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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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Shahzad S, Willcox MDP, Rayamajhee B. A Review of Resistance to Polymyxins and Evolving Mobile Colistin Resistance Gene ( mcr) among Pathogens of Clinical Significance. Antibiotics (Basel) 2023; 12:1597. [PMID: 37998799 PMCID: PMC10668746 DOI: 10.3390/antibiotics12111597] [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: 09/25/2023] [Revised: 10/26/2023] [Accepted: 11/04/2023] [Indexed: 11/25/2023] Open
Abstract
The global rise in antibiotic resistance in bacteria poses a major challenge in treating infectious diseases. Polymyxins (e.g., polymyxin B and colistin) are last-resort antibiotics against resistant Gram-negative bacteria, but the effectiveness of polymyxins is decreasing due to widespread resistance among clinical isolates. The aim of this literature review was to decipher the evolving mechanisms of resistance to polymyxins among pathogens of clinical significance. We deciphered the molecular determinants of polymyxin resistance, including distinct intrinsic molecular pathways of resistance as well as evolutionary characteristics of mobile colistin resistance. Among clinical isolates, Acinetobacter stains represent a diversified evolution of resistance, with distinct molecular mechanisms of intrinsic resistance including naxD, lpxACD, and stkR gene deletion. On the other hand, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa are usually resistant via the PhoP-PhoQ and PmrA-PmrB pathways. Molecular evolutionary analysis of mcr genes was undertaken to show relative relatedness across the ten main lineages. Understanding the molecular determinants of resistance to polymyxins may help develop suitable and effective methods for detecting polymyxin resistance determinants and the development of novel antimicrobial molecules.
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Affiliation(s)
- Shakeel Shahzad
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia;
| | - Mark D. P. Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, NSW 2052, Australia;
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Hathcock T, Raiford D, Conley A, Barua S, Murillo DFB, Prarat M, Kaur P, Scaria J, Wang C. Antimicrobial-Resistant Escherichia coli, Enterobacter cloacae, Enterococcus faecium, and Salmonella Kentucky Harboring Aminoglycoside and Beta-Lactam Resistance Genes in Raw Meat-Based Dog Diets, USA. Foodborne Pathog Dis 2023; 20:477-483. [PMID: 37615516 DOI: 10.1089/fpd.2023.0043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023] Open
Abstract
The practice of feeding raw meat-based diets to dogs has grown in popularity worldwide in recent years. However, there are public health risks in handling and feeding raw meat-based dog diets (RMDDs) to dogs since there are no pathogen reduction steps to reduce the microbial load, which may include antimicrobial-resistant pathogenic bacteria. A total of 100 RMDDs from 63 suppliers were sampled, and selective media were used to isolate bacteria from the diets. Bacterial identification, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) were conducted to identify antimicrobial resistance (AMR). The primary meat sources for RMDDs included in this study were poultry (37%) and beef (24%). Frozen-dry was the main method of product production (68%). In total, 52 true and opportunistic pathogens, including Enterobacterales (mainly Escherichia coli, Enterobacter cloacae) and Enterococcus faecium, were obtained from 30 RMDDs. Resistance was identified to 19 of 28 antimicrobials tested, including amoxicillin/clavulanic acid (23/52, 44%), ampicillin (19/52, 37%), cephalexin (16/52, 31%), tetracycline (7/52, 13%), marbofloxacin (7/52, 13%), and cefazolin (6/52, 12%). All 19 bacterial isolates submitted for WGS harbored at least one type of AMR gene. The identified AMR genes were found to mediate resistance to aminoglycoside (gentamicin, streptomycin, amikacin/kanamycin, gentamicin/kanamycin/tobramycin), macrolide, beta-lactam (carbapenem, cephalosporin), tetracycline, fosfomycin, quinolone, phenicol/quinolone, and sulfonamide. In conclusion, the results of this study suggest that feeding and handling RMDDs may pose a significant public health risk due to the presence of antimicrobial-resistant pathogens, and further research and intervention may be necessary to minimize these risks.
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Affiliation(s)
- Terri Hathcock
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Donna Raiford
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Austin Conley
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | - Subarna Barua
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
| | | | - Melanie Prarat
- Ohio Department of Agriculture, Virology, and Molecular Diagnostics, Reynoldsburg, Ohio, USA
| | - Prabhjot Kaur
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Joy Scaria
- Department of Veterinary & Biomedical Sciences, South Dakota State University, Brookings, South Dakota, USA
| | - Chengming Wang
- Department of Pathobiology, College of Veterinary Medicine, Auburn University, Auburn, Alabama, USA
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Lakshmanan D, Ramasamy D, Subramanyam V, Saravanan SK. Mobile colistin resistance (mcr) genes and recent developments in colistin resistance detection. Lett Appl Microbiol 2023; 76:ovad102. [PMID: 37673673 DOI: 10.1093/lambio/ovad102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/17/2023] [Accepted: 09/05/2023] [Indexed: 09/08/2023]
Abstract
The peptide antibiotic colistin has been reserved as a last resort antibiotic treatment option for cases where other antibiotics including carbapenems have failed. Recent emergence of colistin resistance and discovery of mobile colistin resistance (mcr) genes, which encode the cell wall modifying phosphoethanolamine transferase enzyme, complicates the issue. The mcr genes have been associated with conjugative plasmids and can be horizontally transferred between different bacterial species. The global spread of mcr genes has been extensively documented and this warrants surveillance of the resistance genes in the community. However, susceptibility testing of colistin is fraught with practical challenges owing to the chemical nature of the drug and multiple mechanisms of resistance. Although broth microdilution is the current gold standard for colistin susceptibility testing, the method poses technical challenges. Hence, alternative detection methods for screening colistin resistance are the need of the hour. Several methods have been studied in the recent times to address this issue. In this review, we discuss some of the recent developments in the detection of colistin resistance.
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Affiliation(s)
- Divya Lakshmanan
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed-to-be-University), Pillayarkuppam, Pondicherry 607042, India
| | - Dhamodharan Ramasamy
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed-to-be-University), Pillayarkuppam, Pondicherry 607042, India
| | - Veni Subramanyam
- Mahatma Gandhi Medical Advanced Research Institute (MGMARI), Sri Balaji Vidyapeeth (Deemed-to-be-University), Pillayarkuppam, Pondicherry 607042, India
| | - Suresh Kumar Saravanan
- Mahatma Gandhi Medical Preclinical Research Centre (MGMPRC), Sri Balaji Vidyapeeth (Deemed-to-be-University), Pillayarkuppam, Pondicherry 607402, India
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Slimene K, Ali AA, Mohamed EA, El Salabi A, Suliman FS, Elbadri AA, El-fertas FF, El-awjly A, Shokri SA, Rolain JM, Chouchani C. Isolation of Carbapenem and Colistin Resistant Gram-Negative Bacteria Colonizing Immunocompromised SARS-CoV-2 Patients Admitted to Some Libyan Hospitals. Microbiol Spectr 2023; 11:e0297222. [PMID: 37042782 PMCID: PMC10269485 DOI: 10.1128/spectrum.02972-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 03/16/2023] [Indexed: 04/13/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has had a devastating effect, globally. We describe, for the first time, the occurrence of carbapenem-resistant bacteria colonizing SARS-CoV-2 patients who developed hospital-associated infections with carbapenemase-producing, Gram-negative bacteria at some isolation centers of SARS-CoV-2 in the eastern part of Libya. In total, at first, 109 samples were collected from 43 patients, with the samples being recovered from oral (n = 35), nasal (n = 45), and rectal (n = 29) cavities. Strain identification was performed via matrix assisted laser desorption ionization-time of flight (MALDI-TOF). Antibiotic susceptibility testing was carried out on Mueller-Hinton agar, using the standard disk diffusion method. MIC determination was confirmed via E-TEST and microdilution standard methods. A molecular study was carried out to characterize the carbapenem and colistin resistance in Gram-negative bacterial strains. All of the positive results were confirmed via sequencing. Klebsiella pneumoniae (n = 32), Citrobacter freundii (n = 21), Escherichia coli (n = 7), and Acinetobacter baumannii (n = 21) were the predominant isolated bacteria. Gram-negative isolates were multidrug-resistant and carried different carbapenem resistance-associated genes, including NDM-1 (56/119; 47.05%), OXA-48 (15/119; 12.60%), OXA-23 (19/119; 15.96%), VIM (10/119; 8.40%), and the colistin resistance mobile gene mcr-1 (4/119; 3.36%). The overuse of antimicrobials, particularly carbapenem antibiotics, during the SARS-CoV-2 pandemic has led to the emergence of multidrug-resistant bacteria, mainly K. pneumoniae, A. baumannii, and colistin-resistant E. coli strains. Increased surveillance as well as the rational use of carbapenem antibiotics and, recently, colistin are required to reduce the propagation of multidrug-resistant strains and to optimally maintain the efficacy of these antibiotics. IMPORTANCE In this work, we describe, for the first time, the occurrence of carbapenem-resistant bacteria colonizing COVID-19 patients who developed hospital-associated infections with carbapenemase-producing, Gram-negative bacteria at some isolation centers of COVID-19 in the eastern part of Libya. Our results confirmed that the overuse of antimicrobials, such as carbapenem antibiotics, during the COVID-19 pandemic has led to the emergence of multidrug-resistant bacteria, mainly K. pneumoniae and A. baumannii, as well as colistin resistance.
