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Pasquali F, Crippa C, Parisi A, Lucchi A, Gambi L, Merlotti A, Remondini D, Stonfer M, Manfreda G. Genetic Diversity and Antimicrobial Resistance of Extraintestinal E. coli Populations Pre- and Post-Antimicrobial Therapy on Broilers Affected by Colisepticemia. Animals (Basel) 2023; 13:2590. [PMID: 37627381 PMCID: PMC10451725 DOI: 10.3390/ani13162590] [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] [Received: 06/28/2023] [Revised: 07/31/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The aim of the present study was to investigate the genetic diversity and antimicrobial resistance (AMR) of E. coli during enrofloxacin therapy in broilers affected by colisepticemia. Three unrelated farms with ongoing colibacillosis outbreaks were sampled at day 1 before treatment and at days 5, 10 and 24 post-treatment. A total of 179 E. coli isolates were collected from extraintestinal organs and submitted to serotyping, PFGE and the minimum inhibitory concentration (MIC) against enrofloxacin. PFGE clusters shifted from 3-6 at D1 to 10-16 at D5, D10 and D24, suggesting an increased population diversity after the treatment. The majority of strains belonged to NT or O78 and to ST117 or ST23. PFGE results were confirmed with SNP calling: no persistent isolates were identified. An increase in resistance to fluoroquinolones in E. coli isolates was observed along the treatment. Resistome analyses revealed qnrB19 and qnrS1 genes along with mutations in the gyrA, parC and parE genes. Interestingly, despite a fluoroquinolone selective pressure, qnr-carrying plasmids did not persist. On the contrary, two conjugative AMR plasmid clusters (AB233 and AA474) harboring AMR genes other than qnr were persistent since they were identified in both D1 and D10 genomes in two farms. Further studies should be performed in order to confirm plasmid persistence not associated (in vivo) to antimicrobial selective pressure.
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Affiliation(s)
- Frédérique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum–University of Bologna, 40126 Bologna, Italy (A.L.); (L.G.); (G.M.)
| | - Cecilia Crippa
- Department of Agricultural and Food Sciences, Alma Mater Studiorum–University of Bologna, 40126 Bologna, Italy (A.L.); (L.G.); (G.M.)
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale di Puglia e Basilicata, 71121 Foggia, Italy;
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum–University of Bologna, 40126 Bologna, Italy (A.L.); (L.G.); (G.M.)
| | - Lucia Gambi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum–University of Bologna, 40126 Bologna, Italy (A.L.); (L.G.); (G.M.)
| | - Alessandra Merlotti
- Department of Physics and Astronomy, Alma Mater Studiorum–University of Bologna, 40126 Bologna, Italy; (A.M.); (D.R.)
| | - Daniel Remondini
- Department of Physics and Astronomy, Alma Mater Studiorum–University of Bologna, 40126 Bologna, Italy; (A.M.); (D.R.)
| | | | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, Alma Mater Studiorum–University of Bologna, 40126 Bologna, Italy (A.L.); (L.G.); (G.M.)
