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Bernardino AR, Grosso F, Torres CA, Reis MA, Peixe L. Exploring the biotechnological potential of Acinetobacter soli ANG344B: A novel bacterium for 2-phenylethanol production. Biotechnol Rep (Amst) 2024; 42:e00839. [PMID: 38633817 PMCID: PMC11021914 DOI: 10.1016/j.btre.2024.e00839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/21/2024] [Accepted: 03/24/2024] [Indexed: 04/19/2024]
Abstract
A bacterium, Acinetobacter soli ANG344B, isolated from river water, exhibited an exceptional capacity to produce 2-phenylethanol (2-PE) using L-phenylalanine (L-Phe) as a precursor-a capability typically observed in yeasts rather than bacteria. Bioreactor experiments were conducted to evaluate the production performance, using glucose as the carbon source for cellular growth and L-Phe as the precursor for 2-PE production. Remarkably, A. soli ANG344B achieved a 2-PE concentration of 2.35 ± 0.26 g/L in just 24.5 h of cultivation, exhibiting a global volumetric productivity of 0.10 ± 0.01 g/L.h and a production yield of 0.51 ± 0.01 g2-PE/gL-Phe, a result hitherto reported only for yeasts. These findings position A. soli ANG344B as a highly promising microorganism for 2-PE production. Whole-genome sequencing of A. soli strain ANG344 revealed a genome size of 3.52 Mb with a GC content of 42.7 %. Utilizing the Rapid Annotation using Subsystem Technology (RAST) server, 3418 coding genes were predicted, including genes coding for enzymes previously associated with the metabolic pathway of 2-PE production in other microorganisms, yet unreported in Acinetobacter species. Through gene mapping, 299 subsystems were identified, exhibiting 30 % subsystem coverage. The whole genome sequence data was submitted to NCBI GeneBank with the BioProject ID PRJNA982713. These draft genome data offer significant potential for exploiting the biotechnological capabilities of A. soli strain ANG344 and for conducting further comparative genomic studies.
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Affiliation(s)
- Ana R.S. Bernardino
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- LAQV‑REQUIMTE, Chemistry Department, FCT/Universidade NOVA de Lisboa, 2829‑516 Caparica, Portugal
| | - Filipa Grosso
- UCIBIO – Applied Molecular Biosciences Unit, Faculty of Pharmacy, Department of Biological Sciences, Laboratory of Microbiology, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Cristiana A.V. Torres
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Maria A.M. Reis
- UCIBIO – Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- Laboratory i4HB - Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Luísa Peixe
- UCIBIO – Applied Molecular Biosciences Unit, Faculty of Pharmacy, Department of Biological Sciences, Laboratory of Microbiology, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP – Culture Collection of Porto-Faculty of Pharmacy, University of Porto, Porto, Portugal
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Ribeiro-Almeida M, Mourão J, Magalhães M, Freitas AR, Novais C, Peixe L, Antunes P. Raw meat-based diet for pets: a neglected source of human exposure to Salmonella and pathogenic Escherichia coli clones carrying mcr, Portugal, September 2019 to January 2020. Euro Surveill 2024; 29:2300561. [PMID: 38699902 PMCID: PMC11067432 DOI: 10.2807/1560-7917.es.2024.29.18.2300561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 03/04/2024] [Indexed: 05/05/2024] Open
Abstract
BackgroundThe pet industry is expanding worldwide, particularly raw meat-based diets (RMBDs). There are concerns regarding the safety of RMBDs, especially their potential to spread clinically relevant antibiotic-resistant bacteria or zoonotic pathogens.AimWe aimed to investigate whether dog food, including RMBD, commercially available in Portugal can be a source of Salmonella and/or other Enterobacteriaceae strains resistant to last-line antibiotics such as colistin.MethodsFifty-five samples from 25 brands (21 international ones) of various dog food types from 12 suppliers were screened by standard cultural methods between September 2019 and January 2020. Isolates were characterised by phenotypic and genotypic methods, including whole genome sequencing and comparative genomics.ResultsOnly RMBD batches were contaminated, with 10 of 14 containing polyclonal multidrug-resistant (MDR) Escherichia coli and one MDR Salmonella. One turkey-based sample contained MDR Salmonella serotype 1,4,[5],12:i:- ST34/cgST142761 with similarity to human clinical isolates occurring worldwide. This Salmonella exhibited typical antibiotic resistance (bla TEM + strA-strB + sul2 + tet(B)) and metal tolerance profiles (pco + sil + ars) associated with the European epidemic clone. Two samples (turkey/veal) carried globally dispersed MDR E. coli (ST3997-complexST10/cgST95899 and ST297/cgST138377) with colistin resistance (minimum inhibitory concentration: 4 mg/L) and mcr-1 gene on IncX4 plasmids, which were identical to other IncX4 circulating worldwide.ConclusionSome RMBDs from European brands available in Portugal can be a vehicle for clinically relevant MDR Salmonella and pathogenic E. coli clones carrying genes encoding resistance to the last-line antibiotic colistin. Proactive actions within the One Health context, spanning regulatory, pet-food industry and consumer levels, are needed to mitigate these public health risks.
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Affiliation(s)
- Marisa Ribeiro-Almeida
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Joana Mourão
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Centre for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Mafalda Magalhães
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Ana R Freitas
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (CESPU-CRL), Gandra, Portugal
| | - Carla Novais
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO - Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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Wagner TM, Pöntinen AK, Fenzel CK, Engi D, Janice J, Almeida-Santos AC, Tedim AP, Freitas AR, Peixe L, van Schaik W, Johannessen M, Hegstad K. Interactions between commensal Enterococcus faecium and Enterococcus lactis and clinical isolates of Enterococcus faecium. FEMS Microbes 2024; 5:xtae009. [PMID: 38606354 PMCID: PMC11008740 DOI: 10.1093/femsmc/xtae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 02/15/2024] [Accepted: 03/05/2024] [Indexed: 04/13/2024] Open
Abstract
Enterococcus faecium (Efm) is a versatile pathogen, responsible for multidrug-resistant infections, especially in hospitalized immunocompromised patients. Its population structure has been characterized by diverse clades (A1, A2, and B (reclassified as E. lactis (Ela)), adapted to different environments, and distinguished by their resistomes and virulomes. These features only partially explain the predominance of clade A1 strains in nosocomial infections. We investigated in vitro interaction of 50 clinical isolates (clade A1 Efm) against 75 commensal faecal isolates from healthy humans (25 clade A2 Efm and 50 Ela). Only 36% of the commensal isolates inhibited clinical isolates, while 76% of the clinical isolates inhibited commensal isolates. The most apparent overall differences in inhibition patterns were presented between clades. The inhibitory activity was mainly mediated by secreted, proteinaceous, heat-stable compounds, likely indicating an involvement of bacteriocins. A custom-made database targeting 76 Bacillota bacteriocins was used to reveal bacteriocins in the genomes. Our systematic screening of the interactions between nosocomial and commensal Efm and Ela on a large scale suggests that, in a clinical setting, nosocomial strains not only have an advantage over commensal strains due to their possession of AMR genes, virulence factors, and resilience but also inhibit the growth of commensal strains.
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Affiliation(s)
- Theresa Maria Wagner
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Anna Kaarina Pöntinen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
- Department of Biostatistics, Faculty of Medicine, University of Oslo, 0372 Oslo, Norway
| | - Carolin Kornelia Fenzel
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Daniel Engi
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Jessin Janice
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
| | - Ana C Almeida-Santos
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana P Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CiberES CB22/06/00035), 28029 Madrid, Spain
| | - Ana R Freitas
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 1H- TOXRUN – One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, 4584-116 Gandra, Portugal
| | - Luísa Peixe
- UCIBIO. Departamento de Ciências Biológicas, Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Willem van Schaik
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Mona Johannessen
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kristin Hegstad
- Research group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, 9038 Tromsø, Norway
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Roer L, Kaya H, Tedim AP, Novais C, Coque TM, Aarestrup FM, Peixe L, Hasman H, Hammerum AM, Freitas AR. VirulenceFinder for Enterococcus faecium and Enterococcus lactis: an enhanced database for detection of putative virulence markers by using whole-genome sequencing data. Microbiol Spectr 2024; 12:e0372423. [PMID: 38329344 PMCID: PMC10913372 DOI: 10.1128/spectrum.03724-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/20/2024] [Indexed: 02/09/2024] Open
Abstract
Enterococcus faecium (Efm) is a leading cause of hospital-associated (HA) infections, often enriched in putative virulence markers (PVMs). Recently, the Efm clade B was assigned as Enterococcus lactis (Elts), which usually lack HA-Efm infection markers. Available databases for extracting PVM are incomplete and/or present an intermix of genes from Efm and Enterococcus faecalis, with distinct virulence profiles. In this study, we constructed a new database containing 27 PVMs [acm, scm, sgrA, ecbA, fnm, sagA, hylEfm, ptsD, orf1481, fms15, fms21-fms20 (pili gene cluster 1, PGC-1), fms14-fms17-fms13 (PGC-2), empA-empB-empC (PGC-3), fms11-fms19-fms16 (PGC-4), ccpA, bepA, gls20-glsB1, and gls33-glsB] from nine reference genomes (seven Efm + two Elts). The database was validated against these reference genomes and further evaluated using a collection of well-characterized Efm (n = 43) and Elts (n = 7) control strains, by assessing PVM presence/absence and its variants together with a genomic phylogeny constructed as single-nucleotide polymorphisms. We found a high concordance between the phylogeny and in silico findings of the PVM, with Elts clustering separately and mostly carrying Elts-specific PVM gene variants. Based on our validation results, we recommend using the database with raw reads instead of assemblies to avoid missing gene variants. This newly constructed database of 27 PVMs will enable a more comprehensive characterization of Efm and Elts based on WGS data. The developed database exhibits scalability and boasts a range of applications in public health, including diagnostics, outbreak investigations, and epidemiological studies. It can be further used in risk assessment for distinguishing between safe and unsafe enterococci.IMPORTANCEThe newly constructed database, consisting of 27 putative virulence markers, is highly scalable and serves as a valuable resource for the comprehensive characterization of these closely related species using WGS data. It holds significant potential for various public health applications, including hospital outbreak investigations, surveillance, and risk assessment for probiotics and feed additives.
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Affiliation(s)
- Louise Roer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Hülya Kaya
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana P. Tedim
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Carla Novais
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
| | - Luísa Peixe
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
| | - Henrik Hasman
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anette M. Hammerum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ana R. Freitas
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - On behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM)
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Group for Biomedical Research in Sepsis (BioSepsis), Instituto de Investigación Biomédica de Salamanca, Salamanca, Spain
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
- UCIBIO, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Associate Laboratory i4HB, Faculty of Pharmacy, University of Porto, Institute for Health and Bioeconomy, Porto, Portugal
- Department of Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
- Network Research Centre for Infectious Diseases (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
- Research Group for Genomic Epidemiology, Technical University of Denmark, National Food Institute, Lyngby, Denmark
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
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Novais Â, Gonçalves AB, Ribeiro TG, Freitas AR, Méndez G, Mancera L, Read A, Alves V, López-Cerero L, Rodríguez-Baño J, Pascual Á, Peixe L. Development and validation of a quick, automated, and reproducible ATR FT-IR spectroscopy machine-learning model for Klebsiella pneumoniae typing. J Clin Microbiol 2024; 62:e0121123. [PMID: 38284762 PMCID: PMC10865814 DOI: 10.1128/jcm.01211-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
The reliability of Fourier-transform infrared (FT-IR) spectroscopy for Klebsiella pneumoniae typing and outbreak control has been previously assessed, but issues remain in standardization and reproducibility. We developed and validated a reproducible FT-IR with attenuated total reflectance (ATR) workflow for the identification of K. pneumoniae lineages. We used 293 isolates representing multidrug-resistant K. pneumoniae lineages causing outbreaks worldwide (2002-2021) to train a random forest classification (RF) model based on capsular (KL)-type discrimination. This model was validated with 280 contemporaneous isolates (2021-2022), using wzi sequencing and whole-genome sequencing as references. Repeatability and reproducibility were tested in different culture media and instruments throughout time. Our RF model allowed the classification of 33 capsular (KL)-types and up to 36 clinically relevant K. pneumoniae lineages based on the discrimination of specific KL- and O-type combinations. We obtained high rates of accuracy (89%), sensitivity (88%), and specificity (92%), including from cultures obtained directly from the clinical sample, allowing to obtain typing information the same day bacteria are identified. The workflow was reproducible in different instruments throughout time (>98% correct predictions). Direct colony application, spectral acquisition, and automated KL prediction through Clover MS Data analysis software allow a short time-to-result (5 min/isolate). We demonstrated that FT-IR ATR spectroscopy provides meaningful, reproducible, and accurate information at a very early stage (as soon as bacterial identification) to support infection control and public health surveillance. The high robustness together with automated and flexible workflows for data analysis provide opportunities to consolidate real-time applications at a global level. IMPORTANCE We created and validated an automated and simple workflow for the identification of clinically relevant Klebsiella pneumoniae lineages by FT-IR spectroscopy and machine-learning, a method that can be extremely useful to provide quick and reliable typing information to support real-time decisions of outbreak management and infection control. This method and workflow is of interest to support clinical microbiology diagnostics and to aid public health surveillance.
