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Xu Y, Liu D, Han P, Wang H, Wang S, Gao J, Chen F, Zhou X, Deng K, Luo J, Zhou M, Kuang D, Yang F, Jiang Z, Xu S, Rao G, Wang Y, Qu J. Rapid inference of antibiotic resistance and susceptibility for Klebsiella pneumoniae by clinical shotgun metagenomic sequencing. Int J Antimicrob Agents 2024; 64:107252. [PMID: 38908534 DOI: 10.1016/j.ijantimicag.2024.107252] [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] [Received: 02/19/2024] [Revised: 05/14/2024] [Accepted: 06/07/2024] [Indexed: 06/24/2024]
Abstract
OBJECTIVES The study aimed to develop a genotypic antimicrobial resistance testing method for Klebsiella pneumoniae using metagenomic sequencing data. METHODS We utilized Lasso regression on assembled genomes to identify genetic resistance determinants for six antibiotics (Gentamicin, Tobramycin, Imipenem, Meropenem, Ceftazidime, Trimethoprim/Sulfamethoxazole). The genetic features were weighted, grouped into clusters to establish classifier models. Origin species of detected antibiotic resistant gene (ARG) was determined by novel strategy integrating "possible species," "gene copy number calculation" and "species-specific kmers." The performance of the method was evaluated on retrospective case studies. RESULTS Our study employed machine learning on 3928 K. pneumoniae isolates, yielding stable models with AUCs > 0.9 for various antibiotics. GenseqAMR, a read-based software, exhibited high accuracy (AUC 0.926-0.956) for short-read datasets. The integration of a species-specific kmer strategy significantly improved ARG-species attribution to an average accuracy of 96.67%. In a retrospective study of 191 K. pneumoniae-positive clinical specimens (0.68-93.39% genome coverage), GenseqAMR predicted 84.23% of AST results on average. It demonstrated 88.76-96.26% accuracy for resistance prediction, offering genotypic AST results with a shorter turnaround time (mean ± SD: 18.34 ± 0.87 hours) than traditional culture-based AST (60.15 ± 21.58 hours). Furthermore, a retrospective clinical case study involving 63 cases showed that GenseqAMR could lead to changes in clinical treatment for 24 (38.10%) cases, with 95.83% (23/24) of these changes deemed beneficial. CONCLUSIONS In conclusion, GenseqAMR is a promising tool for quick and accurate AMR prediction in Klebsiella pneumoniae, with the potential to improve patient outcomes through timely adjustments in antibiotic treatment.
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Affiliation(s)
- Yanping Xu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Donglai Liu
- National Institutes for Food and Drug Control, Beijing, China
| | - Peng Han
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Hao Wang
- National Institutes for Food and Drug Control, Beijing, China
| | - Shanmei Wang
- Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jianpeng Gao
- Genskey Medical Technology Co., Ltd, Beijing, China
| | | | - Xun Zhou
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Kun Deng
- Department of Laboratory Medicine, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiajie Luo
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Dai Kuang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Fan Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China; Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Zhi Jiang
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Sihong Xu
- National Institutes for Food and Drug Control, Beijing, China.
| | - Guanhua Rao
- Genskey Medical Technology Co., Ltd, Beijing, China.
| | - Youchun Wang
- National Institutes for Food and Drug Control, Beijing, China.
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China.
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Rodoplu Solovchuk D. Advances in AI-assisted biochip technology for biomedicine. Biomed Pharmacother 2024; 177:116997. [PMID: 38943990 DOI: 10.1016/j.biopha.2024.116997] [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] [Received: 04/24/2024] [Revised: 06/13/2024] [Accepted: 06/15/2024] [Indexed: 07/01/2024] Open
Abstract
The integration of biochips with AI opened up new possibilities and is expected to revolutionize smart healthcare tools within the next five years. The combination of miniaturized, multi-functional, rapid, high-throughput sample processing and sensing capabilities of biochips, with the computational data processing and predictive power of AI, allows medical professionals to collect and analyze vast amounts of data quickly and efficiently, leading to more accurate and timely diagnoses and prognostic evaluations. Biochips, as smart healthcare devices, offer continuous monitoring of patient symptoms. Integrated virtual assistants have the potential to send predictive feedback to users and healthcare practitioners, paving the way for personalized and predictive medicine. This review explores the current state-of-the-art biochip technologies including gene-chips, organ-on-a-chips, and neural implants, and the diagnostic and therapeutic utility of AI-assisted biochips in medical practices such as cancer, diabetes, infectious diseases, and neurological disorders. Choosing the appropriate AI model for a specific biomedical application, and possible solutions to the current challenges are explored. Surveying advances in machine learning models for biochip functionality, this paper offers a review of biochips for the future of biomedicine, an essential guide for keeping up with trends in healthcare, while inspiring cross-disciplinary collaboration among biomedical engineering, medicine, and machine learning fields.
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Affiliation(s)
- Didem Rodoplu Solovchuk
- Institute of Biomedical Engineering and Nanomedicine, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan.
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Guo J, Sun D, Li K, Dai Q, Geng S, Yang Y, Mo M, Zhu Z, Shao C, Wang W, Song J, Yang C, Zhang H. Metabolic Labeling and Digital Microfluidic Single-Cell Sequencing for Single Bacterial Genotypic-Phenotypic Analysis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2402177. [PMID: 39077951 DOI: 10.1002/smll.202402177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/23/2024] [Indexed: 07/31/2024]
Abstract
Accurate assessment of phenotypic and genotypic characteristics of bacteria can facilitate comprehensive cataloguing of all the resistance factors for better understanding of antibiotic resistance. However, current methods primarily focus on individual phenotypic or genotypic profiles across different colonies. Here, a Digital microfluidic-based automated assay for whole-genome sequencing of single-antibiotic-resistant bacteria is reported, enabling Genotypic and Phenotypic Analysis of antibiotic-resistant strains (Digital-GPA). Digital-GPA can efficiently isolate and sequence antibiotic-resistant bacteria illuminated by fluorescent D-amino acid (FDAA)-labeling, producing high-quality single-cell amplified genomes (SAGs). This enables identifications of both minor and major mutations, pinpointing substrains with distinctive resistance mechanisms. Digital-GPA can directly process clinical samples to detect and sequence resistant pathogens without bacterial culture, subsequently provide genetic profiles of antibiotic susceptibility, promising to expedite the analysis of hard-to-culture or slow-growing bacteria. Overall, Digital-GPA opens a new avenue for antibiotic resistance analysis by providing accurate and comprehensive molecular profiles of antibiotic resistance at single-cell resolution.
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Affiliation(s)
- Junnan Guo
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
| | - Di Sun
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Kunjie Li
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
| | - Qi Dai
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
| | - Shichen Geng
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
| | - Yuanyuan Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
| | - Mengwu Mo
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
| | - Zhi Zhu
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
| | - Chen Shao
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jia Song
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200092, China
| | - Chaoyong Yang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Huimin Zhang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, School of Life Sciences, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Xiamen University, Xiamen, 361005, China
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Cui HS, Wu ZR, Shi XY, Dong GQ, Ding SN, Bao N, Yu CM, Wu ZQ. CS/PVP Hydrogel-Based Nanocapillary for Monitoring Bacterial Growth and Rapid Antibiotic Susceptibility Testing. ACS Sens 2024; 9:3540-3548. [PMID: 38908004 DOI: 10.1021/acssensors.4c00381] [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: 06/24/2024]
Abstract
Infection with drug-resistant bacteria poses a significant threat to human health. Judicious use of antibiotics could reduce the likelihood of bacterial resistance, which can be evaluated through antibiotic susceptibility testing (AST). This paper focuses on the application of a needle-like nanocapillary tip filled with chitosan (CS)/polyethylene pyrrolidone (PVP) hydrogel based on its specific pH-sensitive properties. The gel-filled nanocapillary has the potential to be used for electrical pH detection with a sensitivity of 3.06 nA/pH and a linear range from 7.3 to 4.3. Such sensitivity for pH measurement could be extended for monitoring of bacterial (such as Escherichia coli and Streptococcus salivarius) growth because of the relationship between pH and bacterial growth. Bacterial growth curves obtained using the hydrogel-filled nanocapillary showed good agreement with the OD600 method. Moreover, this device could be applied for rapid AST for tetracycline and norfloxacin on E. coli with minimum inhibitory concentrations of 2 and 0.125 μg/mL, respectively. This study expands the application of the hydrogel-based nanocapillary for bacterial research by monitoring changes in pH values.
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Affiliation(s)
- Hai-Shan Cui
- School of Public Health, Nantong University, Nantong, Jiangsu 226019, China
| | - Zhang-Rong Wu
- School of Public Health, Nantong University, Nantong, Jiangsu 226019, China
| | - Xiao-Yan Shi
- Nantong Stomatological Hospital, Nantong, Jiangsu 226019, China
| | - Gang-Qiang Dong
- Amway (China) Botanical R&D Center, Wuxi, Jiangsu 214115, China
| | - Shou-Nian Ding
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, Jiangsu 211189, China
| | - Ning Bao
- School of Public Health, Nantong University, Nantong, Jiangsu 226019, China
| | - Chun-Mei Yu
- School of Public Health, Nantong University, Nantong, Jiangsu 226019, China
| | - Zeng-Qiang Wu
- School of Public Health, Nantong University, Nantong, Jiangsu 226019, China
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Glen KA, Lamont IL. Penicillin-binding protein 3 sequence variations reduce susceptibility of Pseudomonas aeruginosa to β-lactams but inhibit cell division. J Antimicrob Chemother 2024:dkae203. [PMID: 39001778 DOI: 10.1093/jac/dkae203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/03/2024] [Indexed: 07/15/2024] Open
Abstract
BACKGROUND β-lactam antibiotics, which inhibit penicillin-binding protein 3 (PBP3) that is required for cell division, play a key role in treating P. aeruginosa infections. Some sequence variations in PBP3 have been associated with β-lactam resistance but the effects of variations on antibiotic susceptibility and on cell division have not been quantified. Antibiotic efflux can also reduce susceptibility. OBJECTIVES To quantify the effects of PBP3 variations on β-lactam susceptibility and cell morphology in P. aeruginosa. METHODS Nineteen PBP3 variants were expressed from a plasmid in the reference strain P. aeruginosa PAO1 and genome engineering was used to construct five mutants expressing PBP3 variants from the chromosome. The effects of the variations on β-lactam minimum inhibitory concentration (MIC) and cell morphology were measured. RESULTS Some PBP3 variations reduced susceptibility to a variety of β-lactam antibiotics including meropenem, ceftazidime, cefepime and ticarcillin with different variations affecting different antibiotics. None of the tested variations reduced susceptibility to imipenem or piperacillin. Antibiotic susceptibility was further reduced when PBP3 variants were expressed in mutant bacteria overexpressing the MexAB-OprM efflux pump, with some variations conferring clinical levels of resistance. Some PBP3 variations, and sub-MIC levels of β-lactams, reduced bacterial growth rates and inhibited cell division, causing elongated cells. CONCLUSIONS PBP3 variations in P. aeruginosa can increase the MIC of multiple β-lactam antibiotics, although not imipenem or piperacillin. PBP3 variations, or the presence of sub-lethal levels of β-lactams, result in elongated cells indicating that variations reduce the activity of PBP3 and may reduce bacterial fitness.
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Affiliation(s)
- Karl A Glen
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Iain L Lamont
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
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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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Dias MC, Alpizar-Jara R, Lavrador C, Marques C, Broens EM, Duarte EL. Companion Animal Owners' Knowledge, Attitudes and Perceptions Regarding Antibiotic Use in Portugal. Antibiotics (Basel) 2024; 13:533. [PMID: 38927199 PMCID: PMC11201214 DOI: 10.3390/antibiotics13060533] [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: 05/08/2024] [Revised: 06/03/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
While multiple studies have focused on the motivations surrounding antibiotic prescription among veterinarians, little is known about companion animal owners' knowledge, attitude and perception (KAP) regarding the topic. A nationwide survey directed toward Portuguese dog and cat owners was conducted online and at veterinary practices to characterize their KAP regarding antibiotics. After database curation, a total of 423 valid submissions were considered. Although 97.9% of respondents stated that they knew what an antibiotic was, 23.5% and 19.2% answered that they were used to treat viral and fungal infections, respectively. Antimicrobial effectiveness was favored over cost when 87.7% of owners agreed they would prefer to spend more money to identify the appropriate antibiotic. Around 87% of respondents recognized antibiotic resistance as a significant health problem and 74.6% strongly agreed/somewhat agreed that antibiotic use in pets may contribute to resistance development. However, only 25.3% recognized that this could promote resistance dissemination, showing little awareness of the interconnection between human and animal health. Moreover, 55.6% of respondents were neutral when asked whether antibiotics used in veterinary medicine were also important for humans. These findings suggest that communication between veterinarians and pet owners can still be improved to further clarify the impact that antibiotic use has in pets from a One-Health perspective, also enabling antimicrobial stewardship interventions.
