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Huang J, Yue H, Wei W, Shan J, Zhu Y, Feng L, Ma Y, Zou B, Wu H, Zhou G. FARPA-based tube array coupled with quick DNA extraction enables ultra-fast bedside detection of antibiotic-resistant pathogens. Analyst 2024; 149:3607-3614. [PMID: 38767613 DOI: 10.1039/d4an00185k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Rapid and accurate detection of pathogens and antimicrobial-resistant (AMR) genes of the pathogens are crucial for the clinical diagnosis and effective treatment of infectious diseases. However, the time-consuming steps of conventional culture-based methods inhibit the precise and early application of anti-infection therapy. For the prompt treatment of pathogen-infected patients, we have proposed a novel tube array strategy based on our previously reported FARPA (FEN1-aided recombinase polymerase amplification) principle for the ultra-fast detection of antibiotic-resistant pathogens on site. The entire process from "sample to result" can be completed in 25 min by combining quick DNA extraction from a urine sample with FARPA to avoid the usually complicated DNA extraction step. Furthermore, a 36-tube array made from commercial 384-well titre plates was efficiently introduced to perform FARPA in a portable analyser, achieving an increase in the loading sample throughput (from several to several tens), which is quite suitable for the point-of-care testing (POCT) of multiple pathogens and multiple samples. Finally, we tested 92 urine samples to verify the performance of our proposed method. The sensitivities for the detection of E. coli, K. pneumoniae, E. faecium, and E. faecalis were 92.7%, 93.8%, 100% and 88.9%, respectively. The specificities for the detection of the four pathogens were 100%. Consequently, our rapid, low-cost and user-friendly POCT method holds great potential for guiding the rational use of antibiotics and reducing bacterial resistance.
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Affiliation(s)
- Jinling Huang
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
| | - Huijie Yue
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Wei Wei
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Jingwen Shan
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Yue Zhu
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Liying Feng
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Yi Ma
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Bingjie Zou
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Key Laboratory of Drug Quality Control and Pharmacovigilance of Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, 510515, China.
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, Affiliated Hospital of Medical School, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing, 210002, China
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Roque-Borda CA, Primo LMDG, Franzyk H, Hansen PR, Pavan FR. Recent advances in the development of antimicrobial peptides against ESKAPE pathogens. Heliyon 2024; 10:e31958. [PMID: 38868046 PMCID: PMC11167364 DOI: 10.1016/j.heliyon.2024.e31958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Multi-drug resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) are a global health threat. The severity of the problem lies in its impact on mortality, therapeutic limitations, the threat to public health, and the costs associated with managing infections caused by these resistant strains. Effectively addressing this challenge requires innovative approaches to research, the development of new antimicrobials, and more responsible antibiotic use practices globally. Antimicrobial peptides (AMPs) are a part of the innate immune system of all higher organisms. They are short, cationic and amphipathic molecules with broad-spectrum activity. AMPs interact with the negatively charged bacterial membrane. In recent years, AMPs have attracted considerable interest as potential antibiotics. However, AMPs have low bioavailability and short half-lives, which may be circumvented by chemical modification. This review presents recent in vitro and in silico strategies for the modification of AMPs to improve their stability and application in preclinical experiments.
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Affiliation(s)
- Cesar Augusto Roque-Borda
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, Brazil
- Universidad Católica de Santa María, Vicerrectorado de Investigación, Arequipa, Peru
| | | | - Henrik Franzyk
- University of Copenhagen, Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, Denmark
| | - Paul Robert Hansen
- University of Copenhagen, Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology, Denmark
| | - Fernando Rogério Pavan
- São Paulo State University (UNESP), Tuberculosis Research Laboratory, School of Pharmaceutical Sciences, Araraquara, Brazil
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Marrs ECL, Milburn O, Eltringham GJ, Fenwick DJC, Orenga S, Hazırolan G, Zarakolu P, Perry JD. The Use of CHROMID ® Colistin R for the Detection of Colistin-Resistant Gram-Negative Bacteria in Positive Blood Cultures. Antibiotics (Basel) 2024; 13:246. [PMID: 38534681 DOI: 10.3390/antibiotics13030246] [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: 02/19/2024] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/28/2024] Open
Abstract
The aim of this study was to assess the utility of CHROMID® Colistin R for direct detection of colistin-resistant Gram-negative bacteria from positive blood cultures. A total of 390 blood cultures from hospitalised patients containing Gram-negative bacteria were included in this study. These blood cultures were referred to clinical laboratories in the United Kingdom and Türkiye. A further 16 simulated positive blood culture bottles were included that contained a range of colistin-resistant strains as well as susceptible control strains. Fluid from each positive blood culture was diluted 1/200 in saline and 10 µL aliquots cultured onto cystine-lactose-electrolyte-deficient agar and CHROMID® Colistin R. All recovered bacteria were identified, and for Gram-negative bacteria, their minimum inhibitory concentration of colistin was measured using the broth microdilution method. From a total of 443 Gram-negative isolates, 57 colistin-resistant isolates were recovered, of which 53 (93%) grew on CHROMID® Colistin R within 18 h. Of the 377 isolates determined to be colistin-susceptible, only 9 isolates were able to grow, including 6 isolates of Pseudomonas aeruginosa. For positive blood cultures that are shown to contain Gram-negative bacteria, culture on CHROMID® Colistin R is a useful diagnostic tool to detect susceptibility or resistance to colistin within 18 h.