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Affiliation(s)
- Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana Beatriz Gonçalves
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa G. Ribeiro
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Gema Méndez
- CLOVER Bioanalytical Software, Granada, Spain
| | | | - Antónia Read
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Valquíria Alves
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
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6
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Rebelo A, Duarte B, Freitas AR, Almeida A, Azevedo R, Pinto E, Peixe L, Antunes P, Novais C. Uncovering the effects of copper feed supplementation on the selection of copper-tolerant and antibiotic-resistant Enterococcus in poultry production for sustainable environmental practices. Sci Total Environ 2023; 900:165769. [PMID: 37506909 DOI: 10.1016/j.scitotenv.2023.165769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/20/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023]
Abstract
The use of antibiotics in animal production is linked to the emergence and spread of antibiotic-resistant bacteria, a threat to animal, environmental and human health. Copper (Cu) is an essential element in poultry diets and an alternative to antibiotics, supplementing inorganic or organic trace mineral feeds (ITMF/OTMF). However, its contribution to select multidrug-resistant (MDR) and Cu tolerant Enterococcus, a bacteria with a human-animal-environment-food interface, remains uncertain. We evaluated whether feeding chickens with Cu-ITMF or Cu-OTMF contributes to the selection of Cu tolerant and MDR Enterococcus from rearing to slaughter. Animal faeces [2-3-days-old (n = 18); pre-slaughter (n = 16)] and their meat (n = 18), drinking-water (n = 14) and feed (n = 18) from seven intensive farms with ITMF and OTMF flocks (10.000-64.000 animals each; 2019-2020; Portugal) were sampled. Enterococcus were studied by cultural, molecular and whole-genome sequencing methods and Cu concentrations by ICP-MS. Enterococcus (n = 477; 60 % MDR) were identified in 80 % of the samples, with >50 % carrying isolates resistant to tetracycline, quinupristin-dalfopristin, erythromycin, streptomycin, ampicillin or ciprofloxacin. Enterococcus with Cu tolerance genes, especially tcrB ± cueO, were mainly found in faeces (85 %; E. faecium/E. lactis) of ITMF/OTMF flocks. Similar occurrence and load of tcrB ± cueO Enterococcus in the faeces was detected throughout the chickens' lifespan in the ITMF/OTMF flocks, decreasing in meat. Most of the polyclonal MDR Enterococcus population carrying tcrB ± cueO or only cueO (67 %) showed a wild-type phenotype (MICCuSO4 ≤ 12 mM) linked to absence of tcrYAZB or truncated variants, also detected in 85 % of Enterococcus public genomes from poultry. Finally, < 65 μg/g Cu was found in all faecal and meat samples. In conclusion, Cu present in ITMF/OTMF is not selecting Cu tolerant and MDR Enterococcus during chickens' lifespan. However, more studies are needed to assess the minimum concentration of Cu required for MDR bacterial selection and horizontal transfer of antibiotic resistance genes, which would support sustainable practices mitigating antibiotic resistance spread in animal production and the environment beyond.
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Affiliation(s)
- Andreia Rebelo
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; ESS, Polytechnic of Porto, Rua Dr. António Bernardino de Almeida 400, 4200-072, Porto, Portugal
| | - Bárbara Duarte
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Ana R Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Avenida Central de Gandra 1317, 4585-116, Gandra, Portugal
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Rui Azevedo
- LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Edgar Pinto
- ESS, Polytechnic of Porto, Rua Dr. António Bernardino de Almeida 400, 4200-072, Porto, Portugal; LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; Faculty of Nutrition and Food Sciences, University of Porto, Rua do Campo Alegre 823, 4150-180, Porto, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313, Porto, Portugal.
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Sousa M, Ksiezarek M, Perovic SU, Antunes-Lopes T, Grosso F, Ribeiro TG, Peixe L. Gardnerella pickettii sp. nov. (formerly Gardnerella genomic species 3) and Gardnerella greenwoodii sp. nov. (formerly Gardnerella genomic species 8) isolated from female urinary microbiome. Int J Syst Evol Microbiol 2023; 73. [PMID: 37921436 DOI: 10.1099/ijsem.0.006140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023] Open
Abstract
During an ongoing female urinary microbiome research study, strains c17Ua_112T and c31Ua_26T isolated from urine samples of a patient diagnosed with overactive bladder and a healthy postmenopausal woman, respectively, could not be allocated to any Gardnerella species with valid names. In this work, we aimed to characterize these strains. The 16S rRNA gene sequences confirmed that these strains are members of the genus Gardnerella. Phylogenetic analysis based on cpn60 strongly supported two clades, one encompassing c17Ua_112T and nine other strains from the public database, and the other including c31Ua_26T and three other strains, which were distinct from currently recognized species of the genus Gardnerella. Likewise, the phylogenomic tree also showed that strains c17Ua_112T and c31Ua_26T formed independent and robust clusters. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between c17Ua_112T and c31Ua_26T were 79.27 and 27.4 %, respectively. Strain c17Ua_112T showed the highest ANI (94.8 %) and dDDH values (59.8 %) with Gardnerella piotii UGent 18.01T, and strain c31Ua_26T revealed highest ANI (84.2 %) and dDDH (29.1 %) values with Gardnerella swidsinskii GS 9838-1T. Based on the data presented here, the two strains c17Ua_112T and c31Ua_26T represent two novel species of the genus Gardnerella, for which the names Gardnerella pickettii (c17Ua_112T=DSM 113414T=CCP 71T) and Gardnerella greenwoodii (c31Ua_26T=DSM 113415T=CCP 72T) are proposed.
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Affiliation(s)
- Márcia Sousa
- Associate Laboratory i4HB , Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Magdalena Ksiezarek
- Associate Laboratory i4HB , Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Svetlana Ugarcina Perovic
- Associate Laboratory i4HB , Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | | | - Filipa Grosso
- Associate Laboratory i4HB , Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Teresa Gonçalves Ribeiro
- Associate Laboratory i4HB , Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Culture Collection of Porto - Faculty of Pharmacy, University of Porto (CCP), Porto, Portugal
| | - Luísa Peixe
- Associate Laboratory i4HB , Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Culture Collection of Porto - Faculty of Pharmacy, University of Porto (CCP), Porto, Portugal
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Rebelo A, Almeida A, Peixe L, Antunes P, Novais C. Unraveling the Role of Metals and Organic Acids in Bacterial Antimicrobial Resistance in the Food Chain. Antibiotics (Basel) 2023; 12:1474. [PMID: 37760770 PMCID: PMC10525130 DOI: 10.3390/antibiotics12091474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antimicrobial resistance (AMR) has a significant impact on human, animal, and environmental health, being spread in diverse settings. Antibiotic misuse and overuse in the food chain are widely recognized as primary drivers of antibiotic-resistant bacteria. However, other antimicrobials, such as metals and organic acids, commonly present in agri-food environments (e.g., in feed, biocides, or as long-term pollutants), may also contribute to this global public health problem, although this remains a debatable topic owing to limited data. This review aims to provide insights into the current role of metals (i.e., copper, arsenic, and mercury) and organic acids in the emergence and spread of AMR in the food chain. Based on a thorough literature review, this study adopts a unique integrative approach, analyzing in detail the known antimicrobial mechanisms of metals and organic acids, as well as the molecular adaptive tolerance strategies developed by diverse bacteria to overcome their action. Additionally, the interplay between the tolerance to metals or organic acids and AMR is explored, with particular focus on co-selection events. Through a comprehensive analysis, this review highlights potential silent drivers of AMR within the food chain and the need for further research at molecular and epidemiological levels across different food contexts worldwide.
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Affiliation(s)
- Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- ESS, Polytechnic of Porto, 4200-072 Porto, Portugal
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratory of Applied Chemistry, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculty of Nutrition and Food Sciences (FCNAUP), University of Porto, 4150-180 Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Rebelo A, Duarte B, Freitas AR, Peixe L, Antunes P, Novais C. Exploring Peracetic Acid and Acidic pH Tolerance of Antibiotic-Resistant Non-Typhoidal Salmonella and Enterococcus faecium from Diverse Epidemiological and Genetic Backgrounds. Microorganisms 2023; 11:2330. [PMID: 37764174 PMCID: PMC10534362 DOI: 10.3390/microorganisms11092330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/06/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Acid stress poses a common challenge for bacteria in diverse environments by the presence of inorganic (e.g., mammals' stomach) or organic acids (e.g., feed additives; acid-based disinfectants). Limited knowledge exists regarding acid-tolerant strains of specific serotypes, clonal lineages, or sources in human/animal pathogens: namely, non-typhoidal Salmonella enterica (NTS) and Enterococcus faecium (Efm). This study evaluated the acidic pH (Mueller-Hinton acidified with HCl) and peracetic acid (PAA) susceptibility of Efm (n = 72) and NTS (n = 60) from diverse epidemiological/genetic backgrounds and with multiple antibiotic resistance profiles. Efm minimum growth/survival pH was 4.5-5.0/3.0-4.0, and for NTS it was 4.0-4.5/3.5-4.0. Efm distribution among acidic pH values showed that only isolates of clade-non-A1 (non-hospital associated) or the food chain were more tolerant to acidic pH compared to clade-A1 (hospital-associated clones) or clinical isolates (p < 0.05). In the case of NTS, multidrug-resistant (MDR) isolates survived better in acidic pH (p < 0.05). The PAA MIC/MBC for Efm was 70-120/80-150 mg/L, and for NTS, it was 50-70/60-100 mg/L. The distribution of Efm among PAA concentrations showed that clade-A1 or MDR strains exhibited higher tolerance than clade-non-A1 or non-MDR ones (p < 0.05). NTS distribution also showed higher tolerance to PAA among non-MDR and clinical isolates than food chain ones (p < 0.05) but there were no differences among different serogroups. This unique study identifies specific NTS or Efm populations more tolerant to acidic pH or PAA, emphasizing the need for further research to tailor controlled measures of public health and food safety within a One Health framework.
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Affiliation(s)
- Andreia Rebelo
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- ESS, Polytechnic of Porto, 4200-072 Porto, Portugal
| | - Bárbara Duarte
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, 4150-180 Porto, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (A.R.); (B.D.); (A.R.F.); (L.P.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Loiodice M, Ribeiro M, Peixe L, Novais Â. Emergence of NDM-1 and KPC-3 carbapenemases in Kluyvera cryocrescens: Investigating genetic heterogeneity and acquisition routes of bla NDM-1 in Enterobacterales species in Portugal. J Glob Antimicrob Resist 2023; 34:195-198. [PMID: 37468064 DOI: 10.1016/j.jgar.2023.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023] Open
Abstract
OBJECTIVES A higher diversity of species, clones and genes have been increasingly implicated in carbapenemases spread, though the mobile genetic elements responsible for their acquisition and dispersion at local and global levels are less explored, particularly in species other than Klebsiella pneumoniae or Escherichia coli. We aim to explain the emergence of NDM-1 and KPC-3 carbapenemases in a Kluyvera cryocrescens isolate, and to shed light on the heterogeneity of genetic platforms and acquisition routes of blaNDM-1 in diverse Enterobacterales species in Portugal. METHODS A KPC-3 and NDM-1-producing K. cryocrescens colonizing a hospitalized patient in 2019 was characterized by whole-genome sequencing and antibiotic resistance profiling following standard methods. Conjugative transfer of carbapenemases genes was assessed by filter mating. Plasmids were reconstructed with in silico and in vitro approaches. blaNDM-1 genetic context was compared with that of diverse NDM-1-producing Enterobacterales species, previously described in Portugal. RESULTS K. cryocrescens K629 showed a multidrug resistance profile. Resistance gene blaKPC-3 was harboured by a Tn4401d transposon within a worldwide-spread IncN-ST15 plasmid (pKLU-KPC3), whereas blaNDM-1 was located in a Tn3000 within a non-typeable mosaic plasmid (pKLU-NDM1). The heterogeneous blaNDM-1 genetic platforms and variable plasmid backbones identified in various Enterobacterales species suggested multiple introductions of blaNDM-1 in Portugal, mediated by variable insertion sequences. CONCLUSIONS We report the convergence of KPC-3 and NDM-1 in K. cryocrescens and the variable dissemination modes of these carbapenemases in different Enterobacterales species, underlining the need to track down genetic platforms responsible for carbapenemases diffusion.
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Affiliation(s)
- Michele Loiodice
- UCIBIO - Applied Molecular Biosciences Unit, Faculty of Pharmacy, University of Porto, Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Manuela Ribeiro
- Service of Clinical Pathology, Hospital University Centre São João, Porto, Portugal
| | - Luísa Peixe
- UCIBIO - Applied Molecular Biosciences Unit, Faculty of Pharmacy, University of Porto, Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ângela Novais
- UCIBIO - Applied Molecular Biosciences Unit, Faculty of Pharmacy, University of Porto, Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal.
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Mourão J, Ribeiro-Almeida M, Novais C, Magalhães M, Rebelo A, Ribeiro S, Peixe L, Novais Â, Antunes P. From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production. Microbiol Spectr 2023; 11:e0138623. [PMID: 37428073 PMCID: PMC10434174 DOI: 10.1128/spectrum.01386-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Concerns about colistin-resistant bacteria in animal food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae in the whole poultry production chain needs clarification. We assessed colistin-resistant and copper-tolerant K. pneumoniae occurrence in chickens raised with inorganic and organic copper formulas from 1-day-old chicks to meat (7 farms from 2019 to 2020), after long-term colistin withdrawal (>2 years). Clonal diversity and K. pneumoniae adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken flocks (75%) carried K. pneumoniae at early and preslaughter stages, with a significant decrease (P < 0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative K. pneumoniae were observed among fecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant (81%; silA and pcoD positive and with a MICCuSO4 of ≥16 mM) isolates. WGS revealed accumulation of colistin resistance-associated mutations and F type multireplicon plasmids carrying antibiotic resistance and metal/copper tolerance genes. The K. pneumoniae population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146, and ST392-KL27 and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken production as a reservoir/source of clinically relevant K. pneumoniae lineages and genes with potential risk to humans through food and/or environmental exposure. Despite the limited mcr spread due to the long-term colistin ban, this action was ineffective in controlling colistin-resistant/mcr-negative K. pneumoniae, regardless of feed. This study provides crucial insights into the persistence of clinically relevant K. pneumoniae in the poultry production chain and highlights the need for continued surveillance and proactive food safety actions within a One Health perspective. IMPORTANCE The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically relevant Klebsiella pneumoniae throughout the poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative K. pneumoniae in chicken flocks, regardless of inorganic and organic copper formulas use and a long-term colistin ban. Despite the high K. pneumoniae isolate diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human K. pneumoniae exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in the food industry and policymakers tasked with regulating food safety.