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Affiliation(s)
- Margarida Correia Dias
- Department of Veterinary Medicine, School of Science and Technology, Universidade de Évora, 7004-516 Évora, Portugal; (C.L.)
- MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, Universidade de Évora, 7004-516 Évora, Portugal
| | - Russell Alpizar-Jara
- Department of Mathematics, School of Science and Technology & CIMA Research Centre in Mathematics and Applications, Universidade de Évora, 7004-516 Évora, Portugal
| | - Catarina Lavrador
- Department of Veterinary Medicine, School of Science and Technology, Universidade de Évora, 7004-516 Évora, Portugal; (C.L.)
- MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, Universidade de Évora, 7004-516 Évora, Portugal
| | - Cátia Marques
- Faculty of Veterinary Medicine, Lusófona University, 376 Campo Grande, 1749-024 Lisbon, Portugal;
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), CECAV—Animal and Veterinary Research Centre, University of Trás-os-Montes and Alto Douro, Quinta de Prados, 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), Centre for Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
- Genevet, Diagnostic Laboratory and ECVM Satellite Training Center, 1495-191 Carnaxide, Portugal
| | - Els M. Broens
- Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, 3584 CS Utrecht, The Netherlands
| | - Elsa L. Duarte
- Department of Veterinary Medicine, School of Science and Technology, Universidade de Évora, 7004-516 Évora, Portugal; (C.L.)
- MED–Mediterranean Institute for Agriculture, Environment and Development & CHANGE–Global Change and Sustainability Institute, Universidade de Évora, 7004-516 Évora, Portugal
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Cheng ZH, Luo XY, Liu DF, Han J, Wang HD, Min D, Yu HQ. Optimized Antibiotic Resistance Genes Monitoring Scenarios Promote Sustainability of Urban Water Cycle. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:9636-9645. [PMID: 38770702 DOI: 10.1021/acs.est.4c02048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Dissemination of antibiotic resistance genes (ARGs) in urban water bodies has become a significant environmental and health concern. Many approaches based on real-time quantitative PCR (qPCR) have been developed to offer rapid and highly specific detection of ARGs in water environments, but the complicated and time-consuming procedures have hindered their widespread use. Herein, we developed a facile one-step approach for rapid detection of ARGs by leveraging the trans-cleavage activity of Cas12a and recombinase polymerase amplification (RPA). This efficient method matches the sensitivity and specificity of qPCR and requires no complex equipment. The results show a strong correlation between the prevalence of four ARG markers (ARGs: sul1, qnrA-1, mcr-1, and class 1 integrons: intl1) in tap water, human urine, farm wastewater, hospital wastewater, municipal wastewater treatment plants (WWTPs), and proximate natural aquatic ecosystems, indicating the circulation of ARGs within the urban water cycle. Through monitoring the ARG markers in 18 WWTPs in 9 cities across China during both peak and declining stages of the COVID epidemic, we found an increased detection frequency of mcr-1 and qnrA-1 in wastewater during peak periods. The ARG detection method developed in this work may offer a useful tool for promoting a sustainable urban water cycle.
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Affiliation(s)
- Zhou-Hua Cheng
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Xi-Yan Luo
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Dong-Feng Liu
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Jing Han
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Hao-Da Wang
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Di Min
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
| | - Han-Qing Yu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Department of Environmental Science and Engineering, University of Science & Technology of China, Hefei 230026, China
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Rafiee Z, Rezaie M, Choi S. Combined electrical-electrochemical phenotypic profiling of antibiotic susceptibility of in vitro biofilm models. Analyst 2024; 149:3224-3235. [PMID: 38686667 DOI: 10.1039/d4an00393d] [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: 05/02/2024]
Abstract
More than 65% of bacterial infections are caused by biofilms. However, standard biofilm susceptibility tests are not available for clinical use. All conventional biofilm models suffer from a long formation time and fail to mimic in vivo microbial biofilm conditions. Moreover, biofilms make it difficult to monitor the effectiveness of antibiotics. This work creates a powerful yet simple method to form a target biofilm and develops an innovative approach to monitoring the antibiotic's efficacy against a biofilm-associated infection. A paper-based culture platform can provide a new strategy for rapid microbial biofilm formation through capillary action. A combined electrical-electrochemical technique monitors bacterial metabolism rapidly and reliably by measuring microbial extracellular electron transfer (EET) and using electrochemical impedance spectroscopy (EIS) across a microbe-electrode interface. Three representative pathogens, Pseudomonas aeruginosa, Escherichia coli, and Staphylococcus aureus, form their biofilms controllably within an hour. Within another hour their susceptibilities to three frontline antibiotics with different action modes (gentamicin, ciprofloxacin, and ceftazidime) are examined. Our antibiotic susceptibility testing (AST) technique provides a quantifiable minimum inhibitory concentration (MIC) of those antibiotics against the in vitro biofilm models and characterizes their action mechanisms. The results will have an important positive effect because they provide immediately actionable healthcare information at a reduced cost, revolutionizing public healthcare.
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Affiliation(s)
- Zahra Rafiee
- Bioelectronics & Microsystems Laboratory, Department of Electrical & Computer Engineering, State University of New York at Binghamton, Binghamton, New York, 13902, USA.
| | - Maryam Rezaie
- Bioelectronics & Microsystems Laboratory, Department of Electrical & Computer Engineering, State University of New York at Binghamton, Binghamton, New York, 13902, USA.
| | - Seokheun Choi
- Bioelectronics & Microsystems Laboratory, Department of Electrical & Computer Engineering, State University of New York at Binghamton, Binghamton, New York, 13902, USA.
- Center for Research in Advanced Sensing Technologies & Environmental Sustainability, State University of New York at Binghamton, Binghamton, New York, 13902, USA
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Do PC, Assefa YA, Batikawai SM, Abate MA, Reid SA. Policy, practice, and prediction: model-based approaches to evaluating N. gonorrhoeae antibiotic susceptibility test uptake in Australia. BMC Infect Dis 2024; 24:498. [PMID: 38760682 PMCID: PMC11100046 DOI: 10.1186/s12879-024-09393-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) represents a significant threat to global health with Neisseria gonorrhoea emerging as a key pathogen of concern. In Australia, the Australian Gonococcal Surveillance Program (AGSP) plays a critical role in monitoring resistance patterns. However, antibiotic susceptibility test (AST) uptake - a crucial component for effective resistance surveillance - remains to be a limiting factor. The study aims to model the processes involved in generating AST tests for N. gonorrhoea isolates within the Australian healthcare system and assess the potential impact of systematic and policy-level changes. METHODS Two models were developed. The first model was a mathematical stochastic health systems model (SHSM) and a Bayesian Belief Network (BBN) to simulate the clinician-patient dynamics influencing AST initiation. Key variables were identified through systematic literature review to inform the construction of both models. Scenario analyses were conducted with the modification of model parameters. RESULTS The SHSM and BBN highlighted clinician education and the use of clinical support tools as effective strategies to improve AST. Scenario analysis further identified adherence to guidelines and changes in patient-level factors, such as persistence of symptoms and high-risk behaviours, as significant determinants. Both models supported the notion of mandated testing to achieve higher AST initiation rates but with considerations necessary regarding practicality, laboratory constraints, and culture failure rate. CONCLUSION The study fundamentally demonstrates a novel approach to conceptualising the patient-clinician dynamic within AMR testing utilising a model-based approach. It suggests targeted interventions to educational, support tools, and legislative framework as feasible strategies to improve AST initiation rates. However, the research fundamentally highlights substantial research gaps in the underlying understanding of AMR.
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Affiliation(s)
- Phu Cong Do
- School of Public Health, The University of Queensland, Herston, QLD, Australia.
| | | | | | - Megbaru Alemu Abate
- School of Public Health, The University of Queensland, Herston, QLD, Australia
- Department of Medical Laboratory Science, Bahir Dar University, Bahir Dar, Ethiopia
| | - Simon Andrew Reid
- School of Public Health, The University of Queensland, Herston, QLD, Australia
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11
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Zhang H, Mou J, Ding J, Qin W. Rapid antibiotic screening based on E. coli apoptosis using a potentiometric sensor array. Anal Chim Acta 2024; 1297:342378. [PMID: 38438244 DOI: 10.1016/j.aca.2024.342378] [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] [Received: 01/03/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/06/2024]
Abstract
Phenotypic antimicrobial susceptibility testing enables reliable antibiotic screening but requires multiple strategies to identify each phenotypic change induced by different bactericidal mechanisms. Bacteria apoptosis with typical phenotypic features has never been explored for antibiotic screening. Herein, we developed an antibiotic screening method based on the measurement of antibiotic-induced phosphatidylserine (PS) exposure of apoptotic bacteria. Phosphatidylserine externalization of E. coli that can be widely used as an apoptosis marker for antibiotics with different antibacterial mechanisms was explored. A positively charged PS-binding peptide was immobilized on magnetic beads (MBs) to recognize and capture apoptotic E. coli with PS externalization. Apoptotic E. coli binding led to the charge or charge density change of MBs-peptide, resulting in a potential change on a magneto-controlled polymeric membrane potentiometric sensor. Based on the detection of apoptotic E. coli killed by antibiotics, antibiotic screening for different classes of antibiotics and silver nanoparticles was achieved within 1.5 h using a potentiometric sensor array. This approach enables sensitive, general, and time-saving antibiotic screening, and may open up a new path for antibiotic susceptibility testing.
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Affiliation(s)
- Han Zhang
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Junsong Mou
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jiawang Ding
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, 266071, PR China.
| | - Wei Qin
- CAS Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Key Laboratory of Coastal Environmental Processes, YICCAS, Yantai, Shandong, 264003, PR China; Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, PR China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, Shandong, 266071, PR China
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12
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Dillon L, Dimonaco NJ, Creevey CJ. Accessory genes define species-specific routes to antibiotic resistance. Life Sci Alliance 2024; 7:e202302420. [PMID: 38228374 DOI: 10.26508/lsa.202302420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/18/2024] Open
Abstract
A deeper understanding of the relationship between the antimicrobial resistance (AMR) gene carriage and phenotype is necessary to develop effective response strategies against this global burden. AMR phenotype is often a result of multi-gene interactions; therefore, we need approaches that go beyond current simple AMR gene identification tools. Machine-learning (ML) methods may meet this challenge and allow the development of rapid computational approaches for AMR phenotype classification. To examine this, we applied multiple ML techniques to 16,950 bacterial genomes across 28 genera, with corresponding MICs for 23 antibiotics with the aim of training models to accurately determine the AMR phenotype from sequenced genomes. This resulted in a >1.5-fold increase in AMR phenotype prediction accuracy over AMR gene identification alone. Furthermore, we revealed 528 unique (often species-specific) genomic routes to antibiotic resistance, including genes not previously linked to the AMR phenotype. Our study demonstrates the utility of ML in predicting AMR phenotypes across diverse clinically relevant organisms and antibiotics. This research proposes a rapid computational method to support laboratory-based identification of the AMR phenotype in pathogens.
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Affiliation(s)
- Lucy Dillon
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
| | - Nicholas J Dimonaco
- School of Biological Sciences, Queen's University Belfast, Belfast, UK
- https://ror.org/02fa3aq29 Department of Medicine, McMaster University, Hamilton, Ontario, Canada
- https://ror.org/02fa3aq29 Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada
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13
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Sturm A, Jóźwiak G, Verge MP, Munch L, Cathomen G, Vocat A, Luraschi-Eggemann A, Orlando C, Fromm K, Delarze E, Świątkowski M, Wielgoszewski G, Totu RM, García-Castillo M, Delfino A, Tagini F, Kasas S, Lass-Flörl C, Gstir R, Cantón R, Greub G, Cichocka D. Accurate and rapid antibiotic susceptibility testing using a machine learning-assisted nanomotion technology platform. Nat Commun 2024; 15:2037. [PMID: 38499536 PMCID: PMC10948838 DOI: 10.1038/s41467-024-46213-y] [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: 06/01/2023] [Accepted: 02/16/2024] [Indexed: 03/20/2024] Open
Abstract
Antimicrobial resistance (AMR) is a major public health threat, reducing treatment options for infected patients. AMR is promoted by a lack of access to rapid antibiotic susceptibility tests (ASTs). Accelerated ASTs can identify effective antibiotics for treatment in a timely and informed manner. We describe a rapid growth-independent phenotypic AST that uses a nanomotion technology platform to measure bacterial vibrations. Machine learning techniques are applied to analyze a large dataset encompassing 2762 individual nanomotion recordings from 1180 spiked positive blood culture samples covering 364 Escherichia coli and Klebsiella pneumoniae isolates exposed to cephalosporins and fluoroquinolones. The training performances of the different classification models achieve between 90.5 and 100% accuracy. Independent testing of the AST on 223 strains, including in clinical setting, correctly predict susceptibility and resistance with accuracies between 89.5% and 98.9%. The study shows the potential of this nanomotion platform for future bacterial phenotype delineation.
