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El Chaar M, Khoury Y, Douglas GM, El Kazzi S, Jisr T, Soussi S, Merhi G, Moghnieh RA, Shapiro BJ. Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in critical care patients. Microbiol Spectr 2024; 12:e0312823. [PMID: 38171007 PMCID: PMC10846182 DOI: 10.1128/spectrum.03128-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/27/2023] [Indexed: 01/05/2024] Open
Abstract
Colonization with multidrug-resistant Escherichia coli strains causes a substantial health burden in hospitalized patients. We performed a longitudinal genomics study to investigate the colonization of resistant E. coli strains in critically ill patients and to identify evolutionary changes and strain replacement events within patients. Patients were admitted to the intensive care unit and hematology wards at a major hospital in Lebanon. Perianal swabs were collected from participants on admission and during hospitalization, which were screened for extended-spectrum beta-lactamases and carbapenem-resistant Enterobacterales. We performed whole-genome sequencing and analysis on E. coli strains isolated from patients at multiple time points. The E. coli isolates were genetically diverse, with 11 sequence types (STs) identified among 22 isolates sequenced. Five patients were colonized by E. coli sequence type 131 (ST131)-encoding CTX-M-27, an emerging clone not previously observed in clinical samples from Lebanon. Among the eight patients whose resident E. coli strains were tracked over time, five harbored the same E. coli strain with relatively few mutations over the 5 to 10 days of hospitalization. The other three patients were colonized by different E. coli strains over time. Our study provides evidence of strain diversity within patients during their hospitalization. While strains varied in their antimicrobial resistance profiles, the number of resistance genes did not increase over time. We also show that ST131-encoding CTX-M-27, which appears to be emerging as a globally important multidrug-resistant E. coli strain, is also prevalent among critical care patients and deserves further monitoring.IMPORTANCEUnderstanding the evolution of bacteria over time in hospitalized patients is of utmost significance in the field of infectious diseases. While numerous studies have surveyed genetic diversity and resistance mechanisms in nosocomial infections, time series of within-patient dynamics are rare, and high-income countries are over-represented, leaving low- and middle-income countries understudied. Our study aims to bridge these research gaps by conducting a longitudinal survey of critically ill patients in Lebanon. This allowed us to track Escherichia coli evolution and strain replacements within individual patients over extended periods. Through whole-genome sequencing, we found extensive strain diversity, including the first evidence of the emerging E. coli sequence type 131 clone encoding the CTX-M-27 beta-lactamase in a clinical sample from Lebanon, as well as likely strain replacement events during hospitalization.
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Affiliation(s)
- Mira El Chaar
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Yaralynn Khoury
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Gavin M. Douglas
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Samir El Kazzi
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Tamima Jisr
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Shatha Soussi
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Georgi Merhi
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
| | - Rima A. Moghnieh
- Division of Infectious Diseases, Department of Internal Medicine, Lebanese American University Medical Center, Beirut, Lebanon
| | - B. Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montréal, Québec, Canada
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Daaboul D, Oueslati S, Rima M, Kassem II, Mallat H, Birer A, Girlich D, Hamze M, Dabboussi F, Osman M, Naas T. The emergence of carbapenemase-producing Enterobacterales in hospitals: a major challenge for a debilitated healthcare system in Lebanon. Front Public Health 2023; 11:1290912. [PMID: 38074718 PMCID: PMC10699444 DOI: 10.3389/fpubh.2023.1290912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 12/18/2023] Open
Abstract
Background Carbapenem- and extended-spectrum cephalosporin-resistant Enterobacterales (CR-E and ESCR-E, respectively) are increasingly isolated worldwide. Information about these bacteria is sporadic in Lebanon and generally relies on conventional diagnostic methods, which is detrimental for a country that is struggling with an unprecedented economic crisis and a collapsing public health system. Here, CR-E isolates from different Lebanese hospitals were characterized. Materials and methods Non-duplicate clinical ESCR-E or CR-E isolates (N = 188) were collected from three hospitals from June 2019 to December 2020. Isolates were identified by MALDI-TOF, and their antibiotic susceptibility by Kirby-Bauer disk diffusion assay. CR-E isolates (n = 33/188) were further analyzed using Illumina-based WGS to identify resistome, MLST, and plasmid types. Additionally, the genetic relatedness of the CR-E isolates was evaluated using an Infrared Biotyper system and compared to WGS. Results Using the Kirby-Bauer disk diffusion assay, only 90 isolates out of the 188 isolates that were collected based on their initial routine susceptibility profile by the three participating hospitals could be confirmed as ESCR-E or CR-E isolates and were included in this study. This collection comprised E. coli (n = 70; 77.8%), K. pneumoniae (n = 13; 14.4%), Enterobacter spp. (n = 6; 6.7%), and Proteus mirabilis (n = 1; 1.1%). While 57 were only ESBL producers the remaining 33 isolates (i.e., 26 E. coli, five K. pneumoniae, one E. cloacae, and one Enterobacter hormaechei) were resistant to at least one carbapenem, of which 20 were also ESBL-producers. Among the 33 CR-E, five different carbapenemase determinants were identified: blaNDM-5 (14/33), blaOXA-244 (10/33), blaOXA-48 (5/33), blaNDM-1 (3/33), and blaOXA-181 (1/33) genes. Notably, 20 CR-E isolates were also ESBL-producers. The analysis of the genetic relatedness revealed a substantial genetic diversity among CR-E isolates, suggesting evolution and transmission from various sources. Conclusion This study highlighted the emergence and broad dissemination of blaNDM-5 and blaOXA-244 genes in Lebanese clinical settings. The weak AMR awareness in the Lebanese community and the ongoing economic and healthcare challenges have spurred self-medication practices. Our findings highlight an urgent need for transformative approaches to combat antimicrobial resistance in both community and hospital settings.
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Affiliation(s)
- Dina Daaboul
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
- Laboratoire Microbiologie Santé et Environment (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Saoussen Oueslati
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital Le Kremlin-Bicêtre, Paris, France
| | - Mariam Rima
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
| | - Issmat I. Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, Griffin, GA, United States
| | - Hassan Mallat
- Laboratoire Microbiologie Santé et Environment (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Aurélien Birer
- French National Reference Center for Antibiotic Resistance, Clermont-Ferrand, France
| | - Delphine Girlich
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environment (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environment (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY, United States
- Department of Public and Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, United States
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT, United States
| | - Thierry Naas
- Faculty of Medicine, Team "Resist" UMR1184, "Immunology of Viral, Auto-Immune, Hematological and Bacterial Diseases (IMVA-HB)," INSERM, Université Paris-Saclay, CEA, Health and Therapeutic Innovation (HEALTHI), Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital Le Kremlin-Bicêtre, Paris, France
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Cheng MF, Ho PY, Wang JL, Tseng FC, Chang JT, Huang IF, Hung CH. Prevalence and household risk factors for fecal carriage of ESBL-producing, sequence type 131, and extraintestinal pathogenic Escherichia coli among children in southern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:695-707. [PMID: 35513972 DOI: 10.1016/j.jmii.2022.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 03/01/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The rapidly increasing prevalence of antimicrobial-resistant Escherichia coli (E. coli) is a global concern. This study determined the prevalence and risk factors for the fecal carriage of drug-resistant E. coli and extraintestinal pathogenic E. coli (ExPEC) among children. MATERIALS AND METHODS In this prospective study, stool samples from children aged 0-18 years were obtained within three days of hospitalization between April 2016 and March 2019. E. coli were selected and tested for extended-spectrum β-lactamase (ESBL)-production and antimicrobial susceptibility. Multilocus sequence typing, blaCTX-M gene groups and ExPEC were determined using polymerase chain reactions. Questionnaires were recorded for risk factor analysis. RESULTS Among 179 E. coli isolates, 44.1% were multi-drug resistant, 20.7% produced ESBL, and 50.3% were ExPEC. Children carrying ESBL-producing E. coli were younger than those carrying non-ESBL strains. Several anthropogenic factors, including drinking water process, pork consumption, pets and household density might be associated with ESBL-producing E. coli, sequence type (ST) 131 E. coli, or ExPEC fecal carriage. Compared with families who live in less crowded houses, participants with pets had a similar trend of higher risks of ESBL-producing E. coli, ST131 E. coli, and ExPEC fecal carriage among those living in houses accommodating relatively more people. CONCLUSIONS Children accounted for a large proportion of instances of feces carrying ESBL E. coli. In addition to antimicrobial control for people and livestocks, avenues of exposure, such as drinking water, food, pets, household density, and socioeconomic deprivation might present potentially novel opportunities to reduce the burden of nonsusceptible E. coli and ExPEC.