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Affiliation(s)
- Joana Mourão
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Marisa Ribeiro-Almeida
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Mafalda Magalhães
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
- ESS, Polytechnic of Porto, Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ângela Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Nonno R, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Fernández Escámez PS, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Barizzone F, Correia S, Herman L. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 18: Suitability of taxonomic units notified to EFSA until March 2023. EFSA J 2023; 21:e08092. [PMID: 37434788 PMCID: PMC10331572 DOI: 10.2903/j.efsa.2023.8092] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023] Open
Abstract
The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of microorganisms, intended for use in the food or feed chains, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, no new information was found that would change the status of previously recommended QPS TUs. Of 38 microorganisms notified to EFSA between October 2022 and March 2023 (inclusive) (28 as feed additives, 5 as food enzymes, food additives and flavourings, 5 as novel foods), 34 were not evaluated because: 8 were filamentous fungi, 4 were Enterococcus faecium and 2 were Escherichia coli (taxonomic units that are excluded from the QPS evaluation) and 20 were taxonomic units (TUs) that already have a QPS status. Three of the other four TUs notified within this period were evaluated for the first time for a possible QPS status: Anaerobutyricum soehngenii, Stutzerimonas stutzeri (former Pseudomonas stutzeri) and Nannochloropsis oculata. Microorganism strain DSM 11798 has also been notified in 2015 and as its taxonomic unit is notified as a strain not a species, it is not suitable for the QPS approach. A. soehngenii and N. oculata are not recommended for the QPS status due to a limited body of knowledge of its use in the food and feed chains. S. stutzeri is not recommended for inclusion in the QPS list based on safety concerns and limited information about the exposure of animals and humans through the food and feed chains.
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Rodrigues C, Lanza VF, Peixe L, Coque TM, Novais Â. Phylogenomics of Globally Spread Clonal Groups 14 and 15 of Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0339522. [PMID: 37098951 PMCID: PMC10269502 DOI: 10.1128/spectrum.03395-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/26/2023] [Indexed: 04/27/2023] Open
Abstract
Klebsiella pneumoniae sequence type 14 (ST14) and ST15 caused outbreaks of CTX-M-15 and/or carbapenemase producers worldwide, but their phylogeny and global dynamics remain unclear. We clarified the evolution of K. pneumoniae clonal group 14 (CG14) and CG15 by analyzing the capsular locus (KL), resistome, virulome, and plasmidome of public genomes (n = 481) and de novo sequences (n = 9) representing main sublineages circulating in Portugal. CG14 and CG15 evolved independently within 6 main subclades defined according to the KL and the accessory genome. The CG14 (n = 65) clade was structured in two large monophyletic subclades, CG14-I (KL2, 86%) and CG14-II (KL16, 14%), whose emergences were dated to 1932 and 1911, respectively. Genes encoding extended-spectrum β-lactamase (ESBL), AmpC, and/or carbapenemases were mostly observed in CG14-I (71% versus 22%). CG15 clade (n = 170) was segregated into subclades CG15-IA (KL19/KL106, 9%), CG15-IB (variable KL types, 6%), CG15-IIA (KL24, 43%) and CG15-IIB (KL112, 37%). Most CG15 genomes carried specific GyrA and ParC mutations and emerged from a common ancestor in 1989. CTX-M-15 was especially prevalent in CG15 (68% CG15 versus 38% CG14) and in CG15-IIB (92%). Plasmidome analysis revealed 27 predominant plasmid groups (PG), including particularly pervasive and recombinant F-type (n = 10), Col (n = 10), and new plasmid types. While blaCTX-M-15 was acquired multiple times by a high diversity of F-type mosaic plasmids, other antibiotic resistance genes (ARGs) were dispersed by IncL (blaOXA-48) or IncC (blaCMY/TEM-24) plasmids. We first demonstrate an independent evolutionary trajectory for CG15 and CG14 and how the acquisition of specific KL, quinolone-resistance determining region (QRDR) mutations (CG15), and ARGs in highly recombinant plasmids could have shaped the expansion and diversification of particular subclades (CG14-I and CG15-IIA/IIB). IMPORTANCE Klebsiella pneumoniae represents a major threat in the burden of antibiotic resistance (ABR). Available studies to explain the origin, the diversity, and the evolution of certain ABR K. pneumoniae populations have mainly been focused on a few clonal groups (CGs) using phylogenetic analysis of the core genome, the accessory genome being overlooked. Here, we provide unique insights into the phylogenetic evolution of CG14 and CG15, two poorly characterized CGs which have contributed to the global dissemination of genes responsible for resistance to first-line antibiotics such as β-lactams. Our results point out an independent evolution of these two CGs and highlight the existence of different subclades structured by the capsular type and the accessory genome. Moreover, the contribution of a turbulent flux of plasmids (especially multireplicon F type and Col) and adaptive traits (antibiotic resistance and metal tolerance genes) to the pangenome reflect the exposure and adaptation of K. pneumoniae under different selective pressures.
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Affiliation(s)
- Carla Rodrigues
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Val F. Lanza
- Unidad de Genómica Traslacional Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M. Coque
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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Furlan JPR, Ribeiro TG, Novais Â, Cabral H, Peixe L, Stehling EG. Citrobacter meridianamericanus sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2023; 73. [PMID: 36943338 DOI: 10.1099/ijsem.0.005720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
A Gram-stain-negative strain, designated BR102T, isolated from a soil sample in Brazil was characterized by a polyphasic approach. Comparative 16S rRNA gene sequences indicated that strain BR102T belonged to the genus Citrobacter. The recN- and whole-genome-based phylogeny, and multilocus sequence analysis based on concatenated partial fusA, leuS, pyrG and rpoB sequences strongly supported a clade encompassing strain BR102T and a strain from public database that was distinct from currently recognized species of the genus Citrobacter. Average nucleotide identity and digital DNA-DNA hybridization values between strain BR102T and the closest relative Citrobacter freundii ATCC 8090T were 91.8 and 48.8 %, respectively. The ability to metabolize different compounds further discriminated strain BR102T from other closely related species of the genus Citrobacter. The novel variants bla CMY-179 and qnrB97, which encoded a CMY-2-like β-lactamase and a QnrB-type protein, respectively, were identified in strain BR102T. BR102T was resistant to ampicillin, amoxicillin/clavulanate and cefoxitin. The DNA G+C content of strain BR102T is 51.3 mol%. Based on these results, strain BR102T represents a novel species of the genus Citrobacter, for which the name Citrobacter meridianamericanus sp. nov. is proposed. The type strain is BR102T (=MUM 22.55T=IMI 507229T).
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Teresa Gonçalves Ribeiro
- UCIBIO-Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 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, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
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Novais C, Almeida-Santos AC, Paula Pereira A, Rebelo A, Freitas AR, Peixe L. Alert for molecular data interpretation when using Enterococcus faecium reference strains reclassified as Enterococcus lactis. Gene 2023; 851:146951. [PMID: 36261083 DOI: 10.1016/j.gene.2022.146951] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal.
| | - Ana C Almeida-Santos
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Ana Paula Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
| | - Andreia Rebelo
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Abel Salazar Biomedical Sciences Institute (ICBAS), Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Technical-Scientific Area of Environmental Health, School of Health, Polytechnic Institute of Porto, Rua Dr. António Bernardino de Almeida 400, 420-072 Porto, Portugal
| | - Ana R Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Rua Central da Gandra, 1317-4585 Gandra, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Rua Jorge de Viterbo Ferreira 228, 4050-313 Porto, Portugal
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Koutsoumanis K, Allende A, Alvarez‐Ordóñez A, Bolton D, Bover‐Cid S, Chemaly M, De Cesare A, Hilbert F, Lindqvist R, Nauta M, Peixe L, Ru G, Simmons M, Skandamis P, Suffredini E, Cocconcelli PS, Escámez PSF, Maradona MP, Querol A, Sijtsma L, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Update of the list of qualified presumption of safety (QPS) recommended microbiological agents intentionally added to food or feed as notified to EFSA 17: suitability of taxonomic units notified to EFSA until September 2022. EFSA J 2023; 21:e07746. [PMID: 36704192 PMCID: PMC9875162 DOI: 10.2903/j.efsa.2023.7746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The qualified presumption of safety (QPS) approach was developed to provide a regularly updated generic pre-evaluation of the safety of microorganisms, intended for use in the food or feed chains, to support the work of EFSA's Scientific Panels. The QPS approach is based on an assessment of published data for each agent, with respect to its taxonomic identity, the body of relevant knowledge and safety concerns. Safety concerns identified for a taxonomic unit (TU) are, where possible, confirmed at the species/strain or product level and reflected by 'qualifications'. In the period covered by this Statement, new information was found leading to the withdrawal of the qualification 'absence of aminoglycoside production ability' for Bacillus velezensis. The qualification for Bacillus paralicheniformis was changed to 'absence of bacitracin production ability'. For the other TUs, no new information was found that would change the status of previously recommended QPS TUs. Of 52 microorganisms notified to EFSA between April and September 2022 (inclusive), 48 were not evaluated because: 7 were filamentous fungi, 3 were Enterococcus faecium, 2 were Escherichia coli, 1 was Streptomyces spp., and 35 were taxonomic units (TUs) that already have a QPS status. The other four TUs notified within this period, and one notified previously as a different species, which was recently reclassified, were evaluated for the first time for a possible QPS status: Xanthobacter spp. could not be assessed because it was not identified to the species level; Geobacillus thermodenitrificans is recommended for QPS status with the qualification 'absence of toxigenic activity'. Streptoccus oralis is not recommended for QPS status. Ogataea polymorpha is proposed for QPS status with the qualification 'for production purposes only'. Lactiplantibacillus argentoratensis (new species) is included in the QPS list.
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de Almeida MP, Rodrigues C, Novais Â, Grosso F, Leopold N, Peixe L, Franco R, Pereira E. Silver Nanostar-Based SERS for the Discrimination of Clinically Relevant Acinetobacter baumannii and Klebsiella pneumoniae Species and Clones. Biosensors (Basel) 2023; 13:149. [PMID: 36831915 PMCID: PMC9953856 DOI: 10.3390/bios13020149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 06/18/2023]
Abstract
The development of rapid, reliable, and low-cost methods that enable discrimination among clinically relevant bacteria is crucial, with emphasis on those listed as WHO Global Priority 1 Critical Pathogens, such as carbapenem-resistant Acinetobacter baumannii and carbapenem-resistant or ESBL-producing Klebsiella pneumoniae. To address this problem, we developed and validated a protocol of surface-enhanced Raman spectroscopy (SERS) with silver nanostars for the discrimination of A. baumannii and K. pneumoniae species, and their globally disseminated and clinically relevant antibiotic resistant clones. Isolates were characterized by mixing bacterial colonies with silver nanostars, followed by deposition on filter paper for SERS spectrum acquisition. Spectral data were processed with unsupervised and supervised multivariate data analysis methods, including principal component analysis (PCA) and partial least-squares discriminant analysis (PLSDA), respectively. Our proposed SERS procedure using silver nanostars adsorbed to the bacteria, followed by multivariate data analysis, enabled differentiation between and within species. This pilot study demonstrates the potential of SERS for the rapid discrimination of clinically relevant A. baumannii and K. pneumoniae species and clones, displaying several advantages such as the ease of silver nanostars synthesis and the possible use of a handheld spectrometer, which makes this approach ideal for point-of-care applications.