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Affiliation(s)
- Alexander Sturm
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland.
| | | | - Marta Pla Verge
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland
| | - Laura Munch
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland
| | - Gino Cathomen
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland
| | - Anthony Vocat
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland
| | | | - Clara Orlando
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland
| | - Katja Fromm
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland
| | - Eric Delarze
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland
| | | | | | - Roxana M Totu
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland
| | - María García-Castillo
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Km 9,1, 28034, Madrid, Spain
| | - Alexandre Delfino
- Institute of Microbiology, Lausanne University Hospital (CHUV) & University of Lausanne (UNIL), 1011, Lausanne, Switzerland
| | - Florian Tagini
- Institute of Microbiology, Lausanne University Hospital (CHUV) & University of Lausanne (UNIL), 1011, Lausanne, Switzerland
| | - Sandor Kasas
- Laboratory of Biological Electron Microscopy (LBEM), École Polytechnique Fédérale de Lausanne (EPFL) and University of Lausanne (UNIL), 1015, Lausanne, Switzerland
- Centre Universitaire Romand de Médecine Légale (UFAM) & Université de Lausanne (UNIL), 1015, Lausanne, Switzerland
| | - Cornelia Lass-Flörl
- Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Universität Innsbruck, Schöpfstraße 41, 6020, Innsbruck, Austria
| | - Ronald Gstir
- Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Universität Innsbruck, Schöpfstraße 41, 6020, Innsbruck, Austria
| | - Rafael Cantón
- Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Carretera de Colmenar Km 9,1, 28034, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC). Instituto de Salud Carlos III. Sinesio Delgado 4, 28029, Madrid, Spain
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital (CHUV) & University of Lausanne (UNIL), 1011, Lausanne, Switzerland
| | - Danuta Cichocka
- Resistell AG, Hofackerstrasse 40, 4132, Muttenz, Switzerland
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14
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Zhou J, Liao C, Zou M, Villalba MI, Xiong C, Zhao C, Venturelli L, Liu D, Kohler AC, Sekatskii SK, Dietler G, Wang Y, Kasas S. An Optical Fiber-Based Nanomotion Sensor for Rapid Antibiotic and Antifungal Susceptibility Tests. NANO LETTERS 2024; 24:2980-2988. [PMID: 38311846 PMCID: PMC10941246 DOI: 10.1021/acs.nanolett.3c03781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/06/2024]
Abstract
The emergence of antibiotic and antifungal resistant microorganisms represents nowadays a major public health issue that might push humanity into a post-antibiotic/antifungal era. One of the approaches to avoid such a catastrophe is to advance rapid antibiotic and antifungal susceptibility tests. In this study, we present a compact, optical fiber-based nanomotion sensor to achieve this goal by monitoring the dynamic nanoscale oscillation of a cantilever related to microorganism viability. High detection sensitivity was achieved that was attributed to the flexible two-photon polymerized cantilever with a spring constant of 0.3 N/m. This nanomotion device showed an excellent performance in the susceptibility tests of Escherichia coli and Candida albicans with a fast response in a time frame of minutes. As a proof-of-concept, with the simplicity of use and the potential of parallelization, our innovative sensor is anticipated to be an interesting candidate for future rapid antibiotic and antifungal susceptibility tests and other biomedical applications.
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Affiliation(s)
- Jiangtao Zhou
- Laboratory
of Physics of Living Matter (LPMV), École
Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Health Sciences and Technology, ETH Zurich, 8092 Zurich, Switzerland
| | - Changrui Liao
- Guangdong
and Hong Kong Joint Research Centre for Optical Fiber Sensors and
Key Laboratory of Optoelectronic Devices and Systems of the Ministry
of Education and Guangdong Province, College of Physics and Optoelectronic
Engineering, Shenzhen University, Shenzhen 518060, China
| | - Mengqiang Zou
- Guangdong
and Hong Kong Joint Research Centre for Optical Fiber Sensors and
Key Laboratory of Optoelectronic Devices and Systems of the Ministry
of Education and Guangdong Province, College of Physics and Optoelectronic
Engineering, Shenzhen University, Shenzhen 518060, China
| | - Maria Ines Villalba
- Laboratory
of Biological Electron Microscopy (LBEM), École Polytechnique Fédérale de Lausanne (EPFL),
and Department of Fundamental Biology, Faculty of Biology and Medicine,
University of Lausanne (UNIL), CH-1015 Lausanne, Switzerland
| | - Cong Xiong
- Guangdong
and Hong Kong Joint Research Centre for Optical Fiber Sensors and
Key Laboratory of Optoelectronic Devices and Systems of the Ministry
of Education and Guangdong Province, College of Physics and Optoelectronic
Engineering, Shenzhen University, Shenzhen 518060, China
| | - Cong Zhao
- Guangdong
and Hong Kong Joint Research Centre for Optical Fiber Sensors and
Key Laboratory of Optoelectronic Devices and Systems of the Ministry
of Education and Guangdong Province, College of Physics and Optoelectronic
Engineering, Shenzhen University, Shenzhen 518060, China
| | - Leonardo Venturelli
- Laboratory
of Physics of Living Matter (LPMV), École
Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Dan Liu
- Guangdong
and Hong Kong Joint Research Centre for Optical Fiber Sensors and
Key Laboratory of Optoelectronic Devices and Systems of the Ministry
of Education and Guangdong Province, College of Physics and Optoelectronic
Engineering, Shenzhen University, Shenzhen 518060, China
| | - Anne-Celine Kohler
- Laboratory
of Physics of Living Matter (LPMV), École
Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sergey K. Sekatskii
- Laboratory
of Physics of Living Matter (LPMV), École
Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Laboratory
of Biological Electron Microscopy (LBEM), École Polytechnique Fédérale de Lausanne (EPFL),
and Department of Fundamental Biology, Faculty of Biology and Medicine,
University of Lausanne (UNIL), CH-1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Laboratory
of Physics of Living Matter (LPMV), École
Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Yiping Wang
- Guangdong
and Hong Kong Joint Research Centre for Optical Fiber Sensors and
Key Laboratory of Optoelectronic Devices and Systems of the Ministry
of Education and Guangdong Province, College of Physics and Optoelectronic
Engineering, Shenzhen University, Shenzhen 518060, China
| | - Sandor Kasas
- Laboratory
of Biological Electron Microscopy (LBEM), École Polytechnique Fédérale de Lausanne (EPFL),
and Department of Fundamental Biology, Faculty of Biology and Medicine,
University of Lausanne (UNIL), CH-1015 Lausanne, Switzerland
- International
Joint Research Group VUB-EPFL BioNanotechnology & NanoMedicine, 1050 Brussels, Belgium
- Centre
Universitaire Romand de Médecine Légale, UFAM, Université de Lausanne, 1015 Lausanne, Switzerland
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15
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Fernandez-Pittol M, Bosch J, Ballesté-Delpierre C, Gonzalez C, Vasilakopoulou A, Berbel D, Riccobono E, Gatermann S, Kamotsay K, Reissier S, Szabo D, Aszalos AZ, Francius L, Volland H, Stankov-Pugès M, Rosenmöller M, Naas T, Vila J. Multicenter study to assess the use of BL-DetecTool for the detection of CTX-M-type ESBLs and carbapenemases directly from clinical specimens. J Clin Microbiol 2024; 62:e0113623. [PMID: 38319119 PMCID: PMC10935652 DOI: 10.1128/jcm.01136-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
Antimicrobial resistance (AMR) is one of the major public health problems worldwide. Multiple strategies have been put in place to address this problem. One of them is the rapid detection of the mechanisms of resistance, such as extended-spectrum beta-lactamases (ESBLs) and/or carbapenemases. We conducted a multicenter study that included nine European centers for the assessment of prototypes of a novel lateral flow immunoassay-based device (BL-DetecTool) for a rapid detection of ESBL (NG-Test CTX-M-MULTI DetecTool) and/or carbapenemases (NG-Test CARBA 5 DetecTool) from Enterobacterales and Pseudomonas aeruginosa in positive urine, positive blood cultures, and rectal swabs. We performed a prospective analysis between January 2021 and June 2022, including overall 22,010 samples. Based on each hospital information, the sensitivity to detect CTX-M was 84%-100%, 90.9%-100%, and 75%-100% for urine, positive blood cultures, and enriched rectal swabs, respectively. On the other hand, the sensitivity to detect carbapenemases was 42.8%-100%, 75%-100%, and 66.6%-100% for urine, positive blood cultures, and enriched rectal swab, respectively. BL-DetecTool allows a rapid and reliable detection of ESBL and carbapenemases directly from urine, positive blood cultures, or enriched rectal swabs, being an easy technique to implement in the workflow of clinical microbiology laboratories. IMPORTANCE The assessed rapid assay to detect CTX-M beta-lactamases and carbapenemases directly from clinical samples can favor in the rapid detection of these mechanisms of resistance and hence the administration of a more adequate antimicrobial treatment.
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Affiliation(s)
- Mariana Fernandez-Pittol
- Department of Microbiology, Hospital Clinic of Barcelona, Barcelona, Spain
- Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | - Jordi Bosch
- Department of Microbiology, Hospital Clinic of Barcelona, Barcelona, Spain
- Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
| | | | - Camille Gonzalez
- Team "Resist", INSERM Unit 1184, Faculty of Medicine, Université Paris-Saclay, Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital Le Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Alexandra Vasilakopoulou
- Laboratory of Clinical Microbiology, Attikon University General Hospital, Medical School, National Kapodistrian University Athens (Greece), Athens, Greece
| | - Dàmaris Berbel
- Microbiology Department, Hospital de Bellvitge. IDIBELL. UB. CIBERES, Barcelona, Spain
| | - Eleonora Riccobono
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sören Gatermann
- German National Reference Laboratory for Multidrug-Resistant Gram-negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Germany - (Germany), Bochum, Germany
| | - Katalin Kamotsay
- Central Microbiology Laboratory, Central Hospital of Southern Pest National Institute of Hematology and Infectious Disease, Budapest, Hungary
| | - Sophie Reissier
- Department of Bacteriology, Amiens University Hospital, Amiens, France
| | - Dora Szabo
- Semmelweis University, Institute of Medical Microbiology, Budapest, Hungary
| | - Albert Zoltan Aszalos
- Health Services Management Training Centre, Semmelweis University, Budapest, Hungary
| | | | - Hervé Volland
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris Saclay, CEA, INRAE, SPI, Gif-sur-Yvette, France
| | | | | | - Thierry Naas
- Team "Resist", INSERM Unit 1184, Faculty of Medicine, Université Paris-Saclay, Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital Le Kremlin-Bicêtre, Le Kremlin-Bicêtre, France
| | - Jordi Vila
- Department of Microbiology, Hospital Clinic of Barcelona, Barcelona, Spain
- Institute for Global Health (ISGlobal), University of Barcelona, Barcelona, Spain
- Department of Clinical Microbiology - CDB, University of Barcelona, Hospital Clínic, Barcelona, Spain
- CIBER de Enfermedades Infecciosas , Barcelona, Spain
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16
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Rodríguez-Guerrero E, Moya-López J, Expósito-Ruiz M, Navarro-Marí JM, Gutiérrez-Fernández J. Preliminary reading of antibiogram by microdilution for clinical isolates in urine culture. Eur J Clin Microbiol Infect Dis 2024; 43:517-524. [PMID: 38214841 DOI: 10.1007/s10096-024-04747-5] [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] [Received: 07/10/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
Abstract
PURPOSE We evaluated a modification of automated antibiograms in urine cultures designed to facilitate the early interpretation of minimum inhibitory concentrations (MICs) and accelerate the targeted treatment of urinary tract infections (UTIs), METHODS: A prospective study was conducted of 309 isolates (219 Enterobacteriaceae, 75 Enterococcus spp., and 15 non-fermenting Gram-negative bacilli (NFGNB), and a retrospective study of 9 carbapenemase-producing clinical isolates from urine cultures. Colonies grown on conventional isolation plates were inoculated in MicroScan Walkaway system panels and incubated for 7 h, using a MicroScan AutoScan-4 plate reader for preliminary MIC determination by turbidimetry. Resulting antibiograms were compared with definitive antibiograms obtained after incubation for 17 h. RESULTS Preliminary and definitive readings were concordant for 86.7% of Gram-positive cocci isolates (65/75), 61.6% of Enterobacteriaceae (135/219), and 53.3% of NFGNB. The agreement rate was greater than 90% for most antimicrobials against Gram-positive cocci (94.7% or more) and Enterobacteriaceae, (97.2% or more for 10 of 17 antibiotics) except with nitrofurantoin (89%). The agreement rate was 86.7% or more for most antibiotics against NFGNB apart from piperacillin/tazobactam, aztreonam, amikacin, and ciprofloxacin. Gram-negative bacilli showed the highest differences in MIC values between preliminary and definitive readings. CONCLUSIONS A preliminary antibiogram reading may be useful in urine cultures to reduce the delay before targeted antibiotherapy, especially against Enterobacteriaceae and Gram-positive cocci, but not in cases of carbapenemase-producing NFGNB. Further local studies are warranted to evaluate the usefulness of this approach in relation to resistance rates.
