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Khoshbayan A, Narimisa N, Elahi Z, Bostanghadiri N, Razavi S, Shariati A. Global prevalence of mutation in the mgrB gene among clinical isolates of colistin-resistant Klebsiella pneumoniae: a systematic review and meta-analysis. Front Microbiol 2024; 15:1386478. [PMID: 38912352 PMCID: PMC11190090 DOI: 10.3389/fmicb.2024.1386478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/22/2024] [Indexed: 06/25/2024] Open
Abstract
Background Colistin is used as a last resort for managing infections caused by multidrug-resistant bacteria. However, the high emergence of colistin-resistant strains has restricted the clinical use of this antibiotic in the clinical setting. In the present study, we evaluated the global prevalence of the mutation in the mgrB gene, one of the most important mechanisms of colistin resistance in Klebsiella pneumoniae. Methods Several databases, including Scopus, Medline (via PubMed), and Web of Science, were searched (until August 2023) to identify those studies that address the mgrB mutation in clinical isolates of K. pneumoniae. Using Stata software, the pooled prevalence of mgrB mutation and subgroup analyses for the year of publication, country, continent, mgrB mutation types, and detection methods of mgrB mutation were analyzed. Results Out of the 115 studies included in the analysis, the prevalence of mgrB mutations in colistin-resistant K. pneumoniae isolates was estimated at 65% of isolates, and mgrB variations with insertional inactivation had the highest prevalence among the five investigated mutations with 69%. The year subgroup analysis indicated an increase in mutated mgrB from 46% in 2014 to 61% in 2022. Europe had the highest prevalence of mutated mgrB at 73%, while Africa had the lowest at 54%. Conclusion Mutations in the mgrB gene are reported as one of the most common mechanisms of colistin resistance in K. pneumoniae, and the results of the present study showed that 65% of the reported colistin-resistant K. pneumoniae had a mutation in this gene.
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Affiliation(s)
- Amin Khoshbayan
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Negar Narimisa
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Elahi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Vice Chancellery of Education and Research, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Narjess Bostanghadiri
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shabnam Razavi
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Aref Shariati
- Molecular and Medicine research center, Khomein University of Medical Sciences, Khomein, Iran
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
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Carrera Páez LC, Olivier M, Gambino AS, Poklepovich T, Aguilar AP, Quiroga MP, Centrón D. Sporadic clone Escherichia coli ST615 as a vector and reservoir for dissemination of crucial antimicrobial resistance genes. Front Cell Infect Microbiol 2024; 14:1368622. [PMID: 38741889 PMCID: PMC11089171 DOI: 10.3389/fcimb.2024.1368622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
There is scarce information concerning the role of sporadic clones in the dissemination of antimicrobial resistance genes (ARGs) within the nosocomial niche. We confirmed that the clinical Escherichia coli M19736 ST615 strain, one of the first isolates of Latin America that harbors a plasmid with an mcr-1 gene, could receive crucial ARG by transformation and conjugation using as donors critical plasmids that harbor bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, or aadB genes. Escherichia coli M19736 acquired bla CTX-M-15, bla KPC-2, bla NDM-5, bla NDM-1, and aadB genes, being only blaNDM-1 maintained at 100% on the 10th day of subculture. In addition, when the evolved MDR-E. coli M19736 acquired sequentially bla CTX-M-15 and bla NDM-1 genes, the maintenance pattern of the plasmids changed. In addition, when the evolved XDR-E. coli M19736 acquired in an ulterior step the paadB plasmid, a different pattern of the plasmid's maintenance was found. Interestingly, the evolved E. coli M19736 strains disseminated simultaneously the acquired conjugative plasmids in different combinations though selection was ceftazidime in all cases. Finally, we isolated and characterized the extracellular vesicles (EVs) from the native and evolved XDR-E. coli M19736 strains. Interestingly, EVs from the evolved XDR-E. coli M19736 harbored bla CTX-M-15 though the pDCAG1-CTX-M-15 was previously lost as shown by WGS and experiments, suggesting that EV could be a relevant reservoir of ARG for susceptible bacteria. These results evidenced the genetic plasticity of a sporadic clone of E. coli such as ST615 that could play a relevant transitional link in the clinical dynamics and evolution to multidrug/extensively/pandrug-resistant phenotypes of superbugs within the nosocomial niche by acting simultaneously as a vector and reservoir of multiple ARGs which later could be disseminated.
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Affiliation(s)
- Laura Camila Carrera Páez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Martin Olivier
- The Research Institute of the McGill University Health Centre, McGill University, Montréal, QC, Canada
| | - Anahí Samanta Gambino
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Tomás Poklepovich
- Plataforma de Genómica y Bioinformática, Instituto Nacional de Enfermedades Infecciosas - La Administración Nacional de Laboratorios e Institutos de Salud (INEI-ANLIS) “Dr. Carlos G. Malbrán”, Buenos Aires, Argentina
| | - Andrea Pamela Aguilar
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos, Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires - Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Buenos Aires, Argentina
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3
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Mondal AH, Khare K, Saxena P, Debnath P, Mukhopadhyay K, Yadav D. A Review on Colistin Resistance: An Antibiotic of Last Resort. Microorganisms 2024; 12:772. [PMID: 38674716 PMCID: PMC11051878 DOI: 10.3390/microorganisms12040772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Antibiotic resistance has emerged as a significant global public health issue, driven by the rapid adaptation of microorganisms to commonly prescribed antibiotics. Colistin, previously regarded as a last-resort antibiotic for treating infections caused by Gram-negative bacteria, is increasingly becoming resistant due to chromosomal mutations and the acquisition of resistance genes carried by plasmids, particularly the mcr genes. The mobile colistin resistance gene (mcr-1) was first discovered in E. coli from China in 2016. Since that time, studies have reported different variants of mcr genes ranging from mcr-1 to mcr-10, mainly in Enterobacteriaceae from various parts of the world, which is a major concern for public health. The co-presence of colistin-resistant genes with other antibiotic resistance determinants further complicates treatment strategies and underscores the urgent need for enhanced surveillance and antimicrobial stewardship efforts. Therefore, understanding the mechanisms driving colistin resistance and monitoring its global prevalence are essential steps in addressing the growing threat of antimicrobial resistance and preserving the efficacy of existing antibiotics. This review underscores the critical role of colistin as a last-choice antibiotic, elucidates the mechanisms of colistin resistance and the dissemination of resistant genes, explores the global prevalence of mcr genes, and evaluates the current detection methods for colistin-resistant bacteria. The objective is to shed light on these key aspects with strategies for combating the growing threat of resistance to antibiotics.
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Affiliation(s)
- Aftab Hossain Mondal
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kriti Khare
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Prachika Saxena
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Parbati Debnath
- Department of Microbiology, Faculty of Allied Health Sciences, Shree Guru Gobind Singh Tricentenary University, Gurugram 122505, Haryana, India; (A.H.M.); (P.D.)
| | - Kasturi Mukhopadhyay
- Antimicrobial Research Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India; (K.K.); (P.S.); (K.M.)
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 712-749, Republic of Korea
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Ghazawi A, Strepis N, Anes F, Yaaqeib D, Ahmed A, AlHosani A, AlShehhi M, Manzoor A, Habib I, Wani NA, Hays JP, Khan M. First Report of Colistin-Resistant Escherichia coli Carrying mcr-1 IncI2(delta) and IncX4 Plasmids from Camels ( Camelus dromedarius) in the Gulf Region. Antibiotics (Basel) 2024; 13:227. [PMID: 38534662 DOI: 10.3390/antibiotics13030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/28/2024] Open
Abstract
Addressing the emergence of antimicrobial resistance (AMR) poses a significant challenge in veterinary and public health. In this study, we focused on determining the presence, phenotypic background, and genetic epidemiology of plasmid-mediated colistin resistance (mcr) in Escherichia coli bacteria isolated from camels farmed in the United Arab Emirates (UAE). Fecal samples were collected from 50 camels at a Dubai-based farm in the UAE and colistin-resistant Gram-negative bacilli were isolated using selective culture. Subsequently, a multiplex PCR targeting a range of mcr-genes, plasmid profiling, and whole-genome sequencing (WGS) were conducted. Eleven of fifty camel fecal samples (22%) yielded colonies positive for E. coli isolates carrying the mcr-1 gene on mobile genetic elements. No other mcr-gene variants and no chromosomally located colistin resistance genes were detected. Following plasmid profiling and WGS, nine E. coli isolates from eight camels were selected for in-depth analysis. E. coli sequence types (STs) identified included ST7, ST21, ST24, ST399, ST649, ST999, and STdaa2. Seven IncI2(delta) and two IncX4 plasmids were found to be associated with mcr-1 carriage in these isolates. These findings represent the first identification of mcr-1-carrying plasmids associated with camels in the Gulf region. The presence of mcr-1 in camels from this region was previously unreported and serves as a novel finding in the field of AMR surveillance.
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Affiliation(s)
- Akela Ghazawi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Nikolaos Strepis
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), P.O. Box 2040 Rotterdam, The Netherlands
| | - Febin Anes
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Dana Yaaqeib
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Amal Ahmed
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Aysha AlHosani
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Mirah AlShehhi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Ashrat Manzoor
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Ihab Habib
- Veterinary Public Health Research Laboratory, Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Nisar A Wani
- Reproductive Biotechnology Center, Dubai P.O. Box 299003, United Arab Emirates
| | - John P Hays
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), P.O. Box 2040 Rotterdam, The Netherlands
| | - Mushtaq Khan
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
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Stamatiou R, Vasilaki A, Tzini D, Tsolaki V, Zacharouli K, Ioannou M, Fotakopoulos G, Sgantzos M, Makris D. Critical-Illness: Combined Effects of Colistin and Vasoactive Drugs: A Pilot Study. Antibiotics (Basel) 2023; 12:1057. [PMID: 37370376 DOI: 10.3390/antibiotics12061057] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/09/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Colistin is often used as a last resort for treating multidrug-resistant infections, particularly in critically ill patients in intensive care units. Nonetheless, its side effects, including myopathy, require careful monitoring. Vasoconstrictive drugs are also used in intensive care to increase blood pressure and improve blood flow to vital organs, which can be compromised in critically ill patients. The exact mechanism of colistin-induced muscle toxicity is of significant interest due to its potential intensive-care clinical implications. Colistin alone or in combination with vasoconstrictive agents was administrated in non-septic and LPS-induced septic animals for 10 days. Histopathological evaluation of the gastrocnemius muscle and dot-blot protein tissue analysis were performed. Increased intramuscular area, de-organization of the muscle fibers and signs of myopathy were observed in colistin-treated animals. This effect was ameliorated in the presence of vasoconstrictive drugs. Administration of colistin to septic animals resulted in a decrease of AMPK and cyclin-D1 levels, while it had no effect on caspase 3 levels. Vasoconstrictive drugs' administration reversed the effects of colistin on AMPK and cyclin D1 levels. Colistin's effects on muscle depend on septic state and vasoconstriction presence, highlighting the need to consider these factors when administering it in critically ill patients.