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Affiliation(s)
- Miguel Peixoto de Almeida
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
| | - Carla Rodrigues
- UCIBIO—Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ângela Novais
- UCIBIO—Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 4TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU (IUCS-CESPU), 4585-116 Gandra, Portugal
| | - Filipa Grosso
- UCIBIO—Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Nicolae Leopold
- Faculty of Physics, Babeş-Bolyai University, 400084 Cluj-Napoca, Romania
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ricardo Franco
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Departamento de Química, School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Eulália Pereira
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4169-007 Porto, Portugal
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Rebelo A, Duarte B, Ferreira C, Mourão J, Ribeiro S, Freitas AR, Coque TM, Willems R, Corander J, Peixe L, Antunes P, Novais C. Enterococcus spp. from chicken meat collected 20 years apart overcome multiple stresses occurring in the poultry production chain: Antibiotics, copper and acids. Int J Food Microbiol 2023; 384:109981. [DOI: 10.1016/j.ijfoodmicro.2022.109981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/03/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
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Pereira AP, Antunes P, Willems R, Corander J, Coque TM, Peixe L, Freitas AR, Novais C. Evolution of Chlorhexidine Susceptibility and of the EfrEF Operon among Enterococcus faecalis from Diverse Environments, Clones, and Time Spans. Microbiol Spectr 2022; 10:e0117622. [PMID: 35862993 PMCID: PMC9430118 DOI: 10.1128/spectrum.01176-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 06/17/2022] [Indexed: 11/20/2022] Open
Abstract
Chlorhexidine (CHX) is widely used to control the spread of pathogens (e.g., human/animal clinical settings, ambulatory care, food industry). Enterococcus faecalis, a major nosocomial pathogen, is broadly distributed in diverse hosts and environments facilitating its exposure to CHX over the years. Nevertheless, CHX activity against E. faecalis is understudied. Our goal was to assess CHX activity and the variability of ChlR-EfrEF proteins (associated with CHX tolerance) among 673 field isolates and 1,784 E. faecalis genomes from the PATRIC database from different sources, time spans, clonal lineages, and antibiotic-resistance profiles. The CHX MIC (MICCHX) and minimum bactericidal concentration (MBCCHX) against E. faecalis presented normal distributions (0.5 to 64 mg/L). However, more CHX-tolerant isolates were detected in the food chain and recent human infections, suggesting an adaptability of E. faecalis populations in settings where CHX is heavily used. Heterogeneity in ChlR-EfrEF sequences was identified, with isolates harboring incomplete ChlR-EfrEF proteins, particularly the EfrE identified in the ST40 clonal lineage, showing low MICCHX (≤1mg/L). Distinct ST40-E. faecalis subpopulations carrying truncated and nontruncated EfrE were detected, with the former being predominant in human isolates. This study provides a new insight about CHX susceptibility and ChlR-EfrEF variability within diverse E. faecalis populations. The MICCHX/MBCCHX of more tolerant E. faecalis (MICCHX = 8 mg/L; MBCCHX = 64 mg/L) remain lower than in-use concentrations of CHX (≥500 mg/L). However, increased CHX use, combined with concentration gradients occurring in diverse environments, potentially selecting multidrug-resistant strains with different CHX susceptibilities, signals the importance of monitoring the trends of E. faecalis CHX tolerance within a One Health approach. IMPORTANCE Chlorhexidine (CHX) is a disinfectant and antiseptic used since the 1950s and included in the World Health Organization's list of essential medicines. It has been widely applied in hospitals, the community, the food industry, animal husbandry and pets. CHX tolerance in Enterococcus faecalis, a ubiquitous bacterium and one of the leading causes of human hospital-acquired infections, remains underexplored. Our study provides novel and comprehensive insights about CHX susceptibility within the E. faecalis population structure context, revealing more CHX-tolerant subpopulations from the food chain and recent human infections. We further show a detailed analysis of the genetic diversity of the efrEF operon (previously associated with E. faecalis CHX tolerance) and its correlation with CHX phenotypes. The recent strains with a higher tolerance to CHX and the multiple sources where bacteria are exposed to this biocide alert us to the need for the continuous monitoring of E. faecalis adaptation toward CHX tolerance within a One Health approach.
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Affiliation(s)
- Ana P. Pereira
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Rob Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jukka Corander
- Department of Biostatistics, Faculty of Medicine, University of Oslo, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Teresa M. Coque
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain
- Centro de Investigación Biomédica en Enfermedades Infecciosas (CIBER-EII), Madrid, Spain
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- TOXRUN, Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Carla Novais
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, REQUIMTE Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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Martins-Oliveira I, Pérez-Viso B, Silva-Dias A, Gomes R, Peixe L, Novais Â, Cantón R, Pina-Vaz C. Rapid Detection of Plasmid AmpC Beta-Lactamases by a Flow Cytometry Assay. Antibiotics (Basel) 2022; 11:antibiotics11081130. [PMID: 36009999 PMCID: PMC9405432 DOI: 10.3390/antibiotics11081130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 12/02/2022] Open
Abstract
Plasmidic AmpC (pAmpC) enzymes are responsible for the hydrolysis of extended-spectrum cephalosporins but they are not routinely investigated in many clinical laboratories. Phenotypic assays, currently the reference methods, are cumbersome and culture dependent. These methods compare the activity of cephalosporins with and without class C inhibitors and the results are provided in 24–48 h. Detection by molecular methods is quicker, but several genes should be investigated. A new assay for the rapid phenotypic detection of pAmpC enzymes of the Enterobacterales group-I (not usually AmpC producers) based on flow cytometry technology was developed and validated. The technology was evaluated in two sites: FASTinov, a spin-off of Porto University (Portugal) where the technology was developed, and the Microbiology Department of Ramón y Cajal University Hospital in Madrid (Spain). A total of 100 strains were phenotypically screened by disk diffusion for the pAmpC with the new 2 h assay. Molecular detection of the pAmpC genes was also performed on discrepant results. Forty-two percent of the strains were phenotypically classified as pAmpC producers using disk diffusion. The percentage of agreement of the flow cytometric assay was 93.0%, with 95.5% sensitivity and 91.1% specificity. Our proposed rapid assay based on flow cytometry technology can, in two hours, accurately detect pAmpC enzymes.
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Affiliation(s)
- Inês Martins-Oliveira
- FASTinov: S.A., 4450-676 Matosinhos, Portugal
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Blanca Pérez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana Silva-Dias
- FASTinov: S.A., 4450-676 Matosinhos, Portugal
- CINTESIS-Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal
| | | | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- 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, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Correspondence: (R.C.); (C.P.-V.); Tel.: +34-913368832 (R.C.); +351-924393147 (C.P.-V.)
| | - Cidália Pina-Vaz
- FASTinov: S.A., 4450-676 Matosinhos, Portugal
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- CINTESIS-Center for Health Technology and Services Research, Faculty of Medicine, University of Porto, 4200-450 Porto, Portugal
- Correspondence: (R.C.); (C.P.-V.); Tel.: +34-913368832 (R.C.); +351-924393147 (C.P.-V.)
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Ksiezarek M, Grosso F, Ribeiro TG, Peixe L. Genomic diversity of genus Limosilactobacillus. Microb Genom 2022; 8. [PMID: 35838756 PMCID: PMC9455696 DOI: 10.1099/mgen.0.000847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The genus Limosilactobacillus (formerly Lactobacillus) contains multiple species considered to be adapted to vertebrates, yet their genomic diversity has not been explored. In this study, we performed comparative genomic analysis of Limosilactobacillus (22 species; 332 genomes) isolated from different niches, further focusing on human strains (11 species; 74 genomes) and their adaptation features to specific body sites. Phylogenomic analysis of Limosilactobacillus showed misidentification of some strains deposited in public databases and existence of putative novel Limosilactobacillus species. The pangenome analysis revealed a remarkable genomic diversity (only 1.3 % of gene clusters are shared), and we did not observe a strong association of the accessory genome with different niches. The pangenome of Limosilactobacillus reuteri and Limosilactobacillus fermentum was open, suggesting that acquisition of genes is still occurring. Although most Limosilactobacillus were predicted as antibiotic susceptible (83%), acquired antibiotic-resistance genes were common in L. reuteri from food-producing animals. Genes related to lactic acid isoform production (>95 %) and putative bacteriocins (70.2%) were identified in most Limosilactobacillus strains, while prophages (55.4%) and CRISPR-Cas systems (32.0%) were less prevalent. Among strains from human sources, several metabolic pathways were predicted as conserved and completed. Their accessory genome was highly variable and did not cluster according to different human body sites, with some exceptions (urogenital Limosilactobacillus vaginalis, Limosilactobacillus portuensis, Limosilactobacillus urinaemulieris and Limosilactobacillus coleohominis or gastrointestinal Limosilactobacillus mucosae). Moreover, we identified 12 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologues that were significantly enriched in strains from particular body sites. We concluded that evolution of the highly diverse Limosilactobacillus is complex and not always related to niche or human body site origin.
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Affiliation(s)
- Magdalena Ksiezarek
- Laboratory of Microbiology, UCIBIO – Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Filipa Grosso
- Laboratory of Microbiology, UCIBIO – Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Teresa Gonçalves Ribeiro
- Laboratory of Microbiology, UCIBIO – Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Luísa Peixe
- Laboratory of Microbiology, UCIBIO – Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- *Correspondence: Luísa Peixe,
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22
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Ribeiro-Almeida M, Mourão J, Novais Â, Pereira S, Freitas-Silva J, Ribeiro S, Martins da Costa P, Peixe L, Antunes P. High diversity of pathogenic Escherichia coli clones carrying mcr-1 among gulls underlines the need for strategies at the environment-livestock-human interface. Environ Microbiol 2022; 24:4702-4713. [PMID: 35726894 DOI: 10.1111/1462-2920.16111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 06/17/2022] [Accepted: 06/19/2022] [Indexed: 11/30/2022]
Abstract
The expansion of mcr-carrying bacteria is a well-recognized public health problem. Measures to contain mcr spread have mainly been focused on the food-animal production sector. Nevertheless, the spread of MCR-producers at the environmental interface particularly driven by the increasing population of gulls in coastal cities has been less explored. Occurrence of mcr-carrying Escherichia coli in gull's colonies faeces on a Portuguese beach was screened over 7-months. Cultural, molecular, and genomic approaches were used to characterize their diversity, mcr plasmids and adaptive features. Multidrug-resistant mcr-1-carrying E. coli were detected for three consecutive months. Over time, multiple strains were recovered, including zoonotic-related pathogenic E. coli clones (e.g., B2-ST131-H22, A-ST10, and B1-ST162). Diverse mcr-1.1 genetic environments were mainly associated with ST2/ST4-HI2 (ST10, ST131, ST162, ST354 and ST4204) but also IncI2 (ST12990) plasmids or in the chromosome (ST656). Whole-genome sequencing revealed enrichment of these strains on antibiotic resistance, virulence, and metal tolerance genes. Our results underscore gulls as important spreaders of high priority bacteria and genes that may affect the environment, food-animals and/or humans, potentially undermining One-Health strategies to reduce colistin resistance. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marisa Ribeiro-Almeida
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal.,School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Joana Mourão
- Faculty of Sciences and Technology, University of Algarve, Gambelas Campus, Faro, Portugal
| | - Ângela Novais
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Sofia Pereira
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Joana Freitas-Silva
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Sofia Ribeiro
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Paulo Martins da Costa
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal.,CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Matosinhos, Portugal
| | - Luísa Peixe
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal.,Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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23
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Furlan JPR, Stehling EG, Savazzi EA, Peixe L, Novais Â. High occurrence of colistin- and multidrug-resistant strains carrying mcr-1 or an underestimated mcr-1.26 allelic variant along a large Brazilian river. J Glob Antimicrob Resist 2022; 30:127-129. [PMID: 35671988 DOI: 10.1016/j.jgar.2022.05.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/11/2022] [Accepted: 05/31/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo (USP)- Ribeirão Preto, Brasil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto Universidade de São Paulo (USP)- Ribeirão Preto, Brasil
| | | | - 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; 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; 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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Freitas AR, Tedim AP, Almeida-Santos AC, Duarte B, Elghaieb H, Abbassi MS, Hassen A, Novais C, Peixe L. High-Resolution Genotyping Unveils Identical Ampicillin-Resistant Enterococcus faecium Strains in Different Sources and Countries: A One Health Approach. Microorganisms 2022; 10:microorganisms10030632. [PMID: 35336207 PMCID: PMC8948916 DOI: 10.3390/microorganisms10030632] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 11/16/2022] Open
Abstract
Multidrug-resistant (MDR) Enterococcus faecium (Efm) infections continue to increase worldwide, although epidemiological studies remain scarce in lower middle-income countries. We aimed to explore which strains circulate in E. faecium causing human infections in Tunisian healthcare institutions in order to compare them with strains from non-human sources of the same country and finally to position them within the global E. faecium epidemiology by genomic analysis. Antibiotic susceptibility testing was performed and transfer of vancomycin-vanA and ampicillin-pbp5 resistance was performed by conjugation. WGS-Illumina was performed on Tunisian strains, and these genomes were compared with Efm genomes from other regions present in the GenBank/NCBI database (n = 10,701 Efm genomes available May 2021). A comparison of phenotypes with those predicted by the recent ResFinder 4.1-CGE webtool unveiled a concordance of 88%, with discordant cases being discussed. cgMLST revealed three clusters [ST18/CT222 (n = 13), ST17/CT948 strains (n = 6), and ST203/CT184 (n = 3)], including isolates from clinical, healthy-human, retail meat, and/or environmental sources in different countries over large time spans (10–12 years). Isolates within each cluster showed similar antibiotic resistance, bacteriocin, and virulence genetic patterns. pbp5-AmpR was transferred by VanA-AmpR-ST80 (clinical) and AmpR-ST17-Efm (bovine meat). Identical chromosomal pbp5-platforms carrying metabolic/virulence genes were identified between ST17/ST18 strains of clinical, farm animal, and retail meat sources. The overall results emphasize the role of high-resolution genotyping as provided by WGS in depicting the dispersal of MDR-Efm strains carrying relevant adaptive traits across different hosts/regions and the need of a One Health task force to curtail their spread.
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Affiliation(s)
- Ana R. Freitas
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- TOXRUN—Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- Correspondence: or (A.R.F.); (L.P.); Tel.: +351-220-428-580 (L.P.)
| | - Ana P. Tedim
- Grupo de Investigación Biomédica en Sepsis-BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), 47012 Valladollid, Spain;
| | - Ana C. Almeida-Santos
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Bárbara Duarte
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Houyem Elghaieb
- Tunisian Institute of Veterinary Research, University of Tunis El Manar, Tunis 1006, Tunisia; (H.E.); (M.S.A.)
| | - Mohamed S. Abbassi
- Tunisian Institute of Veterinary Research, University of Tunis El Manar, Tunis 1006, Tunisia; (H.E.); (M.S.A.)
| | - Abdennaceur Hassen
- Laboratory of Treatment and Valorisation of Wastewater, Centre of Research and Water Technologies (CERTE), Technopark of Borj-Cédria, Soliman 8020, Tunisia;
| | - Carla Novais
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Luísa Peixe
- Laboratory of Microbiology, UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (B.D.); (C.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Correspondence: or (A.R.F.); (L.P.); Tel.: +351-220-428-580 (L.P.)