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Affiliation(s)
- Enrique Rodríguez-Guerrero
- Laboratory of Microbiology, Virgen de Las Nieves University Hospital & Biosanitary Research Institute of Granada (Ibs.GRANADA), 18016, Granada, Spain.
| | - José Moya-López
- Department of Microbiology, School of Medicine, University of Granada & Biosanitary Research Institute of Granada (Ibs.GRANADA), 18016, Granada, Spain
| | - Manuela Expósito-Ruiz
- Unit of Biostatistics, Department of Statistics, School of Medicine, University of Granada & Biosanitary Research Institute of Granada (Ibs.GRANADA), 18016, Granada, Spain
| | - José María Navarro-Marí
- Laboratory of Microbiology, Virgen de Las Nieves University Hospital & Biosanitary Research Institute of Granada (Ibs.GRANADA), 18016, Granada, Spain
| | - José Gutiérrez-Fernández
- Laboratory of Microbiology, Virgen de Las Nieves University Hospital & Biosanitary Research Institute of Granada (Ibs.GRANADA), 18016, Granada, Spain
- Department of Microbiology, School of Medicine, University of Granada & Biosanitary Research Institute of Granada (Ibs.GRANADA), 18016, Granada, Spain
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17
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Sever EA, Aybakan E, Beşli Y, Karatuna O, Kocagoz T. A novel rapid bioluminescence-based antimicrobial susceptibility testing method based on adenosine triphosphate consumption. Front Microbiol 2024; 15:1357680. [PMID: 38404596 PMCID: PMC10885693 DOI: 10.3389/fmicb.2024.1357680] [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: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction Standard, phenotypic antimicrobial susceptibility testing (AST) methods require 16-20 h of incubation and are considered as the bottleneck in providing timely input for appropriate antimicrobial treatment. In this study, a novel adenosine triphosphate (ATP)-bioluminescence-based method which allows rapid AST within 3 h was described. Methods Standard AST was performed for 56 Enterobacterales isolates using EUCAST disk diffusion (DD) methodology. For the bioluminescence-based rapid AST, suspensions of bacteria were prepared using Mueller-Hinton broth to obtain a turbidity of 0.5 McFarland. The suspensions were distributed into 96-well microtiter plates. ATP (20 mM) and fixed concentrations of different antibiotics were added. Following incubation at 37°C for 1 h, a luminescent reaction mixture, including the substrate luciferin and luciferase enzyme solutions, was added. The chemiluminescence was monitored using an imaging system. Light production demonstrated the presence of ATP, indicating that the isolate was susceptible to the antibiotic in the well. Absence or decrease of light intensity, compared with the growth control well, indicated the use of ATP as an indirect measure of bacterial growth, and therefore resistance to the antibiotic in the well. Results The novel AST method was tested using a total of 348 test wells. Concordance was achieved for 290 (83.3%) of the tests, whereas 52 (14.9%) and 6 (1.7%) tests caused minor and major errors, respectively. Discussion In this study, a bioluminescence-based rapid AST was developed based on the consumption of ATP by bacteria. Our method's uniqueness relies on determining ATP consumption by microorganisms in the presence or absence of an antibiotic. The novel AST method described in this study lays the groundwork for obtaining rapid results, which should be considered as a proof of concept. With further optimization studies, this novel method can provide higher accuracy and be introduced into clinical practice as a routine AST method.
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Affiliation(s)
- Elif Arik Sever
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
| | - Esma Aybakan
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
| | - Yeşim Beşli
- American Hospital Clinical Laboratory, Istanbul, Türkiye
| | - Onur Karatuna
- EUCAST Development Laboratory, Clinical Microbiology, Central Hospital, Växjö, Sweden
| | - Tanil Kocagoz
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
- Department of Medical Microbiology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
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18
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Falconer K, Hammond R, Parcell BJ, Gillespie SH. Rapid determination of antimicrobial susceptibility of Gram-negative bacteria from clinical blood cultures using a scattered light-integrated collection device. J Med Microbiol 2024; 73. [PMID: 38415707 DOI: 10.1099/jmm.0.001812] [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: 02/29/2024] Open
Abstract
Background. A bloodstream infection (BSI) presents a complex and serious health problem, a problem that is being exacerbated by increasing antimicrobial resistance (AMR).Gap Statement. The current turnaround times (TATs) for most antimicrobial susceptibility testing (AST) methods offer results retrospective of treatment decisions, and this limits the impact AST can have on antibiotic prescribing and patient care. Progress must be made towards rapid BSI diagnosis and AST to improve antimicrobial stewardship and reduce preventable deaths from BSIs. To support the successful implementation of rapid AST (rAST) in hospital settings, a rAST method that is affordable, is sustainable and offers comprehensive AMR detection is needed.Aim. To evaluate a scattered light-integrated collection (SLIC) device against standard of care (SOC) to determine whether SLIC could accelerate the current TATs with actionable, accurate rAST results for Gram-negative BSIs.Methods. Positive blood cultures from a tertiary referral hospital were studied prospectively. Flagged positive Gram-negative blood cultures were confirmed by Gram staining and analysed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, Vitek 2, disc diffusion (ceftriaxone susceptibility only) and an SLIC device. Susceptibility to a panel of five antibiotics, as defined by European Committee on Antimicrobial Susceptibility Testing breakpoints, was examined using SLIC.Results. A total of 505 bacterial-antimicrobial combinations were analysed. A categorical agreement of 95.5 % (482/505) was achieved between SLIC and SOC. The 23 discrepancies that occurred were further investigated by the broth microdilution method, with 10 AST results in agreement with SLIC and 13 in agreement with SOC. The mean time for AST was 10.53±0.46 h and 1.94±0.02 h for Vitek 2 and SLIC, respectively. SLIC saved 23.96±1.47 h from positive blood culture to AST result.Conclusion. SLIC has the capacity to provide accurate AST 1 day earlier from flagged positive blood cultures than SOC. This significant time saving could accelerate time to optimal antimicrobial therapy, improving antimicrobial stewardship and management of BSIs.
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Affiliation(s)
- Kerry Falconer
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | - Robert Hammond
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | - Benjamin J Parcell
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
- Ninewells Hospital and Medical School, Dundee, UK
| | - Stephen H Gillespie
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
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Saulnier J, Jose C, Lagarde F. Electrochemical techniques for label-free and early detection of growing microbial cells and biofilms. Bioelectrochemistry 2024; 155:108587. [PMID: 37839250 DOI: 10.1016/j.bioelechem.2023.108587] [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] [Received: 07/07/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/17/2023]
Abstract
Over the past decades, the misuse or abuse of antimicrobial agents to prevent and/or control infections has led to increased resistance of microbes to treatments, and antimicrobial resistance is now a subject of major global concern. In some cases, microbes possess the capacity to attach to biotic or abiotic surfaces, and to produce a protective polymeric matrix, forming biofilms of higher resistance and virulence compared to planktonic forms. To avoid further excessive and inappropriate use of antimicrobials, and to propose new effective treatments, it is very important to detect planktonic microbes and microbial biofilms in their early growth stage and at the point of need. In this review, we provide an overview of currently available electrochemical techniques, in particular impedimetric and voltamperometric methods, highlighting recent advances in the field and illustrating with examples in antibiotic susceptibility testing and microbial biofilm monitoring.
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Affiliation(s)
- Joelle Saulnier
- Universite Claude Bernard Lyon 1, Institute of Analytical Sciences, CNRS, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Catherine Jose
- Universite Claude Bernard Lyon 1, Institute of Analytical Sciences, CNRS, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Florence Lagarde
- Universite Claude Bernard Lyon 1, Institute of Analytical Sciences, CNRS, 5 rue de la Doua, 69100 Villeurbanne, France.
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20
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Aruhomukama D, Magiidu WT, Katende G, Ebwongu RI, Bulafu D, Kasolo R, Nakabuye H, Musoke D, Asiimwe B. Evaluation of three protocols for direct susceptibility testing for gram negative-Enterobacteriaceae from patient samples in Uganda with SMS reporting. Sci Rep 2024; 14:2730. [PMID: 38302620 PMCID: PMC10834995 DOI: 10.1038/s41598-024-53230-w] [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: 10/03/2023] [Accepted: 01/30/2024] [Indexed: 02/03/2024] Open
Abstract
In Uganda, the challenge of generating and timely reporting essential antimicrobial resistance (AMR) data has led to overreliance on empirical antibiotic therapy, exacerbating the AMR crisis. To address this issue, this study aimed to adapt a one-step AMR testing protocol alongside an SMS (Short Message Service) result relay system (SRRS), with the potential to reduce the turnaround time for AMR testing and result communication from 4 days or more to 1 day in Ugandan clinical microbiology laboratories. Out of the 377 samples examined, 54 isolates were obtained. Notably, E. coli (61%) and K. pneumoniae (33%) were the most frequently identified, majority testing positive for ESBL. Evaluation of three AMR testing protocols revealed varying sensitivity and specificity, with Protocol A (ChromID ESBL-based) demonstrating high sensitivity (100%) but no calculable specificity, Protocol B (ceftazidime-based) showing high sensitivity (100%) and relatively low specificity (7.1%), and Protocol C (cefotaxime-based) exhibiting high sensitivity (97.8%) but no calculable specificity. ESBL positivity strongly correlated with resistance to specific antibiotics, including cefotaxime, ampicillin, and aztreonam (100%), cefuroxime (96%), ceftriaxone (93%), and trimethoprim sulfamethoxazole (87%). The potential of integrating an SRRS underscored the crucial role this could have in enabling efficient healthcare communication in AMR management. This study underscores the substantial potential of the tested protocols for accurately detecting ESBL production in clinical samples, potentially, providing a critical foundation for predicting and reporting AMR patterns. Although considerations related to specificity warrant careful assessment before widespread clinical adoption.
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Affiliation(s)
- Dickson Aruhomukama
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Walusimbi Talemwa Magiidu
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - George Katende
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Robert Innocent Ebwongu
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Douglas Bulafu
- Department of Disease Control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Rajab Kasolo
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Hellen Nakabuye
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David Musoke
- Department of Disease Control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Benon Asiimwe
- Department of Medical Microbiology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala, Uganda
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21
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Andretta M, Tavares RDM, Fusieger A, Yamatogi RS, Nero LA. Agreement of methods to assess antimicrobial susceptibility using Escherichia coli isolates as target models. Lett Appl Microbiol 2024; 77:ovae009. [PMID: 38285611 DOI: 10.1093/lambio/ovae009] [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: 07/31/2023] [Revised: 12/08/2023] [Accepted: 01/25/2024] [Indexed: 01/31/2024]
Abstract
Antimicrobial susceptibility tests (AST) conducted in vitro offer a range of methods to assess the antimicrobial resistance (AMR) of microorganisms. Escherichia coli, a widely distributed bacterium, is closely linked to the issue of AMR. In this way, the present study aimed to assess the agreement among different in vitro AST methods, including disk diffusion in agar, broth dilution, and agar dilution method. A total of 100 E. coli isolates were analyzed for their resistance levels against six antibiotics: amoxicillin, ceftiofur, ciprofloxacin, chloramphenicol, tetracycline, and sulfamethoxazole + trimethoprim, using the aforementioned AST methods. Standard breakpoint values were employed to classify isolates as resistant, intermediate, or susceptible, and comparisons among the AST methods were conducted by McNemar's test (P < .05). The obtained data demonstrated equivalence among the AST methods, highlighting the reliability of these standardized classical methodologies. This standardization aids in preventing the inappropriate use of antimicrobials and the dissemination of antimicrobial-resistant microorganisms.