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Affiliation(s)
- Khouloud Slimene
- Université Aix-Marseille, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille Cedex 05, France
- IHU Méditerranée Infection, Marseille Cedex 05, France
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Campus Universitaire, 2098 El-Manar II, Université de Tunis El-Manar, Tunis, Tunisie
- Laboratoire de Recherche des Sciences et Technologies de l’Environnement, Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, BP-1003, Hammam-Lif 2050, Université de Carthage, Tunisie
- Unité de Service en Commun pour la Recherche Plateforme Génomique Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, BP-1003, Hammam-Lif 2050, Université de Carthage, Tunisie
| | - Asrra A. Ali
- Department of Environmental Health, Faculty of Public Health, University of Benghazi, Benghazi, Libya
| | - Elhussan A. Mohamed
- Department of Community Medicine, Omar Al-Mukhtar University, El-Beyda, Libya
| | - Allaaeddin El Salabi
- Department of Environmental Health, Faculty of Public Health, University of Benghazi, Benghazi, Libya
| | - Faraj S. Suliman
- Department of Community Medicine, Omar Al-Mukhtar University, El-Beyda, Libya
- Almansoura Isolation Department of COVID-19 Patients, Shahat Teaching Hospital for Chest Diseases and Tuberculosis, Shahat, Libya
| | - Agela A. Elbadri
- Department of Medicine, Faculty of Medicine, University of Benghazi, Benghazi, Libya
- Alhawari Hospital, Benghazi, Libya
| | | | - Ahmed El-awjly
- Sterilization Service Department, Benghazi Medical Center, Benghazi, Libya
| | - Salah A. Shokri
- Department of Microbiology, Faculty of Science, Misurata University, Misurata, Libya
| | - Jean-Marc Rolain
- Université Aix-Marseille, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille Cedex 05, France
- IHU Méditerranée Infection, Marseille Cedex 05, France
| | - Chedly Chouchani
- Laboratoire des Microorganismes et Biomolécules Actives, Faculté des Sciences de Tunis, Campus Universitaire, 2098 El-Manar II, Université de Tunis El-Manar, Tunis, Tunisie
- Laboratoire de Recherche des Sciences et Technologies de l’Environnement, Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, BP-1003, Hammam-Lif 2050, Université de Carthage, Tunisie
- Unité de Service en Commun pour la Recherche Plateforme Génomique Institut Supérieur des Sciences et Technologies de l’Environnement de Borj-Cedria, BP-1003, Hammam-Lif 2050, Université de Carthage, Tunisie
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El-Sawalhi S, Revol O, Chamieh A, Lacoste A, Annessi A, La Scola B, Rolain JM, Pagnier I. Epidemiological Description and Detection of Antimicrobial Resistance in Various Aquatic Sites in Marseille, France. Microbiol Spectr 2023; 11:e0142622. [PMID: 36976002 PMCID: PMC10101087 DOI: 10.1128/spectrum.01426-22] [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: 04/26/2022] [Accepted: 12/22/2022] [Indexed: 03/29/2023] Open
Abstract
Antibiotic resistance is a worldwide public health concern and has been associated with reports of elevated mortality. According to the One Health concept, antibiotic resistance genes are transferrable to organisms, and organisms are shared among humans, animals, and the environment. Consequently, aquatic environments are a possible reservoir of bacteria harboring antibiotic resistance genes. In our study, we screened water and wastewater samples for antibiotic resistance genes by culturing samples on different types of agar media. Then, we performed real-time PCR to detect the presence of genes conferring resistance to beta lactams and colistin, followed by standard PCR and gene sequencing for verification. We mainly isolated Enterobacteriaceae from all samples. In water samples, 36 Gram-negative bacterial strains were isolated and identified. We found three extended-spectrum β-lactamase (ESBL)-producing bacteria-Escherichia coli and Enterobacter cloacae strains-harboring the CTX-M and TEM groups. In wastewater samples, we isolated 114 Gram-negative bacterial strains, mainly E. coli, Klebsiella pneumoniae, Citrobacter freundii and Proteus mirabilis strains. Forty-two bacterial strains were ESBL-producing bacteria, and they harbored at least one gene belonging to the CTX-M, SHV, and TEM groups. We also detected carbapenem-resistant genes, including NDM, KPC, and OXA-48, in four isolates of E. coli. This short epidemiological study allowed us to identify new antibiotic resistance genes present in bacterial strains isolated from water in Marseille. This type of surveillance shows the importance of tracking bacterial resistance in aquatic environments. IMPORTANCE Antibiotic-resistant bacteria are involved in serious infections in humans. The dissemination of these bacteria in water, which is in close contact with human activities, is a serious problem, especially under the concept of One Health. This study was done to survey and localize the circulation of bacterial strains, along with their antibiotic resistance genes, in the aquatic environment in Marseille, France. The importance of this study is to monitor the frequency of these circulating bacteria by creating and surveying water treatments.
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Affiliation(s)
- Sabah El-Sawalhi
- Aix-Marseille Université, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille CEDEX 05, France
- IHU Méditerranée Infection, Marseille CEDEX 05, France
| | - Océane Revol
- Aix-Marseille Université, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille CEDEX 05, France
- IHU Méditerranée Infection, Marseille CEDEX 05, France
| | - Amanda Chamieh
- Aix-Marseille Université, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille CEDEX 05, France
- IHU Méditerranée Infection, Marseille CEDEX 05, France
| | - Alexandre Lacoste
- Bataillon des Marins Pompiers de Marseille, CIS BMPM, Marseille, France
| | - Alexandre Annessi
- Bataillon des Marins Pompiers de Marseille, CIS BMPM, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille CEDEX 05, France
- IHU Méditerranée Infection, Marseille CEDEX 05, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille CEDEX 05, France
- IHU Méditerranée Infection, Marseille CEDEX 05, France
| | - Isabelle Pagnier
- Aix-Marseille Université, IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Marseille CEDEX 05, France
- IHU Méditerranée Infection, Marseille CEDEX 05, France
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Xiao C, Li X, Huang L, Cao H, Han L, Ni Y, Xia H, Yang Z. Prevalence and molecular characteristics of polymyxin-resistant Enterobacterales in a Chinese tertiary teaching hospital. Front Cell Infect Microbiol 2023; 13:1118122. [PMID: 37143741 PMCID: PMC10151768 DOI: 10.3389/fcimb.2023.1118122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/29/2023] [Indexed: 05/06/2023] Open
Abstract
Introduction Polymyxin-resistant Enterobacterales poses a significant threat to public health globally, but its prevalence and genomic diversity within a sole hospital is less well known. In this study, the prevalence of polymyxin-resistant Enterobacterales in a Chinese teaching hospital was investigated with deciphering of their genetic determinants of drug resistance. Methods Polymyxin-resistant Enterobacterales isolates identified by matrix-assisted laser desorption were collected in Ruijin Hospital from May to December in 2021. Both the VITEK 2 Compact and broth dilution methods were used to determine polymyxin B (PMB) susceptibility. Polymyxin-resistant isolates were further characterized by molecular typing using PCR, multi-locus sequence typing, and sequencing of the whole genome. Results Of the 1,216 isolates collected, 32 (2.6%) across 12 wards were polymyxin-resistant (minimum inhibitory concentration (MIC) range, PMB 4-256 mg/ml, and colistin 4 ≥ 16 mg/ ml). A total of 28 (87.5%) of the polymyxin-resistant isolates had reduced susceptibility to imipenem and meropenem (MIC ≥ 16 mg/ml). Of the 32 patients, 15 patients received PMB treatment and 20 survived before discharge. The phylogenetic tree of these isolates showed they belonged to different clones and had multiple origins. The polymyxin-resistant Klebsiella pneumoniae isolates belonged to ST-11 (85.72%), ST-15 (10.71%), and ST-65 (3.57%), and the polymyxin-resistant Escherichia coli belonged to four different sequence types, namely, ST-69 (25.00%), ST-38 (25.00%), ST-648 (25.00%), and ST-1193 (25.00%). In addition, six mgrB specific mutations (snp_ALT c.323T>C and amino acid change p.Val8Ala) were identified in 15.6% (5/32) of the isolates. mcr-1, a plasmid-mediated polymyxin-resistant gene, was found in three isolates, and non-synonymous mutations including T157P, A246T, G53V, and I44L were also observed. Discussion In our study, a low prevalence of polymyxin-resistant Enterobacterales was observed, but these isolates were also identified as multidrug resistant. Therefore, efficient infection control measures should be implemented to prevent the further spread of resistance to last-line polymyxin therapy.