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Tedim AP, Lanza VF, Rodríguez CM, Freitas AR, Novais C, Peixe L, Baquero F, Coque TM. Fitness cost of vancomycin-resistant Enterococcus faecium plasmids associated with hospital infection outbreaks. J Antimicrob Chemother 2021; 76:2757-2764. [PMID: 34450635 DOI: 10.1093/jac/dkab249] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/14/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Vancomycin resistance is mostly associated with Enterococcus faecium due to Tn1546-vanA located on narrow- and broad-host plasmids of various families. This study's aim was to analyse the effects of acquiring Tn1546-carrying plasmids with proven epidemicity in different bacterial host backgrounds. METHODS Widespread Tn1546-carrying plasmids of different families RepA_N (n = 5), Inc18 (n = 4) and/or pHTβ (n = 1), and prototype plasmids RepA_N (pRUM) and Inc18 (pRE25, pIP501) were analysed. Plasmid transferability and fitness cost were assessed using E. faecium (GE1, 64/3) and Enterococcus faecalis (JH2-2/FA202/UV202) recipient strains. Growth curves (Bioscreen C) and Relative Growth Rates were obtained in the presence/absence of vancomycin. Plasmid stability was analysed (300 generations). WGS (Illumina-MiSeq) of non-evolved and evolved strains (GE1/64/3 transconjugants, n = 49) was performed. SNP calling (Breseq software) of non-evolved strains was used for comparison. RESULTS All plasmids were successfully transferred to different E. faecium clonal backgrounds. Most Tn1546-carrying plasmids and Inc18 and RepA_N prototypes reduced host fitness (-2% to 18%) while the cost of Tn1546 expression varied according to the Tn1546-variant and the recipient strain (9%-49%). Stability of Tn1546-carrying plasmids was documented in all cases, often with loss of phenotypic resistance and/or partial plasmid deletions. SNPs and/or indels associated with essential bacterial functions were observed on the chromosome of evolved strains, some of them linked to increased fitness. CONCLUSIONS The stability of E. faecium Tn1546-carrying plasmids in the absence of selective pressure and the high intra-species conjugation rates might explain the persistence of vancomycin resistance in E. faecium populations despite the significant burden they might impose on bacterial host strains.
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Affiliation(s)
- Ana P Tedim
- Department of Microbiology, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | - Val F Lanza
- Unit of Bioinformatics, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
| | | | - Ana R Freitas
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Fernando Baquero
- Department of Microbiology, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain.,Centres for Biomedical Research in the Epidemiology and Public Health Network (CIBER-ESP), Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, University Hospital Ramón y Cajal-IRYCIS, Madrid, Spain
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27
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Almeida-Santos AC, Novais C, Peixe L, Freitas AR. Enterococcus spp. as a Producer and Target of Bacteriocins: A Double-Edged Sword in the Antimicrobial Resistance Crisis Context. Antibiotics (Basel) 2021; 10:antibiotics10101215. [PMID: 34680796 PMCID: PMC8532689 DOI: 10.3390/antibiotics10101215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 01/10/2023] Open
Abstract
Enterococcus spp. are one of the most frequent producers of bacteriocins (enterocins), which provides them with an advantage to compete in their natural environment, which is the gut of humans and many animals. The enterocins’ activity against microorganisms from different phylogenetic groups has raised interest in Enterococcus spp. in different contexts throughout the last decades, especially in the food industry. Nevertheless, some species can also cause opportunistic life-threatening infections and are frequently multidrug-resistant (MDR). Vancomycin-resistant Enterococcus (VRE), in particular, are an ongoing global challenge given the lack of therapeutic options. In this scenario, bacteriocins can offer a potential solution to this persistent threat, either alone or in combination with other antimicrobials. There are a handful of studies that demonstrate the advantages and applications of bacteriocins, especially against VRE. The purpose of this review is to present a current standpoint about the dual role of Enterococcus spp., from important producers to targets needed to be controlled, and the crucial role that enterocins may have in the expansion of enterococcal populations. Classification and distribution of enterocins, the current knowledge about the bacteriocinome of clinical enterococci, and the challenges of bacteriocin use in the fight against VRE infections are particularly detailed.
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Affiliation(s)
- Ana C. Almeida-Santos
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Carla Novais
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.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 or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Correspondence: (L.P.); or (A.R.F.); Tel.: +351-220428580 (L.P. & A.R.F.)
| | - Ana R. Freitas
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal or (A.C.A.-S.); (C.N.)
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- TOXRUN–Toxicology Research Unit, Department of Sciences, University Institute of Health Sciences, CESPU, CRL, 4585-116 Gandra, Portugal
- Correspondence: (L.P.); or (A.R.F.); Tel.: +351-220428580 (L.P. & A.R.F.)
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28
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Rebelo A, Mourão J, Freitas AR, Duarte B, Silveira E, Sanchez-Valenzuela A, Almeida A, Baquero F, Coque TM, Peixe L, Antunes P, Novais C. Diversity of metal and antibiotic resistance genes in Enterococcus spp. from the last century reflects multiple pollution and genetic exchange among phyla from overlapping ecosystems. Sci Total Environ 2021; 787:147548. [PMID: 34000557 DOI: 10.1016/j.scitotenv.2021.147548] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 04/26/2021] [Accepted: 04/30/2021] [Indexed: 06/12/2023]
Abstract
Arsenic (As), mercury (Hg), and copper (Cu) are among the major historical and contemporary metal pollutants linked to global anthropogenic activities. Enterococcus have been considered indicators of fecal pollution and antibiotic resistance for years, but its largely underexplored metallome precludes understanding their role as metal pollution bioindicators as well. Our goal was to determine the occurrence, diversity, and phenotypes associated with known acquired genes/operons conferring tolerance to As, Hg or Cu among Enterococcus and to identify their genetic context (381 field isolates from diverse epidemiological and genetic backgrounds; 3547 enterococcal genomes available in databases representing a time span during 1900-2019). Genes conferring tolerance to As (arsA), Hg (merA) or Cu (tcrB) were used as biomarkers of widespread metal tolerance operons. Different variants of metal tolerance (MeT) genes (13 arsA, 6 merA, 1 tcrB) were more commonly recovered from the food-chain (arsA, tcrB) or humans (merA), and were shared with 49 other bacterial taxa. Comparative genomics analysis revealed that MeT genes occurred in heterogeneous operons, at least since the 1900s, with an increasing accretion of antibiotic resistance genes since the 1960's, reflecting diverse antimicrobial pollution. Multiple MeT genes were co-located on the chromosome or conjugative plasmids flanked by elements with high potential for recombination, often along with antibiotic resistance genes. Phenotypic analysis of some isolates carrying MeT genes revealed up to 128× fold increase in the minimum inhibitory concentrations to metals. The main distribution of functional MeT genes among Enterococcus faecium and Enterococcus faecalis from different sources, time spans, and clonal lineages, and their ability to acquire diverse genes from multiple taxa bacterial communities places these species as good candidates to be used as model organisms in future projects aiming at the identification and quantification of bioindicators of metal polluted environments by anthropogenic activities.
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Affiliation(s)
- Andreia Rebelo
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Instituto de Ciências Biomédicas de Abel Salazar (ICBAS), Universidade do Porto, Portugal; Área Técnico-científica de Saúde Ambiental, Escola Superior de Saúde, Instituto Politécnico do Porto, Portugal
| | - Joana Mourão
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Centro de Neurociências e Biologia Celular, Universidade de Coimbra, Portugal; Centro de Inovação em Biomedicina e Biotecnologia, Universidade de Coimbra, Portugal; Instituto de Investigação Interdisciplinar, Universidade de Coimbra, Portugal
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Eduarda Silveira
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Centro de Investigação Vasco da Gama (CIVG), Departamento de Ciências Veterinárias, Escola Universitária Vasco da Gama, Coimbra, Portugal; Faculdade de Farmácia, Universidade de Coimbra, Portugal
| | - Antonio Sanchez-Valenzuela
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain
| | - Agostinho Almeida
- LAQV/REQUIMTE, Laboratório de Química Aplicada, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Fernando Baquero
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Teresa M Coque
- Servicio de Microbiologia, Hospital Universitario Ramón y Cajal, Madrid, Spain; Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain; Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Patrícia Antunes
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal; Faculdade de Ciências da Nutrição e Alimentação, Universidade do Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal.
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Ribeiro S, Mourão J, Novais Â, Campos J, Peixe L, Antunes P. From farm to fork: Colistin voluntary withdrawal in Portuguese farms reflected in decreasing occurrence of mcr-1-carrying Enterobacteriaceae from chicken meat. Environ Microbiol 2021; 23:7563-7577. [PMID: 34327794 DOI: 10.1111/1462-2920.15689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/27/2021] [Indexed: 11/27/2022]
Abstract
Expansion of mcr-carrying Enterobacteriaceae (MCR-E) is a well-recognized problem affecting animals, humans and the environment. Ongoing global control actions involve colistin restrictions among food-animal production, but their impact on poultry-derived products is largely unknown, justifying comprehensive farm-to-fork studies. Occurrence of MCR-E among 53 chicken-meat batches supplied from 29 Portuguese farms shortly after colistin withdrawal was evaluated. Strains (FT-IR/MLST/WGS), mcr plasmids and their adaptive features were characterized by cultural, molecular and genomic approaches. We found high rates of chicken-meat batches (80%-100% - 4 months; 12% - the last month) with multiple MDR + mcr-1-carrying Escherichia coli (Ec-including ST117 and ST648-Cplx) and Klebsiella pneumoniae (Kp-ST147-O5:K35) clones, some of them persisting over time. The mcr-1 was located in the chromosome (Ec-ST297/16-farms) or dispersed IncX4 (Ec-ST602/ST6469/5-farms), IncHI2-ST2/ST4 (Ec-ST533/ST6469/5 farms and Kp-ST147/6-farms) or IncI2 (Ec-ST117/1-farm) plasmids. WGS revealed high load and diversity in virulence, antibiotic resistance and metal tolerance genes. This study supports colistin withdrawal potential efficacy in poultry production and highlights both poultry-production chain as a source of mcr-1 and the risk of foodborne transmission to poultry-meat consumers. Finally, in the antibiotic reduction/replacement context, other potential co-selective pressures (e.g., metals-Cu as feed additives) need to be further understood to guide concerted, effective and durable actions under 'One Health' perspective.
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Affiliation(s)
- Sofia Ribeiro
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Joana Mourão
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ângela Novais
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Joana Campos
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,INEB-Institute of Biomedical Engineering, i3S-Institute for Research & Innovation in Health, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Patrícia Antunes
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Faculty of Nutrition and Food Sciences, University of Porto, Porto, 4150-180, Portugal
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Freitas AR, Finisterra L, Tedim AP, Duarte B, Novais C, Peixe L. Linezolid- and Multidrug-Resistant Enterococci in Raw Commercial Dog Food, Europe, 2019-2020. Emerg Infect Dis 2021; 27:2221-2224. [PMID: 34287135 PMCID: PMC8314808 DOI: 10.3201/eid2708.204933] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
We describe enterococci in raw-frozen dog food commercialized in Europe as a source of genes encoding resistance to the antibiotic drug linezolid and of strains and plasmids enriched in antibiotic-resistance and virulence genes in hospitalized patients. Whole-genome sequencing was fundamental to linking isolates from dog food to human cases across Europe.
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Silva L, Grosso F, Rodrigues C, Ksiezarek M, Ramos H, Peixe L. The success of particular Acinetobacter baumannii clones: accumulating resistance and virulence inside a sugary shield. J Antimicrob Chemother 2021; 76:305-311. [PMID: 33150386 DOI: 10.1093/jac/dkaa453] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 10/05/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND In Portugal, carbapenem-resistant Acinetobacter baumannii (CRAB) has been associated with ST98, ST103 and ST208 (Oxford Scheme, Oxf) and a clone has usually been associated with a particular period of time. These clonal shifts were primarily explained by an increased antimicrobial resistance profile. Here we explore genomic and biochemical differences among these and more recent clones, which could further explain the diversity and evolution of this species. METHODS A total of 116 CRAB isolates (2010-15), together with representatives of a previously described CRAB collection (4 isolates, 2001-06) were characterized by attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR) and MLST. Representatives of different FTIR-ATR/MLST clusters were selected for WGS (n = 13), which allowed the in silico extraction of resistance and virulence genes, capsule locus and SNP analysis. RESULTS A. baumannii clonal shifts of OXA-58-producing ST103Oxf (2001-04), OXA-40-producing ST98Oxf (2002-06), OXA-23-producing ST208Oxf (2006-10) and OXA-23-producing ST218Oxf (2010-15) were accompanied by an increase in AMR genes and virulence factors. FTIR-ATR clustering was congruent with sugar composition predicted from the capsular locus: a fucosamine cluster comprising ST98Oxf, ST103Oxf and a single ST218Oxf isolate; a pseudaminic acid cluster of ST208Oxf and ST1557Oxf isolates; and legionaminic acid, resembling the sialic acid from mammalian cells, in a cluster comprising ST218Oxf isolates. The whole-genome phylogenetic tree was congruent with MLST, with isolates presenting 5-28 938 SNPs. ST208Oxf and ST218Oxf presented ∼1900 SNPs while ST103Oxf and ST1557Oxf showed a greater number of SNPs (∼28 000). CONCLUSIONS Clonal shifts of CRAB were promoted, in our country, by consecutive virulence and AMR gene pool enlargement, together with features increasing pathogen-host adaptation. Worldwide dominance of ST218Oxf is supported by the combination of high AMR and virulence levels.