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Affiliation(s)
- Ming-Fang Cheng
- Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan; Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan; School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan; Fooyin University, Kaohsiung, Taiwan
| | - Pei-Yu Ho
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - Jiun-Ling Wang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Fan-Chen Tseng
- Department of Nursing, National Taipei University of Nursing and Health Sciences, Taipei, Taiwan
| | - Jenn-Tzong Chang
- Department of Pediatrics, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
| | - I-Fei Huang
- Department of Pediatrics, Kaohsiung Pojen Hospital, Kaohsiung, Taiwan
| | - Chih-Hsin Hung
- Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan.
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Al-Mir H, Osman M, Drapeau A, Hamze M, Madec JY, Haenni M. Spread of ESC-, carbapenem- and colistin-resistant Escherichia coli clones and plasmids within and between food workers in Lebanon. J Antimicrob Chemother 2021; 76:3135-3143. [PMID: 34534282 DOI: 10.1093/jac/dkab327] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/05/2021] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVES Knowledge on the dynamic of MDR Escherichia coli in the human community is still limited, especially in low- and middle-income countries. Our goal was to decipher the dynamics of E. coli lineages and plasmids resistant to ESC, carbapenem and colistin within and between food workers in Lebanon using genomic-based approaches. METHODS Eighty-four healthy adults working in three bakeries were sampled twice at a 6 monthly interval. E. coli resistant to ESC (ESC-E), carbapenem (CP-E) and colistin (CO-E) were collected on selective plates. Non-duplicate isolates were whole-genome sequenced using the Illumina technology and plasmid transmission was assessed by long-read sequencing. Data were analysed using bioinformatics tools and SNP-based phylogeny. RESULTS ESC-E carriage rate reached 34.5% (t0) and 52.9% (t6), and 15 workers were positive at both t0 and t6. Carbapenem resistance (blaOXA-181, blaOXA-204, blaNDM-5) was found in five workers at t0 and two at t6, while colistin resistance (mcr-1.1) was found in five workers at t0 and one at t6. Forty-seven different STs were identified, of which three STs were predominant (ST131, n = 9; ST10, n = 5; ST69, n = 5). One worker presented the same ESC-E clone at t0 and t6. Twelve different events of clonal transmission among individuals were exemplified while plasmid transmission was only shown once. CONCLUSIONS Our study revealed a high carriage rate of MDR E. coli (60.7%) and the emergence of CP and colistin resistance in the Lebanese community. Incidental and long-term ESC-E carriage was observed in 41.7% and 17.9% of the workers, respectively. The high clonal diversity suggests an important dynamic of acquisition and loss of MDR E. coli and limited plasmid spread.
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Affiliation(s)
- Hiba Al-Mir
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Université de Lyon-ANSES laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.,Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Antoine Drapeau
- Université de Lyon-ANSES laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Jean-Yves Madec
- Université de Lyon-ANSES laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
| | - Marisa Haenni
- Université de Lyon-ANSES laboratoire de Lyon, Unité Antibiorésistance et Virulence Bactériennes, Lyon, France
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Shurina BA, Page RC. Structural Comparisons of Cefotaximase (CTX-M-ase) Sub Family 1. Front Microbiol 2021; 12:688509. [PMID: 34504475 PMCID: PMC8421805 DOI: 10.3389/fmicb.2021.688509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/22/2021] [Indexed: 12/17/2022] Open
Abstract
The cefotaximase or CTX-M, family of serine-β-lactamases represents a significant clinical concern due to the ability for these enzymes to confer resistance to a broad array of β-lactam antibiotics an inhibitors. This behavior lends CTX-M-ases to be classified as extended spectrum β-lactamases (ESBL). Across the family of CTX-M-ases most closely related to CTX-M-1, the structures of CTX-M-15 with a library of different ligands have been solved and serve as the basis of comparison within this review. Herein we focus on the structural changes apparent in structures of CTX-M-15 in complex with diazabicyclooctane (DABCO) and boronic acid transition state analog inhibitors. Interactions between a positive surface patch near the active site and complementary functional groups of the bound inhibitor play key roles in the dictating the conformations of active site residues. The insights provided by analyzing structures of CTX-M-15 in complex with DABCO and boronic acid transition state analog inhibitors and analyzing existing structures of CTX-M-64 offer opportunities to move closer to making predictions as to how CTX-M-ases may interact with potential drug candidates, setting the stage for the further development of new antibiotics and β-lactamase inhibitors.
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Affiliation(s)
- Ben A Shurina
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, United States
| | - Richard C Page
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH, United States.,Cell, Molecular, and Structural Biology Program, Miami University, Oxford, OH, United States
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Salgado-Caxito M, Benavides JA, Adell AD, Paes AC, Moreno-Switt AI. Global prevalence and molecular characterization of extended-spectrum β-lactamase producing- Escherichia coli in dogs and cats - A scoping review and meta-analysis. One Health 2021; 12:100236. [PMID: 33889706 PMCID: PMC8050393 DOI: 10.1016/j.onehlt.2021.100236] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 03/08/2021] [Accepted: 03/14/2021] [Indexed: 11/25/2022] Open
Abstract
Antimicrobial resistance (AMR) represents a major threat to human and animal health. Part of the AMR dimension is the circulation of extended-spectrum β-lactamases producing-Escherichia coli (ESBL-E. coli), which is now commonly reported among companion animals. However, the global perspective of the prevalence and population structure of ESBL-E. coli circulating in dogs and cats has not been estimated limiting our understanding of their role in the dissemination of ESBL-E. coli. The aim of this study was to compare the prevalence of ESBL-E. coli between dogs and cats and across countries through meta-analysis. We also performed a scoping review to summarize the current knowledge on ESBL genes and E. coli clones circulating among companion animals. A total of 128 studies published in PubMed, Web of Science, and Scopus up to April 2020 were selected and contained information on prevalence and/or molecular characterization of ESBL genes and ESBL-E. coli clones. Our review shows an increase in the number of publications between 2000 and 2019, concentrated mainly in Europe. Prevalence varied across continents, ranging from 0.63% (Oceania) to 16.56% (Africa) in dogs and from 0% (Oceania) to 16.82% (Asia) in cats. Although there were twice as many studies reporting prevalence on dogs (n = 61) than on cats (n = 32), and only 9 studies focused exclusively on cats, our meta-analysis showed no difference in the global prevalence of ESBL-E. coli between dogs (6.87% [95% CI: 4.46-10.45%]) and cats (5.04% [95% CI: 2.42-10.22%]). A considerable diversity of ESBL genes (n = 60) and sequence types (ST) (n = 171) were recovered from companion animals. ESBL-E. coli encoded by CTX-M-15 (67.5%, 77/114) and SHV-12 (21.9%, 25/114), along with resistant strains of ST38 (22.7%, 15/66) and ST131 (50%, 33/66) were widespread and detected in all continents. While presence of ESBL-E. coli is widespread, the drivers influencing the observed ESBL-E. coli prevalence and the clinical relevance in veterinary medicine and public health along with economic impact of ESBL-E. coli infections among companion animals need to be further investigated.