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Affiliation(s)
- Rodopi Stamatiou
- Physiology Laboratory, Faculty of Medicine, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Anna Vasilaki
- Laboratory of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, 41221 Larissa, Greece
| | - Dimitra Tzini
- Laboratory of Pharmacology, Faculty of Medicine, School of Health Sciences, University of Thessaly, Biopolis, 41221 Larissa, Greece
| | - Vasiliki Tsolaki
- Intensive Care Unit, Faculty of Medicine, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Konstantina Zacharouli
- Pathology Department, Faculty of Medicine, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Maria Ioannou
- Pathology Department, Faculty of Medicine, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - George Fotakopoulos
- Department of Neurosurgery, University Hospital of Larissa, 41500 Larisa, Greece
| | - Markos Sgantzos
- Anatomy Department, Faculty of Medicine, University of Thessaly, Biopolis, 41500 Larissa, Greece
| | - Demosthenes Makris
- Intensive Care Unit, Faculty of Medicine, University of Thessaly, Biopolis, 41500 Larissa, Greece
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6
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Investigation of mobile colistin resistance (mcr) genes among carbapenem resistance Pseudomonas aeruginosa isolates from bovine mastitis in Mashhad, Iran. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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7
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Ferreira M, Leão C, Clemente L, Albuquerque T, Amaro A. Antibiotic Susceptibility Profiles and Resistance Mechanisms to β-Lactams and Polymyxins of Escherichia coli from Broilers Raised under Intensive and Extensive Production Systems. Microorganisms 2022; 10:microorganisms10102044. [PMID: 36296320 PMCID: PMC9608943 DOI: 10.3390/microorganisms10102044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 01/25/2023] Open
Abstract
The intensive and extensive broiler production systems imply different veterinary interventions, including the use of antimicrobials. This study aimed to compare the antimicrobial susceptibility profiles of Escherichia coli isolated from both systems, characterize resistance mechanisms to β-lactams and polymyxins, and identify genetic elements such as integrons. E. coli isolates recovered from broiler cecal samples were assayed for antimicrobial susceptibility through the broth microdilution technique. The molecular characterization of acquired resistance mechanisms to β-lactams and colistin and the detection of integrons was performed by a multiplex PCR. For most antibiotics tested, the prevalence of reduced susceptibility is higher in commensal and extended-spectrum β-lactamases (ESBL)/AmpC producers from broilers raised in the intensive system, compared with those raised under extensive conditions. SHV-12 was the most common ESBL enzyme found in both production systems. Other ESBL variants such as CTX-M-1, CTX-M-55, CTX-M-14, CTX-M-32, CTX-M-9, TEM-52, and plasmid-encoded AmpC enzyme CMY-2 were also present. MCR-1 was identified in a colistin-resistant isolate from broilers raised under the intensive system. This study highlights the differences in E. coli antibiotic susceptibility from both production types and emphasizes that a great deal of work remains to decrease consumption and antimicrobial resistance levels.
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Affiliation(s)
- Mariana Ferreira
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- University of Évora, 7004-516 Évora, Portugal
| | - Célia Leão
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- MED—Mediterranean Institute for Agriculture, Environment and Development, 7006-554 Évora, Portugal
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Science, University of Lisbon, 1300-477 Lisbon, Portugal
| | - Teresa Albuquerque
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, National Reference Laboratory of Animal Health, INIAV—National Institute of Agrarian and Veterinary Research, 2780-157 Oeiras, Portugal
- Correspondence:
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Adi Wicaksono W, Braun M, Bernhardt J, Riedel K, Cernava T, Berg G. Trade-off for survival: Microbiome response to chemical exposure combines activation of intrinsic resistances and adapted metabolic activity. ENVIRONMENT INTERNATIONAL 2022; 168:107474. [PMID: 35988321 DOI: 10.1016/j.envint.2022.107474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 08/11/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
The environmental microbiota is increasingly exposed to chemical pollution. While the emergence of multi-resistant pathogens is recognized as a global challenge, our understanding of antimicrobial resistance (AMR) development from native microbiomes and the risks associated with chemical exposure is limited. By implementing a lichen asa bioindicatororganism and model for a native microbiome, we systematically examined responses towards antimicrobials (colistin, tetracycline, glyphosate, and alkylpyrazine). Despite an unexpectedly high resilience, we identified potential evolutionary consequences of chemical exposure in terms of composition and functioning of native bacterial communities. Major shifts in bacterial composition were observed due to replacement of naturally abundant taxa; e.g. Chthoniobacterales by Pseudomonadales. A general response, which comprised activation of intrinsic resistance and parallel reduction of metabolic activity at RNA and protein levels was deciphered by a multi-omics approach. Targeted analyses of key taxa based on metagenome-assembled genomes reflected these responses but also revealed diversified strategies of their players. Chemical-specific responses were also observed, e.g., glyphosate enriched bacterial r-strategists and activated distinct ARGs. Our work demonstrates that the high resilience of the native microbiota toward antimicrobial exposure is not only explained by the presence of antibiotic resistance genes but also adapted metabolic activity as a trade-off for survival. Moreover, our results highlight the importance of native microbiomes as important but so far neglected AMR reservoirs. We expect that this phenomenon is representative for a wide range of environmental microbiota exposed to chemicals that potentially contribute to the emergence of antibiotic-resistant bacteria from natural environments.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Maria Braun
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.
| | - Jörg Bernhardt
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.
| | - Katharina Riedel
- Institute of Microbiology, University of Greifswald, Greifswald, Germany.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria.
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria; Leibniz-Institute for Agricultural Engineering and Bioeconomy Potsdam (ATB), Potsdam, Germany; Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Cherak Z, Loucif L, Bendjama E, Moussi A, Benbouza A, Grainat N, Rolain JM. Dissemination of Carbapenemases and MCR-1 Producing Gram-Negative Bacteria in Aquatic Environments in Batna, Algeria. Antibiotics (Basel) 2022; 11:antibiotics11101314. [PMID: 36289972 PMCID: PMC9598638 DOI: 10.3390/antibiotics11101314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/04/2022] [Accepted: 09/13/2022] [Indexed: 12/02/2022] Open
Abstract
Antibiotic-resistant-bacteria are being considered as emerging environmental contaminants where the importance of the surrounding environment in their emergence and dissemination has been emphasized. The aim of this study was to screen for the presence and diversity of carbapenem- and colistin-resistant Gram-negative bacteria (GNBs) in different aquatic environments. Water samples were collected in Batna, Algeria. Carbapenem- and colistin-resistant GNBs were selectively isolated and then identified using matrix-assisted laser desorption and ionization time-of-flight mass spectrometry. After phenotypic antibiotic susceptibility testing, the molecular mechanisms of β-lactams and colistin-resistance were investigated by PCR and sequencing. The clonality of mcr-1 positive Escherichia coli was determined by multi-locus sequence typing. We noticed a high level of resistance in both tap water and wastewater. The most commonly found carbapenem-resistance mechanism was the OXA-48 enzyme, but other carbapenemases were also detected. In addition, the mcr-1 gene was detected in 18 E. coli of different sequence types. Our findings highlight the role of aquatic environments in the dissemination of resistant-bacteria, especially considering that water is a connecting medium between different ecological systems and can easily transmit resistant-bacteria and promote horizontal gene transfer. Thus, the development of effective treatment strategies for eliminating antibiotic-resistance is seriously needed.
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Affiliation(s)
- Zineb Cherak
- Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna 05078, Algeria
| | - Lotfi Loucif
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna 05078, Algeria
- Correspondence: ; Tel.: +213-(0)5-40-92-54-00
| | - Esma Bendjama
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna 05078, Algeria
- Départements de Technologie Alimentaire, Instituts des Sciences Agronomiques et Vétérinaires, Université El Hadj Lakhdar-Batna 1, Batna 05000, Algeria
| | - Abdelhamid Moussi
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bioressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra 07000, Algeria
| | - Amel Benbouza
- Faculté de Médecine, Université de Batna 2, Batna 05078, Algeria
| | - Nadia Grainat
- Faculté de Médecine, Université de Batna 2, Batna 05078, Algeria
| | - Jean-Marc Rolain
- Faculté de Médecine et de Pharmacie, Aix Marseille Université, IRD, MEPHI, 13007 Marseille, France
- IHU Méditerranée Infection, 13005 Marseille, France
- Assistance Publique des Hôpitaux de Marseille, 13005 Marseille, France
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10
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Occurrence of Extended Spectrum Cephalosporin-, Carbapenem- and Colistin-Resistant Gram-Negative Bacteria in Fresh Vegetables, an Increasing Human Health Concern in Algeria. Antibiotics (Basel) 2022; 11:antibiotics11080988. [PMID: 35892378 PMCID: PMC9332692 DOI: 10.3390/antibiotics11080988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 02/06/2023] Open
Abstract
The aim of this study was to screen for extended spectrum cephalosporin-, carbapenem- and colistin-resistant Gram-negative bacteria in fresh vegetables in Batna, Algeria. A total of 400 samples of fresh vegetables were collected from different retail stores. Samples were immediately subjected to selective isolation, then the representative colonies were identified using matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF–MS). Phenotypic and genotypic analyses were carried out in terms of species identification and relative antibiotic resistance. Transferability of the carbapenemase and mcr-bearing plasmids was verified by conjugation. The clonal relationships of carbapenemase and mcr-positive Escherichia coli isolates were studied by multi-locus sequence typing (MLST). Sixty-seven isolates were characterised and were mostly isolated from green leafy vegetables, where the dominant species identified included Citrobacter freundii, Klebsiella pneumoniae, Enterobacter cloacae, Stenotrophomona maltophilia, E. coli and Citrobacter braakii. PCR and sequencing results showed that E. coli was the bacterial species presenting the highest antibiotic resistance level in parallel to blaTEM (n = 16) and blaCTX-M-15 (n = 11), which were the most detected genes. Moreover, five isolates carried carbapenemase genes, including the blaOXA-48 and/or blaVIM-4 genes. The mcr-1 gene was detected in two E. coli isolates. MLST analysis revealed three different E. coli sequence types: ST101 (n = 1), ST216 (n = 1) and ST2298 (n = 1). Conjugation assays confirmed the transferability of the blaOXA-48 and mcr-1 genes. In this study we report, for the first time, the detection of the blaOXA-48 gene in E. coli and C. braakii isolates and the blaVIM-4 gene in vegetables. To the best of our knowledge, this is the first report on the detection of mcr-1 genes from vegetables in Algeria.
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Mitchell JM, June CM, Baggett VL, Lowe BC, Ruble JF, Bonomo RA, Leonard DA, Powers RA. Conformational flexibility in carbapenem hydrolysis drives substrate specificity of the class D carbapenemase OXA-24/40. J Biol Chem 2022; 298:102127. [PMID: 35709986 PMCID: PMC9293634 DOI: 10.1016/j.jbc.2022.102127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/03/2022] Open
Abstract
The evolution of multidrug resistance in Acinetobacter spp. increases the risk of our best antibiotics losing their efficacy. From a clinical perspective, the carbapenem-hydrolyzing class D β-lactamase subfamily present in Acinetobacter spp. is particularly concerning because of its ability to confer resistance to carbapenems. The kinetic profiles of class D β-lactamases exhibit variability in carbapenem hydrolysis, suggesting functional differences. To better understand the structure–function relationship between the carbapenem-hydrolyzing class D β-lactamase OXA-24/40 found in Acinetobacter baumannii and carbapenem substrates, we analyzed steady-state kinetics with the carbapenem antibiotics meropenem and ertapenem and determined the structures of complexes of OXA-24/40 bound to imipenem, meropenem, doripenem, and ertapenem, as well as the expanded-spectrum cephalosporin cefotaxime, using X-ray crystallography. We show that OXA-24/40 exhibits a preference for ertapenem compared with meropenem, imipenem, and doripenem, with an increase in catalytic efficiency of up to fourfold. We suggest that superposition of the nine OXA-24/40 complexes will better inform future inhibitor design efforts by providing insight into the complicated and varying ways in which carbapenems are selected and bound by class D β-lactamases.
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Affiliation(s)
- Joshua M Mitchell
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Cynthia M June
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Vincent L Baggett
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Beth C Lowe
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - James F Ruble
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Robert A Bonomo
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, 10701 East Boulevard, Cleveland, OH; Departments of Medicine, Biochemistry, Molecular Biology and Microbiology, Pharmacology, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH.
| | - David A Leonard
- Department of Chemistry, Grand Valley State University, Allendale, MI
| | - Rachel A Powers
- Department of Chemistry, Grand Valley State University, Allendale, MI.