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Affiliation(s)
- Milimani Andretta
- InsPOA-Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Rafaela de Melo Tavares
- InsPOA-Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Andressa Fusieger
- InovaLeite-Laboratório de Pesquisa em Leites e Derivados, Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Ricardo Seiti Yamatogi
- InsPOA-Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
| | - Luís Augusto Nero
- InsPOA-Laboratório de Inspeção de Produtos de Origem Animal, Departamento de Veterinária, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
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22
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Zhang J, Wang M, Xiao J, Wang M, Liu Y, Gao X. Metabolism-Triggered Plasmonic Nanosensor for Bacterial Detection and Antimicrobial Susceptibility Testing of Clinical Isolates. ACS Sens 2024; 9:379-387. [PMID: 38175523 DOI: 10.1021/acssensors.3c02144] [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: 01/05/2024]
Abstract
Antimicrobial resistance (AMR) is predicted to become the leading cause of death worldwide in the coming decades. Rapid and on-site antibiotic susceptibility testing (AST) is crucial for guiding appropriate antibiotic choices to combat AMR. With this in mind, we have designed a simple and efficient plasmonic nanosensor consisting of Cu2+ and cysteine-modified AuNP (Au/Cys) that utilizes the metabolic activity of bacteria toward Cu2+ for bacterial detection and AST. When Cu2+ is present, it induces the aggregation of Au/Cys. However, in the presence of bacteria, Cu2+ is metabolized to varying extents, resulting in distinct levels of aggregation. Moreover, the metabolic activity of bacteria can be influenced by their antibiotic susceptibility, allowing us to differentiate between susceptible and resistant strains through direct color changes from the Cu2+-Au/Cys platform over approximately 3 h. These color changes can be easily detected using naked-eye observation, smartphone analysis, or absorption readout. We have validated the platform using four clinical isolates and six types of antibiotics, demonstrating a clinical sensitivity and specificity of 95.8%. Given its simplicity, low cost, high speed, and high accuracy, the plasmonic nanosensor holds great potential for point-of-care detection of antibiotic susceptibility across various settings.
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Affiliation(s)
- Jing Zhang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mengna Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Jinru Xiao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Mengqi Wang
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yaqing Liu
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Xia Gao
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, China
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23
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Wei S, Tang Q, Hu X, Ouyang W, Shao H, Li J, Yan H, Chen Y, Liu L. Rapid, Ultrasensitive, and Visual Detection of Pathogens Based on Cation Dye-Triggered Gold Nanoparticle Electrokinetic Agglutination Analysis. ACS Sens 2024; 9:325-336. [PMID: 38214583 DOI: 10.1021/acssensors.3c02014] [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: 01/13/2024]
Abstract
Rapid prescribing of the right antibiotic is the key to treat infectious diseases and decelerate the challenge of bacterial antibiotic resistance. Herein, by targeting the 16S rRNA of bacteria, we developed a cation dye-triggered electrokinetic gold nanoparticle (AuNP) agglutination (CD-TEAA) method, which is rapid, visual, ultrasensitive, culture-independent, and low in cost. The limit of detection (LOD) is as low as 1 CFU mL-1 Escherichia coli. The infection identifications of aseptic fluid samples (n = 11) and urine samples with a clinically suspected urinary tract infection (UTI, n = 78) were accomplished within 50 and 30 min for each sample, respectively. The antimicrobial susceptibility testing (AST) of UTI urine samples was achieved within 2.5 h. In ROC analysis of urine, the sensitivity and specificity were 100 and 96% for infection identification, and 100 and 98% for AST, respectively. Moreover, the overall cost of materials for each test is about US$0.69. Therefore, the CD-TEAA method is a superior approach to existing, time-consuming, and expensive methods, especially in less developed areas.
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Affiliation(s)
- Siqi Wei
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Qing Tang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiumei Hu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Wei Ouyang
- Querrey Simpson Institute for Bioelectronics, Northwestern University, Evanston, Illinois 60208, United States
| | - Huaze Shao
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jincheng Li
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hong Yan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yue Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Lihong Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
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24
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Baker KR, Flentie K, Spears BR, Mozharov S, Roberts K, El ganbour A, Somers M, Calkwood J, Liu J, DaPonte K, Sam N, Kaur G, Chen F, Donato J, Chao A, Lewis A, Sherman J, Mortimer K, Harrington AT, Traczewski M, Carpenter D, Shortridge D, Lindley J, Diep A, Norton E, Green M, Gajewski J, Landrith R, Nalubega F, McCallum J, Beiswenger M, Dolan B, Brennan K, Carpenter A, Vacic A, Flyer AN, Pierce VM, Hooper DC, Lewis II JS, Stern E. Multicenter evaluation of the Selux Next-Generation Phenotyping antimicrobial susceptibility testing system. J Clin Microbiol 2024; 62:e0054623. [PMID: 38051069 PMCID: PMC10793272 DOI: 10.1128/jcm.00546-23] [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: 05/12/2023] [Accepted: 10/12/2023] [Indexed: 12/07/2023] Open
Abstract
The Selux Next-Generation Phenotyping (NGP) system (Charlestown, MA) is a new antimicrobial susceptibility testing system that utilizes two sequential assays performed on all wells of doubling dilution series to determine MICs. A multicenter evaluation of the performance of the Selux NGP system compared with reference broth microdilution was conducted following FDA recommendations and using FDA-defined breakpoints. A total of 2,488 clinical and challenge isolates were included; gram-negative isolates were tested against 24 antimicrobials, and gram-positive isolates were tested against 15 antimicrobials. Data is provided for all organism-antimicrobial combinations evaluated, including those that did and did not meet FDA performance requirements. Overall very major error and major error rates were less than 1% (31/3,805 and 107/15,606, respectively), essential agreement and categorical agreement were >95%, reproducibility was ≥95%, and the average time-to-result (from time of assay start to time of MIC result) was 5.65 hours.
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Affiliation(s)
| | | | | | | | | | | | - Mark Somers
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | - Jamie Liu
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | - Nikitha Sam
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | - Gurleen Kaur
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | - Felicia Chen
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | - Alan Chao
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | - Autumn Lewis
- Selux Diagnostics, Charlestown, Massachusetts, USA
| | | | | | - Amanda T. Harrington
- Pathology and Laboratory Medicine, Loyola University Medical Center, Maywood, Illinois, USA
| | | | | | | | - Jill Lindley
- JMI Laboratories/Element, North Liberty, Iowa, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Virginia M. Pierce
- Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - David C. Hooper
- Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - James S. Lewis II
- Department of Pharmacy Services, Oregon Health and Science University Hospitals and Clinics, Portland, Oregon, USA
| | - Eric Stern
- Selux Diagnostics, Charlestown, Massachusetts, USA
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25
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Javad Jafari M, Golabi M, Ederth T. Antimicrobial susceptibility testing using infrared attenuated total reflection (IR-ATR) spectroscopy to monitor metabolic activity. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123384. [PMID: 37714109 DOI: 10.1016/j.saa.2023.123384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
Fast and accurate detection of antimicrobial resistance in pathogens remains a challenge, and with the increase in antimicrobial resistance due to mis- and overuse of antibiotics, it has become an urgent public health problem. We demonstrate how infrared attenuated total reflection (IR-ATR) can be used as a simple method for assessment of bacterial susceptibility to antibiotics. This is achieved by monitoring the metabolic activities of bacterial cells via nutrient consumption and using this as an indicator of bacterial viability. Principal component analysis of the obtained spectra provides a tool for fast and simple discrimination of antimicrobial resistance in the acquired data. We demonstrate this concept using four bacterial strains and four different antibiotics, showing that the change in glucose concentration in the growth medium after 2 h, as monitored by IR-ATR, can be used as a spectroscopic diagnostic technique, to reduce detection time and to improve quality in the assessment of antimicrobial resistance in pathogens.
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Affiliation(s)
- Mohammad Javad Jafari
- Division of Biophysics and Bioengineering, Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden
| | - Mohsen Golabi
- Department of Biotechnology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan 81746-73441, Iran; Division of Biosensors and Bioelectronics, Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden.
| | - Thomas Ederth
- Division of Biophysics and Bioengineering, Department of Physics, Chemistry and Biology (IFM), Linköping University, SE-581 83 Linköping, Sweden.
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26
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Buppasirakul K, Suginta W, Schulte A. Rapid and directly interpretable antimicrobial susceptibility profiling by continuous microvolume-electroanalysis of ferricyanide-mediated bacterial respiration. Chem Commun (Camb) 2024; 60:308-311. [PMID: 38059564 DOI: 10.1039/d3cc04683d] [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: 12/08/2023]
Abstract
We present a novel method for the electroanalysis of potassium ferricyanide-mediated bacterial electron transport, to rapidly assess viability and construct interpretable antimicrobial susceptibility profiles. Electrochemical minimum inhibitory concentrations (ecMICs) became determinable with a high correlation to the results from conventional assays.
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Affiliation(s)
- Krittamate Buppasirakul
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wang Chan Valley, Rayong 21210, Thailand.
| | - Wipa Suginta
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wang Chan Valley, Rayong 21210, Thailand.
| | - Albert Schulte
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wang Chan Valley, Rayong 21210, Thailand.
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27
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Gillespie SH, Hammond RJH. Rapid Drug Susceptibility Testing to Preserve Antibiotics. Methods Mol Biol 2024; 2833:129-143. [PMID: 38949707 DOI: 10.1007/978-1-0716-3981-8_13] [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: 07/02/2024]
Abstract
Antibiotic resistance is a global challenge likely to cost trillions of dollars in excess costs in the health system and more importantly, millions of lives every year. A major driver of resistance is the absence of susceptibility testing at the time a healthcare worker needs to prescribe an antimicrobial. The effect is that many prescriptions are unintentionally wasted and expose mutable organisms to antibiotics increasing the risk of resistance emerging. Often simplistic solutions are applied to this growing issue, such as a naïve drive to increase the speed of drug susceptibility testing. This puts a spotlight on a technological solution and there is a multiplicity of such candidate DST tests in development. Yet, if we do not define the necessary information and the speed at which it needs to be available in the clinical decision-making progress as well as the necessary integration into clinical pathways, then little progress will be made. In this chapter, we place the technological challenge in a clinical and systems context. Further, we will review the landscape of some promising technologies that are emerging and attempt to place them in the clinic where they will have to succeed.
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Affiliation(s)
- Stephen H Gillespie
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, Scotland, UK.
| | - Robert J H Hammond
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, Scotland, UK
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28
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Ulyashova MM, Presnova GV, Filippova AA, Grigorenko VG, Egorov AM, Rubtsova MY. Multiplex Microarrays in 96-Well Plates Photoactivated with 4-Azidotetrafluorobenzaldehyde for the Identification and Quantification of β-Lactamase Genes and Their RNA Transcripts. Curr Issues Mol Biol 2023; 46:53-66. [PMID: 38275665 PMCID: PMC10814224 DOI: 10.3390/cimb46010005] [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: 11/23/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Antibiotic-resistant bacteria represent a global issue that calls for novel approaches to diagnosis and treatment. Given the variety of genetic factors that determine resistance, multiplex methods hold promise in this area. We developed a novel method to covalently attach oligonucleotide probes to the wells of polystyrene plates using photoactivation with 4-azidotetrafluorobenzaldehyde. Then, it was used to develop the technique of microarrays in the wells. It consists of the following steps: activating polystyrene, hybridizing the probes with biotinylated target DNA, and developing the result using a streptavidin-peroxidase conjugate with colorimetric detection. The first microarray was designed to identify 11 different gene types and 16 single-nucleotide polymorphisms (SNPs) of clinically relevant ESBLs and carbapenemases, which confer Gram-negative bacteria resistance to β-lactam antibiotics. The detection of bla genes in 65 clinical isolates of Enterobacteriaceae demonstrated the high sensitivity and reproducibility of the technique. The highly reproducible spot staining of colorimetric microarrays allowed us to design a second microarray that was intended to quantify four different types of bla mRNAs in order to ascertain their expressions. The combination of reliable performance, high throughput in standard 96-well plates, and inexpensive colorimetric detection makes the microarrays suitable for routine clinical application and for the study of multi-drug resistant bacteria.
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Affiliation(s)
| | | | | | | | | | - Maya Yu. Rubtsova
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia; (M.M.U.); (G.V.P.); (A.A.F.); (V.G.G.); (A.M.E.)
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29
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Khire TS, Gao W, Bales B, Hsieh K, Grossmann G, Park DJM, O’Keefe C, Brown-Countess A, Peterson S, Chen FE, Lenigk R, Trick A, Wang TH, Puleo C. Rapid Minimum Inhibitory Concentration (MIC) Analysis Using Lyophilized Reagent Beads in a Novel Multiphase, Single-Vessel Assay. Antibiotics (Basel) 2023; 12:1641. [PMID: 37998843 PMCID: PMC10669664 DOI: 10.3390/antibiotics12111641] [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: 10/04/2023] [Revised: 10/30/2023] [Accepted: 11/09/2023] [Indexed: 11/25/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global threat fueled by incorrect (and overuse) of antibiotic drugs, giving rise to the evolution of multi- and extreme drug-resistant bacterial strains. The longer time to antibiotic administration (TTA) associated with the gold standard bacterial culture method has been responsible for the empirical usage of antibiotics and is a key factor in the rise of AMR. While polymerase chain reaction (PCR) and other nucleic acid amplification methods are rapidly replacing traditional culture methods, their scope has been restricted mainly to detect genotypic determinants of resistance and provide little to no information on phenotypic susceptibility to antibiotics. The work presented here aims to provide phenotypic antimicrobial susceptibility testing (AST) information by pairing short growth periods (~3-4 h) with downstream PCR assays to ultimately predict minimum inhibitory concentration (MIC) values of antibiotic treatment. To further simplify the dual workflows of the AST and PCR assays, these reactions are carried out in a single-vessel format (PCR tube) using novel lyophilized reagent beads (LRBs), which store dried PCR reagents along with primers and enzymes, and antibiotic drugs separately. The two reactions are separated in space and time using a melting paraffin wax seal, thus eliminating the need to transfer reagents across different consumables and minimizing user interactions. Finally, these two-step single-vessel reactions are multiplexed by using a microfluidic manifold that allows simultaneous testing of an unknown bacterial sample against different antibiotics at varying concentrations. The LRBs used in the microfluidic system showed no interference with the bacterial growth and PCR assays and provided an innovative platform for rapid point-of-care diagnostics (POC-Dx).