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Affiliation(s)
- Liliana Silva
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- ESALD, Instituto Politécnico de Castelo Branco, Castelo Branco, Portugal
| | - Filipa Grosso
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Carla Rodrigues
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Magdalena Ksiezarek
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Helena Ramos
- Hospital Geral de Santo António (HGSA), Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Freitas AR, Tedim AP, Duarte B, Elghaieb H, Abbassi MS, Hassen A, Read A, Alves V, Novais C, Peixe L. Linezolid-resistant (Tn6246::fexB-poxtA) Enterococcus faecium strains colonizing humans and bovines on different continents: similarity without epidemiological link. J Antimicrob Chemother 2021; 75:2416-2423. [PMID: 32607549 DOI: 10.1093/jac/dkaa227] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 04/09/2020] [Accepted: 04/29/2020] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES poxtA is the most recently described gene conferring acquired resistance to linezolid, a relevant antibiotic for treating enterococcal infections. We retrospectively screened for poxtA in diverse enterococci and aimed to characterize its genetic/genomic contexts. METHODS poxtA was screened by PCR in 812 enterococci from 458 samples (hospitals/healthy humans/wastewater/animals/retail food) obtained in Portugal/Angola/Tunisia (1996-2019). Antimicrobial susceptibility testing was performed for 13 antibiotics (EUCAST/CLSI). poxtA stability (∼500 generations), transfer (filter mating), clonality (SmaI-PFGE) and location (S1-PFGE/hybridization) were tested. WGS (Illumina-HiSeq) was performed for clonal representatives. RESULTS poxtA was detected in Enterococcus faecium from six samples (1.3%): a healthy human (rectal swab) in Porto, Portugal (ST32/2001); four farm cows (milk) in Mateur, Tunisia (ST1058/2015); and a hospitalized patient (faeces) in Matosinhos, Portugal (ST1058/2015). All expressed resistance to linezolid (MIC = 8 mg/L), chloramphenicol, tetracycline and erythromycin, with variable resistance to ciprofloxacin and streptomycin. ST1058-poxtA-carrying isolates from Tunisia and Portugal differed by two SNPs and had similar plasmid content. poxtA, located in an IS1216-flanked Tn6246-like element, co-hybridized with fexB on one or more plasmids per isolate (one to three plasmids of 30-100 kb), was stable after several generations and transferred only from ST1058. ST1058 strains carried resistance/virulence genes (Efmqnr/acm) possibly induced under selective quinolone treatment. CONCLUSIONS poxtA has been circulating in Portugal since at least 2001, corresponding to the oldest description worldwide to date. We also extend the reservoir of poxtA to bovines. The similar linezolid-resistant poxtA-carrying strains colonizing humans and livestock on different continents, and without a noticeable relationship, suggests a recent transmission event or convergent evolution of E. faecium populations in different hosts and geographic regions.
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Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Ana P Tedim
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Rio Hortega/Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladolid/Salamanca, Spain
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Unidade de Análises Clínicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Houyem Elghaieb
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Mohamed S Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj Cédria, Soliman, Tunisia
| | - Antónia Read
- Serviço de Patologia Clínica-Microbiologia, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Valquíria Alves
- Serviço de Patologia Clínica-Microbiologia, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Finisterra L, Duarte B, Peixe L, Novais C, Freitas AR. Industrial dog food is a vehicle of multidrug-resistant enterococci carrying virulence genes often linked to human infections. Int J Food Microbiol 2021; 358:109284. [PMID: 34144837 DOI: 10.1016/j.ijfoodmicro.2021.109284] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 05/25/2021] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
The increase in the number of pets in recent years has been followed by an exponential growth of the industrial pet food sector, which has been accompanied by new food safety risks, namely antibiotic resistance. The aim of this study was to investigate whether dog food commercially available in Portugal is a reservoir of clinically-relevant antibiotic resistant Enterococcus. Fifty-five samples (25 brands; 22 wet, 14 raw frozen, 8 dry, 7 treats and 4 semi-wet) were collected on 9 commercial surfaces in the Porto region (September 2019 to January 2020). Most samples were obtained from brands that are commercialized worldwide (n = 21/25). Sample (25 g) processing included pre-enrichment and enrichment steps in culture media without/with 3 antibiotics, and then plating into selective media without/with the same antibiotics. Susceptibility was studied for 13 antibiotics (disk diffusion; Etest; microdilution) according to EUCAST/CLSI. Clinically-relevant species (E. faecium and E. faecalis), antibiotic resistance (vanA, vanB, optrA, poxtA) and virulence (e.g. ptsD, esp, sgrA) genes were identified by PCR. Other species of Enterococcus were identified by MALDI-TOF MS. Clonality was established by MLST in selected isolates. Enterococcus (n = 184; 7 species; >85% E. faecium and E. faecalis) were detected in 30 samples (54%) of different types (14 raw, 16 heat treated-7 dry, 6 wet, 3 treats). E. faecium and E. faecalis were more frequent in dry and wet samples, respectively. More than 40% of enterococci recovered were resistant to erythromycin, tetracycline, quinupristin-dalfopristin, streptomycin, gentamicin, chloramphenicol, ampicillin or ciprofloxacin, and to a lesser extent to linezolid (23%; optrA, poxtA) or vancomycin and teicoplanin (2% each; vanA). Multidrug-resistant isolates (31%), including to vancomycin and linezolid, were obtained mostly from raw foods, although also detected in wet samples or treats, and mainly from culture media supplemented with antibiotics. Samples subjected to thermal treatment mostly carried non-MDR isolates. The variety of clones observed included strains previously identified in hospitalized patients (E. faecium ST17/ST80; E. faecalis ST40), farm animals, pets and environmental strains. This study shows that dog food from international brands is a vehicle of clinically-relevant enterococci carrying resistance to last resort antibiotics and relevant virulence genes, thus positioning pet food as an important source of antibiotic resistance spread within the One Health context. The high incidence of Enterococcus in a variety of dog food samples indicates the need to review selection of raw materials, manufacturing and hygiene practices in an emerging food sector growing worldwide.
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Affiliation(s)
- Liliana Finisterra
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; Departamento de Ciências Biológicas, Unidade de Análises Clínicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; ESCMID Food- and Water-borne Infections Study Group (EFWISG)
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; ESCMID Food- and Water-borne Infections Study Group (EFWISG).
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal; Departmento de Ciências, Instituto Universitário de Ciências da Saúde (IUCS), Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), CRL, Gandra, Portugal; ESCMID Food- and Water-borne Infections Study Group (EFWISG).
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Elghaieb H, Tedim AP, Abbassi MS, Novais C, Duarte B, Hassen A, Peixe L, Freitas AR. From farm to fork: identical clones and Tn6674-like elements in linezolid-resistant Enterococcus faecalis from food-producing animals and retail meat. J Antimicrob Chemother 2021; 75:30-35. [PMID: 31605129 DOI: 10.1093/jac/dkz419] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES Increasing numbers of linezolid-resistant Enterococcus carrying optrA are being reported across different niches worldwide. We aimed to characterize the first optrA-carrying Enterococcus faecalis obtained from food-producing animals and retail meat samples in Tunisia. METHODS Seven optrA-carrying E. faecalis obtained from chicken faeces (n=3, August 2017) and retail chicken meat (n=4, August 2017) in Tunisia were analysed. Antimicrobial susceptibility was determined by disc diffusion, broth microdilution and Etest against 13 antibiotics, linezolid and tedizolid, respectively (EUCAST/CLSI). optrA stability (∼600 bacterial generations), transfer (filter mating) and location (S1-PFGE/hybridization) were characterized. WGS (Illumina-HiSeq) was done for four representatives that were analysed through in silico and genomic mapping tools. RESULTS Four MDR clones carrying different virulence genes were identified in chicken faeces (ST476) and retail meat (the same ST476 clone plus ST21 and ST859) samples. MICs of linezolid and tedizolid were stably maintained at 8 and 1-2 mg/L, respectively. optrA was located in the same transferable chromosomal Tn6674-like element in ST476 and ST21 clones, similar to isolates from pigs in Malaysia and humans in China. ST859 carried a non-conjugative plasmid of ∼40 kb with an impB-fexA-optrA segment, similar to plasmids from pigs and humans in China. CONCLUSIONS The same chromosomal and transferable Tn6674-like element was identified in different E. faecalis clones from humans and animals. The finding of retail meat contaminated with the same linezolid-resistant E. faecalis strain obtained from a food-producing animal highlights the potential role of the food chain in the worrisome dissemination of optrA that can be stably maintained without selective pressure over generations.
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Affiliation(s)
- Houyem Elghaieb
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Ana P Tedim
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Grupo de Investigación Biomédica en Sepsis - BioSepsis, Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Mohamed S Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, 20 rue Jebel Lakhdhar, Bab Saadoun, Tunis, Tunisia
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Bárbara Duarte
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Departamento de Ciências Biológicas, Unidade de Análises Clínicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj Cédria, Soliman, Tunisia
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Ksiezarek M, Ugarcina-Perovic S, Rocha J, Grosso F, Peixe L. Long-term stability of the urogenital microbiota of asymptomatic European women. BMC Microbiol 2021; 21:64. [PMID: 33632119 PMCID: PMC7905919 DOI: 10.1186/s12866-021-02123-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/09/2021] [Indexed: 12/16/2022] Open
Abstract
Background To date, information on healthy female urinary microbiota is available mostly at genus level and at one time point. However, profound species-level characterization of healthy urinary microbiome and its stability over time are essential for further correct interpretation of its role in healthy urogenital tract. In this study, we investigated female urogenital microbiome (FUM) at two timepoints (within 2.5-year interval) in young asymptomatic European women. We used culturomics with accurate isolates’ identification (MALDI-TOF MS and gene markers sequencing) to understand species stability within healthy FUM. Results Extended culturomics of voided midstream urine sample pairs revealed a mean Shannon diversity index of 1.25 and mean of 19 species/sample (range 5–39 species; total of 115 species; 1830 isolates). High overall species variability between individuals was captured by beta diversity and a variety of community structure types, with the largest cluster characterized by Lactobacillus crispatus, often in combination with Gardnerella vaginalis or Gardnerella genomospecies 3. Significant FUM composition differences, related to Finegoldia magna and Streptococcus anginosus, according to smoking status were found. A high species variability within individuals (Shannon index SD > 0.5 in 7 out of 10 sample pairs) with a mean of 29% of shared species (range 9.1–41.7%) was observed. Moreover, 4 out of 10 sample pairs clustered in the same community structure type. The stable FUM sample pairs presented high abundance of Lactobacillus crispatus, Streptococcus agalactiae or Lactobacillus paragasseri and Bifidobacterium spp.. Moreover, Gardnerella vaginalis, Gardnerella genomospecies 3 or Gardnerella swidsinskii were often maintained within individuals in high abundance. Conclusions Shift in species composition at two distant timepoints was frequently observed among urogenital microbiome of European asymptomatic women. This suggests possible interchange of particular species in healthy FUM and the existence of multiple health-associated FUM compositions in certain individuals. Additionally, we provided additional evidence on resilience of particular bacterial communities and identified certain species more prone to persist in urogenital tract. This study revealed important details on the FUM composition complexity relevant for studies aiming to understand microbiota role in the urogenital tract health and for identification of eubiotic and dysbiotic FUM. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02123-3.
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Affiliation(s)
- Magdalena Ksiezarek
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Svetlana Ugarcina-Perovic
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Joana Rocha
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Filipa Grosso
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO-REQUIMTE. Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal.
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Antunes P, Novais C, Novais Â, Grosso F, Ribeiro TG, Mourão J, Perovic SU, Rebelo A, Ksiezarek M, Freitas AR, Peixe L. MicroMundo@UPorto: an experimental microbiology project fostering student's antimicrobial resistance awareness and personal and social development. FEMS Microbiol Lett 2021; 368:6141117. [PMID: 33595643 DOI: 10.1093/femsle/fnab016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/13/2021] [Indexed: 12/30/2022] Open
Abstract
Antimicrobial resistance (AMR) is a global societal challenge requiring the contribution of professionals along with general community citizens for their containment. Portugal is one of the European countries where a lack of knowledge on the correct use of antimicrobials and AMR problematic is preeminent. Moreover, youth demotivation to pursue science careers is emerging. To address these problems an innovative experimental service-learning pedagogical strategy, MicroMundo@UPorto, was implemented in Portugal during 2018 through University of Porto as a partner of the global Citizen Science project 'Tiny Earth' responding to the AMR crisis. In this first edition of MicroMundo@UPorto, university students (n = 41; Pharmaceutical Sciences and Nutrition Sciences) organized in eight teams tutored by university professors/researchers (n = 13) on Microbiology and AMR theoretical and practical aspects as well on communication skills to enable their guidance of younger school students (n = 140/3 schools) in experiments to discover antimicrobial-producing microorganisms while exploring the soil microbial diversity. Post-survey-based evaluation revealed that this project allowed university students to acquire diverse personal, social and scientific skills while increasing AMR awareness, in the One-Health perspective, and interest for science in school students. This University to Society approach can be successfully extended across Portugal and for education in Microbiology in general, with benefits for the future generations contributing to socially responsible and scientifically-literate citizens.