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Worldwide Prevalence of mcr-mediated Colistin-Resistance Escherichia coli in Isolates of Clinical Samples, Healthy Humans, and Livestock-A Systematic Review and Meta-Analysis. Pathogens 2022; 11:pathogens11060659. [PMID: 35745513 PMCID: PMC9230117 DOI: 10.3390/pathogens11060659] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 05/30/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Antimicrobial resistance is a serious public-health problem throughout the world. Escherichia coli, the most common Gram-negative microorganism, has developed different resistance mechanisms, making treating infections difficult. Colistin is considered a last-resort drug in the treatment of infections caused by E. coli. Plasmid-mediated mobile-colistin-resistant (mcr) genes in E. coli, now disseminated globally, are considered a major public-health threat. Humans, chickens, and pigs are the main reservoirs for E. coli and the sources of antibiotic resistance. Hence, an up-to-date and precise estimate of the global prevalence of mcr resistance genes in these reservoirs is necessary to understand more precisely the worldwide spread and to more effectively implement control and prevention strategies. Methodology: Publications were identified in the PubMed database on the basis of the PRISMA guidelines. English full-text articles were selected from December 2014 to March 2021. Descriptive statistics and a meta-analysis were performed in Excel and R software, respectively. Colistin resistance was defined as the molecular-genetic detection of the mcr genes. The crude and estimated prevalence were calculated for each host and continent. The studies were divided into two groups; community-based when they involved isolates from healthy humans, chickens, or pigs, and clinical studies when they involved only hospital, outpatient, or laboratory isolates. Results: A total of 1278 studies were identified and 218 were included in this systematic review and meta-analysis, divided into community studies (159 studies) and clinical studies (59 studies). The general prevalence of mcr-mediated colistin-resistant E. coli (mcrMCRE) was 6.51% (n = 11,583/177,720), reported in 54 countries and on five continents; Asia with 119 studies followed by Europe with 61 studies registered the most articles. Asia reported the major diversity of mcr-variants (eight of nine, except mcr-2). Worldwide, chickens and pigs proved to be the principal reservoir of mcr with an estimated prevalence of 15.8% and 14.9%, respectively. Healthy humans and clinical isolates showed a lower prevalence with 7.4% and 4.2% respectively. Conclusions: In this systematic review and meta-analysis, the worldwide prevalence of mcr in E. coli isolated from healthy humans, chickens, and pigs was investigated. A wide prevalence and distribution of mcr genes was demonstrated on all continents in E. coli isolates from the selected reservoirs. Understanding the epidemiology and occurrence in the reservoirs of mcr in E. coli on different continents of the world facilitates tracing how mcr genes are transmitted and determining the infection risks for humans. This knowledge can be used to reduce the incidence of zoonotic transmission by implementing the appropriate control programs.
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High Carriage of Extended-Spectrum, Beta Lactamase-Producing, and Colistin-Resistant Enterobacteriaceae in Tibetan Outpatients with Diarrhea. Antibiotics (Basel) 2022; 11:antibiotics11040508. [PMID: 35453259 PMCID: PMC9032258 DOI: 10.3390/antibiotics11040508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/04/2022] [Accepted: 04/08/2022] [Indexed: 11/28/2022] Open
Abstract
Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) have been detected in human-impacted habitats, especially in densely populated cities. The Qinghai–Tibet Plateau is located far from the heavily populated regions of China, and Tibetan residents have distinct dietary habits and gut microbes. Antibiotic-resistance monitoring in the Tibetan population is rare. Here, we collected stool samples from Tibetan outpatients with diarrhea. From 59 samples, 48 antibiotic-resistant Enterobacteriaceae isolates were obtained, including 19 extended-spectrum beta lactamase (ESBL)-producing isolates from 16 patients and 29 polymyxin-resistant isolates from 22 patients. Either ESBL or mcr genes were found in 17 Escherichia coli isolates, approximately 58.8% of which were multidrug-resistant, and ten incompatible plasmid types were found. The gene blaCTX-M was a common genotype in the ESBL-producing E. coli isolates. Four E. coli isolates contained mcr-1. The same mcr-1-carrying plasmid was found in distinct E. coli isolates obtained from the same sample, thus confirming horizontal transmission of mcr-1 between bacteria. Genomic clustering of E. coli isolates obtained from Lhasa, with strains from other regions providing evidence of clone spreading. Our results reveal a strong presence of ARB and ARGs in Tibetan outpatients with diarrhea, implying that ARB and ARGs should be monitored in the Tibetan population.
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Dosing Colistimethate Every 8 h Results in Higher Plasma Concentrations of Active Colistin Than Every 12-Hourly Dosing without Increase in Nephrotoxicity: A Phase 1 Pharmacokinetics Trial in Healthy Adult Volunteers. Antibiotics (Basel) 2022; 11:antibiotics11040490. [PMID: 35453240 PMCID: PMC9029538 DOI: 10.3390/antibiotics11040490] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/02/2022] [Accepted: 04/05/2022] [Indexed: 12/04/2022] Open
Abstract
Despite its use for decades, pharmacokinetic (PK) and safety studies on colistin are limited. We conducted a phase l, open-label trial to evaluate the safety and PK of multiple doses of intravenous (IV) and aerosolized colistimethate sodium (CMS) administered separately and in combination. In total, 31 healthy adults were enrolled into three cohorts of 9, 10, and 12 participants, respectively. Each cohort received increasing doses of CMS over three dosing periods as follows: Period 1 (IV only), 2.5 mg/kg every 12 h (q12h) to 3.3 mg/kg every 8 h (q8h); Period 2 (aerosolized only), 75 mg 2–4 doses, and Period 3 (combined IV aerosolized), in which was Periods 1 and 2 combined. Safety assessments, serum and lung concentrations of colistin analytes (colistin A, colistin B, CMS A, and CMS B), and kidney biomarkers were measured at specified time points. Increasing the CMS dose from 2.5 mg/kg q12h to q8h resulted in a 33% increase in serum colistin A concentrations from 3.9 μg/mL to 5.3 μg/mL—well above the accepted target of 2 μg/mL for 6 h after dosing, without evidence of nephrotoxicity. However, there was an increase in neurotoxicity, primarily perioral and lingual paresthesias, and self-limited ataxia. IV administration did not increase the lung concentrations of colistin.
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Hahm C, Chung HS, Lee M. Whole-genome sequencing for the characterization of resistance mechanisms and epidemiology of colistin-resistant Acinetobacter baumannii. PLoS One 2022; 17:e0264335. [PMID: 35245298 PMCID: PMC8896714 DOI: 10.1371/journal.pone.0264335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Background Multidrug-resistant Acinetobacter baumannii is an important causal pathogen of healthcare-associated infections, and colistin-resistant strains have recently emerged owing to the increased use of colistin. Using next-generation sequencing (NGS), a single whole-genome sequencing (WGS) protocol can identify and type pathogens, analyze genetic relationships among different pathogens, predict pathogenic transmissions, and detect antibiotic resistance genes. However, only a few studies have applied NGS in studying the resistance mechanism and epidemiology of colistin-resistant A. baumannii. This study aimed to elucidate the resistance mechanism of colistin-resistant A. baumannii and analyze its molecular epidemiology through WGS. Materials and methods The subjects in this study were patients who visited a university hospital between 2014 and 2018. Thirty colistin-resistant strains with high minimum inhibitory concentrations were selected from various patient samples, and WGS was performed. Comparative genomic analysis was performed for the 27 colistin-resistant A. baumannii strains using a colistin-susceptible strain as the reference genome. Results The WGS analysis found no mutation for lpxA, lpxC, lpx D, pmrA, pmrB, and mcr1, the genes known to be associated with colistin resistance. Fifty-seven coding sequences (CDS) showed differences; they included 13 CDS with known names and functions that contained 21 genes. From the whole-genome multi-locus sequence typing (wgMLST) and single nucleotide polymorphism (SNP) analyses, two major clusters were found for the colistin-resistant A. baumannii strains. However, no differences were observed by the time of detection for each cluster, the samples, the pattern of antibiotic resistance, or the patient characteristics. In the conventional MLST following the Oxford scheme, the typing result showed ST1809, ST451, ST191, ST1837, and ST369 in the global clone 2 (GC2), without any relation with the results of wgMLST and SNP analyses. Conclusion Based on the findings of the resistance gene analysis through WGS and comparative genomic analysis, the potential genes associated with colistin-resistance or CDS were examined. Furthermore, the analysis of molecular epidemiology through WGS regarding colistin-resistant A. baumannii may prove helpful in preventing infection by multidrug-resistant bacteria and controlling healthcare-associated infections.
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Affiliation(s)
- Chorong Hahm
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
- Department of Laboratory Medicine, Eone Laboratories, Incheon, Korea
| | - Hae-Sun Chung
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
- EWHA Education and Research Center for Infection, College of Medicine, Ewha Womans University, Seoul, Korea
| | - Miae Lee
- Department of Laboratory Medicine, College of Medicine, Ewha Womans University, Seoul, Korea
- EWHA Education and Research Center for Infection, College of Medicine, Ewha Womans University, Seoul, Korea
- * E-mail:
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Sonnevend Á, Alali WQ, Mahmoud SA, Ghazawi A, Bharathan G, Melegh S, Rizvi TA, Pál T. Molecular Characterization of MCR-1 Producing Enterobacterales Isolated in Poultry Farms in the United Arab Emirates. Antibiotics (Basel) 2022; 11:antibiotics11030305. [PMID: 35326769 PMCID: PMC8944778 DOI: 10.3390/antibiotics11030305] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/18/2022] [Accepted: 02/20/2022] [Indexed: 02/04/2023] Open
Abstract
Data on the prevalence of MCR-producing Enterobacterales of animal origin are scarce from the Arabian Peninsula. We investigated the presence and variety of such strains from fecal specimens of poultry collected in four farms in the United Arab Emirates. Colonies from ten composite samples per farm grown on colistin-supplemented plates were PCR-screened for alleles of the mcr gene. Thirty-nine isolates selected based on species, colony morphology, and plasmid profile were subjected to whole genome sequencing. The panel of their resistance and virulence genes, MLST and cgMLST were established. Transferability and incompatibility types of the MCR-plasmids were determined. mcr-1.1 positive strains were identified in 36 of the 40 samples. Thirty-four multi-drug resistant Escherichia coli of 16 different sequence types, two Escherichia albertii, two Klebsiella pneumoniae and one Salmonella minnesota were identified. Beyond various aminoglycoside, tetracycline, and co-trimoxazole resistance genes, seven of them also carried ESBL genes and one blaCMY-2. Six IncHI2, 26 IncI2 and 4 IncX4 MCR-plasmids were mobilized, in case of the IncHI2 plasmids co-transferring ampicillin, chloramphenicol and tetracycline resistance. The diversity of mcr-1 positive strains suggest a complex local epidemiology calling for a coordinated surveillance including animals, retail meat and clinical cases.
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Affiliation(s)
- Ágnes Sonnevend
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Á.S.); (S.M.)
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
| | - Walid Q. Alali
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Kuwait University, Safat, Kuwait City 13110, Kuwait;
| | - Sara A. Mahmoud
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
| | - Greeshma Bharathan
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
- Department of Food Science, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Szilvia Melegh
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Á.S.); (S.M.)
| | - Tahir A. Rizvi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Tibor Pál
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, 7624 Pécs, Hungary; (Á.S.); (S.M.)
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates; (S.A.M.); (A.G.); (G.B.); (T.A.R.)
- Correspondence:
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Hou J, Mao D, Zhang Y, Huang R, Li L, Wang X, Luo Y. Long-term spatiotemporal variation of antimicrobial resistance genes within the Serratia marcescens population and transmission of S. marcescens revealed by public whole-genome datasets. JOURNAL OF HAZARDOUS MATERIALS 2022; 423:127220. [PMID: 34844350 DOI: 10.1016/j.jhazmat.2021.127220] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 09/05/2021] [Accepted: 09/10/2021] [Indexed: 06/13/2023]
Abstract
The development of antimicrobial resistance (AMR) is accelerated by the selective pressure exerted by the widespread use of antimicrobial drugs, posing an increasing danger to public health. However, long-term spatiotemporal variation in AMR genes in microorganisms, particularly in bacterial pathogens in response to antibiotic consumption, is not fully understood. Here, we used the NCBI RefSeq database to collect 478 whole-genome sequences for Serratia marcescens ranging from 1961 up to 2019, to document global long-term AMR trends in S. marcescens populations. In total, 100 AMR gene subtypes (16 AMR gene types) were detected in the genomes of S. marcescens populations. We identified 3 core resistance genes in S. marcescens genomes, and a high diversity of AMR genes was observed in S. marcescens genomes after corresponding antibiotics were discovered and introduced into clinical practice, suggesting the adaptation of S. marcescens populations to challenges with therapeutic antibiotics. Our findings indicate spatiotemporal variation of AMR genes in S. marcescens populations in relation to antibiotic consumption and suggest the potential transmission of S. marcescens isolates harboring AMR genes among countries and between the environment and the clinic, representing a public health threat that necessitates international solidarity to overcome.