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Majewski P, Gutowska A, Smith DGE, Hauschild T, Majewska P, Hryszko T, Gizycka D, Kedra B, Kochanowicz J, Glowiński J, Drewnowska J, Swiecicka I, Sacha PT, Wieczorek P, Iwaniuk D, Sulewska A, Charkiewicz R, Makarewicz K, Zebrowska A, Czaban S, Radziwon P, Niklinski J, Tryniszewska EA. Plasmid Mediated mcr-1.1 Colistin-Resistance in Clinical Extraintestinal Escherichia coli Strains Isolated in Poland. Front Microbiol 2021; 12:547020. [PMID: 34956105 PMCID: PMC8703133 DOI: 10.3389/fmicb.2021.547020] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/02/2021] [Indexed: 01/27/2023] Open
Abstract
Objectives: The growing incidence of multidrug-resistant (MDR) bacteria is an inexorable and fatal challenge in modern medicine. Colistin is a cationic polypeptide considered a “last-resort” antimicrobial for treating infections caused by MDR Gram-negative bacterial pathogens. Plasmid-borne mcr colistin resistance emerged recently, and could potentially lead to essentially untreatable infections, particularly in hospital and veterinary (livestock farming) settings. In this study, we sought to establish the molecular basis of colistin-resistance in six extraintestinal Escherichia coli strains. Methods: Molecular investigation of colistin-resistance was performed in six extraintestinal E. coli strains isolated from patients hospitalized in Medical University Hospital, Bialystok, Poland. Complete structures of bacterial chromosomes and plasmids were recovered with use of both short- and long-read sequencing technologies and Unicycler hybrid assembly. Moreover, an electrotransformation assay was performed in order to confirm IncX4 plasmid influence on colistin-resistance phenotype in clinical E. coli strains. Results: Here we report on the emergence of six mcr-1.1-producing extraintestinal E. coli isolates with a number of virulence factors. Mobile pEtN transferase-encoding gene, mcr-1.1, has been proved to be encoded within a type IV secretion system (T4SS)-containing 33.3 kbp IncX4 plasmid pMUB-MCR, next to the PAP2-like membrane-associated lipid phosphatase gene. Conclusion: IncX4 mcr-containing plasmids are reported as increasingly disseminated among E. coli isolates, making it an “epidemic” plasmid, responsible for (i) dissemination of colistin-resistance determinants between different E. coli clones, and (ii) circulation between environmental, industrial, and clinical settings. Great effort needs to be taken to avoid further dissemination of plasmid-mediated colistin resistance among clinically relevant Gram-negative bacterial pathogens.
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Affiliation(s)
- Piotr Majewski
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Anna Gutowska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - David G E Smith
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Tomasz Hauschild
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | | | - Tomasz Hryszko
- Second Department of Nephrology and Hypertension with Dialysis Unit, Medical University of Białystok, Białystok, Poland
| | - Dominika Gizycka
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Boguslaw Kedra
- Second Department of General and Gastroenterological Surgery, Medical University of Białystok, Białystok, Poland
| | - Jan Kochanowicz
- Department of Neurology, Medical University of Białystok, Białystok, Poland
| | - Jerzy Glowiński
- Department of Vascular Surgery and Transplantation, Medical University of Białystok, Białystok, Poland
| | - Justyna Drewnowska
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | - Izabela Swiecicka
- Department of Microbiology, Institute of Biology, University of Białystok, Białystok, Poland
| | - Pawel T Sacha
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Piotr Wieczorek
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Dominika Iwaniuk
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
| | - Anetta Sulewska
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | - Radoslaw Charkiewicz
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | | | | | - Slawomir Czaban
- Department of Anesthesiology and Intensive Care, Medical University of Białystok, Białystok, Poland
| | - Piotr Radziwon
- Regional Centre for Transfusion Medicine, Białystok, Poland.,Department of Hematology, Medical University of Białystok, Białystok, Poland
| | - Jacek Niklinski
- Department of Clinical Molecular Biology, Medical University of Białystok, Białystok, Poland
| | - Elzbieta A Tryniszewska
- Department of Microbiological Diagnostics and Infectious Immunology, Medical University of Białystok, Białystok, Poland
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Książczyk M, Dudek B, Kuczkowski M, O'Hara R, Korzekwa K, Wzorek A, Korzeniowska-Kowal A, Upton M, Junka A, Wieliczko A, Ratajszczak R, Bugla-Płoskońska G. The Phylogenetic Structure of Reptile, Avian and Uropathogenic Escherichia coli with Particular Reference to Extraintestinal Pathotypes. Int J Mol Sci 2021; 22:1192. [PMID: 33530493 DOI: 10.3390/ijms22031192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/14/2020] [Accepted: 12/18/2020] [Indexed: 11/24/2022] Open