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Affiliation(s)
- Emma C L Marrs
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Olivia Milburn
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | - Gary J Eltringham
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
| | | | - Sylvain Orenga
- Research & Development Microbiology, bioMérieux SA, 38 390 La Balme-les-Grottes, France
| | - Gulsen Hazırolan
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06230, Türkiye
| | - Pinar Zarakolu
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06230, Türkiye
| | - John D Perry
- Microbiology Department, Freeman Hospital, Newcastle upon Tyne NE7 7DN, UK
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Lim AL, Miller BW, Lin Z, Fisher MA, Barrows LR, Haygood MG, Schmidt EW. Resistance mechanisms for Gram-negative bacteria-specific lipopeptides, turnercyclamycins, differ from that of colistin. Microbiol Spectr 2023; 11:e0230623. [PMID: 37882570 PMCID: PMC10714751 DOI: 10.1128/spectrum.02306-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/13/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Bacterial resistance to antibiotics is a crisis. Acinetobacter baumannii is among the CDC urgent threat pathogens in part for this reason. Lipopeptides known as turnercyclamycins are produced by symbiotic bacteria that normally live in marine mollusks, where they may be involved in shaping their symbiotic niche. Turnercyclamycins killed Gram-negative pathogens including drug-resistant Acinetobacter, but how do the mechanisms of resistance compare to other lipopeptide drugs? Here, we define resistance from a truncation of MlaA, a protein involved in regulating bacterial membrane phospholipids. Intriguingly, this resistance mechanism only affected one turnercyclamycin variant, which differed only in two atoms in the lipid tail of the compounds. We could not obtain significant resistance to the second turnercyclamycin variant, which was also effective in an infection model. This study reveals an unexpected subtlety in resistance to lipopeptide antibiotics, which may be useful in the design and development of antibiotics to combat drug resistance.
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Affiliation(s)
- Albebson L. Lim
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Bailey W. Miller
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Mark A. Fisher
- Department of Pathology and ARUP Laboratories, University of Utah, Salt Lake City, Utah, USA
| | - Louis R. Barrows
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah, USA
| | - Margo G. Haygood
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, USA
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, Utah, 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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Lu C, Wang J, Pan L, Gu X, Lu W, Chen D, Zhang C, Ye Q, Xiao C, Liu P, Tang Y, Tang B, Huang G, Fang J, Jiang H. Rapid detection of multiple resistance genes to last-resort antibiotics in Enterobacteriaceae pathogens by recombinase polymerase amplification combined with lateral flow dipstick. Front Microbiol 2023; 13:1062577. [PMID: 36687650 PMCID: PMC9850091 DOI: 10.3389/fmicb.2022.1062577] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 12/12/2022] [Indexed: 01/07/2023] Open
Abstract
The worrying emergence of multiple resistance genes to last-resort antibiotics in food animals and human populations throughout the food chain and relevant environments has been increasingly reported worldwide. Enterobacteriaceae pathogens are considered the most common reservoirs of such antibiotic resistance genes (ARGs). Thus, a rapid, efficient and accurate detection method to simultaneously screen and monitor such ARGs in Enterobacteriaceae pathogens has become an urgent need. Our study developed a recombinase polymerase amplification (RPA) assay combined with a lateral flow dipstick (LFD) for simultaneously detecting predominant resistance genes to last-resort antibiotics of Enterobacteriaceae pathogens, including mcr-1, blaNDM-1 and tet(X4). It is allowed to complete the entire process, including crude DNA extraction, amplification as well as reading, within 40 min at 37°C, and the detection limit is 101 copies/μl for mcr-1, blaNDM-1 and tet(X4). Sensitivity analysis showed obvious association of color signals with the template concentrations of mcr-1, blaNDM-1 and tet(X4) genes in Enterobacteriaceae pathogens using a test strip reader (R 2 = 0.9881, R 2 = 0.9745, and R 2 = 0.9807, respectively), allowing for quantitative detection using multiplex RPA-LFD assays. Therefore, the RPA-LFD assay can suitably help to detect multiple resistance genes to last-resort antibiotics in foodborne pathogens and has potential applications in the field.