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Affiliation(s)
- Jie Hou
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Daqing Mao
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Yulin Zhang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Ruiyang Huang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Linyun Li
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Xiaolong Wang
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China
| | - Yi Luo
- College of Environmental Science and Engineering, Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, Nankai University, Tianjin 300071, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210093, China.
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Gut microbiome in the emergence of antibiotic-resistant bacterial pathogens. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 192:1-31. [DOI: 10.1016/bs.pmbts.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Masterson K, Meade E, Garvey M, Lynch M, Major I, Rowan NJ. Development of a low-temperature extrusion process for production of GRAS bioactive-polymer loaded compounds for targeting antimicrobial-resistant (AMR) bacteria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149545. [PMID: 34399333 DOI: 10.1016/j.scitotenv.2021.149545] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/05/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Antimicrobial resistance (AMR) is recognised globally as one of the greatest threats to human and animal health; thus, discovery of alternative antibacterial agents to address AMR is a priority challenge. This study constitutes the first report of a low-melting temperature, polymer- extrusion process for the smart delivery of thermally-sensitive antimicrobial bioactives, including generally-regarded-as-safe (GRAS) bioactives derived from various sources. Bioactives were assessed before and after extrusion by determining their respective minimum inhibitory concentrations (MIC). WHO-priority AMR-bacterial isolates causing zoonotic infections were evaluated along with use of standard ATCC strains. Findings revealed that this copolymer method was capable of delivering thermally-sensitive bioactives with varying degrees of growth inhibition against the AMR-bacterial strains. The extrusion process was found to increase the effect of nisin against MRSA (4-fold increase) and L. monocytogenes (6.4-fold increase), silver nitrate (AgNO3) against E. coli (3.6-fold increase) and S. epidermidis (1.25-fold increase), and chitosan against S. aureus (1.25-fold). Findings show the potential applicability of this polymer extrusion process for developing future bioactive-loaded polymer compounds; thus, highlighting the potential of converging bio-based industry with novel materials for enabling 'One-Health' solutions.
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Affiliation(s)
- Kevin Masterson
- Bioscience Research Institute, Athlone Institute of Technology, Ireland.
| | - Elaine Meade
- Department of Life Science, Sligo Institute of Technology, Ash Lane, Sligo, Ireland
| | - Mary Garvey
- Department of Life Science, Sligo Institute of Technology, Ash Lane, Sligo, Ireland
| | - Mark Lynch
- Bioscience Research Institute, Athlone Institute of Technology, Ireland
| | - Ian Major
- Materials Research Institute, Athlone Institute of Technology, Ireland
| | - Neil J Rowan
- Bioscience Research Institute, Athlone Institute of Technology, Ireland; Centre for Disinfection, Sterilization and Biosecurity, Athlone Institute of Technology, Ireland
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Mobile Colistin Resistance Genetic Determinants of Non-Typhoid Salmonella enterica Isolates from Russia. Microorganisms 2021; 9:microorganisms9122515. [PMID: 34946117 PMCID: PMC8705591 DOI: 10.3390/microorganisms9122515] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/23/2022] Open
Abstract
Polymyxin resistance, determined by mcr genes located on plasmid DNA, currently poses a high epidemiological threat. Non-typhoid Salmonella (NTS) are one of the key pathogens causing diarrheal diseases. Here, we report the isolation and whole genome sequencing of multidrug colistin-resistant/susceptible isolates of non-typhoid Salmonella enterica serovars carrying mcr genes. Non-typhoid strains of Salmonella enterica subsp. enterica were isolated during microbiological monitoring of the environment, food, and diarrheal disease patients between 2018 and 2020 in Russia (n = 586). mcr-1 genes were detected using a previously developed qPCR assay, and whole genome sequencing of mcr positive isolates was performed by both short-read (Illumina) and long-read (Oxford Nanopore) approaches. Three colistin-resistant isolates, including two isolates of S. Enteritidis and one isolate of S. Bovismorbificans, carried the mcr-1.1 gene located on IncX4 and IncI2 conjugative plasmids, respectively. The phenotypically colistin-susceptible isolate of S. Typhimurium carried a mcr-9 gene on plasmid IncHI2. In conclusion, we present the first three cases of mcr gene-carrying NTS isolates detected in Russia with both outbreak and sporadic epidemiological backgrounds.
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Portes AB, Rodrigues G, Leitão MP, Ferrari R, Conte Junior CA, Panzenhagen P. Global distribution of plasmid-mediated colistin resistance mcr gene in Salmonella: A systematic review. J Appl Microbiol 2021; 132:872-889. [PMID: 34480840 DOI: 10.1111/jam.15282] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/04/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
This systematic review focuses on obtaining the most relevant information from multiple studies that detected a mobilized colistin resistance mcr gene in Salmonella for a better comprehension of its global distribution. A group of strategic and systematic keywords were combined to retrieve research data on the detection frequency of the mcr gene globally from four database platforms (Google Scholar, Science Direct, PubMed and Scielo). Forty-eight studies attended all the eligibility criteria and were selected. China was the country with the highest frequency of Salmonella strains with the mcr gene, and Europe exhibited a wide diversity of countries with positive mcr strains. In addition, animals and humans carried the highest frequency of positive strains for the mcr gene. Salmonella Typhimurium was the most frequent serovar carrying the mcr gene. Apparently, colistin overuse in animal husbandry has increased the selective pressure of antimicrobial resistance, resulting in the emergence of a plasmid-mediated colistin resistance mcr gene in China. The mcr-positive Salmonella strains are recently predominant worldwide, which is probably due to the capacity of this gene to be swiftly horizontally transmissible. The transmission ability of mcr-positive Salmonella strains to humans through the consumption of contaminated animal-based food is a public health concern.
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Affiliation(s)
- Ana Beatriz Portes
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Grazielle Rodrigues
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Mylenna Palma Leitão
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Rafaela Ferrari
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Carlos Adam Conte Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói, RJ, Brazil.,Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
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Cherak Z, Loucif L, Moussi A, Rolain JM. Epidemiology of mobile colistin resistance (mcr) genes in aquatic environments. J Glob Antimicrob Resist 2021; 27:51-62. [PMID: 34438108 DOI: 10.1016/j.jgar.2021.07.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/11/2021] [Accepted: 07/25/2021] [Indexed: 02/05/2023] Open
Abstract
Colistin is one of the last-line therapies against multidrug-resistant Gram-negative pathogens, especially carbapenemase-producing isolates, making resistance to this compound a major global public-health crisis. Until recently, colistin resistance in Gram-negative bacteria was known to arise only by chromosomal mutations. However, a plasmid-mediated colistin resistance mechanism was described in late 2015. This mechanism is encoded by different mobile colistin resistance (mcr) genes that encode phosphoethanolamine (pEtN) transferases. These enzymes catalyse the addition of a pEtN moiety to lipid A in the bacterial outer membrane leading to colistin resistance. MCR-producing Gram-negative bacteria have been largely disseminated worldwide. However, their environmental dissemination has been underestimated. Indeed, water environments act as a connecting medium between different environments, allowing them to play a crucial role in the spread of antibiotic resistance between the natural environment and humans and other animals. For a better understanding of the role of such environments as reservoirs and/or dissemination routes of mcr genes, this review discusses primarily the various water habitats contributing to the spread of antibiotic resistance. Thereafter, we provide an overview of existing knowledge regarding the global epidemiology of mcr genes in water environments. This review confirms the global distribution of mcr genes in several water environments, including wastewater from different origins, surface water and tap water, making these environments reservoirs and dissemination routes of concern for this resistance mechanism.
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Affiliation(s)
- Zineb Cherak
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bio-ressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra, Algeria
| | - Lotfi Loucif
- Laboratoire de Biotechnologie des Molécules Bioactives et de la Physiopathologie Cellulaire (LBMBPC), Département de Microbiologie et de Biochimie, Faculté des Sciences de la Nature et de la Vie, Université de Batna 2, Batna, Algeria.
| | - Abdelhamid Moussi
- Laboratoire de Génétique, Biotechnologie et Valorisation des Bio-ressources (GBVB), Faculté des Sciences Exactes et des Sciences de la Nature et de la Vie, Université Mohamed Khider, Biskra, Algeria
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, MEPHI, Faculté de Médecine et de Pharmacie, Marseille, France; IHU Méditerranée Infection, Marseille, France; Assistance Publique des Hôpitaux de Marseille, Marseille, France
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23
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Coker ME, Oaikhena AO, Ajayi TO. Antimicrobial activity of extracts and fractions of Euphorbia lateriflora (Schum. and Thonn) on microbial isolates of the urinary tract. Saudi J Biol Sci 2021; 28:4723-4731. [PMID: 34354460 PMCID: PMC8324943 DOI: 10.1016/j.sjbs.2021.04.086] [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: 02/07/2021] [Revised: 04/25/2021] [Accepted: 04/26/2021] [Indexed: 12/04/2022] Open
Abstract
Euphorbia lateriflora is used in ethnomedicine for treating several conditions, including genital and urinary tract infections (UTI). Although ethnobotanical claims support its use in therapy, there is limited evidence on its effect on UTI, even though UTI remains a public health problem in Nigeria especially due to increasing antimicrobial resistance. We investigated the activity of E. lateriflora extracts and fractions on bacterial and fungal isolates from symptomatic urinary tract infections and vaginosis respectively. Qualitative phytochemical screening was conducted on dried pulverised leaves. Successive gradient extraction was carried out with the aid of a soxhlet extractor with n-Hexane, ethyl acetate and methanol respectively. Bioactivity guided fractionation was conducted on the ethyl acetate extract using Vacuum Liquid Chromatography. Antimicrobial susceptibility testing by disc diffusion was conducted on test isolates. Antimicrobial susceptibility of isolates to extracts and fractions was done using the agar well diffusion technique. Minimum Inhibitory Concentrations (MIC) and Minimum Biocidal Concentrations (MBC) were determined by agar and broth dilutions respectively. Time-kill assay of the ethyl acetate extract was conducted using the viable count technique. Phytochemicals present include saponins, tannins and flavonoids. The majority of isolates used in this study were multidrug resistant. Extracts and fractions of E. lateriflora produced appreciable zones of inhibition on both antibiotic susceptible and resistant bacteria with MICs of 6.25 mg/mL and MBC ranging from 6.25–50 mg/mL. Bactericidal activity of the ethyl acetate extract was concentration and time dependent with 100% kill at 25 mg/mL after 6 h for E. coli and 2 h for C. albicans. Euphorbia lateriflora contains phytochemicals which possess antimicrobial activity on antibiotic resistant bacteria and has potential in the development of chemotherapeutics for bacterial and fungal infections.
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Affiliation(s)
- Morenike E Coker
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Anderson O Oaikhena
- Department of Pharmaceutical Microbiology, University of Ibadan, Ibadan, Nigeria
| | - Temitayo O Ajayi
- Department of Phamacognosy, University of Ibadan, Ibadan, Nigeria
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Wang C, Hong T, Cui P, Wang J, Xia J. Antimicrobial peptides towards clinical application: Delivery and formulation. Adv Drug Deliv Rev 2021; 175:113818. [PMID: 34090965 DOI: 10.1016/j.addr.2021.05.028] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 05/14/2021] [Accepted: 05/30/2021] [Indexed: 02/07/2023]
Abstract
Antimicrobial peptides hold promise to supplement small molecules antibiotics and combat the multidrug resistant microbes. There are however technical hurdles towards the clinical applications, largely due to the inherent limitations of peptides including stability, cytotoxicity and bioavailability. Here we review recent studies concerning the delivery and formulation of antimicrobial peptides, by categorizing the different strategies as driven by physical interactions or chemical conjugation reactions, and carriers ranging from inorganic based ones (including gold, silver and silica based solid nanoparticles) to organic ones (including micelle, liposome and hydrogel) are covered. Besides, targeted delivery of antimicrobial peptides or using antimicrobial peptides as the targeting moiety, and responsive release of the peptides after delivery are also reviewed. Lastly, strategies towards the increase of oral bioavailability, from both physical or chemical methods, are highlighted. Altogether, this article provides a comprehensive review of the recent progress of the delivery and formulation of antimicrobial peptides towards clinical application.