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Affiliation(s)
- Marília Salgado-Caxito
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Julio A. Benavides
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Departamento de Ecología y Biodiversidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
- Centro de Investigación para la Sustentabilidad, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile
| | - Aiko D. Adell
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Escuela de Medicina Veterinaria, Universidad Andres Bello, Santiago, Chile
| | - Antonio Carlos Paes
- Department of Animal Production and Preventive Veterinary Medicine, School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Andrea I. Moreno-Switt
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Santiago, Chile
- Escuela de Medicina Veterinaria, Pontificia Universidad Católica de Chile, Santiago, Chile
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Abboud Z, Galuppo L, Tolone M, Vitale M, Puleio R, Osman M, Loria GR, Hamze M. Molecular Characterization of Antimicrobial Resistance and Virulence Genes of Bacterial Pathogens from Bovine and Caprine Mastitis in Northern Lebanon. Microorganisms 2021; 9:1148. [PMID: 34071800 PMCID: PMC8228836 DOI: 10.3390/microorganisms9061148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/08/2021] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
Mastitis is an infectious disease encountered in dairy animals worldwide that is currently a growing concern in Lebanon. This study aimed at investigating the etiology of the main mastitis-causing pathogens in Northern Lebanon, determining their antimicrobial susceptibility profiles, and identifying their antimicrobial resistance (AMR) genes. A total of 101 quarter milk samples were collected from 77 cows and 11 goats presenting symptoms of mastitis on 45 dairy farms. Bacterial identification was carried out through matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Antimicrobial susceptibility was tested by disc diffusion and broth microdilution methods. Molecular characterization included polymerase chain reaction (PCR) screening for genes encoding extended-spectrum beta-lactamases (ESBLs) and plasmid-mediated AmpC among Enterobacterales isolates, and virulence factors among Staphylococcus isolates. Escherichia coli isolates were subjected to phylogenetic typing by a quadruplex PCR method. The most frequently identified species were Streptococcus uberis (19.2%), Streptococcus agalactiae (15.1%), E. coli (12.3%), and Staphylococcus aureus (10.96%). Gram-positive bacteria were resistant to macrolides and tetracycline, whereas gram-negative bacteria displayed resistance to ampicillin and tetracycline. Two ESBL genes, blaTEM (83.3%) and blaOXA (16.7%), and one AmpC beta-lactamase gene, blaCMY-II (16.7%), were detected among six E. coli isolates, which mainly belonged to phylogenetic group B1. Among Staphylococcus spp., the mecA gene was present in three isolates. Furthermore, four isolates contained at least one toxin gene, and all S. aureus isolates carried the ica operon. These findings revealed the alarming risk of AMR in the Lebanese dairy chain and the importance of monitoring antimicrobial usage.
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Affiliation(s)
- Zahie Abboud
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli P.O. Box 146404, Lebanon;
| | - Lucia Galuppo
- Istituto Zooprofilattico Sperimentale della Sicilia, Via G. Marinuzzi 3, 90129 Palermo, Italy; (L.G.); (M.V.); (R.P.)
| | - Marco Tolone
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128 Palermo, Italy;
| | - Maria Vitale
- Istituto Zooprofilattico Sperimentale della Sicilia, Via G. Marinuzzi 3, 90129 Palermo, Italy; (L.G.); (M.V.); (R.P.)
| | - Roberto Puleio
- Istituto Zooprofilattico Sperimentale della Sicilia, Via G. Marinuzzi 3, 90129 Palermo, Italy; (L.G.); (M.V.); (R.P.)
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli P.O. Box 146404, Lebanon;
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA
| | - Guido Ruggero Loria
- Istituto Zooprofilattico Sperimentale della Sicilia, Via G. Marinuzzi 3, 90129 Palermo, Italy; (L.G.); (M.V.); (R.P.)
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement, Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli P.O. Box 146404, Lebanon;
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8
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Plassard V, Gisbert P, Granier SA, Millemann Y. Surveillance of Extended-Spectrum β-Lactamase-, Cephalosporinase- and Carbapenemase-Producing Gram-Negative Bacteria in Raw Milk Filters and Healthy Dairy Cattle in Three Farms in Île-de-France, France. Front Vet Sci 2021; 8:633598. [PMID: 33644154 PMCID: PMC7902890 DOI: 10.3389/fvets.2021.633598] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 01/11/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this work was to test a surveillance protocol able to detect extended-spectrum β-lactamase (ESBL)-, cephalosporinase (AmpC)- and carbapenemase (CP)-producing gram-negative bacteria in three conveniently chosen dairy farms with known prior occurrences of ESBL- and CP-producing strains. The protocol was applied monthly for a year. At each visit, 10 healthy lactating dairy cows were rectally swabbed, and raw milk filters (RMFs) were sampled in two of the three farms. Bacterial isolation was based on a first screening step with MacConkey agar supplemented with 1 mg/L cefotaxime and commercial carbapenem-supplemented media. We failed to detect CP-producing strains but showed that ESBL-Escherichia strains, found in one farm only (13 strains), were closely associated with multi-drug resistance (12 out of 13). The limited number of conveniently selected farms and the fact that RMFs could not be retrieved from one of them limit the validity of our findings. Still, our results illustrate that ESBL-status changes monthly based on fecal swabs and negative herds should be qualified as “unsuspected” as proposed by previous authors. Although surveillance of farm statuses based on RMF analysis could theoretically allow for a better sensitivity than individual swabs, we failed to illustrate it as both farms where RMFs could be retrieved were constantly negative. Determination of CP herd-level status based on RMFs and our surveillance protocol was hindered by the presence of intrinsically resistant bacteria or strains cumulating multiple non-CP resistance mechanisms which means our protocol is not specific enough for routine monitoring of CP in dairy farms.
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Affiliation(s)
| | | | - Sophie A Granier
- Agence Nationale de Sécurité Sanitaire de l'Alimentation, de l'Environnement et du Travail, Fougères, France
| | - Yves Millemann
- Ecole Nationale Vétérinaire d'Alfort, Maisons-Alfort, France.,Laboratoire de Sécurité des Aliments de l'ANSES, Maisons-Alfort, France
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9
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Rochegüe T, Haenni M, Cazeau G, Metayer V, Madec JY, Ferry T, Lupo A. An inventory of 44 qPCR assays using hydrolysis probes operating with a unique amplification condition for the detection and quantification of antibiotic resistance genes. Diagn Microbiol Infect Dis 2021; 100:115328. [PMID: 33819858 DOI: 10.1016/j.diagmicrobio.2021.115328] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/22/2021] [Accepted: 01/24/2021] [Indexed: 01/28/2023]
Abstract
Early antibiotic resistance determinants (ARDs) detection in humans or animals is crucial to counteract their propagation. The ARDs quantification is fundamental to understand the perturbation caused by disruptors, such as antibiotics, during therapies. Forty-three qPCRs on the most diffused ARDs and integrons among human and animal Enterobacterales, and one on the 16S rDNA for bacteria quantification, were developed. The qPCRs, using hydrolysis probes, operated with a unique amplification condition and were tested analytically and diagnostically performing 435 reactions on five positive and negative controls for each qPCR. Diagnostic sensitivity and specificity were confirmed by PCR and genome sequencing of control isolates, demonstrating 100% performance for all qPCRs. An easy and rapid discrimination method for the epidemiologically relevant blaCTX-Ms is provided. This large, noncommercial qPCRs inventory could serve for precise quantification of ARDs, but also as a rapid screening tool for surveillance purposes, providing the basis for further high-throughput developments.