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Affiliation(s)
- Patrícia Antunes
- Faculty of Nutrition and Food Sciences, University of Porto. Rua do Campo Alegre, 823 / 4150-180 Porto Portugal.,UCIBIO/REQUIMTE, University of Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, University of Porto, Portugal.,Faculty of Pharmacy, University of Porto. Rua de Jorge Viterbo Ferreira n°. 228, 4050-313 Porto, Portugal
| | | | | | | | | | | | | | | | | | - Luísa Peixe
- UCIBIO/REQUIMTE, University of Porto, Portugal.,Faculty of Pharmacy, University of Porto. Rua de Jorge Viterbo Ferreira n°. 228, 4050-313 Porto, Portugal
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Freitas AR, Pereira AP, Novais C, Peixe L. Multidrug-resistant high-risk Enterococcus faecium clones: can we really define them? Int J Antimicrob Agents 2020; 57:106227. [PMID: 33207280 DOI: 10.1016/j.ijantimicag.2020.106227] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 10/26/2020] [Accepted: 11/07/2020] [Indexed: 12/13/2022]
Abstract
Enterococcus faecium is a significant opportunistic human pathogen with a broad host range, including humans, farm animals, pets and wildlife. Specialised subpopulations have globally evolved towards a powerful and convergent adaption to the healthcare environment by acquiring a cocktail of key antimicrobial resistance and virulence genes, enabling them to thrive in the disturbed microbiota of hospitalised patients. These populations can also be found in different community reservoirs, but the relevance of their dispersal in non-human hosts is greatly unknown and is here discussed. This review provides a brief historical overview of what we have been considering E. faecium high-risk clones worldwide alongside the advances in strain typing technologies that have revolutionised our understanding of the genetic evolution of this species over the last three decades.
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Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira n° 228, 4050-313 Porto, Portugal
| | - Ana P Pereira
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira n° 228, 4050-313 Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira n° 228, 4050-313 Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira n° 228, 4050-313 Porto, Portugal.
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38
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Guerra AM, Lira A, Lameirão A, Selaru A, Abreu G, Lopes P, Mota M, Novais Â, Peixe L. Multiplicity of Carbapenemase-Producers Three Years after a KPC-3-Producing K. pneumoniae ST147-K64 Hospital Outbreak. Antibiotics (Basel) 2020; 9:E806. [PMID: 33202755 PMCID: PMC7696612 DOI: 10.3390/antibiotics9110806] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/05/2020] [Accepted: 11/07/2020] [Indexed: 11/16/2022] Open
Abstract
Carbapenem resistance rates increased exponentially between 2014 and 2017 in Portugal (~80%), especially in Klebsiella pneumoniae. We characterized the population of carbapanemase-producing Enterobacterales (CPE) infecting or colonizing hospitalized patients (2017-2018) in a central hospital from northern Portugal, where KPC-3-producing K. pneumoniae capsular type K64 has caused an initial outbreak. We gathered phenotypic (susceptibility data), molecular (population structure, carbapenemase, capsular type) and biochemical (FT-IR) data, together with patients' clinical and epidemiological information. A high diversity of Enterobacterales species, clones (including E. coli ST131) and carbapenemases (mainly KPC-3 but also OXA-48 and VIM) was identified three years after the onset of carbapenemases spread in the hospital studied. ST147-K64 K. pneumoniae, the initial outbreak clone, is still predominant though other high-risk clones have emerged (e.g., ST307, ST392, ST22), some of them with pandrug resistance profiles. Rectal carriage, previous hospitalization or antibiotherapy were presumptively identified as risk factors for subsequent infection. In addition, our previously described Fourier Transform infrared (FT-IR) spectroscopy method typed 94% of K. pneumoniae isolates with high accuracy (98%), and allowed to identify previously circulating clones. This work highlights an increasing diversity of CPE infecting or colonizing patients in Portugal, despite the infection control measures applied, and the need to improve the accuracy and speed of bacterial strain typing, a goal that can be met by simple and cost-effective FT-IR based typing.
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Affiliation(s)
| | - Agostinho Lira
- Centro Hospitalar Vila Nova de Gaia/Espinho, 4434-502 Vila Nova de Gaia, Portugal; (A.L.); (A.L.); (A.S.); (G.A.); (P.L.); (M.M.)
| | - Angelina Lameirão
- Centro Hospitalar Vila Nova de Gaia/Espinho, 4434-502 Vila Nova de Gaia, Portugal; (A.L.); (A.L.); (A.S.); (G.A.); (P.L.); (M.M.)
| | - Aurélia Selaru
- Centro Hospitalar Vila Nova de Gaia/Espinho, 4434-502 Vila Nova de Gaia, Portugal; (A.L.); (A.L.); (A.S.); (G.A.); (P.L.); (M.M.)
| | - Gabriela Abreu
- Centro Hospitalar Vila Nova de Gaia/Espinho, 4434-502 Vila Nova de Gaia, Portugal; (A.L.); (A.L.); (A.S.); (G.A.); (P.L.); (M.M.)
| | - Paulo Lopes
- Centro Hospitalar Vila Nova de Gaia/Espinho, 4434-502 Vila Nova de Gaia, Portugal; (A.L.); (A.L.); (A.S.); (G.A.); (P.L.); (M.M.)
| | - Margarida Mota
- Centro Hospitalar Vila Nova de Gaia/Espinho, 4434-502 Vila Nova de Gaia, Portugal; (A.L.); (A.L.); (A.S.); (G.A.); (P.L.); (M.M.)
| | - Ângela Novais
- UCIBIO, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal;
| | - Luísa Peixe
- UCIBIO, Faculdade de Farmácia, Universidade do Porto, 4050-313 Porto, Portugal;
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Botelho J, Mourão J, Roberts AP, Peixe L. Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria. Microb Genom 2020; 6:mgen000424. [PMID: 32841111 PMCID: PMC7660259 DOI: 10.1099/mgen.0.000424] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 08/02/2020] [Indexed: 12/24/2022] Open
Abstract
Carbapenemases inactivate most β-lactam antibiotics, including carbapenems, and have frequently been reported among Enterobacteriaceae, Acinetobacter spp. and Pseudomonas spp. Traditionally, the horizontal gene transfer of carbapenemase-encoding genes (CEGs) has been linked to plasmids. However, given that integrative and conjugative elements (ICEs) are possibly the most abundant conjugative elements among prokaryotes, we conducted an in silico analysis to ascertain the likely role of ICEs in the spread of CEGs among all bacterial genomes (n=182 663). We detected 17 520 CEGs, of which 66 were located within putative ICEs among several bacterial species (including clinically relevant bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae and Escherichia coli). Most CEGs detected within ICEs belong to the IMP, NDM and SPM metallo-beta-lactamase families, and the serine beta-lactamase KPC and GES families. Different mechanisms were likely responsible for acquisition of these genes. The majority of CEG-bearing ICEs belong to the MPFG, MPFT and MPFF classes and often encode resistance to other antibiotics (e.g. aminoglycosides and fluoroquinolones). This study provides a snapshot of the different CEGs associated with ICEs among available bacterial genomes and sheds light on the underappreciated contribution of ICEs to the spread of carbapenem resistance globally.
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Affiliation(s)
- João Botelho
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
- Present address: Antibiotic Resistance Evolution Group, Max-Planck-Institute for Evolutionary Biology, 24306 Plön, Germany; Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts-Universität zu Kiel, 24118 Kiel, Germany
| | - Joana Mourão
- University of Coimbra, Center for Innovative Biomedicine and Biotechnology, Coimbra, Portugal
- University of Coimbra, Center for Neuroscience and Cell Biology, Coimbra, Portugal
- University of Coimbra, Institute for Interdisciplinary Research, Coimbra, Portugal
| | - Adam P. Roberts
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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40
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Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Atypical Non-H 2S-Producing Monophasic Salmonella Typhimurium ST3478 Strains from Chicken Meat at Processing Stage Are Adapted to Diverse Stresses. Pathogens 2020; 9:pathogens9090701. [PMID: 32859122 PMCID: PMC7557518 DOI: 10.3390/pathogens9090701] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 01/23/2023] Open
Abstract
Poultry products are still an important cause of Salmonella infections worldwide, with an increasingly reported expansion of less-frequent serotypes or atypical strains that are frequently multidrug-resistant. Nevertheless, the ability of Salmonella to survive antimicrobials promoted in the context of antibiotic reducing/replacing and farming rethinking (e.g., organic acids and copper in feed/biocides) has been scarcely explored. We investigated Salmonella occurrence (conventional and molecular assays) among chicken meat at the processing stage (n = 53 batches/29 farms) and characterized their tolerance to diverse stress factors (antibiotics, copper, acid pH, and peracetic acid). Whole-genome sequencing was used to assess adaptive features and to perform comparative analysis. We found a low Salmonella occurrence (4%) and identified S. Enteritidis/ST11 plus atypical non-H2S-producing S. 1,4,[5],12:i:-/ST3478. The ST3478 presented the ability to grow under diverse stresses (antibiotics, copper, and acid-pH). Comparative genomics among ST3478 isolates showed similar antibiotic/metal resistance gene repertoires and identical nonsense phsA thiosulfate reductase mutations (related to H2S-negative phenotype), besides their close phylogenetic relationship by cgMLST and SNPs. This study alerts for the ongoing national and international spread of an emerging monophasic Salmonella Typhimurium clonal lineage with an enlarged ability to survive to antimicrobials/biocides commonly used in poultry production, being unnoticed by conventional Salmonella detection approaches due to an atypical non-H2S-producing phenotype.
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Affiliation(s)
- Joana Mourão
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
- Institute for Interdisciplinary Research, University of Coimbra, 3030-789 Coimbra, Portugal
| | - Andreia Rebelo
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- Scientific Area of Environmental Health, School of Health, Polytechnic Institute of Porto, 4200-465 Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- ESCMID Food- and Water-borne Infections Study Group (EFWISG), 4010 Basel, Switzerland
| | - Carla Novais
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- ESCMID Food- and Water-borne Infections Study Group (EFWISG), 4010 Basel, Switzerland
| | - Patrícia Antunes
- UCIBIO/REQUIMTE, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (J.M.); (A.R.); (S.R.); (L.P.); (C.N.)
- ESCMID Food- and Water-borne Infections Study Group (EFWISG), 4010 Basel, Switzerland
- Faculty of Nutrition and Food Sciences, University of Porto, 4150-180 Porto, Portugal
- Correspondence: ; Tel.: +351-507-4320
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Elghaieb H, Freitas AR, Abbassi MS, Novais C, Zouari M, Hassen A, Peixe L. Dispersal of linezolid-resistant enterococci carrying poxtA or optrA in retail meat and food-producing animals from Tunisia. J Antimicrob Chemother 2020; 74:2865-2869. [PMID: 31243458 DOI: 10.1093/jac/dkz263] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 05/02/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022] Open
Abstract
OBJECTIVES The epidemiology of Enterococcus resistant to priority antibiotics including linezolid has mainly been investigated in developed countries and especially in hospitals. We aimed to evaluate the contribution of different non-human reservoirs for the burden of MDR enterococci in Tunisia, where scarce data are available. METHODS Samples (n = 287) were collected from urban wastewater (n = 57), retail meat (n = 29; poultry/bovine/ovine), milk (n = 89; bovine/ovine), farm animal faeces (n = 80; poultry/bovine/ovine) and pets (n = 32; rabbit/dogs/cats/birds) in different Tunisian regions (2014-17). They were plated onto Slanetz-Bartley agar after pre-enrichment without antibiotics. Standard methods were used for bacterial identification and characterization of antibiotic resistance and virulence genes (PCR), antibiotic susceptibility testing (disc diffusion/broth microdilution; EUCAST/CLSI) and clonality (SmaI-PFGE/MLST). RESULTS All samples carried Enterococcus (n = 377 isolates) resistant to antibiotics considered to be critical or highly important by WHO. Even without antibiotic selection, 38% of Enterococcus faecalis (Efs) and 22% of Enterococcus faecium (Efm) were identified as MDR. Linezolid-resistant isolates (5%; MIC = 8 mg/L) comprised six poxtA-carrying Efm (cow milk), seven optrA-carrying Efs (chicken faeces/meat) and five Efm lacking cfr/optrA/poxtA (poultry/bovine/ovine/wastewater). Clinically relevant Efm clones (clade A1) were identified in animal/meat sources. Ampicillin resistance (1%) was confined to ST18/ST78-like MDR Efm clones from bovine meat/milk samples carrying relevant virulence markers (e.g. ptsD/IS16). CONCLUSIONS This study provides evidence of the contribution of livestock and foodstuffs to the dispersal of acquired linezolid resistance genes including poxtA and optrA. We report the first poxtA-carrying Efm in Tunisia, and for the first time in bovine samples, stressing the urgent need for alternative measures to counteract the spread of linezolid-resistant enterococci globally.
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Affiliation(s)
- Houyem Elghaieb
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, Tunis, Tunisia
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Mohamed Salah Abbassi
- Université de Tunis El Manar, Institut de la Recherche Vétérinaire de Tunisie, Tunis, Tunisia
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | | | - Abdennaceur Hassen
- Laboratoire de Traitement des Eaux Usées, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj Cédria, Hammam-Lif, Tunisia
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Ribeiro TG, Rocha J, Ksiezarek M, Perovic SU, Grosso F, Peixe L. The status of the species Lactobacillus fornicalis Dicks et al. 2000. Request for an opinion. Int J Syst Evol Microbiol 2020; 70:3953-3954. [PMID: 32515725 DOI: 10.1099/ijsem.0.004259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During a recent study on members of the genus Lactobacillus we realized that cultures of Lactobacillus fornicalis TV 1018T (=DSM 13171T=ATCC 700934T) are no longer available from the online catalogue of the German Collection of Microorganisms and Cell Cultures GmbH, being displayed as Lactobacillus plantarum at the American Type Culture Collection. Based on data currently available, the organism deposited as ATCC 700934T is a member of the species Lactobacillus plantarum subs. plantarum. Therefore, the type strain of Lactobacillus fornicalis cannot be included in any further scientific comparative study. This matter is referred to the Judicial Commission, asking for an opinion on the status of the species.