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Affiliation(s)
- Chenlu Xiao
- Department of Laboratory Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Clinical Microbiology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuming Li
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Lianjiang Huang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Huiluo Cao
- Department of Microbiology, The University of Hongkong, Hong Kong, Hong Kong SAR, China
| | - Lizhong Han
- Department of Laboratory Medicine, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Clinical Microbiology, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yuxing Ni
- Department of Infection Control, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Han Xia
- Department of Scientific Affairs, Hugobiotech Co., Ltd., Beijing, China
| | - Zhitao Yang
- Department of Emergency, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Zhitao Yang,
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Hamame A, Davoust B, Hasnaoui B, Mwenebitu DL, Rolain JM, Diene SM. Screening of colistin-resistant bacteria in livestock animals from France. Vet Res 2022; 53:96. [DOI: 10.1186/s13567-022-01113-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/26/2022] [Indexed: 11/24/2022] Open
Abstract
AbstractColistin is frequently used as a growth factor or treatment against infectious bacterial diseases in animals. The Veterinary Division of the European Medicines Agency (EMA) restricted colistin use as a second-line treatment to reduce colistin resistance. In 2020, 282 faecal samples were collected from chickens, cattle, sheep, goats, and pigs in the south of France. In order to track the emergence of mobilized colistin resistant (mcr) genes in pigs, 111 samples were re-collected in 2021 and included pig faeces, food, and water from the same location. All samples were cultured in a selective Lucie Bardet Jean-Marc Rolain (LBJMR) medium and colonies were identified using MALDI-TOF mass spectrometry and then antibiotic susceptibility tests were performed. PCR and Sanger sequencing were performed to screen for the presence of mcr genes. The selective culture revealed the presence of 397 bacteria corresponding to 35 different bacterial species including Gram-negative and Gram-positive. Pigs had the highest prevalence of colistin-resistant bacteria with an abundance of intrinsically colistin-resistant bacteria and from these samples one strain harbouring both mcr-1 and mcr-3 has been isolated. The second collection allowed us to identify 304 bacteria and revealed the spread of mcr-1 and mcr-3 in pigs. In the other samples, naturally, colistin-resistant bacteria were more frequent, nevertheless the mcr-1 variant was the most abundant gene found in chicken, sheep, and goat samples and one cattle sample was positive for the mcr-3 gene. Animals are potential reservoir of colistin-resistant bacteria which varies from one animal to another. Interventions and alternative options are required to reduce the emergence of colistin resistance and to avoid zoonotic transmissions.
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Laidoudi Y, Ngaiganam EP, Marié JL, Pagnier I, Rolain JM, Mouhamadou Diene S, Davoust B. Colistin Resistance Mechanism in Enterobacter hormaechei subsp. steigerwaltii Isolated from Wild Boar (Sus scrofa) in France. Pathogens 2022; 11:pathogens11091022. [PMID: 36145454 PMCID: PMC9504195 DOI: 10.3390/pathogens11091022] [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: 08/17/2022] [Revised: 09/03/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Wild animals may act as efficient antimicrobial-resistance reservoirs and epidemiological links between humans, livestock, and natural environments. By using phenotypic and genotypic characterization, the present study highlighted the occurrence of an antimicrobial-resistant (i.e., amoxicillin, amoxicillin–clavulanic acid, cephalothin, and colistin) Enterobacter hormaechei subsp. steigerwaltii strain in wild boar (Sus scrofa) from France. The molecular analysis conducted showed non-synonymous mutations in the pmrA/pmrB and phoQ/phoP operons and the phoP/Q regulator mgrB gene, leading to colistin resistance. The present data highlight the need for continuous monitoring of multidrug-resistant bacteria in wild animals to limit the spread of these threatening pathogens.
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Affiliation(s)
- Younes Laidoudi
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Edgarthe Priscilla Ngaiganam
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Jean-Lou Marié
- Animal Epidemiology Expert Group, French Military Health Service, 37076 Tours, France
| | - Isabelle Pagnier
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Seydina Mouhamadou Diene
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Bernard Davoust
- Aix Marseille Université, IRD, APHM, MEPHI, IHU-Méditerranée Infection, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France
- Animal Epidemiology Expert Group, French Military Health Service, 37076 Tours, France
- Correspondence:
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10
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Jangir PK, Yang Q, Shaw LP, Caballero JD, Ogunlana L, Wheatley R, Walsh T, MacLean RC. Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of resistance to a last-resort antibiotic. eLife 2022; 11:e78834. [PMID: 35943060 PMCID: PMC9363117 DOI: 10.7554/elife.78834] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 07/22/2022] [Indexed: 12/17/2022] Open
Abstract
Bacterial pathogens show high levels of chromosomal genetic diversity, but the influence of this diversity on the evolution of antibiotic resistance by plasmid acquisition remains unclear. Here, we address this problem in the context of colistin, a 'last line of defence' antibiotic. Using experimental evolution, we show that a plasmid carrying the MCR-1 colistin resistance gene dramatically increases the ability of Escherichia coli to evolve high-level colistin resistance by acquiring mutations in lpxC, an essential chromosomal gene involved in lipopolysaccharide biosynthesis. Crucially, lpxC mutations increase colistin resistance in the presence of the MCR-1 gene, but decrease the resistance of wild-type cells, revealing positive sign epistasis for antibiotic resistance between the chromosomal mutations and a mobile resistance gene. Analysis of public genomic datasets shows that lpxC polymorphisms are common in pathogenic E. coli, including those carrying MCR-1, highlighting the clinical relevance of this interaction. Importantly, lpxC diversity is high in pathogenic E. coli from regions with no history of MCR-1 acquisition, suggesting that pre-existing lpxC polymorphisms potentiated the evolution of high-level colistin resistance by MCR-1 acquisition. More broadly, these findings highlight the importance of standing genetic variation and plasmid/chromosomal interactions in the evolutionary dynamics of antibiotic resistance.
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Affiliation(s)
- Pramod K Jangir
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Liam P Shaw
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | | | - Lois Ogunlana
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - Rachel Wheatley
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - Timothy Walsh
- Department of Zoology, University of OxfordOxfordUnited Kingdom
| | - R Craig MacLean
- Department of Zoology, University of OxfordOxfordUnited Kingdom
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11
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Phenotypic and Genotypic Screening of Colistin Resistance Associated with Emerging Pathogenic Escherichia coli Isolated from Poultry. Vet Sci 2022; 9:vetsci9060282. [PMID: 35737334 PMCID: PMC9229556 DOI: 10.3390/vetsci9060282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 05/31/2022] [Accepted: 06/06/2022] [Indexed: 11/23/2022] Open
Abstract
Chickens continue to be an important reservoir of zoonotic multidrug-resistant illnesses. Antimicrobial resistance correlated with colistin has emerged as a critical concern worldwide in the veterinary field and the public health sector. The current study investigated the prevalence of multidrug-resistant avian pathogenic Escherichia coli among chicken farms in three Egyptian governorates, focusing on colistin resistance assessment. A total of 56 Escherichia coli isolates were recovered out of 120 pooled samples obtained from diseased chicken broilers (46.7%). The E. coli isolates were serotyped to nine different serotypes; the highest incidence was for O125 (n = 18). The E. coli isolates demonstrated multidrug-resistant patterns against 10 antibiotics, especially clindamycin, tetracycline, streptomycin and ampicillin, by 100, 100, 96.4 and 92.9%, respectively. On the other hand, colistin resistance was 41.1% using AST. All E. coli isolates displayed positive colistin resistance growth on chromogenic medium, but only 25% represented this positivity via MIC estimation and Sensititre kit. PCR results revealed that all isolates harbored mcr-1, but no isolates harbored the other 2–5 mcr genes. In conclusion, the study demonstrated the emergence of multidrug-resistant, especially colistin-resistant, E. coli among chicken broiler flocks, and mcr-1 is the master gene of the colistin resistance feature.
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12
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Perrin-Guyomard A, Granier SA, Slettemeås JS, Anjum M, Randall L, AbuOun M, Pauly N, Irrgang A, Hammerl JA, Kjeldgaard JS, Hammerum A, Franco A, Skarżyńska M, Kamińska E, Wasyl D, Dierikx C, Börjesson S, Geurts Y, Haenni M, Veldman K. Multicentre evaluation of a selective isolation protocol for detection of mcr-positive E. coli and Salmonella spp. in food-producing animals and meat. Lett Appl Microbiol 2022; 75:224-233. [PMID: 35388505 PMCID: PMC9544698 DOI: 10.1111/lam.13717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/01/2022] [Accepted: 04/01/2022] [Indexed: 12/01/2022]
Abstract
This study was conducted to evaluate the performance of a screening protocol to detect and isolate mcr‐positive Escherichia coli and Salmonella spp. from animal caecal content and meat samples. We used a multicentre approach involving 12 laboratories from nine European countries. All participants applied the same methodology combining a multiplex PCR performed on DNA extracted from a pre‐enrichment step, followed by a selective culture step on three commercially available chromogenic agar plates. The test panel was composed of two negative samples and four samples artificially contaminated with E. coli and Salmonella spp. respectively harbouring mcr‐1 or mcr‐3 and mcr‐4 or mcr‐5 genes. PCR screening resulted in a specificity of 100% and a sensitivity of 83%. Sensitivity of each agar medium to detect mcr‐positive colistin‐resistant E. coli or Salmonella spp. strains was 86% for CHROMID® Colistin R, 75% for CHROMagarTM COL‐APSE and 70% for COLISTIGRAM. This combined method was effective to detect and isolate most of the E. coli or Salmonella spp. strains harbouring different mcr genes from food‐producing animals and food products and might thus be used as a harmonized protocol for the screening of mcr genes in food‐producing animals and food products in Europe.