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Affiliation(s)
- Tony Rochegüe
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Marisa Haenni
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Géraldine Cazeau
- ANSES - Université de Lyon, Unité Epidémiologie et Appui à la Surveillance (EAS), Lyon, France
| | - Véronique Metayer
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Jean-Yves Madec
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France
| | - Tristan Ferry
- Service des maladies infectieuses et tropicales, CHU de Lyon, Hôpital de la Croix-Rousse, Lyon, France; Centre International de Recherche en Infectiologie, CIRI, Inserm U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Agnese Lupo
- ANSES - Université de Lyon, Unité Antibiorésistance et Virulence Bactériennes (AVB), Lyon, France.
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10
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Ramos S, Silva V, Dapkevicius MDLE, Caniça M, Tejedor-Junco MT, Igrejas G, Poeta P. Escherichia coli as Commensal and Pathogenic Bacteria Among Food-Producing Animals: Health Implications of Extended Spectrum β-lactamase (ESBL) Production. Animals (Basel) 2020; 10:ani10122239. [PMID: 33260303 PMCID: PMC7761174 DOI: 10.3390/ani10122239] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/22/2022] Open
Abstract
Simple Summary This revision is about the problem of Escherichia coli as a commensal and pathogenic bacterium among food-producing animals and health implications. Escherichia coli may play an important ecological role and can be used as a bioindicator of antimicrobial resistance. All animal species used for food production, as well as humans, carry E. coli in their intestinal tract; plus, the genetic flexibility and adaptability of this bacteria to constantly changing environments allows it to acquire a great number of antimicrobial resistance mechanisms. The majority of E. coli strains are commensals inhabiting the intestinal tract of humans and warm-blooded animals and rarely causes diseases. However, E. coli also remains as one of the most frequent causes of several common bacterial infections in humans and animals. All over the word, antibiotic resistance is commonly detected among commensal bacteria from food-producing animals, raising important questions on the potential impact of antibiotic use in animals and the possible transmission of these resistant bacteria to humans through the food chain. The use, in food-producing animals, of antibiotics that are critically important in human medicine has been implicated in the emergence of new forms of resistant bacteria, including new strains of multidrug-resistant foodborne bacteria, such as extended spectrum β-lactamase (ESBL)-producing E. coli. Abstract Escherichia coli are facultative, anaerobic Gram-negative rods with many facets. Within resistant bacterial populations, they play an important ecological role and can be used as a bioindicator of antimicrobial resistance. All animal species used for food production, as well as humans, carry E. coli in their intestinal tracts; plus, the genetic flexibility and adaptability of this bacteria to constantly changing environments allows it to acquire a great number of antimicrobial resistance mechanisms. Thus, the prevalence of antimicrobial resistance in these commensal bacteria (or others, such as enterococci) can be a good indicator for the selective pressure caused by the use of antimicrobial agents, providing an early warning of the emergence of antimicrobial resistance in pathogens. As many as 90% of E. coli strains are commensals inhabiting the intestinal tracts of humans and warm-blooded animals. As a commensal, it lives in a mutually beneficial association with its hosts and rarely causes diseases. However, E. coli also remains as one of the most frequent causes of several common bacterial infections in humans and animals. In humans, it is the prominent cause of enteritis, community- and hospital-acquired urinary tract infection (UTI), septicemia, postsurgical peritonitis, and other clinical infections, such as neonatal meningitis, while, in farm animals, it is more prominently associated with diarrhea. On a global scale, E. coli can be considered the most important human pathogen, causing severe infection along with other major bacterial foodborne agents, such as Salmonella spp. and Campylobacter. Thus, the importance of resistance in E. coli, typically considered a benign commensal, should not be underestimated.
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Affiliation(s)
- Sónia Ramos
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal; (S.R.); (V.S.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal
| | - Vanessa Silva
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal; (S.R.); (V.S.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisbon, Portugal
| | - Maria de Lurdes Enes Dapkevicius
- Faculty of Agricultural and Environmental Sciences, University of the Azores, 9500-321 Angra do Heroísmo, Portugal;
- Institute of Agricultural and Environmental Research and Technology (IITAA), University of the Azores, 9500-321 Angra do Heroísmo, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections (NRL-AMR/HAI), Department of Infectious Diseases, National Institute of Health Dr Ricardo Jorge, Av. Padre Cruz, 1649-016 Lisbon, Portugal;
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, Oporto University, 4051-401 Oporto, Portugal
| | - María Teresa Tejedor-Junco
- Research Institute of Biomedical and Health Sciences, University of Las Palmas de Gran Canaria, 35001 Canary Islands, Spain;
- Department of Clinical Sciences, University of Las Palmas de Gran Canaria, 35001 Canary Islands, Spain
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5001-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisbon, Portugal
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5001-801 Vila Real, Portugal; (S.R.); (V.S.)
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 2829-516 Lisbon, Portugal
- Correspondence: ; Tel./Fax: +351-259-350-466
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11
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Adefioye OJ, Weinreich J, Rödiger S, Schierack P, Olowe OA. Phylogenetic Characterization and Multilocus Sequence Typing of Extended-Spectrum Beta Lactamase-Producing Escherichia coli from Food-Producing Animals, Beef, and Humans in Southwest Nigeria. Microb Drug Resist 2020; 27:111-120. [PMID: 32522073 DOI: 10.1089/mdr.2019.0397] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Multidrug-resistant extended-spectrum beta lactamase (ESBL)-producing Escherichia coli strains are emerging globally in both humans and animals. Antimicrobial susceptibility testing and ESBL screening were performed on pure cultures of 216 E. coli isolates from human and animal fecal samples as well as beef. Polymerase chain reaction was performed for the detection of resistance genes. Representative isolates of ESBL-producing E. coli were randomly selected for multilocus sequence typing and pulsed field gel electrophoresis (PFGE). Sixty of the isolates were identified as ESBL producers, and seven resistance genes were amplified in them: TEM (61.7%), blaCTX-M-15 (51.7%), AAC-6-LB (43.3%), blaCTX-M-1 (38.3%), blaCTX-M-9 (33.3%), blaCTX-M-2 (21.7%), and SHV (11.7%); they were classified into four phylogroups: A (25%), B1 (45%), B2 (20%), and D (10%). Thirty of these isolates were clustered into 10 sequence types with ST131 being mostly prevalent. Six PFGE types were discovered, each of which was shared by isolates from different subjects and had the same phylogroups and resistance gene profiles. There was a dissemination of PFGE types across various groups among humans, animals, and beef. This underlines the fact that the spread of ESBL E. coli could be from humans to animals, from animals to humans, as well as across animal species.