Abstract
The impact of the Gram-negative bacterium Escherichia coli (E. coli) on the microbiomic and pathogenic phenomena occurring in humans and other warm-blooded animals is relatively well-recognized. At the same time, there are scant data concerning the role of E. coli strains in the health and disease of cold-blooded animals. It is presently known that reptiles are common asymptomatic carriers of another human pathogen, Salmonella, which, when transferred to humans, may cause a disease referred to as reptile-associated salmonellosis (RAS). We therefore hypothesized that reptiles may also be carriers of specific E. coli strains (reptilian Escherichia coli, RepEC) which may differ in their genetic composition from the human uropathogenic strain (UPEC) and avian pathogenic E. coli (APEC). Therefore, we isolated RepECs (n = 24) from reptile feces and compared isolated strains’ pathogenic potentials and phylogenic relations with the aforementioned UPEC (n = 24) and APEC (n = 24) strains. To this end, we conducted an array of molecular analyses, including determination of the phylogenetic groups of E. coli, virulence genotyping, Pulsed-Field Gel Electrophoresis-Restriction Analysis (RA-PFGE) and genetic population structure analysis using Multi-Locus Sequence Typing (MLST). The majority of the tested RepEC strains belonged to nonpathogenic phylogroups, with an important exception of one strain, which belonged to the pathogenic group B2, typical of extraintestinal pathogenic E. coli. This strain was part of the globally disseminated ST131 lineage. Unlike RepEC strains and in line with previous studies, a high percentage of UPEC strains belonged to the phylogroup B2, and the percentage distribution of phylogroups among the tested APEC strains was relatively homogenous, with most coming from the following nonpathogenic groups: C, A and B1. The RA-PFGE displayed a high genetic diversity among all the tested E. coli groups. In the case of RepEC strains, the frequency of occurrence of virulence genes (VGs) was lower than in the UPEC and APEC strains. The presented study is one of the first attempting to compare the phylogenetic structures of E. coli populations isolated from three groups of vertebrates: reptiles, birds and mammals (humans).
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Delannoy S, Beutin L, Mariani-Kurkdjian P, Fleiss A, Bonacorsi S, Fach P. The Escherichia coli Serogroup O1 and O2 Lipopolysaccharides Are Encoded by Multiple O-antigen Gene Clusters. Front Cell Infect Microbiol 2017; 7:30. [PMID: 28224115 PMCID: PMC5293828 DOI: 10.3389/fcimb.2017.00030] [Citation(s) in RCA: 14] [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: 11/21/2016] [Accepted: 01/23/2017] [Indexed: 01/10/2023] Open
Abstract
Escherichia coli strains belonging to serogroups O1 and O2 are frequently associated with human infections, especially extra-intestinal infections such as bloodstream infections or urinary tract infections. These strains can be associated with a large array of flagellar antigens. Because of their frequency and clinical importance, a reliable detection of E. coli O1 and O2 strains and also the frequently associated K1 capsule is important for diagnosis and source attribution of E. coli infections in humans and animals. By sequencing the O-antigen clusters of various O1 and O2 strains we showed that the serogroups O1 and O2 are encoded by different sets of O-antigen encoding genes and identified potentially new O-groups. We developed qPCR-assays to detect the various O1 and O2 variants and the K1-encoding gene. These qPCR assays proved to be 100% sensitive and 100% specific and could be valuable tools for the investigations of zoonotic and food-borne infection of humans with O1 and O2 extra-intestinal (ExPEC) or Shiga toxin-producing E. coli (STEC) strains.
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Affiliation(s)
- Sabine Delannoy
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
| | - Lothar Beutin
- National Reference Laboratory for Escherichia coli, Federal Institute for Risk Assessment (BfR)Berlin, Germany; Department of Biology, Chemistry, Pharmacy, Institute for Biology - Microbiology, Freie Universität BerlinBerlin, Germany
| | - Patricia Mariani-Kurkdjian
- CNR Associé Escherichia coli, Service de Microbiologie, Hôpital Robert-DebréParis, France; IAME, UMR 1137, INSERMParis, France; IAME, UMR 1137, University Paris Diderot, Sorbonne Paris CitéParis, France
| | - Aubin Fleiss
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
| | - Stéphane Bonacorsi
- CNR Associé Escherichia coli, Service de Microbiologie, Hôpital Robert-DebréParis, France; IAME, UMR 1137, INSERMParis, France; IAME, UMR 1137, University Paris Diderot, Sorbonne Paris CitéParis, France
| | - Patrick Fach
- IdentyPath Platform, Food Safety Laboratory, Anses, Université Paris-Est Maisons-Alfort, France
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