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Affiliation(s)
- Agnès Perrin-Guyomard
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères Laboratory, France
| | - Sophie A Granier
- French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Fougères Laboratory, France
| | | | - Muna Anjum
- Animal and Plant Health Agency, United Kingdom
| | | | | | - Natalie Pauly
- German Federal Institute for Risk Assessment, Germany
| | | | | | | | | | - Alessia Franco
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana, Italy
| | | | | | | | - Cindy Dierikx
- National Institute for Public Health and the Environment, the Netherlands
| | - Stefan Börjesson
- National Veterinary Institute (SVA), Sweden and Public Health Agency of Sweden, Sweden
| | - Yvon Geurts
- Wageningen Bioveterinary Research, the Netherlands
| | - Marisa Haenni
- Lyon University - French Agency for Food, Environmental and Occupational Health & Safety (ANSES), Lyon laboratory, France
| | - Kees Veldman
- Wageningen Bioveterinary Research, the Netherlands
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13
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Abdallah R, Kuete Yimagou E, Hadjadj L, Mediannikov O, Ibrahim A, Davoust B, Barciela A, Hernandez-Aguilar RA, Diatta G, Sokhna C, Raoult D, Rolain JM, Baron SA. Population Diversity of Antibiotic Resistant Enterobacterales in Samples From Wildlife Origin in Senegal: Identification of a Multidrug Resistance Transposon Carrying blaCTX–M–15 in Escherichia coli. Front Microbiol 2022; 13:838392. [PMID: 35369484 PMCID: PMC8971907 DOI: 10.3389/fmicb.2022.838392] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/18/2022] [Indexed: 01/08/2023] Open
Abstract
Introduction The role of wildlife in the transmission of antimicrobial resistant (AMR) is suspected but scarcely reported in current studies. Therefore, we studied the dynamics and prevalence of antibiotic-resistant Enterobacterales in antibiotic-limited areas of Senegal. Materials and Methods We collected fecal samples from monkeys and apes (N = 226) and non-fecal environmental samples (N = 113) from Senegal in 2015 and 2019. We grew the samples on selective media, subsequently isolated AMR Enterobacterales, and then sequenced their genomes. Results We isolated 72 different Enterobacterales among which we obtained a resistance rate of 65% for colistin (N = 47/72) and 29% for third generation-cephalosporin (C3G) (29%, N = 21/72). Interestingly, almost 46% of our isolates, among Enterobacter sp., Citrobacter cronae and Klebsiella aerogenes, belong to 34 new STs. Moreover, the genes blaCTX–M–15, blaTEM1B, sul2, dfrA14, qnrs, aph(3′′), aph(6), tetA, and tetR harbored within a transposon on the IncY plasmid of ST224 Escherichia coli were transferred and inserted into a ST10 E. coli phage coding region. Conclusion Wildlife constitutes a rich, unexplored reservoir of natural microbial diversity, AMR genes and international resistant clones pathogenic in humans. The presence of a transposon that carries AMR genes is intriguing since no antibiotics are used in the non-human primates we studied.
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Affiliation(s)
- Rim Abdallah
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Edmond Kuete Yimagou
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Linda Hadjadj
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Oleg Mediannikov
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Ahmad Ibrahim
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Bernard Davoust
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Amanda Barciela
- Dindefelo Biological Station, Jane Goodall Institute Spain and Senegal, Kedougou, Senegal
| | - R. Adriana Hernandez-Aguilar
- Dindefelo Biological Station, Jane Goodall Institute Spain and Senegal, Kedougou, Senegal
- Department of Social Psychology and Quantitative Psychology, Faculty of Psychology, Serra Hunter Programme, University of Barcelona, Barcelona, Spain
| | - Georges Diatta
- VITROME IRD 257, Campus International de Recherche IRD-UCAD de Hann, Dakar, Senegal
| | - Cheikh Sokhna
- IHU Méditerranée Infection, Marseille, France
- VITROME IRD 257, Campus International de Recherche IRD-UCAD de Hann, Dakar, Senegal
| | - Didier Raoult
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
| | - Sophie Alexandra Baron
- IRD, APHM, MEPHI, Faculté de Médecine et de Pharmacie, Aix Marseille University, Marseille, France
- IHU Méditerranée Infection, Marseille, France
- *Correspondence: Sophie Alexandra Baron,
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14
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Screening of Colistin-Resistant Bacteria in Domestic Pets from France. Animals (Basel) 2022; 12:ani12050633. [PMID: 35268202 PMCID: PMC8909117 DOI: 10.3390/ani12050633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Zoonotic transmission from pets to their owners is a major health problem, especially when dealing with human pathogens. It is important to determine the reservoir of colistin-resistant bacteria in pets to avoid the risk factors for human transmission. This study investigated the screening of colistin-resistant bacteria in pets in Marseille, France. Overall, cats and dogs have various reservoirs of colistin-resistant bacteria, including naturally colistin-resistant bacteria and mcr gene carriers (n = 14). Pets are the best human companions; therefore, vigilance would be required to avoid zoonotic transmission of colistin-resistant bacteria. Although colistin use is restricted in France, we report here for the first time that cats and dogs have various colistin-resistant bacteria including mcr-1 gene carriers. Abstract Background: Pets are the closest animals to humans with a considerable risk of zoonotic transmission. This study aimed to screen colistin-resistant bacteria from stools of dogs and cats from Marseille, France. Screening of mcr genes in pets has never been reported in France. Methods: Fecal samples (n = 157) were cultivated on the selective Lucie-Bardet Jean-Marc-Rolain medium (LBJMR). Bacteria were identified using Microflex LS MALDI-TOF. The antibiotic resistance phenotype was investigated for several antibiotics (β-lactams, aminoside, cephalosporine, tetracycline, and sulfonamide). PCR techniques were performed to detect mcr genes. Results: A total of 218 bacteria were identified. For cats, intrinsically colistin-resistant bacteria were significantly higher than mcr-1 gene carriers (n = 4). Dogs had more bacteria with the mcr-1 gene (n = 10). Furthermore, cats had a high prevalence of Gram-positive bacteria (GPB), whereas dogs had GNB equal to GPB. The diversity of identified bacteria was due to the constitution of the pets’ microorganisms. Even though colistin use is monitored in France, pets harbor various colistin-resistant bacteria. Additionally, in this geographical area, bacteria bearing mcr-1 gene from dogs and cats were detected for the first time. Conclusions: The current study opens a new perspective: the spread of colistin resistance is independent of colistin use. What are the most factors related to the emergence of colistin resistance? The surveillance of pets must be considered a priority to avoid the spread of mcr genes. It is important to know the contribution that pets make to the pool of multidrug-resistant mcr-1-containing bacteria.
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Azyzov IS, Martinovich А. Detection of mcr-1-mediated resistance to polymyxins in Enterobacterales using colistin disk chelator application. CLINICAL MICROBIOLOGY AND ANTIMICROBIAL CHEMOTHERAPY 2022. [DOI: 10.36488/cmac.2022.3.254-260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Objective.
To evaluate the possibility of using the colistin disk chelator application (CDCA) method as simple and available screening tool for detection of mcr-1-mediated resistance to polymyxins in Enterobacterales.
Materials and Methods.
A total of 47 colistin-resistant Enterobacterales isolates obtained in 2014–2020 within multicenter MARATHON study were included in the experiment. Colistin susceptibility testing was performed using Mueller–Hinton broth microdilution method according to ISO 20776-1:2006. Interpretation of the results was performed according to EUCAST v.12.0 clinical breakpoints. MCR-genes were detected by multiplex real-time PCR. Phenotypic screening for mcr-expression was performed on Mueller–Hinton agar by application of dipicolinic acid in concentration of 1,000 mcg/disk in 10 µL volume per disk and 0.5 M solution of EDTA in 5 µL volume per disk. Chelating effect was registered by differences in zone of growth inhibition around colistin disks with and without chelator. Measurements were performed with the help of caliper in millimeters. Statistical data processing was carried out in accordance with guidelines for statistical analysis in medical researches using MS-Excel tool.
Results.
In 25 of 47 included in the experiment enterobacteria isolates mcr-genes were detected by molecular method. MCR-detection by CDCA method identified the average difference value of the zones of growth inhibition for colistin and its combination with EDTA and DPA as 4.1 mm and 3.7 mm respectively for mcr-positive isolates and 1.7 mm and 1.2 mm respectively for mcr-negative isolates. Statistical analysis estimated that a difference of ≥ 3 mm in zone of growth inhibition for combination of colistin with one of the chelating agents when compared to colistin only allows us to conclude that a studied isolated carries mcr-1-mediated resistance to polymyxins. In addition, sensitivity of the test was 96% and specificity was 91% if DPA is used, while EDTA showed only 88% sensitivity and 77% specificity.
Conclusions.
Proposed method appears as available technique for phenotypic screening of the Enterobacterales order for mcr-1-mediated resistance to polymyxins for practical laboratories in present conditions. The use of DPA is preferred because of better specificity and sensitivity rates.