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Affiliation(s)
- Chenze Lu
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Jingwen Wang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Leiming Pan
- Zhejiang Hongzheng Testing Co., Ltd, Ningbo, Zhejiang, China
| | - Xiuying Gu
- Zhejiang Gongzheng Testing Center Co., Ltd, Hangzhou, Zhejiang, China
| | - Wenjing Lu
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Di Chen
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Cen Zhang
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Qin Ye
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Chaogeng Xiao
- Institute of Food Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Pengpeng Liu
- Key Laboratory of Biosafety Detection for Zhejiang Market Regulation, Zhejiang Fangyuan Testing Group LO.T, Hangzhou, Zhejiang, China
| | - Yulong Tang
- Hangzhou Tiannie Technology Co., Ltd, Hangzhou, Zhejiang, China
| | - Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products and Institute of Agro-Product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Guangrong Huang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China
| | - Jiehong Fang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China,*Correspondence: Jiehong Fang, ✉
| | - Han Jiang
- Key Laboratory of Specialty Agri-Products Quality and Hazard Controlling Technology of Zhejiang Province, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, China,Han Jiang, ✉
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Anyanwu MU, Jaja IF, Nwobi OC, Mgbeahuruike AC, Ikpendu CN, Okafor NA, Oguttu JW. Epidemiology and Traits of Mobile Colistin Resistance ( mcr) Gene-Bearing Organisms from Horses. Microorganisms 2022; 10:microorganisms10081499. [PMID: 35893557 PMCID: PMC9394310 DOI: 10.3390/microorganisms10081499] [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: 06/30/2022] [Revised: 07/18/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
Mobile colistin resistance (mcr) genes (mcr-1 to mcr-10) threaten the efficacy of colistin (COL), a polymyxin antibiotic that is used as a last-line agent for the treatment of deadly infections caused by multidrug-resistant and extensively drug-resistant bacteria in humans and animals. COL has been used for more than 60 years for the prophylactic control and treatment of infections in livestock husbandry but not in horses. Polymyxin B is used for the prophylactic control and empirical treatment of infections in horses without conducting sensitivity tests. The lack of sensitivity testing exerts selection pressure for the acquisition of the mcr gene. By horizontal transfer, mcr-1, mcr-5, and mcr-9 have disseminated among horse populations globally and are harbored by Escherichia coli, Klebsiella, Enterobacter, Citrobacter, and Salmonella species. Conjugative plasmids, insertion sequences, and transposons are the backbone of mcr genes in the isolates, which co-express genes conferring multi- to extensive-drug resistance, including genes encoding extended-spectrum β-lactamase, ampicillinase C, fosfomycin, and fluoroquinolone resistance, and virulence genes. The transmission of mcr genes to/among bacterial strains of equine origin is non-clonal. Contact with horses, horse manure, feed/drinking water, farmers, farmers’ clothing/farm equipment, the consumption of contaminated horse meat and its associated products, and the trading of horses, horse meat, and their associated products are routes for the transmission of mcr-gene-bearing bacteria in, to, and from the equine industry.