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Affiliation(s)
- Olusolabomi J Adefioye
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Ladoke Akintola University of Technology, Osogbo, Nigeria
| | - Jörg Weinreich
- Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Stefan Rödiger
- Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Peter Schierack
- Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Olugbenga Adekunle Olowe
- Department of Medical Microbiology and Parasitology, College of Health Sciences, Ladoke Akintola University of Technology, Osogbo, Nigeria
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12
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Dandachi I, Fayad E, Sleiman A, Daoud Z, Rolain JM. Dissemination of Multidrug-Resistant and mcr-1 Gram-Negative Bacilli in Broilers, Farm Workers, and the Surrounding Environment in Lebanon. Microb Drug Resist 2020; 26:368-377. [DOI: 10.1089/mdr.2019.0137] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Iman Dandachi
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Elie Fayad
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Ahmad Sleiman
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Ziad Daoud
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
- Division of Clinical Microbiology, Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Jean-Marc Rolain
- Aix Marseille University, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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13
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Dantas Palmeira J, Ferreira HMN. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in cattle production - a threat around the world. Heliyon 2020; 6:e03206. [PMID: 32042963 PMCID: PMC7002838 DOI: 10.1016/j.heliyon.2020.e03206] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/01/2019] [Accepted: 01/09/2020] [Indexed: 01/19/2023] Open
Abstract
Food producing animal is a global challenge in terms of antimicrobial resistance spread. Extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae are relevant opportunistic pathogens that may spread in many ecological niches of the One Health approach as human, animal and environment due to intestinal selection of antimicrobial resistant commensals in food production animals. Cattle production is a relevant ecological niche for selection of commensal bacteria with antimicrobial resistance from microbiota. Enterobacteriaceae show importance in terms of circulation of resistant-bacteria and antimicrobial resistance genes via food chain creating a resistance reservoir, setting up a threat for colonization of humans and consequent health risk. ESBL-producing Enterobacteriaceae are a threat in terms of human health responsible for life threatening outbreaks and silent enteric colonization of community populations namely the elder population. Food associated colonization is a risk difficult to handle and control. In a time of globalization of food trading, population intestinal colonization is a mirror of food production and in that sense this work aims to make a picture of ESBL-producing Enterobacteriaceae in animal production for food over the world in order to make some light in this reality of selection of resistant threats in food producing animal.
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Affiliation(s)
- Josman Dantas Palmeira
- Microbiology - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Portugal
| | - Helena Maria Neto Ferreira
- Microbiology - Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal.,UCIBIO - Research Unit on Applied Molecular Biosciences, REQUIMTE, Portugal
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14
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Dandachi I, Chaddad A, Hanna J, Matta J, Daoud Z. Understanding the Epidemiology of Multi-Drug Resistant Gram-Negative Bacilli in the Middle East Using a One Health Approach. Front Microbiol 2019; 10:1941. [PMID: 31507558 PMCID: PMC6716069 DOI: 10.3389/fmicb.2019.01941] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022] Open
Abstract
In the last decade, extended-spectrum cephalosporin and carbapenem resistant Gram-negative bacilli (GNB) have been extensively reported in the literature as being disseminated in humans but also in animals and the environment. These resistant organisms often cause treatment challenges due to their wide spectrum of antibiotic resistance. With the emergence of colistin resistance in animals and its subsequent detection in humans, the situation has worsened. Several studies reported the transmission of resistant organisms from animals to humans. Studies from the middle east highlight the spread of resistant organisms in hospitals and to a lesser extent in livestock and the environment. In view of the recent socio-economical conflicts that these countries are facing in addition to the constant population mobilization; we attempt in this review to highlight the gaps of the prevalence of resistance, antibiotic consumption reports, infection control measures and other risk factors contributing in particular to the spread of resistance in these countries. In hospitals, carbapenemases producers appear to be dominant. In contrast, extended spectrum beta lactamases (ESBL) and colistin resistance are becoming a serious problem in animals. This is mainly due to the continuous use of colistin in veterinary medicine even though it is now abandoned in the human sphere. In the environment, despite the small number of reports, ESBL and carbapenemases producers were both detected. This highlights the importance of the latter as a bridge between humans and animals in the transmission chain. In this review, we note that in the majority of the Middle Eastern area, little is known about the level of antibiotic consumption especially in the community and animal farms. Furthermore, some countries are currently facing issues with immigrants, poverty and poor living conditions which has been imposed by the civil war crisis. This all greatly facilitates the dissemination of resistance in all environments. In the one health concept, this work re-emphasizes the need to have global intervention measures to avoid dissemination of antibiotic resistance in humans, animals and the environment in Middle Eastern countries.
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Affiliation(s)
- Iman Dandachi
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Amer Chaddad
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Jason Hanna
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Jessika Matta
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
| | - Ziad Daoud
- Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand, Beirut, Lebanon
- Division of Clinical Microbiology, Saint George Hospital University Medical Center, Beirut, Lebanon
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15
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Osman M, Al Mir H, Rafei R, Dabboussi F, Madec JY, Haenni M, Hamze M. Epidemiology of antimicrobial resistance in Lebanese extra-hospital settings: An overview. J Glob Antimicrob Resist 2019; 17:123-129. [DOI: 10.1016/j.jgar.2018.11.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/07/2018] [Accepted: 11/26/2018] [Indexed: 01/14/2023] Open
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16
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Jammoul A, El Darra N. Evaluation of Antibiotics Residues in Chicken Meat Samples in Lebanon. Antibiotics (Basel) 2019; 8:antibiotics8020069. [PMID: 31141997 PMCID: PMC6627442 DOI: 10.3390/antibiotics8020069] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 01/21/2023] Open
Abstract
Antibiotic residue in chicken is a human health concern due to its harmful effects on consumer health. This study aims at screening the antibiotic residues from 80 chicken samples collected from farms located in different regions of Lebanon. An optimized multi-class method for identification and quantification of 30 antibiotics from four different chemical classes (sulfonamides, tetracyclines, quinolones, and beta-lactams) has been developed by using liquid chromatography–mass spectrometry. The evaluation of antibiotics residues in 80 chicken muscles samples has shown that 77.5% of samples were at least contaminated with antibiotics residues, out of which 53.75% were exposed to co-occurrence of multidrug residues. The screening of the four antibiotics families has shown that ciprofloxacin (quinolones) represents the highest occurrence percentage (32.5%), followed by amoxicillin (β-lactams) (22.5%) and then tetracyclines (17.5%). Means of sarafloxacin, amoxicillin, and penicillin G residues levels were above the Maximum Residue Limit (MRL) recommended limit according to the European Union EC. This study revealed that chicken samples collected from Lebanese farms contain antibiotic residues. Guidelines for prudent use of antimicrobials agents for chicken should be adopted to reduce the prevalence of resistant Salmonella in chicken.
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Affiliation(s)
- Adla Jammoul
- Lebanese Agricultural Research Institute, Food Department, Fanar, P.O.Box: 2611, Lebanon.
| | - Nada El Darra
- Beirut Arab University, Faculty of Heath Sciences, Tarik El Jedidah - Beirut, P.O.Box: 115020, Riad EL Solh 1107 2809, Lebanon.