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16
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Hamame A, Davoust B, Rolain JM, Diene SM. Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France. J Glob Antimicrob Resist 2022; 28:174-179. [DOI: 10.1016/j.jgar.2022.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
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Clonal Dissemination of Plasmid-Mediated Carbapenem and Colistin Resistance in Refugees Living in Overcrowded Camps in North Lebanon. Antibiotics (Basel) 2021; 10:antibiotics10121478. [PMID: 34943690 PMCID: PMC8698793 DOI: 10.3390/antibiotics10121478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/22/2021] [Accepted: 11/29/2021] [Indexed: 11/26/2022] Open
Abstract
Carbapenem and colistin-resistant bacteria represent a global public health problem. Refugees carrying these bacteria and living in inadequate shelters can spread these microorganisms. The aim of this study was to investigate the intestinal carriage of these bacteria in Syrian refugees in Lebanon. Between June and July 2019, 250 rectal swabs were collected from two refugee camps in North Lebanon. Swabs were cultured on different selective media. Antibiotic susceptibility testing was performed using the disk diffusion method. Carbapenemase-encoding genes and mcr genes were investigated using real-time polymerase chain reaction (RT-PCR) and standard polymerase chain reaction (PCR). Epidemiological relatedness was studied using multilocus sequence typing (MLST). From 250 rectal swabs, 16 carbapenem-resistant, 5 colistin-resistant, and 4 colistin and carbapenem-resistant Enterobacteriaceae were isolated. The isolates exhibited multidrug-resistant phenotypes. Seven Klebsiella pneumoniae isolates harboured the blaOXA-48 gene, and in addition four K. pneumoniae had mutations in the two component systems pmrA/pmrB, phoP/phoQ and co-harboured the blaNDM-1 gene. Moreover, the blaNDM-1 gene was detected in six Escherichia coli and three Enterobacter cloacae isolates. The remaining five E. coli isolates harboured the mcr-1 gene. MLST results showed several sequence types, with a remarkable clonal dissemination. An urgent strategy needs to be adopted in order to avoid the spread of such resistance in highly crowded underserved communities.
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Smelikova E, Tkadlec J, Krutova M. How to: screening for mcr-mediated resistance to colistin. Clin Microbiol Infect 2021; 28:43-50. [PMID: 34537365 DOI: 10.1016/j.cmi.2021.09.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 11/03/2022]
Abstract
BACKGROUND Colistin belongs to the last-resort antibiotics. The discovery of plasmid-bound colistin resistance mediated by the mcr-gene(s) is of great concern because, given its biological potential, there is a risk of its rapid spread. OBJECTIVES To discuss the current literature on the methods for the screening for mcr-mediated resistance to colistin. SOURCES Literature was drawn from a search of PubMed from 1 January 2016 to 26 April 2021. CONTENT The selective culture-based or culture-independent approach can be used for the screening of mcr-mediated resistance to colistin in clinical samples. Rapid Polymyxin NP, Colistin Drop or Colistin Agar Spot tests are applicable for the selection of isolates with a suspected resistance to colistin that has to be confirmed by broth microdilution. The mcr-mediated resistance to colistin can be confirmed by the detection of the causal gene(s) or by phenotype using EDTA-colistin broth disc elution; production of the MCR-1 enzyme can be confirmed with lateral flow immunoassay, using matrix-assisted laser desorption/ionization time-of flight or liquid chromatography-based mass spectrometry. Whole-genome sequencing (WGS) is the ultimate typing method. When a WGS platform is not available at a healthcare facility, a WGS-outsourced service, in combination with freely available bioinformatics tools, allows for the characterization of the mcr-gene(s) carrying isolates. IMPLICATIONS mcr-mediated colistin resistance should be monitored through active targeted screening. The broth microdilution method is required for colistin susceptibility testing but as only a selected number of clinical isolates are tested, colistin resistance, including mcr-mediated, may remain undetected. In mcr-1-positive Escherichia coli isolates, the MIC to colistin can range from 2 to 8 mg/L, so it is proposed that Enterobacterales with a colistin MIC of 2 mg/L should also be included in the mcr-mediated colistin resistance screening and those with a confirmed mcr-genotype and/or MCR-phenotype should be considered to be colistin-resistant.
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Affiliation(s)
- Eva Smelikova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Czech Republic
| | - Jan Tkadlec
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Czech Republic
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Czech Republic.
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Gogry FA, Siddiqui MT, Sultan I, Haq QMR. Current Update on Intrinsic and Acquired Colistin Resistance Mechanisms in Bacteria. Front Med (Lausanne) 2021; 8:677720. [PMID: 34476235 PMCID: PMC8406936 DOI: 10.3389/fmed.2021.677720] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/09/2021] [Indexed: 01/07/2023] Open
Abstract
Colistin regained global interest as a consequence of the rising prevalence of multidrug-resistant Gram-negative Enterobacteriaceae. In parallel, colistin-resistant bacteria emerged in response to the unregulated use of this antibiotic. However, some Gram-negative species are intrinsically resistant to colistin activity, such as Neisseria meningitides, Burkholderia species, and Proteus mirabilis. Most identified colistin resistance usually involves modulation of lipid A that decreases or removes early charge-based interaction with colistin through up-regulation of multistep capsular polysaccharide expression. The membrane modifications occur by the addition of cationic phosphoethanolamine (pEtN) or 4-amino-l-arabinose on lipid A that results in decrease in the negative charge on the bacterial surface. Therefore, electrostatic interaction between polycationic colistin and lipopolysaccharide (LPS) is halted. It has been reported that these modifications on the bacterial surface occur due to overexpression of chromosomally mediated two-component system genes (PmrAB and PhoPQ) and mutation in lipid A biosynthesis genes that result in loss of the ability to produce lipid A and consequently LPS chain, thereafter recently identified variants of plasmid-borne genes (mcr-1 to mcr-10). It was hypothesized that mcr genes derived from intrinsically resistant environmental bacteria that carried chromosomal pmrC gene, a part of the pmrCAB operon, code three proteins viz. pEtN response regulator PmrA, sensor kinase protein PmrAB, and phosphotransferase PmrC. These plasmid-borne mcr genes become a serious concern as they assist in the dissemination of colistin resistance to other pathogenic bacteria. This review presents the progress of multiple strategies of colistin resistance mechanisms in bacteria, mainly focusing on surface changes of the outer membrane LPS structure and other resistance genetic determinants. New handier and versatile methods have been discussed for rapid detection of colistin resistance determinants and the latest approaches to revert colistin resistance that include the use of new drugs, drug combinations and inhibitors. Indeed, more investigations are required to identify the exact role of different colistin resistance determinants that will aid in developing new less toxic and potent drugs to treat bacterial infections. Therefore, colistin resistance should be considered a severe medical issue requiring multisectoral research with proper surveillance and suitable monitoring systems to report the dissemination rate of these resistant genes.
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Affiliation(s)
| | | | - Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
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Multidrug-Resistant Klebsiella pneumoniae Clones from Wild Chimpanzees and Termites in Senegal. Antimicrob Agents Chemother 2021; 65:e0255720. [PMID: 34152818 DOI: 10.1128/aac.02557-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antibiotic resistance genes exist naturally in various environments far from human usage. Here, we investigated multidrug-resistant Klebsiella pneumoniae, a common pathogen of chimpanzees and humans. We screened antibiotic-resistant K. pneumoniae from 48 chimpanzee stools and 38 termite mounds (n = 415 samples) collected in protected areas in Senegal. The microsatellite method was used to identify chimpanzee individuals (n = 13). Whole-genome sequencing was performed on K. pneumoniae complex isolates to identify antibiotic-resistant genes and characterize clones. We found a high prevalence of carbapenem-resistant K. pneumoniae among chimpanzee isolates (18/48 samples from 7/13 individuals) and ceftriaxone resistance among both chimpanzee individuals (19/48) and termite mounds (7/415 termites and 3/38 termite mounds). The blaOXA-48 and the blaKPC-2 genes were carried by international pOXA-48 and pKPC-2 plasmids, respectively. The ESBL plasmid carried blaCTX-M-15, blaTEM-1B, and blaOXA-1 genes. Genome sequencing of 56 isolates identified two major clones associated with hospital-acquired infections of K. pneumoniae (ST307 and ST147) in chimpanzees and termites, suggesting circulation of strains between the two species, as chimpanzees feed on termites. The source and selection pressure of these clones in this environment need to be explored.