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Affiliation(s)
| | - Wei Gao
- GE Global Research, Niskayuna, NY 12309, USA (G.G.); (S.P.); (R.L.)
| | - Brian Bales
- GE Global Research, Niskayuna, NY 12309, USA (G.G.); (S.P.); (R.L.)
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; (K.H.); (D.J.M.P.); (C.O.); (T.-H.W.)
| | - Greg Grossmann
- GE Global Research, Niskayuna, NY 12309, USA (G.G.); (S.P.); (R.L.)
| | - Dong Jin M. Park
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; (K.H.); (D.J.M.P.); (C.O.); (T.-H.W.)
| | - Christine O’Keefe
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; (K.H.); (D.J.M.P.); (C.O.); (T.-H.W.)
| | | | - Sara Peterson
- GE Global Research, Niskayuna, NY 12309, USA (G.G.); (S.P.); (R.L.)
| | - Fan-En Chen
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; (F.-E.C.); (A.T.)
| | - Ralf Lenigk
- GE Global Research, Niskayuna, NY 12309, USA (G.G.); (S.P.); (R.L.)
| | - Alex Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; (F.-E.C.); (A.T.)
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; (K.H.); (D.J.M.P.); (C.O.); (T.-H.W.)
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA; (F.-E.C.); (A.T.)
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Rosłon I, Japaridze A, Rodenhuis S, Hamoen L, Ghatkesar MK, Steeneken P, Dekker C, Alijani F. Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria. iScience 2023; 26:108268. [PMID: 38026160 PMCID: PMC10654606 DOI: 10.1016/j.isci.2023.108268] [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: 05/31/2023] [Revised: 08/28/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Bacteria that are resistant to antibiotics present an increasing burden on healthcare. To address this emerging crisis, novel rapid antibiotic susceptibility testing (AST) methods are eagerly needed. Here, we present an optical AST technique that can determine the bacterial viability within 1 h down to a resolution of single bacteria. The method is based on measuring intensity fluctuations of a reflected laser focused on a bacterium in reflective microwells. Using numerical simulations, we show that both refraction and absorption of light by the bacterium contribute to the observed signal. By administering antibiotics that kill the bacteria, we show that the variance of the detected fluctuations vanishes within 1 h, indicating the potential of this technique for rapid sensing of bacterial antibiotic susceptibility. We envisage the use of this method for massively parallelizable AST tests and fast detection of drug-resistant pathogens.
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Affiliation(s)
- Ireneusz Rosłon
- Delft University of Technology, Mekelweg 2, Delft 2628 CD, the Netherlands
- SoundCell B.V., Raamweg 20D, The Hague 2596HL, the Netherlands
| | - Aleksandre Japaridze
- Delft University of Technology, Mekelweg 2, Delft 2628 CD, the Netherlands
- SoundCell B.V., Raamweg 20D, The Hague 2596HL, the Netherlands
| | - Stef Rodenhuis
- Delft University of Technology, Mekelweg 2, Delft 2628 CD, the Netherlands
| | - Lieke Hamoen
- Delft University of Technology, Mekelweg 2, Delft 2628 CD, the Netherlands
| | | | - Peter Steeneken
- Delft University of Technology, Mekelweg 2, Delft 2628 CD, the Netherlands
| | - Cees Dekker
- Delft University of Technology, Mekelweg 2, Delft 2628 CD, the Netherlands
| | - Farbod Alijani
- Delft University of Technology, Mekelweg 2, Delft 2628 CD, the Netherlands
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31
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Lin R, Xing Z, Liu X, Chai Q, Xin Z, Huang M, Zhu C, Luan C, Gao H, Du Y, Deng X, Zhang H, Ma D. Performance of targeted next-generation sequencing in the detection of respiratory pathogens and antimicrobial resistance genes for children. J Med Microbiol 2023; 72. [PMID: 37910007 DOI: 10.1099/jmm.0.001771] [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: 11/03/2023] Open
Abstract
Introduction. Respiratory tract infection, which is associated with high morbidity and mortality, occurs frequently in children. At present, the main diagnostic method is culture. However, the low pathogen detection rate of the culture approach prevents timely and accurate diagnosis. Fortunately, next-generation sequencing (NGS) can compensate for the deficiency of culture, and its application in clinical diagnostics has become increasingly available.Gap Statement. Targeted NGS (tNGS) is a platform that can select and enrich specific regions before data enter the NGS pipeline. However, the performance of tNGS in the detection of respiratory pathogens and antimicrobial resistance genes (ARGs) in infections in children is unclear.Aim and methodology. In this study, we estimated the performance of tNGS in the detection of respiratory pathogens and ARGs in 47 bronchoalveolar lavage fluid (BALF) specimens from children using conventional culture and antimicrobial susceptibility testing (AST) as the gold standard.Results. RPIP (Respiratory Pathogen ID/AMR enrichment) sequencing generated almost 500 000 reads for each specimen. In the detection of pathogens, RPIP sequencing showed targeted superiority in detecting difficult-to-culture bacteria, including Mycoplasma pneumoniae. Compared with the results of culture, the sensitivity and specificity of RPIP were 84.4 % (confidence interval 70.5-93.5 %) and 97.7 % (95.9 -98.8%), respectively. Moreover, RPIP results showed that a single infection was detected in 10 of the 47 BALF specimens, and multiple infections were detected in 34, with the largest number of bacterial/viral coinfections. Nevertheless, there were also three specimens where no pathogen was detected. Furthermore, we analysed the drug resistance genes of specimens containing Streptococcus pneumoniae, which was detected in 25 out of 47 specimens in the study. A total of 58 ARGs associated with tetracycline, macrolide-lincosamide-streptogramin, beta-lactams, sulfonamide and aminoglycosides were identified by RPIP in 19 of 25 patients. Using the results of AST as a standard, the coincidence rates of erythromycin, tetracycline, penicillin and sulfonamides were 89.5, 79.0, 36.8 and 42.1 %, respectively.Conclusion. These results demonstrated the superiority of RPIP in pathogen detection, particularly for multiple and difficult-to-culture pathogens, as well as in predicting resistance to erythromycin and tetracycline, which has significance for the accurate diagnosis of pathogenic infection and in the guidance of clinical treatment.
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Affiliation(s)
- Ruihong Lin
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Zhihao Xing
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Xiaorong Liu
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Qiang Chai
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Zefeng Xin
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Meng Huang
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Chunqing Zhu
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Ce Luan
- Department of Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing 400042, PR China
| | - Hongdan Gao
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Yao Du
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Xuwen Deng
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Hetong Zhang
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
| | - Dongli Ma
- Shenzhen Pediatrics Institute of Shantou University Medical College, Shenzhen 518026, Guangdong, PR China
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Zhang X, Yang Q, Ma L, Zhang D, Lin W, Schlensky N, Cheng H, Zheng Y, Luo X, Ding C, Zhang Y, Hou X, Lu F, Yan H, Wang R, Li CZ, Qu K. Automatically showing microbial growth kinetics with a high-performance microbial growth analyzer. Biosens Bioelectron 2023; 239:115626. [PMID: 37643493 DOI: 10.1016/j.bios.2023.115626] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/11/2023] [Accepted: 08/20/2023] [Indexed: 08/31/2023]
Abstract
It is difficult to show microbial growth kinetics online when they grow in complex matrices. We presented a novel strategy to address this challenge by developing a high-performance microbial growth analyzer (HPMGA), which employed a unique 32-channel capacitively coupled contactless conductivity detector as a sensing element and fixed with a CellStatz software. It was capable of online showing accurate and repeatable growth curves of well-dispersed and bad-dispersed microbes, whether they grew in homogeneous simple culture broth or heterogeneous complex matrices. Moreover, it could automatically report key growth kinetics parameters. In comparison to optical density (OD), plate counting and broth microdilution (BMD) methods, we demonstrated its practicability in five scenarios: 1) the illustration of the growth, growth rate, and acceleration curves of Escherichia coli (E. coli); 2) the antimicrobial susceptibility testing (AST) of Oxacillin against Staphylococcus aureus (S. aureus); 3) the determination of Ag nanoparticle toxicity on Providencia rettgeri (P. rettgeri); 4) the characterization of milk fermentation; and 5) the enumeration of viable pathogenic Vibrio in shrimp body. Results highlighted that the HPMGA method had the advantages of universality and effectivity. This technology would significantly facilitate the routine analysis of microbial growth in many fields (biology, medicine, clinic, life, food, environment, and ecology), paving an avenue for microbiologists to achieve research goals that have been inhibited for years due to a lack of practical analytical methods.
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Affiliation(s)
- Xuzhi Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Qianqian Yang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Liangyu Ma
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Dahai Zhang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China.
| | - Wentao Lin
- eDAQ Pty Ltd, 6 Doig Ave, Denistone East, NSW, 2112, Australia
| | - Nick Schlensky
- eDAQ Pty Ltd, 6 Doig Ave, Denistone East, NSW, 2112, Australia
| | - Hongrui Cheng
- College of Chemistry, Fuzhou University, Fuzhou, 350116, China
| | - Yuanhui Zheng
- College of Chemistry, Fuzhou University, Fuzhou, 350116, China.
| | - Xiliang Luo
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Caifeng Ding
- College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Yan Zhang
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Xiangyi Hou
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Feng Lu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Hua Yan
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Ruoju Wang
- Key Laboratory of Marine Chemistry Theory and Technology, Ministry of Education, Ocean University of China, Qingdao, 266100, China
| | - Chen-Zhong Li
- Biosensors & Bioelectronics Center, Biomedical Engineering, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen, 518172, China.
| | - Keming Qu
- Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
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Song S, Jang H, Lee D, Jeong W, Bae EH, Kim H, Choi YS, Shin M, Kim SM, Jeon TJ. Portable Colorimetric Hydrogel Beads for Point-of-Care Antimicrobial Susceptibility Testing. ACS Sens 2023; 8:3754-3761. [PMID: 37801584 DOI: 10.1021/acssensors.3c01155] [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: 10/08/2023]
Abstract
Sepsis is a life-threatening condition with systemic inflammatory responses caused by bacterial infections. Considering the emergence of antibiotic-resistant bacteria such as methicillin-resistant Staphylococcus aureus (MRSA), sepsis is a great threat to public health. The gold standard methods for antimicrobial susceptibility testing (AST), however, take at least approximately 3 days to implement the entire blood culture, pure culture, and AST processes. To overcome the time-consuming nature of conventional AST, a method employing a chromatic biosensor composed of poly(diacetylene), alginate, and LB broth (PAL) is introduced in this study. Compared to the gold standards, AST with PAL biosensors can be completed within a time frame as short as 16 h. Such a significant reduction in time is possible because the consecutive cultures and AST are carried out simultaneously by encapsulating the bacterial nutrients and detection molecules into a single component. The bead-like hydrogel sensors were used in their freeze-dried form, which endows them with portability and stability, thus making them adequate for point-of-care testing. The PAL biosensor yields minimum inhibitory concentrations comparable to those from the Clinical and Laboratory Standards Institute, and the applicability of the biosensor is further shown in MRSA-infected mice.
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Affiliation(s)
- Seoyoon Song
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Huisoo Jang
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Deborah Lee
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Woojin Jeong
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
| | - Eun Hwan Bae
- Department of Microbiology, College of Medicine, Inha University, Incheon 22212, Republic of Korea
| | - Hoon Kim
- Department of Emergency Medicine, Inje University Ilsan Paik Hospital, Goyang, Gyeonggi-do 10380, Republic of Korea
| | - Yong Sung Choi
- Department of Pediatrics, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Minhye Shin
- Department of Microbiology, College of Medicine, Inha University, Incheon 22212, Republic of Korea
| | - Sun Min Kim
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
- Department of Mechanical Engineering, Inha University, Incheon 22212, Republic of Korea
| | - Tae-Joon Jeon
- Department of Biological Sciences and Bioengineering, Inha University, Incheon 22212, Republic of Korea
- Department of Biological Engineering, Inha University, Incheon 22212, Republic of Korea
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Yamin D, Uskoković V, Wakil AM, Goni MD, Shamsuddin SH, Mustafa FH, Alfouzan WA, Alissa M, Alshengeti A, Almaghrabi RH, Fares MAA, Garout M, Al Kaabi NA, Alshehri AA, Ali HM, Rabaan AA, Aldubisi FA, Yean CY, Yusof NY. Current and Future Technologies for the Detection of Antibiotic-Resistant Bacteria. Diagnostics (Basel) 2023; 13:3246. [PMID: 37892067 PMCID: PMC10606640 DOI: 10.3390/diagnostics13203246] [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: 09/30/2023] [Revised: 10/14/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
Antibiotic resistance is a global public health concern, posing a significant threat to the effectiveness of antibiotics in treating bacterial infections. The accurate and timely detection of antibiotic-resistant bacteria is crucial for implementing appropriate treatment strategies and preventing the spread of resistant strains. This manuscript provides an overview of the current and emerging technologies used for the detection of antibiotic-resistant bacteria. We discuss traditional culture-based methods, molecular techniques, and innovative approaches, highlighting their advantages, limitations, and potential future applications. By understanding the strengths and limitations of these technologies, researchers and healthcare professionals can make informed decisions in combating antibiotic resistance and improving patient outcomes.