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Affiliation(s)
- Cheng Wang
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Tingting Hong
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Pengfei Cui
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China
| | - Jianhao Wang
- Jiangsu Key Laboratory of Advanced Catalytic Materials and Technology, School of Pharmacy, Changzhou University, Changzhou, Jiangsu 213164, China.
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region.
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Kong Y, Li C, Chen H, Zheng W, Sun Q, Xie X, Zhang J, Ruan Z. In vivo Emergence of Colistin Resistance in Carbapenem-Resistant Klebsiella pneumoniae Mediated by Premature Termination of the mgrB Gene Regulator. Front Microbiol 2021; 12:656610. [PMID: 34234754 PMCID: PMC8256851 DOI: 10.3389/fmicb.2021.656610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
Multidrug-resistant (MDR) Klebsiella pneumoniae is a severe threat to public health worldwide. Worryingly, colistin resistance, one of the last-line antibiotics for the treatment of MDR K. pneumoniae infection, has been increasingly reported. This study aims to investigate the emergence of evolved colistin resistance in a carbapenem-resistant K. pneumoniae isolate during colistin treatment. In this study, a pair of sequential carbapenem-resistant K. pneumoniae isolates were recovered from the same patient before and after colistin treatment, named KP1-1 and KP1-2, respectively. Antibiotic susceptibility testing was performed by the microdilution broth method. Whole genome sequencing was performed, and putative gene variations were analyzed in comparison of the genome sequence of both isolates. The bacterial whole genome sequence typing and source tracking analysis were performed by BacWGSTdb 2.0 server. Validation of the role of these variations in colistin resistance was examined by complementation experiments. The association between colistin resistance and the expression level of PhoP/PhoQ signaling system and its regulated genes was evaluated by quantitative real-time PCR (qRT-PCR) assay. Our study indicated that KP1-1 displayed extensively antibiotic resistant trait, but only susceptible to colistin. KP1-2 showed additional resistance to colistin. Both isolates belonged to Sequence Type 11 (ST11). The whole genome sequence analysis uncovered multiple resistance genes and virulence genes in both isolates. No plasmid-mediated mcr genes were found, but genetic variations in five chromosomal genes, especially the Gln30∗ alteration in MgrB, were detected in colistin-resistant isolate KP1-2. Moreover, only complementation with wild-type mgrB gene restored colistin susceptibility, with colistin MIC decreased from 32 to 1 mg/L. Expression assays revealed an overexpression of the phoP, phoQ, and pmrD genes in the mgrB-mutated isolate KP1-2 compared to the wild-type isolate KP1-1, confirming the MgrB alterations was responsible for increased expression levels of those genes. This study provides direct in vivo evidence that Gln30∗ alteration of MgrB is a critical region responsible for colistin resistance in K. pneumoniae clinical strains.
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Affiliation(s)
- Yingying Kong
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chao Li
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hangfei Chen
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wei Zheng
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qingyang Sun
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyou Xie
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Zhang
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhi Ruan
- Department of Clinical Laboratory, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Madi-Moussa D, Coucheney F, Drider D. Expression of five class II bacteriocins with activity against Escherichia coli in Lacticaseibacillus paracasei CNCM I-5369, and in a heterologous host. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2021; 30:e00632. [PMID: 34136365 PMCID: PMC8181189 DOI: 10.1016/j.btre.2021.e00632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 02/06/2023]
Abstract
Five open reading frames viz orf010, orf12, orf023, orf030 and orf038 coding class II bacteriocins in Lacticaseibacillus paracasei CNCM I-5369 strain previously isolated from an Algerian dairy product, were found to be expressed after 24 h of growth. The strain has also shown anti-E. coli activity in a narrow pH range between 4.5 and 5. Then, expression and purification of these bacteriocins was conducted in the heterologous host E. coli. This strategy enabled us to purify the peptide encoded by orf030 in large quantities, in contrast to other peptides that were produced but required to be released from the insoluble fraction following 4 M urea and desalting treatments. All peptides heterologously produced were characterized by MALDI TOF Mass spectrometry and successfully tested for their anti-E. coli activity. Furthermore, in silico transcriptional analysis was determined by Findterm tool and with Bagel4 software permitted to locate potential promoters and co-transcription events.
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Affiliation(s)
- Désiré Madi-Moussa
- UMR Transfrontalière BioEcoAgro1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV – Institut Charles Viollette, F-59000 Lille, France
| | - Françoise Coucheney
- UMR Transfrontalière BioEcoAgro1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV – Institut Charles Viollette, F-59000 Lille, France
| | - Djamel Drider
- UMR Transfrontalière BioEcoAgro1158, Univ. Lille, INRAE, Univ. Liège, UPJV, YNCREA, Univ. Artois, Univ. Littoral Côte d’Opale, ICV – Institut Charles Viollette, F-59000 Lille, France
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Takiguchi S, Homma H, Fujisawa T, Hirota-Takahata Y, Ono Y, Kizuka M, Ishii Y, Yoshimura S, Nishi T. Syntheses and antimicrobial activities of ogipeptin derivatives. Bioorg Med Chem Lett 2021; 42:128093. [PMID: 33964447 DOI: 10.1016/j.bmcl.2021.128093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/19/2021] [Accepted: 04/28/2021] [Indexed: 11/30/2022]
Abstract
Novel cyclic peptide derivatives based on ogipeptins A, B, C, and D were synthesized. Starting with a mixture of ogipeptins A-D, a practical four-step synthetic procedure was followed to prepare novel derivatives with various kinds of acyl side chains. Among the 45 new synthetic derivatives identified, the antibacterial activities of compounds 8-3 and 8-38 were comparable with those of ogipeptin A. In in vitro nephrotoxicity screening using LLC-PK1 cells, compounds 8-3 and 8-38 showed significantly lower cytotoxicity (LD20 > 480 μM) than colistin (LD20 = 44.2 μM).
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Affiliation(s)
- Shingo Takiguchi
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan.
| | - Hidehito Homma
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Tetsunori Fujisawa
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Yuki Hirota-Takahata
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Yasunori Ono
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Masaaki Kizuka
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Yuki Ishii
- Daiichi Sankyo RD Novare Co., Ltd., 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Satomichi Yoshimura
- Organization for Research Initiatives, Yamaguchi University, 1-1-1 Minami-Kogushi, Ube, Yamaguchi 755-8505, Japan
| | - Takahide Nishi
- School of Pharmaceutical Sciences, Health Sciences University of Hokkaido, 1757 Kanazawa, Ishikari-Tobetsu, Hokkaido 061-0293, Japan.
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Fam NS, Mohamed SH, Gamal D, Wasfy RM, Soliman MS, El-Kholy AA. Reliability of phenotypic methods for detection of colistin resistance among carbapenem-resistant Acinetobacter baumannii clinical isolates from Egypt. Germs 2020; 10:303-309. [PMID: 33489945 DOI: 10.18683/germs.2020.1222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/11/2020] [Accepted: 07/22/2020] [Indexed: 11/08/2022]
Abstract
Introduction Acinetobacter baumannii is a challenging pathogen responsible for serious nosocomial infections. Colistin resistance in carbapenem-resistant A. baumannii strains is a critical health problem as it limits the available therapeutic options. The current work aimed to study the reliability of several phenotypic methods for the detection of colistin resistance among carbapenem-resistant A. baumannii isolates in Egypt. Methods A total of 22 carbapenem-resistant A. baumannii isolates were recovered. Colistin minimum inhibitory concentrations (MICs) were determined using broth microdilution (BMD) and compared to agar dilution (AD), automated system (VITEK-2) and gradient test (E-test) and were analyzed by statistical methods. Results Phenotypic testing showed that nine of 22 isolates (40.9%) were colistin-resistant by BMD and seven of them were also resistant by AD, with the categorical agreement (CA) of 72.7% and essential agreement (EA) of 90.9%. Colistin MIC results ranged from 1-8 µg/mL and 1-32 µg/mL by both AD and BMD respectively. Detection of colistin resistance by gradient test and automated system showed high very major error (VME) rates (40.9%) compared to BMD with a lack of CA between them. AD gave moderate agreement with BMD by 90.9% EA, 72.7% CA and only 9.1% VME. Conclusions In delineating colistin breakpoints BMD followed by AD method are defined as the only reliable phenotypic methods for colistin resistance evaluation. More rapid and reliable tests, other than BMD and AD, are required for the convenient detection of colistin resistance in the routine clinical microbiology laboratory daily workflow.
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Affiliation(s)
- Nevine S Fam
- MD, Department of Microbiology, Theodor Bilharz Research Institute, PM Box 30 Imbaba, Giza, Egypt
| | - Sara H Mohamed
- PhD, Department of Microbiology, National Organization for Drug Control and Research, Giza, Egypt
| | - Doaa Gamal
- MD, Department of Microbiology, Theodor Bilharz Research Institute, PM Box 30 Imbaba, Giza, Egypt
| | - Reham M Wasfy
- MSc, Department of Microbiology, Theodor Bilharz Research Institute, PM Box 30 Imbaba, Giza, Egypt
| | - May S Soliman
- MD, Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Amani A El-Kholy
- MD, Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
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Simple Phenotypic Tests To Improve Accuracy in Screening Chromosomal and Plasmid-Mediated Colistin Resistance in Gram-Negative Bacilli. J Clin Microbiol 2020; 59:JCM.01701-20. [PMID: 33115847 DOI: 10.1128/jcm.01701-20] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 10/19/2020] [Indexed: 11/20/2022] Open
Abstract
CLSI and EUCAST recommend that only broth microdilution (BMD) should be used for routine colistin susceptibility testing; however, this technique can be difficult to perform in resource-poor settings. The purpose of this study was to evaluate the accuracy of a colistin agar spot test (COL-AS) and a colistin drop test (COL-DT) compared to BMD. COL-AS and COL-DT were assessed with a collection of 271 Gram-negative bacilli clinical isolates: 195 Enterobacterales (including 63 mcr-1 positive strains), 37 Acinetobacter spp., and 39 Pseudomonas aeruginosa For COL-AS, 3.0 μg/ml (final concentration) of colistin was added to a Mueller-Hinton agar plate and subsequently swabbed with a 0.5 McFarland standard suspension of the tested strain within a 1 cm2 spot. For COL-DT, 10 μl of a 16 μg/ml colistin solution was dripped on the surface of a Mueller-Hinton agar plate, previously inoculated with a lawn of the tested strain (0.5 McFarland standard). Colistin solution was made either by dissolving powder or by disk elution in cation-adjusted Mueller-Hinton broth (CA-MHB). Overall, 141/271 (52%) isolates were categorized as colistin resistant by reference BMD. COL-AS yielded a categorical agreement (CA) of 95.5% compared to BMD, with 0.7% very major errors and 3.8% major errors. COL-DT yielded a CA of 96.2% compared to BMD, with 0.7% and 0% very major errors and 3.1% and 3.8% major errors, for colistin powder and disk elution solutions, respectively. Most major errors occurred for mcr-1 strains with MICs that fluctuated from 2 to 4 μg/ml according to the method used. In conclusion, we developed and validated methods suited to the systematic screening of resistance to colistin in Gram-negative bacilli.