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Leshaba TMS, Mbelle NM, Osei Sekyere J. Current and emerging polymyxin resistance diagnostics: A systematic review of established and novel detection methods. J Appl Microbiol 2021; 132:8-30. [PMID: 34152057 DOI: 10.1111/jam.15184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 05/09/2021] [Accepted: 06/16/2021] [Indexed: 01/19/2023]
Abstract
The emergence of polymyxin resistance, due to transferable mcr genes, threatens public and animal health as there are limited therapeutic options. As polymyxin is one of the last-line antibiotics, there is a need to contain the spread of its resistance to conserve its efficacy. Herein, we describe current and emerging polymyxin resistance diagnostics to inform faster clinical diagnostic choices. A literature search in diverse databases for studies published between 2016 and 2020 was performed. English articles evaluating colistin resistance methods/diagnostics were included. Screening resulted in the inclusion of 93 journal articles. Current colistin resistance diagnostics are either phenotypic or molecular. Broth microdilution is currently the only gold standard for determining colistin MICs (minimum inhibitory concentration). Phenotypic methods comprise of agar-based methods such as CHROMagar™ Col-APSE, SuperPolymyxin, ChromID® Colistin R, LBJMR and LB medium; manual MIC-determiners viz., UMIC, MICRONAUT MIC-Strip and ComASP Colistin; automated antimicrobial susceptibility testing systems such as BD Phoenix, MICRONAUT-S, MicroScan, Sensititre and Vitek 2; MCR-detectors such as lateral flow immunoassay (LFI) and chelator-based assays including EDTA- and DPA-based tests, that is, combined disk test, modified colistin broth-disk elution (CBDE), Colispot, and Colistin MAC test as well as biochemical colorimetric tests, that is, Rapid Polymyxin NP test and Rapid ResaPolymyxin NP test. Molecular methods only characterize mobile colistin resistance; they include PCR, LAMP and whole-genome sequencing. Due to the faster turnaround time (≤3 h), improved sensitivity (84%-100%) and specificity (93.3%-100%) of the Rapid ResaPolymyxin NP test and Fastinov® , we recommend this test for initial screening of colistin-resistant isolates. This can be followed by CBDE with EDTA or the LFI as they both have 100% sensitivity and a specificity of ≥94.3% for the rapid screening of mcr genes. However, molecular assays such as LAMP and PCR may be considered in well-equipped clinical laboratories.
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Affiliation(s)
- Tumisho Mmatumelo Seipei Leshaba
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Ibrahim A, Peyclit L, Abdallah R, Khelaifia S, Chamieh A, Rolain JM, Bittar F. SCA Medium: A New Culture Medium for the Isolation of All Candida auris Clades. J Fungi (Basel) 2021; 7:jof7060433. [PMID: 34072592 PMCID: PMC8226795 DOI: 10.3390/jof7060433] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/23/2021] [Accepted: 05/28/2021] [Indexed: 12/11/2022] Open
Abstract
Candida auris is an emerging multidrug-resistant yeast causing nosocomial infections and associated with high mortality in immunocompromised patients. Rapid identification and characterisation are necessary for diagnosis and containing its spread. In this study, we present a selective culture medium for all C. auris clades. This medium is sensitive with a limit of detection ranging between 101 and 102 CFU/mL. The 100% specificity of SCA (specific C. auris) medium is confirmed on a set of 135 Candida strains, 50 bacterial species and 200 human stool samples. Thus, this medium specifically selects for C. auris isolation from clinical samples, allowing the latter to study its phenotypic profile.
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Affiliation(s)
- Ahmad Ibrahim
- Aix Marseille University, IRD, APHM, MEPHI, 13005 Marseille, France; (A.I.); (L.P.); (R.A.); (S.K.); (A.C.); (J.-M.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Lucie Peyclit
- Aix Marseille University, IRD, APHM, MEPHI, 13005 Marseille, France; (A.I.); (L.P.); (R.A.); (S.K.); (A.C.); (J.-M.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Rim Abdallah
- Aix Marseille University, IRD, APHM, MEPHI, 13005 Marseille, France; (A.I.); (L.P.); (R.A.); (S.K.); (A.C.); (J.-M.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Saber Khelaifia
- Aix Marseille University, IRD, APHM, MEPHI, 13005 Marseille, France; (A.I.); (L.P.); (R.A.); (S.K.); (A.C.); (J.-M.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Amanda Chamieh
- Aix Marseille University, IRD, APHM, MEPHI, 13005 Marseille, France; (A.I.); (L.P.); (R.A.); (S.K.); (A.C.); (J.-M.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Jean-Marc Rolain
- Aix Marseille University, IRD, APHM, MEPHI, 13005 Marseille, France; (A.I.); (L.P.); (R.A.); (S.K.); (A.C.); (J.-M.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France
| | - Fadi Bittar
- Aix Marseille University, IRD, APHM, MEPHI, 13005 Marseille, France; (A.I.); (L.P.); (R.A.); (S.K.); (A.C.); (J.-M.R.)
- IHU-Méditerranée Infection, 13005 Marseille, France
- Correspondence:
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Conceição-Neto OC, da Costa BS, Pontes LS, Santos ICO, Silveira MC, Cordeiro-Moura JR, Pereira NF, Tavares-Teixeira CB, Picão RC, Rocha-de-Souza CM, Carvalho-Assef APD. Difficulty in detecting low levels of polymyxin resistance in clinical Klebsiella pneumoniae isolates: evaluation of Rapid Polymyxin NP test, Colispot Test and SuperPolymyxin medium. New Microbes New Infect 2020; 36:100722. [PMID: 32642069 PMCID: PMC7334411 DOI: 10.1016/j.nmni.2020.100722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/06/2020] [Accepted: 06/22/2020] [Indexed: 01/29/2023] Open
Abstract
Polymyxins are important therapeutic options for treating infections, mainly those caused by carbapenem-resistant Klebsiella pneumoniae. Specific chemical characteristics of polymyxins make it difficult to perform antimicrobial susceptibility testing, especially within the clinical laboratory. Here we aimed to evaluate the performance of three phenotypic methods: Rapid NP Polymyxin Test, ColiSpot test and the SuperPolymyxin medium. To accomplish this, 170 non-duplicate clinical K. pneumoniae isolates were analysed (123 colistin-resistant and 47 susceptible). The sensitivity and specificity obtained for Rapid Polymyxin NP Test, Colispot and SuperPolymyxin medium were, respectively, 90% and 94%, 74% and 100%, and 82% and 85%. Very major errors occurred more frequently in low-level colistin-resistant isolates (MICs 4 and 8 μg/mL). Rapid Polymyxin NP proved to be a method capable of identifying colistin-resistant strains in acceptable categorical agreement. However, major errors and very major errors of this method were considered unacceptable for colistin-resistance screening. Although the Colispot test is promising and easy to perform and interpret, the results did not reproduce well in the isolates tested. The colistin-containing selective medium (SuperPolymyxin) showed limitations, including quantification of mucoid colonies and poor stability. Nevertheless, Colispot and SuperPolymyxin medium methods did not present acceptable sensitivity, specificity and categorical agreement. It is essential to use analytical tools that faithfully reproduce bacterial resistance in vitro, especially in last-line drugs, such as polymyxins, when misinterpretation of a test can result in therapeutic ineffectiveness.
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Affiliation(s)
- O C Conceição-Neto
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - B S da Costa
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - L S Pontes
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - I C O Santos
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - M C Silveira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - J R Cordeiro-Moura
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - N F Pereira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - C B Tavares-Teixeira
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - R C Picão
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - C M Rocha-de-Souza
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - A P D Carvalho-Assef
- Laboratório de Pesquisa em Infecção Hospitalar, Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
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Shedko ED, Timoshina O, Azyzov IS. Molecular epidemiology of mcr gene group. CLINICAL MICROBIOLOGY AND ANTIMICROBIAL CHEMOTHERAPY 2020. [DOI: 10.36488/cmac.2020.4.287-300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Colistin and polymyxin B are the “last reserve” antimicrobials for the treatment of extensively drug-resistant Gram-negative bacterial infections. The rapidly increasing prevalence of polymyxin resistance mediated by the mcr gene localized on plasmid DNA currently poses a high epidemiological threat. In order to control a distribution of mcr genes, it is necessary to develop highly accurate, highly sensitive and easy-to-use diagnostic tools. This paper provides a review of the most relevant studies on the molecular epidemiology as well as current approaches to microbiological and molecular detection of mcr group genes.
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Stefaniuk EM, Tyski S. Colistin Resistance in Enterobacterales Strains - A Current View. Pol J Microbiol 2019; 68:417-427. [PMID: 31880886 PMCID: PMC7260631 DOI: 10.33073/pjm-2019-055] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 02/07/2023] Open
Abstract
Colistin is a member of cationic polypeptide antibiotics known as polymyxins. It is widely used in animal husbandry, plant cultivation, animal and human medicine and is increasingly used as one of the last available treatment options for patients with severe infections with carbapenem-resistant Gram-negative bacilli. Due to the increased use of colistin in treating infections caused by multidrug-resistant (MDR) bacteria, the resistance to this antibiotic ought to be monitored. Bacterial resistance to colistin may be encoded on transposable genetic elements (e.g. plasmids with the mcr genes). Thus far, nine variants of the mcr gene, mcr-1 – mcr-9, have been identified. Chromosomal resistance to colistin is associated with the modification of lipopolysaccharide (LPS). Various methods, from classical microbiology to molecular biology methods, are used to detect the colistin-resistant bacterial strains and to identify resistance mechanisms. The broth dilution method is recommended for susceptibility testing of bacteria to colistin.