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17
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Dandachi I, Chabou S, Daoud Z, Rolain JM. Prevalence and Emergence of Extended-Spectrum Cephalosporin-, Carbapenem- and Colistin-Resistant Gram Negative Bacteria of Animal Origin in the Mediterranean Basin. Front Microbiol 2018; 9:2299. [PMID: 30323797 PMCID: PMC6172473 DOI: 10.3389/fmicb.2018.02299] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 09/10/2018] [Indexed: 11/13/2022] Open
Abstract
In recent years, extended ESBL and carbapenemase producing Gram negative bacteria have become widespread in hospitals, community settings and the environment. This has been triggered by the few therapeutic options left when infections with these multi-drug resistant organisms occur. The emergence of resistance to colistin, the last therapeutic option against carbapenem-resistant bacteria, worsened the situation. Recently, animals were regarded as potent antimicrobial reservoir and a possible source of infection to humans. Enteric Gram negative bacteria in animals can be easily transmitted to humans by direct contact or indirectly through the handling and consumption of undercooked/uncooked animal products. In the Mediterranean basin, little is known about the current overall epidemiology of multi-drug resistant bacteria in livestock, companion, and domestic animals. This review describes the current epidemiology of ESBL, carbapenemase producers and colistin resistant bacteria of animal origin in this region of the world. The CTX-M group 1 seems to prevail in animals in this area, followed by SHV-12 and CTX-M group 9. The dissemination of carbapenemase producers and colistin resistance remains low. Isolated multi-drug resistant bacteria were often co-resistant to non-beta-lactam antibiotics, frequently used in veterinary medicine as treatment, growth promoters, prophylaxis and in human medicine for therapeutic purposes. Antibiotics used in veterinary medicine in this area include mainly tetracycline, aminoglycosides, fluoroquinolones, and polymyxins. Indeed, it appears that the emergence of ESBL and carbapenemase producers in animals is not related to the use of beta-lactam antibiotics but is, rather, due to the co-selective pressure applied by the over usage of non-beta-lactams. The level of antibiotic consumption in animals should be, therefore, re-considered in the Mediterranean area especially in North Africa and western Asia where no accurate data are available about the level of antibiotic consumption in animals.
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Affiliation(s)
- Iman Dandachi
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, Marseille, France
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Selma Chabou
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, Marseille, France
| | - Ziad Daoud
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix Marseille Université, Marseille, France
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18
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Dandachi I, Fayad E, El-Bazzal B, Daoud Z, Rolain JM. Prevalence of Extended-Spectrum Beta-Lactamase-Producing Gram-Negative Bacilli and Emergence of mcr-1 Colistin Resistance Gene in Lebanese Swine Farms. Microb Drug Resist 2018; 25:233-240. [PMID: 30142027 DOI: 10.1089/mdr.2018.0110] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Livestock are considered reservoirs of multidrug-resistant organisms that can be transferred to humans through direct/indirect routes. Once transmitted, these organisms can be responsible for infections with therapeutic challenges. The aim of this study was to determine the prevalence of extended-spectrum cephalosporin and colistin-resistant Gram-negative bacilli in Lebanese swine farms. In May 2017, 114 fecal samples were collected from swine farms in south Lebanon. Separate media supplemented with cefotaxime, ertapenem, and colistin were used for the screening of resistant organisms. Double-disk synergy test and ampC disk test were performed to detect extended-spectrum beta-lactamase (ESBL) and ampC producers, respectively. Detection of beta-lactamase and mcr genes was performed using real time PCR. Of 114 fecal samples, 76 showed growth on the medium with cefotaxime. In total, 111 strains were isolated with 94.5% being Escherichia coli. Phenotypic tests showed that 98, 6, and 7 strains were ESBL, ampC, and ESBL/ampC producers, respectively. CTX-M and CMY were the main beta-lactamase genes detected. On the medium with colistin, 19 samples showed growth. In total, 23 colistin-resistant E. coli strains harboring the mcr-1 gene were isolated. This is the first study in Lebanon determining multidrug resistance epidemiology in pigs. The prevalence of ESBLs is high and the emergence of colistin resistance is alarming.
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Affiliation(s)
- Iman Dandachi
- 1 Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand , Beirut, Lebanon .,2 IRD, APHM, MEPHI, IHU-Méditerranée-Infection, Aix Marseille University , Marseille, France
| | - Elie Fayad
- 1 Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand , Beirut, Lebanon
| | | | - Ziad Daoud
- 1 Faculty of Medicine and Medical Sciences, Clinical Microbiology Laboratory, University of Balamand , Beirut, Lebanon
| | - Jean-Marc Rolain
- 2 IRD, APHM, MEPHI, IHU-Méditerranée-Infection, Aix Marseille University , Marseille, France
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19
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Dandachi I, Sokhn ES, Dahdouh EA, Azar E, El-Bazzal B, Rolain JM, Daoud Z. Prevalence and Characterization of Multi-Drug-Resistant Gram-Negative Bacilli Isolated From Lebanese Poultry: A Nationwide Study. Front Microbiol 2018; 9:550. [PMID: 29628921 PMCID: PMC5876231 DOI: 10.3389/fmicb.2018.00550] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Currently, antimicrobial resistance is one of the most prominent public health issues. In fact, there is increasing evidence that animals constitute a reservoir of antimicrobial resistance. In collaboration with the Lebanese Ministry of Agriculture, the aim of this study was to determine the prevalence of intestinal carriage of multi-drug-resistant Gram-negative Bacilli in poultry farms at the national level. Between August and December 2015, 981 fecal swabs were obtained from 49 poultry farms distributed across Lebanon. The swabs were subcultured on MacConkey agar supplemented with cefotaxime (2 μg/ml). Isolated strains were identified using MALDI-TOF mass spectrometry. Multilocus sequence typing analysis was performed for Escherichia coli. Phenotypic detection of extended spectrum β-lactamases (ESBL) and AmpC production was performed using double disk synergy and the ampC disk test, respectively. β-lactamase encoding genes blaCTX-M, blaTEM, blaSHV, blaFOX, blaMOX, blaEBC, blaACC, blaDHA, and blaCMY using PCR amplification. Out of 981 fecal swabs obtained, 203 (20.6%) showed bacterial growth on the selective medium. Of the 235 strains isolated, 217 were identified as E. coli (92%), eight as Klebsiella pneumoniae (3%), three as Proteus mirabilis (1%) and three as Enterobacter cloacae (1%). MLST analysis of E. coli isolates showed the presence of ST156, ST5470, ST354, ST155, and ST3224. The phenotypic tests revealed that 43.5, 28.5, and 20.5% of the strains were ampC, ESBL, and ampC/ESBL producers, respectively. The putative TEM gene was detected in 83% of the isolates, SHV in 20%, CTX-M in 53% and CMY ampC β-lactamase gene in 65%. Our study showed that chicken farms in Lebanon are reservoirs of ESBL and AmpC producing Gram-negative bacilli. The level of antibiotic consumption in the Lebanese veterinary medicine should be evaluated. Future studies should focus on the risk factors associated with the acquisition of multi-drug-resistant organisms in farm animals in Lebanon.