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The Household Resistome: Frequency of β-Lactamases, Class 1 Integrons, and Antibiotic-Resistant Bacteria in the Domestic Environment and Their Reduction during Automated Dishwashing and Laundering. Appl Environ Microbiol 2020; 86:AEM.02062-20. [PMID: 32978137 PMCID: PMC7657631 DOI: 10.1128/aem.02062-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/20/2020] [Indexed: 11/20/2022] Open
Abstract
Households provide a habitat for bacteria originating from humans, animals, foods, contaminated clothes, or other sources. Thus, bacteria carrying antibiotic resistance genes (ARGs) may be introduced via household members, animals, or the water supply from external habitats into private households and vice versa. Since data on antibiotic resistance (ABR) in the domestic environment are limited, this study aimed to determine the abundance of β-lactamase, mobile colistin resistance, and class 1 integron genes and the correlation of their presence and to characterize phenotypically resistant strains in 54 private households in Germany. Additionally, the persistence of antibiotic-resistant bacteria during automated dishwashing compared to that during laundering was assessed. Shower drains, washing machines, and dishwashers were sampled and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using a Vitek 2 system. The results showed a significantly higher relative ARG abundance of 0.2367 ARG copies/16S rRNA gene copies in shower drains than in dishwashers (0.1329 ARG copies/16S rRNA gene copies) and washing machines (0.0006 ARG copies/16S rRNA gene copies). bla CMY-2, bla ACT/MIR, and bla OXA-48 were the most prevalent ARG, and intI1 occurred in 96.3% of the households, while no mcr genes were detected. Several β-lactamase genes co-occurred, and the resistance of bacterial isolates correlated positively with genotypic resistance, with carbapenemase genes dominating across isolates. Antibiotic-resistant bacteria were significantly reduced during automated dishwashing as well as laundering tests and did not differ from susceptible strains. Overall, the domestic environment may represent a potential reservoir of β-lactamase genes and β-lactam-resistant bacteria, with shower drains being the dominant source of ABR.IMPORTANCE The abundance of antibiotic-resistant bacteria and ARGs is steadily increasing and has been comprehensively analyzed in natural environments, animals, foods, and wastewater treatment plants. In this respect, β-lactams and colistin are of particular interest due to the emergence of multidrug-resistant Gram-negative bacteria. Despite the connection of private households to these environments, only a few studies have focused on the domestic environment so far. Therefore, the present study further investigated the occurrence of ARGs and antibiotic-resistant bacteria in shower drains, washing machines, and dishwashers. The analysis of the domestic environment as a potential reservoir of resistant bacteria is crucial to determine whether households contribute to the spread of ABR or may be a habitat where resistant bacteria from the natural environment, humans, food, or water are selected due to the use of detergents, antimicrobial products, and antibiotics. Furthermore, ABR could limit the options for the treatment of infections arising in the domestic environment.
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Liao W, Lin J, Jia H, Zhou C, Zhang Y, Lin Y, Ye J, Cao J, Zhou T. Resistance and Heteroresistance to Colistin in Escherichia coli Isolates from Wenzhou, China. Infect Drug Resist 2020; 13:3551-3561. [PMID: 33116674 PMCID: PMC7553605 DOI: 10.2147/idr.s273784] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
Background Colistin is being administered as last-line therapy for patients that have failed to respond to other available antibiotics that are active against Escherichia coli. The underlying mechanisms of colistin resistance and heteroresistance remain largely uncharacterized. The present study investigated the mechanisms of resistance and heteroresistance to colistin in Escherichia coli isolates from Wenzhou, China. Materials and Methods Colistin resistance was detected by the broth microdilution method (BMD). Colistin heteroresistance was determined by population analysis profiles (PAPs). The polymerase chain reaction (PCR) was conducted to detect mcr-1, mcr-2, mcr-3, pmrA, pmrB, phoP, phoQ and mgrB, and quantitative real-time PCR (qRT-PCR) was used to determine the expression levels of mcr-1, pmrC, pmrA and pmrB. Lipid A characterization was conducted by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). Results 0.69% (2/291) of Escherichia coli strains were resistant to colistin, whereas the heteroresistance rate reached 1.37% (4/291). mcr-1, the mobile colistin-resistance gene, was present in the two resistant isolates. The substitutions in PmrB were detected in the two heteroresistant isolates. The transcripts levels of the pmrCAB operon were upregulated in two of the heteroresistant isolates. carbonylcyanide m-chlorophenylhydrazone (CCCP) was able to reverse colistin resistance of all isolates tested and exhibited a significantly higher effect on colistin-heteroresistant isolates. MALDI-TOF MS indicated that the additional phosphoethanolamine (PEtn) moieties in lipid A profiles were present both in colistin-resistant and heteroresistant isolates. Conclusion The present study was the first to investigate the differential mechanisms between colistin resistance and heteroresistance. The development of colistin heteroresistance should be addressed in future clinical surveillance.
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Affiliation(s)
- Wenli Liao
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Jie Lin
- Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Huaiyu Jia
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Ying Zhang
- Department of Medical Laboratory Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Yishuai Lin
- Department of Medical Laboratory Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Jianzhong Ye
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Jianming Cao
- Department of Medical Laboratory Science, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, People's Republic of China
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Molecular mechanisms and prevalence of colistin resistance of Klebsiella pneumoniae in the Middle East region: A review over the last 5 years. J Glob Antimicrob Resist 2020; 22:625-630. [DOI: 10.1016/j.jgar.2020.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/06/2020] [Accepted: 06/12/2020] [Indexed: 12/21/2022] Open
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Carratalá JV, Serna N, Villaverde A, Vázquez E, Ferrer-Miralles N. Nanostructured antimicrobial peptides: The last push towards clinics. Biotechnol Adv 2020; 44:107603. [PMID: 32738381 DOI: 10.1016/j.biotechadv.2020.107603] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 06/24/2020] [Accepted: 07/16/2020] [Indexed: 12/15/2022]
Abstract
Peptide drugs hold great potential for the treatment of infectious diseases due to their unconventional mechanisms of action, biocompatibility, biodegradability and ease of synthesis and modification. The increasing rising of bacterial strains resistant to classical antibiotics have pushed the development of new peptide-based antimicrobial therapies. In this context, over the past few years, different approaches have reached a clinical approval. Furthermore, the application of nanotechnological principles to the design of antimicrobial peptide-based composites increases even more the already known benefits of antimicrobial peptides as competent protein drugs. Then, we provide here an overview of the current strategies for antimicrobial peptide discovery and modification and the status of such peptides already under clinical development. In addition, we summarize the innovative formulation strategies for their application, focusing on the controlled self-assembly for the fabrication of antimicrobial nanostructures without the assistance of external nanocarriers, and with emphasis on bioengineering, design of ultra-short peptides and rising insights in bacterial selectivity.
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Affiliation(s)
- Jose Vicente Carratalá
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona 08193, Spain
| | - Naroa Serna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona 08193, Spain.
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona 08193, Spain.
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona 08193, Spain.
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Bellaterra, Barcelona 08193, Spain
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Adiguzel MC, Baran A, Wu Z, Cengiz S, Dai L, Oz C, Ozmenli E, Goulart DB, Sahin O. Prevalence of Colistin Resistance in Escherichia coli in Eastern Turkey and Genomic Characterization of an mcr-1 Positive Strain from Retail Chicken Meat. Microb Drug Resist 2020; 27:424-432. [PMID: 32721263 DOI: 10.1089/mdr.2020.0209] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Colistin is one of the most effective antibiotics against multidrug resistant Gram-negative bacteria. However, the recent emergence of plasmid-borne mobilized colistin resistance (mcr) genes is considered a serious antimicrobial resistance challenge worldwide. In this study, we report detection of an mcr-1 carrying Escherichia coli isolate (named ATAVET mcr-1 Turkey) from retail raw chicken meat in Turkey. Of the 11 (from 500 total tested) phenotypically colistin-resistant isolates, 1 was shown to carry the mcr-1 gene by PCR. Whole-genome sequencing indicated that mcr-1 was located on a ∼13 kb-long contig that was almost identical to the corresponding part in pZJ1635, an IncI2 plasmid encoding mcr-1 in the same genetic context in another E. coli strain. In addition, ATAVET mcr-1 Turkey harbored blaCTX-M-8, qnrB19, mdf(A), tet(A), sul2, aph(3″)-Ib, aph(6)-Id, and floR resistance genes. Phylogenetic analysis based on whole genome and multilocus sequence typing indicated that ATAVET mcr-1 Turkey was more closely related to mcr-1 carrying E. coli isolates from food and human clinical samples previously reported from different parts of the world than to those from Turkey. These findings further emphasize the worldwide emergence and spread of mcr meditated colistin resistance in bacteria with zoonotic potential within animals and the food chain.
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Affiliation(s)
- Mehmet Cemal Adiguzel
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, Erzurum, Turkey.,Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Alper Baran
- Department of Food Quality Control and Analysis, Erzurum Vocational School, Ataturk University, Erzurum, Turkey
| | - Zuowei Wu
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Seyda Cengiz
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, Erzurum, Turkey
| | - Lei Dai
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Cihan Oz
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, Erzurum, Turkey
| | - Esma Ozmenli
- Department of Microbiology, Faculty of Veterinary Medicine, Ataturk University, Erzurum, Turkey
| | - Debora Brito Goulart
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
| | - Orhan Sahin
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, USA
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Resistance to Colistin Mediated by mcr-1 among Multidrug Resistant Gram Negative Pathogens at a Tertiary Care Hospital, Egypt. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2020. [DOI: 10.22207/jpam.14.2.07] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
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Fodor A, Abate BA, Deák P, Fodor L, Gyenge E, Klein MG, Koncz Z, Muvevi J, Ötvös L, Székely G, Vozik D, Makrai L. Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review. Pathogens 2020; 9:pathogens9070522. [PMID: 32610480 PMCID: PMC7399985 DOI: 10.3390/pathogens9070522] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.
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Affiliation(s)
- András Fodor
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
| | - Birhan Addisie Abate
- Ethiopian Biotechnology Institute, Agricultural Biotechnology Directorate, Addis Ababa 5954, Ethiopia;
| | - Péter Deák
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
| | - Ervin Gyenge
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
| | - Michael G. Klein
- Department of Entomology, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA;
| | - Zsuzsanna Koncz
- Max-Planck Institut für Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Köln, Germany;
| | | | - László Ötvös
- OLPE, LLC, Audubon, PA 19403-1965, USA;
- Institute of Medical Microbiology, Semmelweis University, H-1085 Budapest, Hungary
- Arrevus, Inc., Raleigh, NC 27612, USA
| | - Gyöngyi Székely
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania
| | - Dávid Vozik
- Research Institute on Bioengineering, Membrane Technology and Energetics, Faculty of Engineering, University of Veszprem, H-8200 Veszprém, Hungary; or or
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
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Bustamante P, Iredell JR. The roles of HicBA and a novel toxin-antitoxin-like system, TsxAB, in the stability of IncX4 resistance plasmids in Escherichia coli. J Antimicrob Chemother 2020; 74:553-556. [PMID: 30535076 DOI: 10.1093/jac/dky491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 11/05/2018] [Accepted: 11/06/2018] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES To identify toxin-antitoxin (TA)-like plasmid stability loci on IncX4 plasmids. METHODS TA-like loci were identified bioinformatically and their contribution to stability of the IncX4 plasmid pJIE143 was tested in optimal growth conditions in vitro. The conservation of the TA-like loci identified was analysed within an updated IncX plasmid database. RESULTS A novel TA-like locus, tsxAB, was identified on the IncX4 plasmid pJIE143, carrying the important plasmid-borne antibiotic resistance gene blaCTX-M-15. pJIE143 (the WT plasmid) and its tsxA mutant are stable for 80 bacterial generations in the absence of selective pressure but a tsxB deletion mutant of pJIE143 is relatively quickly lost without positive selection (91.1% ± 1.5% loss after 50 generations). Nine IncX subclasses were identified among 272 fully sequenced IncX plasmids, dominated by those identified as IncX3, IncX1 and IncX4 subclasses in PlasmidFinder. The novel TA-like locus, tsxAB, appears to be a feature of IncX4 plasmids, being present in 64 of 67 so identified, but only present in a single IncX1 plasmid (of 79 identified) and present in no other IncX plasmids. CONCLUSIONS tsxAB, a novel TA-like stability locus, is highly conserved in IncX4 plasmids associated with transmission of important antibiotic resistance genes. Previous in silico analysis indicated that IncX4 encodes only HicBA among the known TA systems. Here we show that HicBA does not contribute to plasmid stability in optimal growth conditions for Escherichia coli and instead demonstrate this role for a completely novel TA-like system, TsxAB, that appears both necessary and sufficient for E. coli addiction to IncX4 resistance plasmids.