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Affiliation(s)
- Elżbieta M Stefaniuk
- Department of Antibiotics and Microbiology, National Medicines Institute , Warsaw , Poland
| | - Stefan Tyski
- Department of Antibiotics and Microbiology, National Medicines Institute , Warsaw , Poland ; Department of Pharmaceutical and Microbiology, Medical University of Warsaw , Warsaw , Poland
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Wang M, Deng B, Fu X, Sun H, Xu Z. Characterizations of microbial diversity and machine oil degrading microbes in machine oil contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 255:113190. [PMID: 31541828 DOI: 10.1016/j.envpol.2019.113190] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/02/2019] [Accepted: 09/05/2019] [Indexed: 06/10/2023]
Abstract
Microbial diversity in machine oil contaminated soil was determined by high-throughput amplicon sequencing technology. The diversity of culturable microbes in the contaminated soil was further characterized using polymerase chain reaction method. Proteobacteria and Bacteroidetes were the most dominant phyla and occupied 52.73 and 16.77%, respectively, while the most abundant genera were Methylotenera (21.62%) and Flavobacterium (3.06%) in the soil. In the culturable microbes, the major phyla were Firmicutes (46.15%) and Proteobacteria (37.36%) and the most abundant genera were Bacillus (42.86%) and Aeromonas (34.07%). Four isolated microbes with high machine oil degradation efficiency were selected to evaluate their characteristics on the oil degradation. All of them reached their highest oil degradation rate after 7 days of incubation. Most of them significantly increased their oil degradation rate by additional carbon or organic nitrogen source in the incubation medium. The oil degradation rate by combination of the four microbes at the same inoculation level was also higher than the rate from each individual microbe. The protocol and findings of this study are very useful for developing micro-bioremediation method to eliminate machine oil contaminants from soil.
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Affiliation(s)
- Mengjiao Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China; Shaanxi Provincial Engineering Research Center of Edible and Medicinal Microbes, Shaanxi University of Technology, Hanzhong, Shaanxi, China; Shaanxi Key Laboratory of Bio-resources, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Baiwan Deng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China; Shaanxi Provincial Engineering Research Center of Edible and Medicinal Microbes, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Xun Fu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Haiyan Sun
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China; Shaanxi Key Laboratory of Bio-resources, Shaanxi University of Technology, Hanzhong, Shaanxi, China
| | - Zhimin Xu
- School of Nutrition and Food Sciences, Louisiana State University, Baton Rouge, LA, USA.
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27
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Ngaiganam EP, Pagnier I, Chaalal W, Leangapichart T, Chabou S, Rolain JM, Diene SM. Investigation of urban birds as source of β-lactamase-producing Gram-negative bacteria in Marseille city, France. Acta Vet Scand 2019; 61:51. [PMID: 31672159 PMCID: PMC6822345 DOI: 10.1186/s13028-019-0486-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 10/22/2019] [Indexed: 01/18/2023] Open
Abstract
Background We investigate here the presence of multidrug-resistant bacteria isolated from stool samples of yellow-legged gulls and chickens (n = 136) in urban parks and beaches of Marseille, France. Bacterial isolation was performed on selective media, including MacConkey agar with ceftriaxone and LBJMR medium. Antibiotic resistance genes, including extended-spectrum β-lactamases (ESBL) (i.e. blaCTX-M, blaTEM and blaSHV), carbapenemases (blaKPC, blaVIM, blaNDM, blaOXA-23, blaOXA-24, blaOXA-48 and blaOXA-58) and colistin resistance genes (mcr-1 to mcr-5) were screened by real-time PCR and standard PCR and sequenced when found. Results Of the 136 stools samples collected, seven ESBL-producing Gram-negative bacteria (BGN) and 12 colistin-resistant Enterobacteriaceae were isolated. Among them, five ESBL-producing Escherichia coli and eight colistin-resistant Hafnia alvei strains were identified. Four blaTEM-1 genes were detected in yellow-legged gulls and chickens. Three CTX-M-15 genes were detected in yellow-legged gulls and pigeons, and one CTX-M-1 in a yellow-legged gull. No mcr-1 to mcr-5 gene were detected in colistin-resistant isolates. Genotyping of E. coli strains revealed four different sequence types already described in humans and animals and one new sequence type. Conclusions Urban birds, which are believed to have no contact with antibiotics appear as potential source of ESBL genes. Our findings highlight the important role of urban birds in the proliferation of multidrug-resistant bacteria and also the possible zoonotic transmission of such bacteria from wild birds to humans.
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Emergence of Escherichia coli harbouring mcr-1 and mcr-3 genes in North West Algerian farmlands. J Glob Antimicrob Resist 2019; 21:132-137. [PMID: 31606428 DOI: 10.1016/j.jgar.2019.10.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 09/27/2019] [Accepted: 10/02/2019] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVES Colistin resistance has emerged worldwide, threatening the efficacy of colistin treatment of Gram-negative bacterial infections. Farms have been recognised as an important reservoir of genes conferring resistance to colistin. This study aimed to isolate and characterise colistin-resistant bacteria in farmlands located in the region of Oran, northwest Algeria. METHODS Forty environmental samples were collected between May 2016 and March 2018 at eight agricultural sites in the Oran region. RESULTS From the 40 samples, 103 colistin-resistant isolates were isolated from agricultural soil (n = 52), irrigation water (n = 31) and manure (n = 20). Eight isolates were identified as Escherichia coli, including six and two isolates carrying the mcr-1 and mcr-3 gene, respectively. All eight E. coli isolates were non-susceptible to amoxicillin, amoxicillin/clavulanic acid, ticarcillin, nalidixic acid, ciprofloxacin, gentamicin, trimethoprim/sulfamethoxazole and rifamycin; two were also non-susceptible to cefotaxime, cefepime and aztreonam and carried the blaTEM-12 gene in addition to mcr-1. The six mcr-1-carrying E. coli isolates (MIC ≥ 2 μg/mL) belonged to three sequences types, including ST10 (n = 3), ST405 (n = 2) and ST345 (n = 1), whereas the two mcr-3-carrying isolates were assigned to ST155. The conjugation assay was positive only for two mcr-1-positive isolates. CONCLUSION These results show that farms are an important reservoir of colistin-resistant E. coli as well as other antimicrobial resistance genes such as ESBL genes. Transfer of manure from animals to soil and irrigation water might be disseminating a mix of multiple resistances, posing a worrying threat to human health.
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Dafopoulou K, Vourli S, Tsakris A, Pournaras S. An update on polymyxin susceptibility testing methods for Acinetobacter baumannii. Expert Rev Anti Infect Ther 2019; 17:699-713. [DOI: 10.1080/14787210.2019.1667230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Konstantina Dafopoulou
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Greece
- Laboratory of Clinical Microbiology, Attikon University Hospital, Athens, Greece
| | - Sophia Vourli
- Laboratory of Clinical Microbiology, Attikon University Hospital, Athens, Greece
| | - Athanasios Tsakris
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Greece
| | - Spyros Pournaras
- Department of Microbiology, Medical School, National and Kapodistrian University of Athens, Greece
- Laboratory of Clinical Microbiology, Attikon University Hospital, Athens, Greece
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Li Z, Cao Y, Yi L, Liu JH, Yang Q. Emergent Polymyxin Resistance: End of an Era? Open Forum Infect Dis 2019; 6:5550895. [PMID: 31420655 PMCID: PMC6767968 DOI: 10.1093/ofid/ofz368] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Indexed: 12/03/2022] Open
Abstract
Until recently, the polymyxin antibiotics were used sparingly due to dose limiting toxicities. However, the lack of therapeutic alternatives for infections caused by highly resistant Gram-negative bacteria has led to the increased use of the polymyxins. Unfortunately, the world has witnessed increased rates of polymyxin resistance in the last decade, which is likely in part due to its irrational use in human and veterinary medicine. The spread of polymyxin resistance has been aided by the dissemination of the transferable polymyxin-resistance gene, mcr, in humans and the environment. The mortality of colistin-resistant bacteria (CoRB) infections varies in different reports. However, poor clinical outcome was associated with prior colistin treatment, illness severity, complications, and multidrug resistance. Detection of polymyxin resistance in the clinic is possible through multiple robust and practical tests, including broth microdilution susceptibility testing, chromogenic agar testing, and molecular biology assays. There are multiple risk factors that increase a person’s risk for infection with a polymyxin-resistant bacteria, including age, prior colistin treatment, hospitalization, and ventilator support. For patients that are determined to be infected by polymyxin-resistant bacteria, various antibiotic treatment options currently exist. The rising trend of polymyxin resistance threatens patient care and warrants effective control.