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Affiliation(s)
- Iman Dandachi
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon.,IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Elie S Sokhn
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Elias A Dahdouh
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | - Eid Azar
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
| | | | - Jean-Marc Rolain
- IRD, APHM, MEPHI, IHU-Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Ziad Daoud
- Clinical Microbiology Laboratory, Faculty of Medicine and Medical Sciences, University of Balamand, Beirut, Lebanon
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Diab M, Hamze M, Bonnet R, Saras E, Madec JY, Haenni M. Extended-spectrum beta-lactamase (ESBL)- and carbapenemase-producing Enterobacteriaceae in water sources in Lebanon. Vet Microbiol 2018; 217:97-103. [PMID: 29615264 DOI: 10.1016/j.vetmic.2018.03.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/07/2018] [Accepted: 03/09/2018] [Indexed: 02/06/2023]
Abstract
Extended-spectrum beta-lactamases (ESBLs) have been recurrently reported in both human and veterinary medicine, and carbapenemases have also emerged in these two sectors. Such resistance phenotypes were increasingly reported in the environment, which both receives and further disseminates multidrug-resistant (MDR) bacteria. Here, we report the high contamination of water samples (68.2%; 15/22) collected in estuaries in Lebanon. From these 15 contaminated sites, a total of 21 ESBL-producing (mostly harbouring the blaCTX-M-15 gene) and four carbapenemase-producing (two blaOXA-48 and two blaOXA-244) Enterobacteriaceae were recovered. ESBL contamination was also identified in water samples collected from rural wells and spring water, although at a lower frequency. Indeed, 1.9% (3/155) and 6.1% (7/115) of the wells and springs were contaminated, respectively, and all identified isolates were CTX-M-15-producing E. coli. Interestingly, sequence types (STs) previously associated both with animal and human reservoirs were detected (ST38, ST10 and ST131), suggesting a complex source of contamination. This situation is alarming since water drawn from wells or springs is directly intended for human consumption in Lebanon without any further treatment. Moreover, even though water from estuaries is not intended for human consumption, it is used to water animals and irrigate crops. Consequently, water contamination by ESBLs and carbapenemases in Lebanon is potentially a major risk to public health. Part of this work was presented at the 7th Symposium on Antimicrobial Resistance in Animals and the Environment (ARAE).
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Affiliation(s)
- Mohamad Diab
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale en Sciences et Technologies, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon; Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Agence Nationale de Sécurité Sanitaire (ANSES), Lyon, France; Clermont Université, Université d'Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale en Sciences et Technologies, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Richard Bonnet
- Clermont Université, Université d'Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France
| | - Estelle Saras
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Agence Nationale de Sécurité Sanitaire (ANSES), Lyon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Agence Nationale de Sécurité Sanitaire (ANSES), Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Agence Nationale de Sécurité Sanitaire (ANSES), Lyon, France.
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Molecular Epidemiology of Dairy Cattle-Associated Escherichia coli Carrying blaCTX-M Genes in Washington State. Appl Environ Microbiol 2018; 84:AEM.02430-17. [PMID: 29305512 DOI: 10.1128/aem.02430-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 12/20/2017] [Indexed: 12/31/2022] Open
Abstract
An increase in the prevalence of commensal Escherichia coli carrying blaCTX-M genes among dairy cattle was observed between 2008 and 2012 in Washington State. To study the molecular epidemiology of this change, we selected 126 blaCTX-M-positive and 126 blaCTX-M-negative isolates for determinations of the multilocus sequence types (MLSTs) and antibiotic resistance phenotypes from E. coli obtained during a previous study. For 99 isolates, we also determined the blaCTX-M alleles using PCR and sequencing and identified the replicon types of blaCTX-M-carrying plasmids. The blaCTX-M-negative E. coli isolates comprised 76 sequence types (STs) compared with 32 STs in blaCTX-M-positive E. coli isolates. The blaCTX-M-positive E. coli isolates formed three MLST clonal complexes, accounting for 83% of these isolates; 52% of blaCTX-M-negative E. coli isolates clustered into 10 clonal complexes, and the remainder were singletons. Overall, blaCTX-M-negative E. coli isolates had more diverse genotypes that were distinct to farms, whereas blaCTX-M-positive E. coli isolates had a clonal population structure and were widely disseminated on farms in both regions included in the study. Plasmid replicon types included IncI1 which predominated, followed by IncFIB and IncFIA/FIB. blaCTX-M-15 was the predominant CTX-M gene allele, followed by blaCTX-M-27 and blaCTX-M-14 There was no significant association between plasmid replicon types and bacterial STs, and neither clonal complexes nor major plasmid groups were associated with two discrete dairy-farming regions of Washington State.IMPORTANCE Infections caused by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli occur globally and present treatment challenges because of their resistance to multiple antimicrobial drugs. Cattle are potential reservoirs of ESBL-producing Enterobacteriaceae, and so understanding the causes of successful dissemination of blaCTX-M genes in commensal bacteria will inform future approaches for the prevention of antibiotic-resistant pathogen emergence.
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Rebbah N, Messai Y, Châtre P, Haenni M, Madec JY, Bakour R. Diversity of CTX-M Extended-Spectrum β-Lactamases in Escherichia coli Isolates from Retail Raw Ground Beef: First Report of CTX-M-24 and CTX-M-32 in Algeria. Microb Drug Resist 2017; 24:896-908. [PMID: 29227186 DOI: 10.1089/mdr.2017.0171] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The aim of this study was to investigate the prevalence and molecular features of extended-spectrum cephalosporin resistance in Escherichia coli isolates contaminating ground beef at retail in Algeria. Of 371 ground beef samples, 27.5% were found to contain cefotaxime-resistant E. coli isolates distributed into A (24.5%), B1 (60.8%), and D (14.7%) phylogroups. A rate of 88.2% of isolates had a multidrug-resistance phenotype. All strains were producers of CTX-M type extended-spectrum β-lactamases (ESBLs): CTX-M-1, CTX-M-3, CTX-M-14, CTX-M-15, CTX-M-24, or CTX-M-32. Conjugation assays allowed the transfer of blaCTX-M-1 in association with IncI1 plasmids, blaCTX-M-15 with IncI1 and IncK+B/O plasmids, blaCTX-M-3 with IncK plasmids, and blaCTX-M-14 with IncF1B or IncK plasmids. Sequence analysis of gyrA and parC genes showed mutations in 98.6% of ciprofloxacin-resistant isolates. The patterns "GyrA: S83L+D87N, ParC: S80I" (46.5%) and "ParC: S80I" (42.3%) were predominant. qnrS1, qnrB, and aac(6')-Ib-cr were detected in 18.7% of isolates. The tet genes, tetA, tetB, and tetA+tetB, were present in 95.7% of tetracycline-resistant isolates. The sul genes (sul1, sul2, sul3, sul1+sul2, sul2+sul3, and sul1+sul3) and the dfr gene clusters (dfrA1, dfrA5, dfrA7, dfrA8, dfrA12, dfrA5+dfrA12, dfrA1+dfrA5, dfrA7+dfrA12, dfrA5+dfrA7, and dfrA1+dfrA5+dfrA7) were found in 96.4% and 85.5% of sulfamethoxazole/trimethoprim-resistant isolates, respectively. Classes 1 and 2 integrons were detected in 67.6% and 9.8% of isolates, respectively. This study highlighted the significant presence of resistance genes, in particular those of CTXM ESBLs, in the beef meat, with the risk of their transmission to humans through food chain.