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Affiliation(s)
- Paula Bustamante
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital, Westmead, NSW, Australia
| | - Jonathan R Iredell
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney, Westmead Hospital, Westmead, NSW, Australia
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Tha S, Shakya S, Malla R, Aryal P. Prospects of Indole derivatives as methyl transfer inhibitors: antimicrobial resistance managers. BMC Pharmacol Toxicol 2020; 21:33. [PMID: 32366298 PMCID: PMC7197119 DOI: 10.1186/s40360-020-00402-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/06/2020] [Indexed: 12/02/2022] Open
Abstract
Background It is prudent that novel classes of antibiotics be urgently developed to manage the WHO prioritized multi-drug resistant (MDR) pathogens posing an unprecedented medical crisis. Simultaneously, multiple essential proteins have to be targeted to prevent easy resistance development. Methods An integration of structure-based virtual screening and ligand-based virtual screening was employed to explore the antimicrobial properties of indole derivatives from a compound database. Results Whole-genome sequences of the target pathogens were aligned exploiting DNA alignment potential of MAUVE to identify putative common lead target proteins. S-adenosyl methionine (SAM) biosynthesizing MetK was taken as the lead target and various literature searches revealed that SAM is a critical metabolite. Furthermore, SAM utilizing CobA involved in the B12 biosynthesis pathway, Dam in the regulation of replication and protein expression, and TrmD in methylation of tRNA were also taken as drug targets. The ligand library of 715 indole derivatives chosen based on kinase inhibition potential of indoles was created from which 102 were pursued based on ADME/T scores. Among these, 5 potential inhibitors of MetK in N. gonorrhoeae were further expanded to molecular docking studies in MetK proteins of all nine pathogens among which 3 derivatives exhibited inhibition potential. These 3 upon docking in other SAM utilizing enzymes, CobA, Dam, and TrmD gave 2 potential compounds with multiple targets. Further, docking with human MetK homolog also showed probable inhibitory effects however SAM requirements can be replenished from external sources since SAM transporters are present in humans. Conclusions We believe these molecules 3-[(4-hydroxyphenyl)methyl]-6-(1H-indol-3-ylmethyl)piperazine-2,5-dione (ZINC04899565) and 1-[(3S)-3-[5-(1H-indol-3-ylmethyl)-1,3,4-oxadiazol-2-yl]pyrrolidin-1-yl]ethanone (ZINC49171024) could be a starting point to help develop broad-spectrum antibiotics against infections caused by N. gonorrhoeae, A. baumannii, C. coli, K. pneumoniae, E. faecium, H. pylori, P. aeruginosa, S. aureus and S. typhi.
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Affiliation(s)
- Suprim Tha
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Sapana Shakya
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Rajani Malla
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal
| | - Pramod Aryal
- Central Department of Biotechnology, Tribhuvan University, Kirtipur, Kathmandu, Nepal.
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Chandler JC, Franklin AB, Bevins SN, Bentler KT, Bonnedahl J, Ahlstrom CA, Bisha B, Shriner SA. Validation of a screening method for the detection of colistin-resistant E. coli containing mcr-1 in feral swine feces. J Microbiol Methods 2020; 172:105892. [DOI: 10.1016/j.mimet.2020.105892] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 12/28/2022]
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Schages L, Wichern F, Kalscheuer R, Bockmühl D. Winter is coming - Impact of temperature on the variation of beta-lactamase and mcr genes in a wastewater treatment plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 712:136499. [PMID: 31945531 DOI: 10.1016/j.scitotenv.2020.136499] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/18/2019] [Accepted: 01/01/2020] [Indexed: 05/29/2023]
Abstract
Wastewater treatment plants (WWTP) play a key role in the dissemination of antibiotic resistance and analyzing the abundance of antibiotic resistance genes (ARGs) and resistant bacteria is necessary to evaluate the risk of proliferation caused by WWTPs. Since few studies investigated the seasonal variation of antibiotic resistance, this study aimed to determine the abundance of beta-lactamase and mcr genes and to characterize phenotypic resistant strains in a WWTP in Germany over the seasons. Wastewater, sewage sludge and effluent samples were collected over a one year period and analyzed using quantitative real-time PCR. Resistant strains were isolated, followed by identification and antibiotic susceptibility testing using VITEK 2. The results show a significantly higher occurrence of nearly all investigated ARGs in the wastewater compared to sewage sludge and effluent. ARG abundance and temperature showed a negative correlation in wastewater and significant differences between ARG abundance during warmer and colder seasons were determined, indicating a seasonal effect. Co-occurrence of mcr-1 and carbapenemase genes in a multi-drug resistant Enterobacter cloacae and Escherichia coli producing extended-spectrum beta-lactamase (ESBL) was determined. To the best of our knowledge, this is the first detection of mcr-1, blaVIM and blaOXA-48 in an ESBL-producing E. coli. Although wastewater treatment reduced the abundance of ARGs and resistant strains, a dissemination into the river might be possible because carbapenemase-, CTX-M- and mcr-1-gene harboring strains were still present in the effluent.
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Affiliation(s)
- Laura Schages
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany; Heinrich-Heine University Düsseldorf, Institute of Pharmaceutical Biology and Biotechnology, Germany
| | - Florian Wichern
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany
| | - Rainer Kalscheuer
- Heinrich-Heine University Düsseldorf, Institute of Pharmaceutical Biology and Biotechnology, Germany
| | - Dirk Bockmühl
- Rhine-Waal University of Applied Sciences, Faculty of Life Sciences, Kleve, Germany.
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Nwaiwu O, Aduba CC. An in silico analysis of acquired antimicrobial resistance genes in Aeromonas plasmids. AIMS Microbiol 2020; 6:75-91. [PMID: 32226916 PMCID: PMC7099201 DOI: 10.3934/microbiol.2020005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 03/13/2020] [Indexed: 12/17/2022] Open
Abstract
Sequences of 105 Aeromonas species plasmids were probed for acquired anti-microbial resistance (AMR) genes using a bioinformatics approach. The plasmids showed no positive linear correlation between size and GC content and up to 55 acquired AMR genes were found in 39 (37%) plasmids after in silico screening for resistance against 15 antibiotic drug classes. Overall, potential multiple antibiotic resistance (p-MAR) index ranged from 0.07 to 0.53. Up to 18 plasmids were predicted to mediate multiple drug resistance (MDR). Plasmids pS121-1a (A. salmonicida), pWCX23_1 (A. hydrophila) and pASP-a58 (A. veronii) harboured 18, 15 and 14 AMR genes respectively. The five most occurring drug classes for which AMR genes were detected were aminoglycosides (27%), followed by beta-lactams (17%), sulphonamides (13%), fluoroquinolones (13%), and phenicols (10%). The most prevalent genes were a sulphonamide resistant gene Sul1, the gene aac (6')-Ib-cr (aminoglycoside 6'-N-acetyl transferase type Ib-cr) resistant to aminoglycosides and the blaKPC-2 gene, which encodes carbapenemase-production. Plasmid acquisition of AMR genes was mainly inter-genus rather than intra-genus. Eighteen plasmids showed template or host genes acquired from Pseudomonas monteilii, Salmonella enterica or Escherichia coli. The most occurring antimicrobial resistance determinants (ARDs) were beta-lactamase, followed by aminoglycosides acetyl-transferases, and then efflux pumps. Screening of new isolates in vitro and in vivo is required to ascertain the level of phenotypic expression of colistin and other acquired AMR genes detected.
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Affiliation(s)
- Ogueri Nwaiwu
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, United Kingdom
| | - Chiugo Claret Aduba
- Department of Science Laboratory Technology, University of Nigeria, Nsukka, Nigeria
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Chen L, Lin J, Lu H, Zhang X, Wang C, Liu H, Zhang X, Li J, Cao J, Zhou T. Deciphering colistin heteroresistance in Acinetobacter baumannii clinical isolates from Wenzhou, China. J Antibiot (Tokyo) 2020; 73:463-470. [DOI: 10.1038/s41429-020-0289-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 01/01/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
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Aira A, Fehér C, Rubio E, Soriano A. The Intestinal Microbiota as a Reservoir and a Therapeutic Target to Fight Multi-Drug-Resistant Bacteria: A Narrative Review of the Literature. Infect Dis Ther 2019; 8:469-482. [PMID: 31654298 PMCID: PMC6856238 DOI: 10.1007/s40121-019-00272-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Indexed: 12/12/2022] Open
Abstract
The appearance and dissemination of antibiotic-resistant bacteria, particularly in specific closed environments such as intensive care units of acute care hospitals, have become a major health concern. The intestinal microbiota has various functions including host protection from overgrowth or colonization by unwanted bacteria. The exposure to antibiotics significantly reduces the bacterial density of intestinal microbiota leaving an ecologic void that can be occupied by potentially pathogenic and/or resistant bacteria frequently present in hospital settings. Consequently, the intestinal microbiota of inpatients acts as a major reservoir and plays a critical role in perpetuating the spread of resistant bacteria. There are novel innovative methods to protect the host microbiota during antibiotic treatment, but they do not offer a solution for already established colonization by resistant microorganisms. Fecal microbiota transfer (FMT) is a promising intervention to achieve this goal; however, controlled trials report lower success rates than initial retrospective studies, especially in case of gram negatives. The aim of the present article is to highlight the importance of the intestinal microbiota in the global spread of multi-drug-resistant (MDR) microorganisms and to review the recent advances to protect the human microbiota from the action of antibiotics as well as a critical discussion about the evidence of decolonization of MDR microorganisms by FMT.
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Affiliation(s)
- Andrea Aira
- Department of Infectious Diseases, Hospital Clínic, IDIBAPS, Catalonia, Barcelona, Spain
| | - Csaba Fehér
- Department of Infectious Diseases, Hospital Clínic, IDIBAPS, Catalonia, Barcelona, Spain
| | - Elisa Rubio
- Department of Clinical Microbiology, Hospital Clínic, Catalonia, Barcelona, Spain
| | - Alex Soriano
- Department of Infectious Diseases, Hospital Clínic, IDIBAPS, Catalonia, Barcelona, Spain.
- University of Barcelona, IDIBAPS, Catalonia, Barcelona, Spain.
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Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT. Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination. Nat Med 2019; 25:1858-1864. [PMID: 31768064 PMCID: PMC6930013 DOI: 10.1038/s41591-019-0650-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/11/2019] [Indexed: 12/13/2022]
Abstract
Multidrug resistant organisms (MDROs) are a serious threat to human health1,2. Fast, accurate antibiotic susceptibility testing (AST) is a critical need in addressing escalating antibiotic resistance, since delays in identifying MDROs increase mortality3,4 and use of broad-spectrum antibiotics, further selecting for resistant organisms. Yet current growth-based AST assays, such as broth microdilution5, require several days before informing key clinical decisions. Rapid AST would transform the care of infected patients while ensuring that our antibiotic arsenal is deployed as efficiently as possible. Growth-based assays are fundamentally constrained in speed by doubling time of the pathogen, and genotypic assays are limited by the ever-growing diversity and complexity of bacterial antibiotic resistance mechanisms. Here, we describe a rapid assay for combined Genotypic and Phenotypic AST through RNA detection, GoPhAST-R, that classifies strains with 94–99% accuracy by coupling machine learning analysis of early antibiotic-induced transcriptional changes with simultaneous detection of key genetic resistance determinants to increase accuracy of resistance detection, facilitate molecular epidemiology, and enable early detection of emerging resistance mechanisms. This two-pronged approach provides phenotypic AST 24–36 hours faster than standard workflows, with <4 hour assay time on a pilot instrument for hybridization-based multiplexed RNA detection implemented directly from positive blood cultures.