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Affiliation(s)
- Zekun Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuping Cao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lingxian Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jian-Hua Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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Lalaoui R, Djukovic A, Bakour S, Sanz J, Gonzalez-Barbera EM, Salavert M, López-Hontangas JL, Sanz MA, Xavier KB, Kuster B, Debrauwer L, Ubeda C, Rolain JM. Detection of plasmid-mediated colistin resistance, mcr-1 gene, in Escherichia coli isolated from high-risk patients with acute leukemia in Spain. J Infect Chemother 2019; 25:605-609. [PMID: 31023570 DOI: 10.1016/j.jiac.2019.03.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND Bacterial infections in immunocompromised patients are associated with a high mortality and morbidity rate. In this high-risk group, the presence of multidrug-resistant (MDR) bacteria, particularly bacteria that harbor a transferable antibiotic resistance gene, complicates the management of bacterial infections. In this study, we investigated the presence of the transferable colistin resistance mcr genes in patients with leukemia in Spain. METHODS 217 fecal samples collected in 2013-2015 from 56 patients with acute leukemia and colonized with MDR Enterobacteriaceae strains, were screened on September 2017 for the presence of the colistin resistance mcr genes (mcr-1 to -5) by multiplex PCR. mcr positive strains selected on LBJMR and MacConkey supplemented with colistin (2 μg/ml) media were phenotypically and molecularly characterized by antimicrobial susceptibility testing, minimum inhibitory concentration, multilocus sequence typing and plasmid characterization. RESULTS Among 217 fecal samples, 5 samples collected from 3 patients were positive for the presence of the mcr-1 colistin-resistance gene. Four Escherichia coli strains were isolated and exhibited resistance to colistin with MIC = 4 μg/ml. Other genes conferring the resistance to β-lactam antibiotics have also been identified in mcr-1 positive strains, including blaTEM-206 and blaTEM-98. Three different sequence types were identified, including ST1196, ST140 and ST10. Plasmid characterization allowed us to detect the mcr-1 colistin resistance gene on conjugative IncP plasmid type. CONCLUSION To the best of our knowledge, we have identified the mcr-1 gene for the first time in leukemia patients in Spain. In light of these results, strict measures have been implemented to prevent its dissemination.
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Affiliation(s)
- Rym Lalaoui
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Ana Djukovic
- Centro Superior de Investigación en Salud Pública - FISABIO, Valencia, Spain
| | - Sofiane Bakour
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France
| | - Jaime Sanz
- Department of Medicine, Hospital Universitari i Politecnic La Fe, University of Valencia, and Centro de Investigación Biomédica en Red de Cáncer, Instituto Carlos III, Valencia, Spain
| | | | | | | | - Miguel A Sanz
- Department of Medicine, Hospital Universitari i Politecnic La Fe, University of Valencia, and Centro de Investigación Biomédica en Red de Cáncer, Instituto Carlos III, Valencia, Spain
| | | | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Munich, Germany; Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technische Universität München, Gregor-Mendel-Strasse 4, 85354 Freising, Germany
| | - Laurent Debrauwer
- Toxalim, Université de Toulouse, INRA, INP-ENVT, INP-EI-Purpan, Université de Toulouse 3 Paul Sabatier, F-31027, Toulouse, France; Axiom Platform, UMR 1331 Toxalim, MetaToul-MetaboHUB, National Infrastructure of Metabolomics and Fluxomics, F-31027, Toulouse, France
| | - Carles Ubeda
- Centro Superior de Investigación en Salud Pública - FISABIO, Valencia, Spain; Centers of Biomedical Research Network (CIBER) in Epidemiology and Public Health, Madrid, Spain
| | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, Marseille, France; IHU-Méditerranée Infection, Marseille, France.
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Bardet L, Okdah L, Le Page S, Baron SA, Rolain JM. Comparative evaluation of the UMIC Colistine kit to assess MIC of colistin of gram-negative rods. BMC Microbiol 2019; 19:60. [PMID: 30885126 PMCID: PMC6421643 DOI: 10.1186/s12866-019-1424-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/21/2019] [Indexed: 12/11/2022] Open
Abstract
Background The recent description of the first plasmid-mediated colistin-resistant gene mcr-1, conferring transferable and low-level resistance to colistin, raised concern about the need to implement a rapid and reliable screening method to detect colistin-resistant clinical isolates. The only valid method to assess the MIC of colistin is the broth microdilution according to the joint CLSI-EUCAST Polymyxin Breakpoints Working Group. UMIC Colistine is a ready-to-use broth microdilution kit developed to easily assess colistin MIC by proposing unitary polystyrene strips containing 11 concentrations of dehydrated colistin. Here, we evaluated the UMIC Colistine kit on 235 Gram-negative rods (176 Enterobacterales, including 70 harboring a mcr gene, and 59 non-fermentative), through comparison to the reference broth microdilution method prepared in accordance with EN ISO 20776-1:2006 standard. Reproducibility of the UMIC Colistine was assayed with the three recommended quality control strains E. coli ATCC 25922, E. coli NCTC 13846 (mcr-1 positive), and P. aeruginosa ATCC 27853, as for stability testing. Results Categorical agreement was 100% with 63.4% (n = 149) of colistin-resistant strains, and 36.6% (n = 86) of colistin-susceptible strains with both methods (S ≤ 2 μg/mL and R > 2 μg/mL). No major error or very major error was reported. Essential agreement was 94.0% (n = 221), and 100% for detection of colistin-resistant strains as compared to the reference method. Pearson’s correlation between UMIC Colistine and the reference method was 0.98. Reproducibility of the UMIC Colistine system was 97.8% with MICs of the quality control strains within the target ranges. However, some isolates had lower MIC with UMIC Colistine, but that did not change their categorization as colistin-susceptible, and this phenomenon should be further explored. Conclusions The UMIC Colistine kit is an easy to perform unitary device that showed excellent results when compared to the reference method. The UMIC Colistine system is a rapid and reliable broth microdilution method that is suitable to assess the colistin MIC of clinical isolates in clinical microbiology laboratories.
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Affiliation(s)
- Lucie Bardet
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Liliane Okdah
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Stéphanie Le Page
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | | | - Jean-Marc Rolain
- Aix Marseille Univ, IRD, APHM, MEPHI, IHU-Méditerranée Infection, Marseille, France. .,IHU-Méditerranée Infection, Marseille, France.
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Bardet L, Rolain JM. Development of New Tools to Detect Colistin-Resistance among Enterobacteriaceae Strains. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2018; 2018:3095249. [PMID: 30631384 PMCID: PMC6305056 DOI: 10.1155/2018/3095249] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/11/2018] [Indexed: 12/27/2022]
Abstract
The recent discovery of the plasmid-mediated mcr-1 gene conferring resistance to colistin is of clinical concern. The worldwide screening of this resistance mechanism among samples of different origins has highlighted the urgent need to improve the detection of colistin-resistant isolates in clinical microbiology laboratories. Currently, phenotypic methods used to detect colistin resistance are not necessarily suitable as the main characteristic of the mcr genes is the low level of resistance that they confer, close to the clinical breakpoint recommended jointly by the CLSI and EUCAST expert systems (S ≤ 2 mg/L and R > 2 mg/L). In this context, susceptibility testing recommendations for polymyxins have evolved and are becoming difficult to implement in routine laboratory work. The large number of mechanisms and genes involved in colistin resistance limits the access to rapid detection by molecular biology. It is therefore necessary to implement well-defined protocols using specific tools to detect all colistin-resistant bacteria. This review aims to summarize the current clinical microbiology diagnosis techniques and their ability to detect all colistin resistance mechanisms and describe new tools specifically developed to assess plasmid-mediated colistin resistance. Phenotyping, susceptibility testing, and genotyping methods are presented, including an update on recent studies related to the development of specific techniques.
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Affiliation(s)
- Lucie Bardet
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, IRD, AP-HM, MEPHI, IHU-Méditerranée Infection, Marseille, France
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Osei Sekyere J. Mcr colistin resistance gene: a systematic review of current diagnostics and detection methods. Microbiologyopen 2018; 8:e00682. [PMID: 29974640 PMCID: PMC6530528 DOI: 10.1002/mbo3.682] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 05/21/2018] [Accepted: 06/07/2018] [Indexed: 11/23/2022] Open
Abstract
Resistance to colistin, mediated by chromosomal mutations and more recently, by plasmid‐borne mcr genes, is increasingly being reported in bacterial isolates taken from humans, animals, farms, foods, and the environment. To easily identify and contain this quickly spreading menace, efficient diagnostics that are cheaper, faster, simpler, sensitive, and specific have become indispensable and urgently necessary. A thorough and systematic review of the literature available at Pubmed, ScienceDirect and Web of Science was thus undertaken to identify articles describing novel and efficient colistin resistance‐ and mcr gene‐detecting methods. From the final 23 studies included in this review, both phenotypic and molecular tests were found. The phenotypic tests consisted of novel culture media viz., SuperPolymyxin™, CHROMagar COL‐APSE and LBJMR media, commercial automated MIC‐determining instruments such as MICRONAUT‐S, Vitek 2, BD Phoenix, Sensititre and MicroScan, and novel assays such as Colistin MAC test, Colispot, rapid polymxin NP test (RPNP), alteration of Zeta potential, modified RPNP test, MICRONAUT‐MIC Strip, MIC Test Strip, UMIC System, and Sensitest™ Colistin. Molecular diagnostics consisted of the CT103XL microarray, eazyplex® SuperBug kit, and Taqman®/SYBR Green® real‐time PCR assays, with 100% sensitivity and specificity plus a shorter turnaround time (<3 hr). Based on the sensitivity, specificity, cost, required skill and turnaround time, the RPNP test and/or novel culture media is recommended for under‐resourced laboratories while the Multiplex PCR or Taqman®/SYBR Green® real‐time PCR assay alongside the RPNP or novel culture media is suggested for well‐resourced ones.
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Affiliation(s)
- John Osei Sekyere
- Department of Pharmaceutics, Faculty of Pharmacy and Pharmaceutical Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Medical Microbiology, Prinshof Medical School Campus, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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