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Affiliation(s)
- Madubuike Umunna Anyanwu
- Microbiology Unit, Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka 400001, Nigeria;
- Correspondence: (M.U.A.); (I.F.J.); Tel.: +27-78-549-2098 (I.F.J.); Fax: +27-86-770-6869 (I.F.J.)
| | - Ishmael Festus Jaja
- Department of Agriculture and Animal Health, Florida Campus, University of South Africa, Johannesburg 1709, South Africa;
- Correspondence: (M.U.A.); (I.F.J.); Tel.: +27-78-549-2098 (I.F.J.); Fax: +27-86-770-6869 (I.F.J.)
| | - Obichukwu Chisom Nwobi
- Department of Veterinary Public Health and Preventive Medicine, University of Nigeria, Nsukka 400001, Nigeria;
| | | | - Chinaza Nnenna Ikpendu
- Department of Veterinary Microbiology, Michael Okpara University of Agriculture, Umudike 440101, Nigeria;
| | | | - James Wabwire Oguttu
- Department of Agriculture and Animal Health, Florida Campus, University of South Africa, Johannesburg 1709, South Africa;
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Performance Evaluation of the VITEK2 and Sensititre Systems to Determine Colistin Resistance and MIC for Acinetobacter baumannii. Diagnostics (Basel) 2022; 12:diagnostics12061487. [PMID: 35741297 PMCID: PMC9221671 DOI: 10.3390/diagnostics12061487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 11/26/2022] Open
Abstract
Performances of the colistin antimicrobial susceptibility testing (AST) systems of Acinetobacter baumannii vary depending on the manufacturer, and data on colistin-resistant A. baumannii are limited. We evaluated the VITEK2 and Sensititre systems to determine colistin resistance and minimum inhibitory concentration (MIC) for A. baumannii isolated from a clinical microbiology laboratory. A total of 213 clinical A. baumannii isolates were tested, including 81 colistin-resistant A. baumannii. ASTs were performed using the VITEK2 and Sensititre systems according to the manufacturer’s instructions. Reference MICs for colistin were determined using the manual broth microdilution method (BMD). The results of the two AST methods were compared with the BMD results. VITEK2 and Sensititre systems showed category agreements of 95.3% and 99.1%, respectively. VITEK2 had a relatively high very major error (VME) rate (9.9%). Sensititre reported higher MICs than the reference method for the susceptible isolates and showed low essential agreement. In conclusion, the automated systems investigated in this study showed good category agreements for colistin AST of A. baumannii. However, VITEK2 had a high VME rate, and Sensititre had differences in MIC results. Colistin AST remains a challenging task in the clinical laboratory.
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A prospective matched case-control study on the genomic epidemiology of colistin-resistant Enterobacterales from Dutch patients. COMMUNICATIONS MEDICINE 2022; 2:55. [PMID: 35607432 PMCID: PMC9122983 DOI: 10.1038/s43856-022-00115-6] [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: 10/06/2021] [Accepted: 04/20/2022] [Indexed: 11/08/2022] Open
Abstract
Abstract
Background
Colistin is a last-resort treatment option for infections with multidrug-resistant Gram-negative bacteria. However, colistin resistance is increasing.
Methods
A six-month prospective matched case-control study was performed in which 22 Dutch laboratories with 32 associated hospitals participated. Laboratories were invited to send a maximum of five colistin-resistant Escherichia coli or Klebsiella pneumoniae (COLR-EK) isolates and five colistin-susceptible isolates (COLS-EK) to the reference laboratory, matched for patient location, material of origin and bacterial species. Epidemiological/clinical data were collected and included in the analysis. Characteristics of COLR-EK/COLS-EK isolates were compared using logistic regression with correction for variables used for matching. Forty-six ColR-EK/ColS-EK pairs were analysed by next-generation sequencing (NGS) for whole-genome multi-locus sequence typing and identification of resistance genes, including mcr genes. To identify chromosomal mutations potentially leading to colistin resistance, NGS reads were mapped against gene sequences of pmrAB, phoPQ, mgrB and crrB.
Results
In total, 72 COLR-EK/COLS-EK pairs (75% E. coli and 25% K. pneumoniae) were included. Twenty-one percent of COLR-EK patients had received colistin, in contrast to 3% of COLS-EK patients (OR > 2.9). Of COLR-EK isolates, five contained mcr-1 and two mcr-9. One isolate lost mcr-9 after repeated sub-culturing, but retained colistin resistance. Among 46 sequenced COLR-EK isolates, genetic diversity was large and 19 (41.3%) isolates had chromosomal mutations potentially associated with colistin resistance.
Conclusions
Colistin resistance is present but uncommon in the Netherlands and caused by the mcr gene in a minority of COLR-EK isolates. There is a need for surveillance of colistin resistance using appropriate susceptibility testing methods.
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