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Affiliation(s)
- Roby P Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nirmalya Bandyopadhyay
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Peijun Ma
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sophie S Son
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jamin Liu
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lorrie L He
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lidan Wu
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Rich Boykin
- NanoString Technologies, Inc., Seattle, WA, USA
| | - Gustavo C Cerqueira
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Personal Genome Diagnostics, Ellicott City, MD, USA
| | - Alejandro Pironti
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Robert F Rudy
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Milesh M Patel
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rui Yang
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jennifer Skerry
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kimberly A Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jill Taylor
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Virginia M Pierce
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lisa A Cosimi
- Infectious Diseases Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Noam Shoresh
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Deborah T Hung
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
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Bloodstream infections caused by Escherichia coli carrying mcr-1 gene in hospitalized patients in northern Italy from 2012 to 2018. Infection 2019; 48:223-230. [PMID: 31758437 DOI: 10.1007/s15010-019-01377-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 11/11/2019] [Indexed: 01/02/2023]
Abstract
PURPOSE The recurrence of multi-drug resistant (MDR) pathogens to the latest antibiotics and the limited development of new antibacterial agents have reduced the options for the treatment of severe infections. The reintroduction of old antibiotics, such as colistin, represents an effective strategy, since the latest antibiotics are over-consumed and ineffective against MDR pathogens. In 2015, Liu (Lancet Infect Dis 16:161-168, 2016) reported Escherichia coli (E. coli) isolates carrying plasmid-mediated colistin resistance gene mcr-1. The first of mcr-1 positive colistin-resistant (col-R) E. coli from a human blood culture was observed in 2012 in Latin America, while in Italy was reported for the first time by our center in 2016. The present study aimed to describe the prevalence of mcr-1 positive col-R strains in E. coli-related bloodstream infection among patients hospitalized in Fondazione IRCCS Policlinico San Matteo in Pavia, Italy, from 2012 to 2018, including the three cases already published. METHODS All col-R E. coli strains isolated from blood cultures collected during the study period were analyzed. The minimal inhibitory concentration of colistin was determined using broth microdilution and detection of mcr-1 and mcr-2 genes was performed by PCR. The sequence type of E. coli mcr-1 positive was determined according to Multilocus sequence typing. RESULTS Out of 1557 samples, 14 strains (0.90%) were col-R. and positive for the presence of the mcr-1 gene, with no mcr-2 detected. The most common ST was ST10 (n = 3), followed by ST410 (n = 2). The remaining strains exhibited different MLST profiles, indicating that they were genetically unrelated. CONCLUSIONS Proper reporting of the presence of mcr-1 genes is an essential component to anticipate the spread of colistin resistance. This public health issue is particularly alarming in Italy due to the consistent circulation of MDR bacteria.
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Global Burden of Colistin-Resistant Bacteria: Mobilized Colistin Resistance Genes Study (1980-2018). Microorganisms 2019; 7:microorganisms7100461. [PMID: 31623244 PMCID: PMC6843232 DOI: 10.3390/microorganisms7100461] [Citation(s) in RCA: 170] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/12/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Colistin is considered to be an antimicrobial of last-resort for the treatment of multidrug-resistant Gram-negative bacterial infections. The recent global dissemination of mobilized colistin resistance (mcr) genes is an urgent public health threat. An accurate estimate of the global prevalence of mcr genes, their reservoirs and the potential pathways for human transmission are required to implement control and prevention strategies, yet such data are lacking. Publications from four English (PubMed, Scopus, the Cochrane Database of Systematic Reviews and Web of Science) and two Chinese (CNKI and WANFANG) databases published between 18 November 2015 and 30 December 2018 were identified. In this systematic review and meta-analysis, the prevalence of mcr genes in bacteria isolated from humans, animals, the environment and food products were investigated. A total of 974 publications were identified. 202 observational studies were included in the systematic review and 71 in the meta-analysis. mcr genes were reported from 47 countries across six continents and the overall average prevalence was 4.7% (0.1–9.3%). China reported the highest number of mcr-positive strains. Pathogenic Escherichia coli (54%), isolated from animals (52%) and harboring an IncI2 plasmid (34%) were the bacteria with highest prevalence of mcr genes. The estimated prevalence of mcr-1 pathogenic E. coli was higher in food-animals than in humans and food products, which suggests a role for foodborne transmission. This study provides a comprehensive assessment of prevalence of the mcr gene by source, organism, genotype and type of plasmid.
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Cahill N, O'Connor L, Mahon B, Varley Á, McGrath E, Ryan P, Cormican M, Brehony C, Jolley KA, Maiden MC, Brisse S, Morris D. Hospital effluent: A reservoir for carbapenemase-producing Enterobacterales? THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 672:618-624. [PMID: 30974353 PMCID: PMC6525273 DOI: 10.1016/j.scitotenv.2019.03.428] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 05/03/2023]
Abstract
Antimicrobial resistance is a major public health concern. Carbapenemase-producing Enterobacterales (CPE) represent a significant health threat as some strains are resistant to almost all available antibiotics. The aim of this research was to examine hospital effluent and municipal wastewater in an urban area in Ireland for CPE. Samples of hospital effluent (n = 5), municipal wastewater before (n = 5) and after (n = 4) the hospital effluent stream joined the municipal wastewater stream were collected over a nine-week period (May-June 2017). All samples were examined for CPE by direct plating onto Brilliance CRE agar. Isolates were selected for susceptibility testing to 15 antimicrobial agents in accordance with EUCAST criteria. Where relevant, isolates were tested for carbapenemase-encoding genes by real-time PCR. CPE were detected in five samples of hospital effluent, one sample of pre-hospital wastewater and three samples of post-hospital wastewater. Our findings suggest hospital effluent is a major contributor to CPE in municipal wastewater. Monitoring of hospital effluent for CPE could have important applications in detection and risk management of unrecognised dissemination of CPE in both the healthcare setting and the environment.
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Affiliation(s)
- Niamh Cahill
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for Health from Environment, Ryan Institute, National University of Ireland, Galway, Ireland.
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for Health from Environment, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Bláthnaid Mahon
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for Health from Environment, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Áine Varley
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Elaine McGrath
- Carbapenemase-Producing Enterobacterales Reference Laboratory, Department of Medical Microbiology, University Hospital Galway, Galway, Ireland
| | - Phelim Ryan
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Martin Cormican
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for Health from Environment, Ryan Institute, National University of Ireland, Galway, Ireland; Carbapenemase-Producing Enterobacterales Reference Laboratory, Department of Medical Microbiology, University Hospital Galway, Galway, Ireland
| | - Carina Brehony
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Keith A Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Martin C Maiden
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland; Centre for Health from Environment, Ryan Institute, National University of Ireland, Galway, Ireland
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48
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Evaluation of a novel epidemiological screening approach for detection of colistin resistant human Enterobacteriaceae isolates using a selective SuperPolymyxin medium. J Microbiol Methods 2019; 160:117-123. [DOI: 10.1016/j.mimet.2019.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 11/17/2022]
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49
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Manageiro V, Clemente L, Romão R, Silva C, Vieira L, Ferreira E, Caniça M. IncX4 Plasmid Carrying the New mcr-1.9 Gene Variant in a CTX-M-8-Producing Escherichia coli Isolate Recovered From Swine. Front Microbiol 2019; 10:367. [PMID: 30923516 PMCID: PMC6426780 DOI: 10.3389/fmicb.2019.00367] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/12/2019] [Indexed: 11/22/2022] Open
Abstract
We studied a commensal colistin-resistant Escherichia coli isolated from a swine cecum sample collected at a slaughter, in Portugal. Antimicrobial susceptibility phenotype of E. coli LV23529 showed resistance to colistin at a minimum inhibitory concentration of 4 mg/L. Whole genome of E. coli LV23529 was sequenced using a MiSeq system and the assembled contigs were analyzed for the presence of antibiotic resistance and plasmid replicon types using bioinformatics tools. We report a novel mcr-1 gene variant (mcr-1.9), carried by an IncX4 plasmid, where one-point mutation at nucleotide T1238C leads to Val413Ala substitution. The mcr-1.9 genetic context was characterized by an IS26 element upstream of the mcr-pap2 element and by the absence of ISApl1. Bioinformatic analysis also revealed genes conferring resistance to β-lactams, sulphamethoxazole, trimethoprim, chloramphenicol and colistin, corresponding to the phenotype noticed. Moreover, we highlight the presence of mcr-1.9 plus blaCTX-M-8, a blaESBL gene rarely detected in Europe in isolates of animal origin; these two genes were located on different plasmids with 33,303 and 89,458 bp, respectively. MCR-1.9-harboring plasmid showed high identity to other X4-type mcr-1-harboring plasmids characterized worldwide, which strongly suggests that the presence of PMCR-encoding genes in food-producing animals, such as MCR-1.9, represent a potential threat to humans, as it is located in mobile genetic elements that have the potential to spread horizontally.
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Affiliation(s)
- Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.,Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal
| | - Lurdes Clemente
- Bacteriology and Mycology Laboratory, INIAV - National Institute of Agrarian and Veterinary Research, Oeiras, Portugal
| | - Raquel Romão
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Catarina Silva
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, Department of Human Genetics, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Eugénia Ferreira
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.,Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal.,Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal
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50
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Thiry D, Berrah A, Evrard J, Duprez JN, Mainil JG, Saulmont M. Assessment of two selective agar media to isolate colistin-resistant bovine Escherichia coli: Correlation with minimal inhibitory concentration and presence of mcr genes. J Microbiol Methods 2019; 159:174-178. [PMID: 30858004 DOI: 10.1016/j.mimet.2019.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/05/2019] [Accepted: 03/07/2019] [Indexed: 11/30/2022]
Abstract
The identification of colistin-resistant enterobacteria in veterinary medicine is impaired by the absence of first-line reliable phenotypic assay. The purpose of this study was to assess two selective agar media for the detection of colistin-resistant bovine pathogenic Escherichia coli. A total of 158 E. coli (46 R <resistant>, 96 I <intermediate> and 16 S <sensitive> at the disk diffusion assay) isolated between 2013 and 2018 from <3 month-old calves suffering enteritis or septicaemia, were (i) tested by the broth dilution assay to determine colistin Minimal Inhibitory Concentrations (MIC); (ii) streaked on CHROMID® Colistin_R and CHROMagar™ COL-APSE agar plates; (iii) submitted to a pentaplex PCR to identify the presence of mcr-1 to mcr-5 genes. Of the 92 E. coli growing on both agar media, 90 had a MIC > 2.0 μg/ml as had the 3 E. coli that grew only on the CHROMID® Colistin_R agar medium and one E. coli that grew on neither agar media. Therefore, the positive predictive values of the CHROMID® Colistin_R and CHROMagar™ COL-APSE agar media were both 0.98 whereas their negative predictive values were 0.98 and 0.94, respectively. Also noteworthy 43 of the 46 R isolates had a MIC > 2.0 μg/ml and grew on both selective media as did half of the 96 I isolates and only 1 of the S isolates. Conversely, only 30 of the 90 isolates that grew on both agar media and with a MIC > 2.0 μg/ml tested positive for the mcr-1 or mcr-2 genes with the pentaplex PCR. These two selective agar media can be used to reliably detect colistin-resistant E. coli. Positive growth was highly correlated with R results at the disk diffusion assay, but not with the presence of mcr genes.
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Affiliation(s)
- Damien Thiry
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, FARAH (Fundamental and Applied Research for Animals and Health) Centre, University of Liège, Liège B-4000, Belgium
| | - Anis Berrah
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, FARAH (Fundamental and Applied Research for Animals and Health) Centre, University of Liège, Liège B-4000, Belgium
| | - Julien Evrard
- ARSIA (Association Régionale de Santé et d'Identification Animale), Ciney B5590, Belgium
| | - Jean-Noël Duprez
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, FARAH (Fundamental and Applied Research for Animals and Health) Centre, University of Liège, Liège B-4000, Belgium
| | - Jacques G Mainil
- Bacteriology, Department of Infectious Diseases, Faculty of Veterinary Medicine, FARAH (Fundamental and Applied Research for Animals and Health) Centre, University of Liège, Liège B-4000, Belgium.
| | - Marc Saulmont
- ARSIA (Association Régionale de Santé et d'Identification Animale), Ciney B5590, Belgium
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