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Affiliation(s)
- Teresa Gonçalves Ribeiro
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Joana Rocha
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Magdalena Ksiezarek
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Svetlana Ugarcina Perovic
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Filipa Grosso
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
| | - Luísa Peixe
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Portugal
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Freitas AR, Novais C, Coque TM, Peixe L. Comment on: Emergence of plasmid-mediated oxazolidinone resistance gene poxtA from CC17 Enterococcus faecium of pig origin. J Antimicrob Chemother 2020; 75:1358-1359. [PMID: 31617898 DOI: 10.1093/jac/dkz432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Teresa M Coque
- Servicio de Microbiologia, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.,Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBER-ESP), Madrid, Spain.,Unidad de Resistencia a Antibióticos y Virulencia Bacteriana asociada al Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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Mourão J, Rebelo A, Ribeiro S, Peixe L, Novais C, Antunes P. Tolerance to arsenic contaminant among multidrug‐resistant and copper‐tolerant
Salmonella
successful clones is associated with diverse
ars
operons and genetic contexts. Environ Microbiol 2020; 22:2829-2842. [DOI: 10.1111/1462-2920.15016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/13/2020] [Accepted: 04/08/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Joana Mourão
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Center for Innovative Biomedicine and BiotechnologyUniversity of Coimbra Coimbra Portugal
- Center for Neuroscience and Cell BiologyUniversity of Coimbra Coimbra Portugal
- Institute for Interdisciplinary Research, University of Coimbra Coimbra Portugal
| | - Andreia Rebelo
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Scientific Area of Environmental HealthSchool of Health, Polytechnic Institute of Porto Porto Portugal
| | - Sofia Ribeiro
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Carla Novais
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
| | - Patrícia Antunes
- UCIBIO/REQUIMTEDepartment of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto Porto Portugal
- Faculty of Nutrition and Food SciencesUniversity of Porto Porto Portugal
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Freitas AR, Tedim AP, Novais C, Lanza VF, Peixe L. Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes. Microb Genom 2020; 6. [PMID: 32149599 PMCID: PMC7371108 DOI: 10.1099/mgen.0.000350] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if optrA is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 27 publicly available optrA-positive E. faecalis genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from Firmicutes. Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010–2017) could be phylogenetically related (3–126 SNPs difference). optrA was located on the chromosome within a Tn6674-like element (n=10) or on medium-size plasmids (30–60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was generally identical in chromosomal (Tn6674) or plasmid (impB-fexA-optrA) backbones. Tn6674 was always inserted into the same ∆radC integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012–2017. This platform is conserved among hundreds of E. faecalis genomes and proposed as a chromosomal hotspot for optrA integration. The finding of optrA in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.
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Affiliation(s)
- Ana R Freitas
- UCIBIO/REQUIMTE. Departamento de Ciências Biológicas. Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto. Porto, Porto, Portugal
| | - Ana P Tedim
- Grupo de Investigación Biomédica en Sepsis - BioSepsis. Hospital Universitario Río Hortega, Instituto de Investigación Biomédica de Salamanca (IBSAL), Valladollid, Spain
| | - Carla Novais
- UCIBIO/REQUIMTE. Departamento de Ciências Biológicas. Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto. Porto, Porto, Portugal
| | - Val F Lanza
- Departamento de Bioinformática. Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Luísa Peixe
- UCIBIO/REQUIMTE. Departamento de Ciências Biológicas. Laboratório de Microbiologia. Faculdade de Farmácia. Universidade do Porto. Porto, Porto, Portugal
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Rocha J, Botelho J, Ksiezarek M, Perovic SU, Machado M, Carriço JA, Pimentel LL, Salsinha S, Rodríguez-Alcalá LM, Pintado M, Ribeiro TG, Peixe L. Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group. Int J Syst Evol Microbiol 2020; 70:1522-1527. [DOI: 10.1099/ijsem.0.003901] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
One Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, and coccobacilli-shaped strain, designated c10Ua161MT, was isolated from a urine sample from a reproductive-age healthy woman. Comparative 16S rRNA gene sequence analysis indicated that strain c10Ua161MT belonged to the genus
Lactobacillus
. Phylogenetic analysis based on pheS and rpoA gene sequences strongly supported a clade encompassing strains c10Ua161MT and eight other strains from public databases, distinct from currently recognized species of the genus Lactobacillus. In silico Average Nucleotide Identity (ANI) and Genome-to-Genome Distance Calculator (GGDC), showed 87.9 and 34.3 % identity to the closest relative
Lactobacillus jensenii
, respectively. The major fatty acids of strain c10Ua161MT were C18 : 1ω9c (65.0%), C16 : 0 (17.8%), and summed feature 8 (10.2 %; comprising C18 : 1ω7c, and/or C18 : 1ω6c). The DNA G+C content of the strains is 34.2 mol%. On the basis of data presented here, strain c10Ua161MT represents a novel species of the genus
Lactobacillus
, for which the name Lactobacillus mulieris sp. nov. is proposed. The type strain is c10Ua161MT (=CECT 9755T=DSM 108704T).
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Affiliation(s)
- Joana Rocha
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - João Botelho
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Magdalena Ksiezarek
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Svetlana Ugarcina Perovic
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Miguel Machado
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - João André Carriço
- Instituto de Microbiologia, Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Lígia L. Pimentel
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Sofia Salsinha
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Luís M. Rodríguez-Alcalá
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Manuela Pintado
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa, Porto, Portugal
| | - Teresa G. Ribeiro
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO-REQUIMTE. Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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47
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Novais C, Freitas AR, León-Sampedro R, Peixe L, Coque TM. Methods to Quantify DNA Transfer in Enterococcus. Methods Mol Biol 2020; 2075:111-122. [PMID: 31584158 DOI: 10.1007/978-1-4939-9877-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA uptake in Enterococcus normally occurs by conjugation, a natural process that is replicated in biomedical research to assess the transferability of different mobile genetic elements and chromosomal regions as well as to study the host range of plasmids and other conjugative elements. More efficient artificial methods to transform cells with foreign DNA as chemotransformation and electroporation are widely used in molecular genetics. Here, we described conjugation protocols to quantify DNA transfer among Enterococcus and revise current perspectives and lab strains. Protocols of electrotransformation have been previously described in this series.
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Affiliation(s)
- Carla Novais
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, UCIBIO/REQUIMTE, University of Porto, Porto, Portugal.
| | - Ana R Freitas
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, UCIBIO/REQUIMTE, University of Porto, Porto, Portugal
| | - Ricardo León-Sampedro
- Department of Microbiology, Ramón y Cajal Health Research Institute (IRYCIS), Unidad de Resistencia a Antibióticos y Virulencia Bacteriana (RYC-CSIC), CIBER en Epidemiología y Salud Pública (CIBER-ESP), Ramón y Cajal University Hospital, Madrid, Spain
| | - Luísa Peixe
- Laboratory of Microbiology, Biological Sciences Department, Faculty of Pharmacy, UCIBIO/REQUIMTE, University of Porto, Porto, Portugal
| | - Teresa M Coque
- Department of Microbiology, Ramón y Cajal Research Institute (IRYCIS), Madrid, Spain.
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain.
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48
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Abstract
Microorganisms vehiculated by food might benefit health, cause minimal change within the equilibrium of the host microbial community or be associated with foodborne diseases. In this chapter we will focus on human pathogenic bacteria for which food is conclusively demonstrated as their transmission mode to human. We will describe the impact of foodborne diseases in public health, the reservoirs of foodborne pathogens (the environment, human and animals), the main bacterial pathogens and food vehicles causing human diseases, and the drivers for the transmission of foodborne diseases related to the food-chain, host or bacteria features. The implication of food-chain (foodborne pathogens and commensals) in the transmission of resistance to antibiotics relevant to the treatment of human infections is also evidenced. The multiplicity and interplay of drivers related to intensification, diversification and globalization of food production, consumer health status, preferences, lifestyles or behaviors, and bacteria adaptation to different challenges (stress tolerance and antimicrobial resistance) from farm to human, make the prevention of bacteria-food-human transmission a modern and continuous challenge. A global One Health approach is mandatory to better understand and minimize the transmission pathways of human pathogens, including multidrug-resistant pathogens and commensals, through food-chain.
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Affiliation(s)
- Patrícia Antunes
- Faculdade de Ciências da Nutrição e Alimentação, Universidade do Porto, Porto, Portugal
| | - Carla Novais
- Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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49
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Botelho J, Lood C, Partridge SR, van Noort V, Lavigne R, Grosso F, Peixe L. Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain. Emerg Microbes Infect 2019; 8:1186-1194. [PMID: 31381486 PMCID: PMC6713103 DOI: 10.1080/22221751.2019.1648182] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Horizontal transfer of plasmids plays a pivotal role in dissemination of antibiotic resistance genes and emergence of multidrug-resistant bacteria. Plasmid sequencing is thus paramount for accurate epidemiological tracking in hospitals and routine surveillance. Combining Nanopore and Illumina sequencing allowed full assembly of a carbapenemase-encoding megaplasmid carried by multidrug-resistant clinical isolate FFUP_PS_41. Average nucleotide identity analyses revealed that FFUP_PS_41 belongs to the recently proposed new species Pseudomonas shirazica, related to the P. putida phylogenetic group. FFUP_PS_41 harbours a 498,516-bp megaplasmid (pJBCL41) with limited similarity to publicly-available plasmids. pJBCL41 contains genes predicted to encode replication, conjugation, partitioning and maintenance functions and heavy metal resistance. The |aacA7|blaVIM-2|aacA4| cassette array (resistance to carbapenems and aminoglycosides) is located within a class 1 integron that is a defective Tn402 derivative. This transposon lies within a 50,273-bp region bound by Tn3-family 38-bp inverted repeats and flanked by 5-bp direct repeats (DR) that composes additional transposon fragments, five insertion sequences and a Tn3-Derived Inverted-Repeat Miniature Element. The hybrid Nanopore/Illumina approach allowed full resolution of a carbapenemase-encoding megaplasmid from P. shirazica. Identification of novel megaplasmids sheds new light on the evolutionary effects of gene transfer and the selective forces driving antibiotic resistance.
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Affiliation(s)
- João Botelho
- a UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto , Porto , Portugal
| | - Cédric Lood
- b Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven , Leuven , Belgium.,c Laboratory of Gene Technology, Department of Biosystems, KU Leuven , Leuven , Belgium
| | - Sally R Partridge
- d Centre for Microbiology and Infectious Diseases, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital , Sydney , Australia
| | - Vera van Noort
- b Centre of Microbial and Plant Genetics, Department of Microbial and Molecular Systems, KU Leuven , Leuven , Belgium.,e Institute of Biology, Leiden University , Leiden , The Netherlands
| | - Rob Lavigne
- c Laboratory of Gene Technology, Department of Biosystems, KU Leuven , Leuven , Belgium
| | - Filipa Grosso
- a UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto , Porto , Portugal
| | - Luísa Peixe
- a UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto , Porto , Portugal
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50
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Trigo da Roza F, Couto N, Carneiro C, Cunha E, Rosa T, Magalhães M, Tavares L, Novais Â, Peixe L, Rossen JW, Lamas LP, Oliveira M. Commonality of Multidrug-Resistant Klebsiella pneumoniae ST348 Isolates in Horses and Humans in Portugal. Front Microbiol 2019; 10:1657. [PMID: 31379799 PMCID: PMC6657530 DOI: 10.3389/fmicb.2019.01657] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 07/04/2019] [Indexed: 11/17/2022] Open
Abstract
Multidrug-resistant (MDR) Klebsiella pneumoniae is considered a major global concern by the World Health Organization. Evidence is growing on the importance of circulation of MDR bacterial populations between animals and humans. Horses have been shown to carry commensal isolates of this bacterial species and can act as human MDR bacteria reservoirs. In this study, we characterized an extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae sequence type (ST) 348 isolate from a horse, an ST reported for the first time in an animal, using next-generation sequencing. We compared it with six other MDR K. pneumoniae ST348 human isolates previously identified in health-care facilities in Portugal using a core genome multi-locus sequence typing approach to evaluate a possible genetic link. The horse isolate was resistant to most of the antimicrobials tested, including 3rd generation cephalosporins, fluoroquinolones, and aminoglycosides, and presented several antimicrobial resistance genes, including blaESBL. Twenty-one allele differences were found between the horse isolate and the most similar human isolate, suggesting a recent common ancestor. Other similarities were observed regarding the content on antimicrobial resistance genes, plasmid incompatibility groups, and capsular and somatic antigens. This study illustrates the relevance of the dissemination of MDR strains, and enhances that identification of these types of bacterial strains in both human and veterinary settings is of significant relevance in order to understand and implement combined control strategies for MDR bacteria in animals and humans.
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Affiliation(s)
- Filipa Trigo da Roza
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Carla Carneiro
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Eva Cunha
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Teresa Rosa
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Mariana Magalhães
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Luís Tavares
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Ângela Novais
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - John W Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Luís P Lamas
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
| | - Manuela Oliveira
- CIISA-Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
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