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Affiliation(s)
- Dina Yamin
- Al-Karak Public Hospital, Karak 61210, Jordan;
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
| | - Vuk Uskoković
- TardigradeNano LLC., Irvine, CA 92604, USA;
- Department of Mechanical Engineering, San Diego State University, San Diego, CA 92182, USA
| | - Abubakar Muhammad Wakil
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, University Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia;
- Department of Veterinary Physiology and Biochemistry, Faculty of Veterinary Medicine, University of Maiduguri, Maiduguri 600104, Borno, Nigeria
| | - Mohammed Dauda Goni
- Public Health and Zoonoses Research Group, Faculty of Veterinary Medicine, University Malaysia Kelantan, Pengkalan Chepa 16100, Kelantan, Malaysia;
| | - Shazana Hilda Shamsuddin
- Department of Pathology, School of Medical Sciences, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia;
| | - Fatin Hamimi Mustafa
- Department of Electronic & Computer Engineering, Faculty of Electrical Engineering, University Teknologi Malaysia, Johor Bharu 81310, Johor, Malaysia;
| | - Wadha A. Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait;
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Mohammed Alissa
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia;
| | - Amer Alshengeti
- Department of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi Arabia;
- Department of Infection Prevention and Control, Prince Mohammad Bin Abdulaziz Hospital, National Guard Health Affairs, Al-Madinah 41491, Saudi Arabia
| | - Rana H. Almaghrabi
- Pediatric Department, Prince Sultan Medical Military City, Riyadh 12233, Saudi Arabia;
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
| | - Mona A. Al Fares
- Department of Internal Medicine, King Abdulaziz University Hospital, Jeddah 21589, Saudi Arabia;
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University, Abu Dhabi 127788, United Arab Emirates;
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi 51900, United Arab Emirates
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran 61441, Saudi Arabia;
| | - Hamza M. Ali
- Department of Medical Laboratories Technology, College of Applied Medical Sciences, Taibah University, Madinah 41411, Saudi Arabia;
| | - Ali A. Rabaan
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia;
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | | | - Chan Yean Yean
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, University Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Nik Yusnoraini Yusof
- Institute for Research in Molecular Medicine, University Sains Malaysia, Health Campus, Kubang Kerian 16150, Kelantan, Malaysia
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Elbehiry A, Marzouk E, Moussa I, Anagreyyah S, AlGhamdi A, Alqarni A, Aljohani A, Hemeg HA, Almuzaini AM, Alzaben F, Abalkhail A, Alsubki RA, Najdi A, Algohani N, Abead B, Gazzaz B, Abu-Okail A. Using Protein Fingerprinting for Identifying and Discriminating Methicillin Resistant Staphylococcus aureus Isolates from Inpatient and Outpatient Clinics. Diagnostics (Basel) 2023; 13:2825. [PMID: 37685363 PMCID: PMC10486511 DOI: 10.3390/diagnostics13172825] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/25/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
In hospitals and other clinical settings, Methicillin-resistant Staphylococcus aureus (MRSA) is a particularly dangerous pathogen that can cause serious or even fatal infections. Thus, the detection and differentiation of MRSA has become an urgent matter in order to provide appropriate treatment and timely intervention in infection control. To ensure this, laboratories must have access to the most up-to-date testing methods and technology available. This study was conducted to determine whether protein fingerprinting technology could be used to identify and distinguish MRSA recovered from both inpatients and outpatients. A total of 326 S. aureus isolates were obtained from 2800 in- and outpatient samples collected from King Faisal Specialist Hospital and Research Centre in Riyadh, Saudi Arabia, from October 2018 to March 2021. For the phenotypic identification of 326 probable S. aureus cultures, microscopic analysis, Gram staining, a tube coagulase test, a Staph ID 32 API system, and a Vitek 2 Compact system were used. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), referred to as protein fingerprinting, was performed on each bacterial isolate to determine its proteomic composition. As part of the analysis, Principal Component Analysis (PCA) and a single-peak analysis of MALDI-TOF MS software were also used to distinguish between Methicillin-sensitive Staphylococcus aureus (MSSA) and MRSA. According to the results, S. aureus isolates constituted 326 out of 2800 (11.64%) based on the culture technique. The Staph ID 32 API system and Vitek 2 Compact System were able to correctly identify 262 (80.7%) and 281 (86.2%) S. aureus strains, respectively. Based on the Oxacillin Disc Diffusion Method, 197 (62.23%) of 326 isolates of S. aureus exhibited a cefoxitin inhibition zone of less than 21 mm and an oxacillin inhibition zone of less than 10 mm, and were classified as MRSA under Clinical Laboratory Standards Institute guidelines. MALDI-TOF MS was able to correctly identify 100% of all S. aureus isolates with a score value equal to or greater than 2.00. In addition, a close relationship was found between S. aureus isolates and higher peak intensities in the mass ranges of 3990 Da, 4120 Da, and 5850 Da, which were found in MRSA isolates but absent in MSSA isolates. Therefore, protein fingerprinting has the potential to be used in clinical settings to rapidly detect and differentiate MRSA isolates, allowing for more targeted treatments and improved patient outcomes.
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Affiliation(s)
- Ayman Elbehiry
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32511, Egypt
| | - Eman Marzouk
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sulaiman Anagreyyah
- Family Medicine Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Abdulaziz AlGhamdi
- Medical Director Office, North Area Armed Forces Hospital, King Khalid Military City 39747, Saudi Arabia
| | - Ali Alqarni
- Respiratory Therapy Department, Armed Forces Hospital Dhahran, Dhahran 34641, Saudi Arabia
| | - Ahmed Aljohani
- Patient Affairs Department, Sharourah Armed Forces Hospital, Sharourah 68372, Saudi Arabia
| | - Hassan A. Hemeg
- Department of Medical Technology/Microbiology, College of Applied Medical Science, Taibah University, Madina 30001, Saudi Arabia
| | - Abdulaziz M. Almuzaini
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Adil Abalkhail
- Department of Public Health, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
| | - Roua A. Alsubki
- Department of Clinical Laboratory Science, College of Applied Medical Science, King Saud University, Riyadh 11433, Saudi Arabia
| | - Ali Najdi
- Northern Area Armed Forces Hospital, King Khalid Military City 39748, Saudi Arabia
| | - Nawaf Algohani
- Consultant Forensic Medicine, Forensic Medicine Center, Madina 42319, Saudi Arabia
| | - Banan Abead
- Support Service Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia;
| | - Bassam Gazzaz
- Patient Affairs Department, King Fahad Armed Forces Hospital, Jeddah 23311, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Medicine, College of Agriculture and Veterinary Medicine, Qassim University, Buraydah 52571, Saudi Arabia
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Baranova AA, Tyurin AP, Korshun VA, Alferova VA. Sensing of Antibiotic-Bacteria Interactions. Antibiotics (Basel) 2023; 12:1340. [PMID: 37627760 PMCID: PMC10451291 DOI: 10.3390/antibiotics12081340] [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: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
Sensing of antibiotic-bacteria interactions is an important area of research that has gained significant attention in recent years. Antibiotic resistance is a major public health concern, and it is essential to develop new strategies for detecting and monitoring bacterial responses to antibiotics in order to maintain effective antibiotic development and antibacterial treatment. This review summarizes recent advances in sensing strategies for antibiotic-bacteria interactions, which are divided into two main parts: studies on the mechanism of action for sensitive bacteria and interrogation of the defense mechanisms for resistant ones. In conclusion, this review provides an overview of the present research landscape concerning antibiotic-bacteria interactions, emphasizing the potential for method adaptation and the integration of machine learning techniques in data analysis, which could potentially lead to a transformative impact on mechanistic studies within the field.
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Affiliation(s)
| | | | | | - Vera A. Alferova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (A.A.B.); (A.P.T.); (V.A.K.)
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37
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Maganga R, Sindiyo E, Musyoki VM, Shirima G, Mmbaga BT. Comparative analysis of clinical breakpoints, normalized resistance interpretation and epidemiological cut-offs in interpreting antimicrobial resistance of Escherichia coli isolates originating from poultry in different farm types in Tanzania. Access Microbiol 2023; 5:acmi000540.v4. [PMID: 37601443 PMCID: PMC10436012 DOI: 10.1099/acmi.0.000540.v4] [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: 12/12/2022] [Accepted: 06/13/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Existing breakpoint guidelines are not optimal for interpreting antimicrobial resistance (AMR) data from animal studies and low-income countries, and therefore their utility for analysing such data is limited. There is a need to integrate diverse data sets, such as those from low-income populations and animals, to improve data interpretation. Gap statement There is very limited research on the relative merits of clinical breakpoints, epidemiological cut-offs (ECOFFs) and normalized resistance interpretation (NRI) breakpoints in interpreting microbiological data, particularly in animal studies and studies from low-income countries. Aim The aim of this study was to compare antimicrobial resistance in Escherichia coli isolates using ECOFFs, CLSI and NRI breakpoints. Methodology A total of 59 non-repetitive poultry isolates were selected for investigation based on lactose fermentation on MacConkey agar and subsequent identification and confirmation as E. coli using chromogenic agar and uidA PCR. Kirby Bauer disc diffusion was used for susceptibility testing. For each antimicrobial agent, inhibition zone diameters were measured, and ECOFFs, CLSI and NRI bespoke breakpoints were used for resistance interpretation. Results According to the interpretation of all breakpoints except ECOFFs, tetracycline resistance was significantly higher (TET) (67.8 -69.5 %), than those for ciprofloxacin (CIPRO) (18.6 -32.2 %), imipenem (IMI) (3.4 -35 %) and ceftazidime (CEF) (1.7 -45.8 %). Prevalence estimates of AMR using CLSI and NRI bespoke breakpoints did not differ for CEF (1.7 % CB and 1.7 % COWT), IMI (3.4 % CB and 4.0 % COWT) and TET (67.8 % CB and 69.5 % COWT). However, with ECOFFs, AMR estimates for CEF, IMI and CIP were significantly higher (45.8, 35.6 and 64.4 %, respectively; P<0.05). Across all the three breakpoints, resistance to ciprofloxacin varied significantly (32.2 % CB, 64.4 % ECOFFs and 18.6 % COWT, P<0.05). Conclusion AMR interpretation is influenced by the breakpoint used, necessitating further standardization, especially for microbiological breakpoints, in order to harmonize outputs. The AMR ECOFF estimates in the present study were significantly higher compared to CLSI and NRI.
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Affiliation(s)
- Ruth Maganga
- University of Birmingham, Birmingham, B15 2TT, UK
- University of Glasgow, Glasgow, G12 8QQ, UK
- Kilimanjaro Christian Medical Center/Kilimanjaro Clinical Research Institute, PO Box 2236, Moshi, Tanzania
| | - Emmanuel Sindiyo
- The Nelson Mandela African Institution of Science and Technology, PO Box 447, Arusha, Tanzania
| | - Victor Moses Musyoki
- Department of Medical Microbiology, University of Nairobi, PO Box 19676-00202, Nairobi, Kenya
| | - Gabriel Shirima
- The Nelson Mandela African Institution of Science and Technology, PO Box 447, Arusha, Tanzania
| | - Blandina T. Mmbaga
- Kilimanjaro Christian Medical Center/Kilimanjaro Clinical Research Institute, PO Box 2236, Moshi, Tanzania
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Hisada A, Matsumoto E, Hirano R, Konomi M, Bou Khalil JY, Raoult D, Ominami Y. Detection of antimicrobial impact on gram-negative bacterial cell envelope based on single-cell imaging by scanning electron microscopy. Sci Rep 2023; 13:11258. [PMID: 37438469 DOI: 10.1038/s41598-023-38198-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
Rapid determination of drug efficacy against bacterial pathogens is needed to detect potentially resistant bacteria and allow for more rational use of antimicrobials. As an indicator of the antimicrobial effect for rapid detection, we found changes in image brightness in antimicrobial-affected bacteria by scanning electron microscopy (SEM). The cell envelopes of unaffected bacteria were stained with phosphotungstic acid (PTA), whereas the entire cells of affected bacteria were stained. Since tungsten density increases backscattered electron intensity, brighter bacterial images indicate lethal damage. We propose a simplified method for determining antimicrobial efficacy by detecting damage that occurs immediately after drug administration using tabletop SEM. This method enabled the visualization of microscopic deformations while distinguishing bacterial-cell-envelope damage on gram-negative bacteria due to image-brightness change. Escherichia coli, Acinetobacter baumannii, Enterobacter cloacae, Klebsiella pneumoniae, and Pseudomonas aeruginosa were exposed to imipenem and colistin, which affect the cell envelope through different mechanisms. Classification of single-cell images based on brightness was quantified for approximately 500 bacteria per sample, and the bright images predominated within 5 to 60 min of antimicrobial treatment, depending on the species. Using intracellular PTA staining and characteristic deformations as indicators, it was possible to determine the efficacy of antimicrobials in causing bacterial-cell-envelope damage.