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Affiliation(s)
- Nesrine Rebbah
- 1 Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene , Algiers, Algeria
| | - Yamina Messai
- 1 Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene , Algiers, Algeria
| | - Pierre Châtre
- 2 Unité Antibiorésistance et Virulence Bactériennes, Université Lyon-ANSES Site de Lyon , Lyon, France
| | - Marisa Haenni
- 2 Unité Antibiorésistance et Virulence Bactériennes, Université Lyon-ANSES Site de Lyon , Lyon, France
| | - Jean Yves Madec
- 2 Unité Antibiorésistance et Virulence Bactériennes, Université Lyon-ANSES Site de Lyon , Lyon, France
| | - Rabah Bakour
- 1 Laboratory of Cellular and Molecular Biology, Faculty of Biological Sciences, University of Sciences and Technology Houari Boumediene , Algiers, Algeria
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Diab M, Hamze M, Bonnet R, Saras E, Madec JY, Haenni M. OXA-48 and CTX-M-15 extended-spectrum beta-lactamases in raw milk in Lebanon: epidemic spread of dominant Klebsiella pneumoniae clones. J Med Microbiol 2017; 66:1688-1691. [DOI: 10.1099/jmm.0.000620] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Mohamad Diab
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale en Sciences et Technologies, Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Agence Nationale de Sécurité Sanitaire (Anses), Lyon, France
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale en Sciences et Technologies, Faculté de Santé Publique, Université Libanaise, Tripoli, Liban
| | - Richard Bonnet
- Clermont Université, Université d'Auvergne, Inserm U1071, INRA USC2018, Clermont-Ferrand, France
| | - Estelle Saras
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Agence Nationale de Sécurité Sanitaire (Anses), Lyon, France
| | - Jean-Yves Madec
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Agence Nationale de Sécurité Sanitaire (Anses), Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université de Lyon - Agence Nationale de Sécurité Sanitaire (Anses), Lyon, France
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Draft genome sequences of two fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST90 (ST23 complex) isolated from a calf and a dairy cow in South America. J Glob Antimicrob Resist 2017; 11:145-147. [PMID: 29111480 DOI: 10.1016/j.jgar.2017.10.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 10/09/2017] [Accepted: 10/19/2017] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVES Farm animals have been recognised as important carriers and reservoirs of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli. The aim of this study was to report the draft genome sequences of two multidrug-resistant (MDR) CTX-M-15-producing E. coli strains (47VL and 13B) isolated from different bovine hosts (a calf and a dairy cow), housed separately in a commercial dairy farm in Brazil. METHODS Total genomic DNA of the E. coli isolates was sequenced using an Illumina MiSeq paired-end 300-bp sequencing platform. Sequence reads were de novo assembled using the A5-miseq pipeline and polishing assembly in Geneious v.R9. The NCBI Prokaryotic Genome Annotation Pipeline v.3.2 was used for genome annotation, whereas whole-genome sequences were analysed using bioinformatic tools from the Center of Genomic Epidemiology and EnteroBase. RESULTS E. coli 47VL generated a total of 3238770 and E. coli 13B a total of 1422808 paired-end reads of ca. 190× and ca. 80×, respectively. The resistome revealed that both isolates carried resistance genes to aminoglycosides, β-lactams, macrolides, sulphonamides, trimethoprim and tetracycline. Comparative analyses revealed clonal relatedness. In fact, both isolates belonged to sequence type ST90 (clonal complex CC23) and phylogroup AxB1. CONCLUSION To our knowledge, these are the first draft genome sequences of CTX-M-15-producing E. coli ST90 isolated from bovines in South America. These data can be used to elucidate genetic features that contribute to colonisation and adaptation of CTX-M-15-producing E. coli in dairy cattle.
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Characteristics and genetic diversity of multi-drug resistant extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolated from bovine mastitis. Oncotarget 2017; 8:90144-90163. [PMID: 29163817 PMCID: PMC5685738 DOI: 10.18632/oncotarget.21496] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 08/23/2017] [Indexed: 11/25/2022] Open
Abstract
A characterization of the drug resistance profiles, identification of PCR-based replicon typing, and multilocus sequence typing (MLST) and analysis of 46 ESBL-producing Escherichia coli from cows with mastitis are described. All multidrug-resistant isolates of various phylogenetic groups (A = 31, B1= 3, B2 = 2, D = 10) were ESBL-producers of genotypes CTX-M-15 (29), CTX-M-55 (4), CTX-M-14 (4), CTX-M-3 (1), CTX-M-1 (1), TEM (22) and SHV (8) that were found on conjugative plasmids of diverse incompatibility groups (primarily IncF). Transconjugation experiments indicated successful (100%) trans-conjugation, which was verified phenotypically and genotypically. A total of 28 sequence types (ST) were identified, with 10% of isolates being ST410, and 9 other ST that were assigned arbitrary numbers, reflecting the degree of diversity. Multilocus sequence analysis revealed two lineages, a dominant and a small lineage. Split-decomposition showed intraspecies recombination clearly contributed in genetic recombination generating genotypic diversity among the isolates, and a lack of interspecies recombination. This coherent analysis on genetic structure of multidrug-resistant pathogenic E. coli population isolated from mastitic-milk weaponized with resistance elements from a large, rapidly developing country will be a helpful contribution for epidemiology and surveillance of drug resistance patterns, and understanding their global diversity.
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Runcharoen C, Raven KE, Reuter S, Kallonen T, Paksanont S, Thammachote J, Anun S, Blane B, Parkhill J, Peacock SJ, Chantratita N. Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand. Genome Med 2017; 9:81. [PMID: 28877757 PMCID: PMC5588602 DOI: 10.1186/s13073-017-0471-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/22/2017] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Tackling multidrug-resistant Escherichia coli requires evidence from One Health studies that capture numerous potential reservoirs in circumscribed geographic areas. METHODS We conducted a survey of extended β-lactamase (ESBL)-producing E. coli isolated from patients, canals and livestock wastewater in eastern Thailand between 2014 and 2015, and analyzed isolates using whole genome sequencing. RESULTS The bacterial collection of 149 isolates consisted of 84 isolates from a single hospital and 65 from the hospital sewer, canals and farm wastewater within a 20 km radius. E. coli ST131 predominated the clinical collection (28.6%), but was uncommon in the environment. Genome-based comparison of E. coli from infected patients and their immediate environment indicated low genetic similarity overall between the two, although three clinical-environmental isolate pairs differed by ≤ 5 single nucleotide polymorphisms. Thai E. coli isolates were dispersed throughout a phylogenetic tree containing a global E. coli collection. All Thai ESBL-positive E. coli isolates were multidrug resistant, including high rates of resistance to tobramycin (77.2%), gentamicin (77.2%), ciprofloxacin (67.8%) and trimethoprim (68.5%). ESBL was encoded by six different CTX-M elements and SHV-12. Three isolates from clinical samples (n = 2) or a hospital sewer (n = 1) were resistant to the carbapenem drugs (encoded by NDM-1, NDM-5 or GES-5), and three isolates (clinical (n = 1) and canal water (n = 2)) were resistant to colistin (encoded by mcr-1); no isolates were resistant to both carbapenems and colistin. CONCLUSIONS Tackling ESBL-producing E. coli in this setting will be challenging based on widespread distribution, but the low prevalence of resistance to carbapenems and colistin suggests that efforts are now required to prevent these from becoming ubiquitous.
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Affiliation(s)
- Chakkaphan Runcharoen
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Sandra Reuter
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Teemu Kallonen
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Suporn Paksanont
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand
| | - Jeeranan Thammachote
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, 24000, Thailand
| | - Suthatip Anun
- Division of Clinical Microbiology, Medical Technology Department, Bhuddhasothon Hospital, Chachoengsao, 24000, Thailand
| | - Beth Blane
- Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Sharon J Peacock
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand.,Department of Medicine, University of Cambridge, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0QQ, UK.,The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.,London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Narisara Chantratita
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, 420/6 Rajvithi Road, Bangkok, 10400, Thailand.
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