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Affiliation(s)
- Akiko Hisada
- Healthcare Innovation Center, Research and Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji-shi, Tokyo, 185-8601, Japan.
| | - Erino Matsumoto
- Healthcare Innovation Center, Research and Development Group, Hitachi, Ltd., 1-280, Higashi-Koigakubo, Kokubunji-shi, Tokyo, 185-8601, Japan
| | - Ryo Hirano
- Core Technology and Solutions Group, Hitachi High-Tech Corporation, Tokyo, 105-6409, Japan
| | - Mami Konomi
- Core Technology and Solutions Group, Hitachi High-Tech Corporation, Tokyo, 105-6409, Japan
| | | | - Didier Raoult
- Consulting Infection Marseille, 13008, Marseille, France
| | - Yusuke Ominami
- Core Technology and Solutions Group, Hitachi High-Tech Corporation, Tokyo, 105-6409, Japan
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Guliy OI, Zaitsev BD, Borodina IA. Electroacoustic Biosensor Systems for Evaluating Antibiotic Action on Microbial Cells. SENSORS (BASEL, SWITZERLAND) 2023; 23:6292. [PMID: 37514587 PMCID: PMC10383298 DOI: 10.3390/s23146292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/07/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023]
Abstract
Antibiotics are widely used to treat infectious diseases. This leads to the presence of antibiotics and their metabolic products in the ecosystem, especially in aquatic environments. In many countries, the growth of pathogen resistance to antibiotics is considered a threat to national security. Therefore, methods for determining the sensitivity/resistance of bacteria to antimicrobial drugs are important. This review discusses the mechanisms of the formation of antibacterial resistance and the various methods and sensor systems available for analyzing antibiotic effects on bacteria. Particular attention is paid to acoustic biosensors with active immobilized layers and to sensors that analyze antibiotics directly in liquids. It is shown that sensors of the second type allow analysis to be done within a short period, which is important for timely treatment.
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Affiliation(s)
- Olga I Guliy
- Institute of Biochemistry and Physiology of Plants and Microorganisms-Subdivision of the Federal State Budgetary Research Institution Saratov Federal Scientific Centre of the Russian Academy of Sciences (IBPPM RAS), Saratov 410049, Russia
| | - Boris D Zaitsev
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Saratov Branch, Saratov 410019, Russia
| | - Irina A Borodina
- Kotelnikov Institute of Radio Engineering and Electronics, Russian Academy of Sciences, Saratov Branch, Saratov 410019, Russia
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40
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Troiano C, De Ninno A, Casciaro B, Riccitelli F, Park Y, Businaro L, Massoud R, Mangoni ML, Bisegna P, Stella L, Caselli F. Rapid Assessment of Susceptibility of Bacteria and Erythrocytes to Antimicrobial Peptides by Single-Cell Impedance Cytometry. ACS Sens 2023. [PMID: 37421371 PMCID: PMC10391704 DOI: 10.1021/acssensors.3c00256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2023]
Abstract
Antimicrobial peptides (AMPs) represent a promising class of compounds to fight antibiotic-resistant infections. In most cases, they kill bacteria by making their membrane permeable and therefore exhibit low propensity to induce bacterial resistance. In addition, they are often selective, killing bacteria at concentrations lower than those at which they are toxic to the host. However, clinical applications of AMPs are hindered by a limited understanding of their interactions with bacteria and human cells. Standard susceptibility testing methods are based on the analysis of the growth of a bacterial population and therefore require several hours. Moreover, different assays are required to assess the toxicity to host cells. In this work, we propose the use of microfluidic impedance cytometry to explore the action of AMPs on both bacteria and host cells in a rapid manner and with single-cell resolution. Impedance measurements are particularly well-suited to detect the effects of AMPs on bacteria, due to the fact that the mechanism of action involves perturbation of the permeability of cell membranes. We show that the electrical signatures of Bacillus megaterium cells and human red blood cells (RBCs) reflect the action of a representative antimicrobial peptide, DNS-PMAP23. In particular, the impedance phase at high frequency (e.g., 11 or 20 MHz) is a reliable label-free metric for monitoring DNS-PMAP23 bactericidal activity and toxicity to RBCs. The impedance-based characterization is validated by comparison with standard antibacterial activity assays and absorbance-based hemolytic activity assays. Furthermore, we demonstrate the applicability of the technique to a mixed sample of B. megaterium cells and RBCs, which paves the way to study AMP selectivity for bacterial versus eukaryotic cells in the presence of both cell types.
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Affiliation(s)
- Cassandra Troiano
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Adele De Ninno
- Institute for Photonics and Nanotechnologies, Italian National Research Council, 00133 Rome, Italy
| | - Bruno Casciaro
- Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185 Rome, Italy
| | - Francesco Riccitelli
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Yoonkyung Park
- Department of Biomedical Science, College of Natural science, Chosun University, Gwangju 61452, Republic of Korea
| | - Luca Businaro
- Institute for Photonics and Nanotechnologies, Italian National Research Council, 00133 Rome, Italy
| | - Renato Massoud
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Maria Luisa Mangoni
- Laboratory affiliated to Pasteur Italia-Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 00185 Rome, Italy
| | - Paolo Bisegna
- Department of Civil Engineering and Computer Science, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Federica Caselli
- Department of Civil Engineering and Computer Science, University of Rome Tor Vergata, 00133 Rome, Italy
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Doganay MT, Chelliah CJ, Tozluyurt A, Hujer AM, Obaro SK, Gurkan U, Patel R, Bonomo RA, Draz M. 3D Printed Materials for Combating Antimicrobial Resistance. MATERIALS TODAY (KIDLINGTON, ENGLAND) 2023; 67:371-398. [PMID: 37790286 PMCID: PMC10545363 DOI: 10.1016/j.mattod.2023.05.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Three-dimensional (3D) printing is a rapidly growing technology with a significant capacity for translational applications in both biology and medicine. 3D-printed living and non-living materials are being widely tested as a potential replacement for conventional solutions for testing and combating antimicrobial resistance (AMR). The precise control of cells and their microenvironment, while simulating the complexity and dynamics of an in vivo environment, provides an excellent opportunity to advance the modeling and treatment of challenging infections and other health conditions. 3D-printing models the complicated niches of microbes and host-pathogen interactions, and most importantly, how microbes develop resistance to antibiotics. In addition, 3D-printed materials can be applied to testing and delivering antibiotics. Here, we provide an overview of 3D printed materials and biosystems and their biomedical applications, focusing on ever increasing AMR. Recent applications of 3D printing to alleviate the impact of AMR, including developed bioprinted systems, targeted bacterial infections, and tested antibiotics are presented.
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Affiliation(s)
- Mert Tunca Doganay
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Cyril John Chelliah
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Abdullah Tozluyurt
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Andrea M Hujer
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
| | | | - Umut Gurkan
- Mechanical and Aerospace Engineering Department, Case Western Reserve University, Cleveland, Ohio, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology and Division of Public Health, Infectious Diseases, and Occupational medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robert A Bonomo
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Research Service, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, OH, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES) Cleveland, OH, USA
| | - Mohamed Draz
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
- Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA
- Department of Biomedical Engineering, Cleveland Clinic, Cleveland, OH 44106, USA
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Fontana C, Favaro M, Pelliccioni M, Minelli S, Bossa MC, Altieri A, D'Orazi C, Paliotta F, Cicchetti O, Minieri M, Prezioso C, Limongi D, D'agostini C. Laboratory Automation in Microbiology: Impact on Turnaround Time of Microbiological Samples in COVID Time. Diagnostics (Basel) 2023; 13:2243. [PMID: 37443637 DOI: 10.3390/diagnostics13132243] [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: 05/10/2023] [Revised: 06/08/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
BACKGROUND Laboratory Automation (LA) is an innovative technology that is currently available for microbiology laboratories. LA can be a game changer by revolutionizing laboratory workflows through efficiency improvement and is also effective in the organization and standardization of procedures, enabling staff requalification. It can provide an important return on investment (time spent redefining the workflow as well as direct costs of instrumentation) in the medium to long term. METHODS Here, we present our experience with the WASPLab® system introduced in our lab during the COVID-19 pandemic. We evaluated the impact due to the system by comparing the TAT recorded on our samples before, during, and after LA introduction (from 2019 to 2021). We focused our attention on blood cultures (BCs) and biological fluid samples (BLs). RESULTS TAT recorded over time showed a significant decrease: from 97 h to 53.5 h (Δ43.5 h) for BCs and from 73 h to 58 h (Δ20 h) for BLs. Despite the introduction of the WASPLab® system, we have not been able to reduce the number of technical personnel units dedicated to the microbiology lab, but WASPLab® has allowed us to direct some of the staff resources toward other laboratory activities, including those required by the pandemic. CONCLUSIONS LA can significantly enhance laboratory performance and, due to the significant reduction in reporting time, can have an effective impact on clinical choices and therefore on patient outcomes. Therefore, the initial costs of LA adoption must be considered worthwhile.
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Affiliation(s)
- Carla Fontana
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, 00149 Rome, Italy
| | - Marco Favaro
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
| | - Marco Pelliccioni
- Laboratory of Microbiology, Polyclinic of "Tor Vergata", 00133 Rome, Italy
| | - Silvia Minelli
- Laboratory of Microbiology, Polyclinic of "Tor Vergata", 00133 Rome, Italy
| | | | - Anna Altieri
- Laboratory of Microbiology, Polyclinic of "Tor Vergata", 00133 Rome, Italy
| | - Carlo D'Orazi
- Laboratory of Microbiology, Polyclinic of "Tor Vergata", 00133 Rome, Italy
| | - Federico Paliotta
- Laboratory of Microbiology, Polyclinic of "Tor Vergata", 00133 Rome, Italy
| | - Oriana Cicchetti
- Laboratory of Microbiology, Polyclinic of "Tor Vergata", 00133 Rome, Italy
| | - Marilena Minieri
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Department of Laboratory Medicine, Polyclinic Tor Vergata, Viale Oxford 81, 00133 Rome, Italy
| | - Carla Prezioso
- Laboratory of Microbiology of Chronic-Neurodegenerative Diseases, IRCCS San Raffaele Roma, 00166 Rome, Italy
| | - Dolores Limongi
- Laboratory of Microbiology of Chronic-Neurodegenerative Diseases, IRCCS San Raffaele Roma, 00166 Rome, Italy
- Department of Human Sciences and Quality of Life Promotion, San Raffaele University, 00166 Rome, Italy
| | - Cartesio D'agostini
- Department of Experimental Medicine, University of Rome Tor Vergata, 00133 Rome, Italy
- Laboratory of Microbiology, Polyclinic of "Tor Vergata", 00133 Rome, Italy
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Humphries RM, Miller L, Zimmer B, Matuschek E, Hindler JA. Contemporary Considerations for Establishing Reference Methods for Antibacterial Susceptibility Testing. J Clin Microbiol 2023; 61:e0188622. [PMID: 36971571 PMCID: PMC10281161 DOI: 10.1128/jcm.01886-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
Antibacterial susceptibility testing (AST) is performed to guide therapy, perform resistance surveillance studies, and support development of new antibacterial agents. For 5 decades, broth microdilution (BMD) has served as the reference method to assess in vitro activity of antibacterial agents against which both novel agents and diagnostic tests have been measured. BMD relies on in vitro inhibition or killing of bacteria. It is associated with several limitations: it is a poor mimic of the in vivo milieu of bacterial infections, requires multiple days to perform, and is associated with subtle, difficult to control variability. In addition, new reference methods will soon be needed for novel agents whose activity cannot be evaluated by BMD (e.g., those that target virulence). Any new reference methods must be standardized, correlated with clinical efficacy and be recognized internationally by researchers, industry, and regulators. Herein, we describe current reference methods for in vitro assessment of antibacterial activity and highlight key considerations for the generation of novel reference methods.
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Affiliation(s)
- Romney M. Humphries
- Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Linda Miller
- CMID Pharma Consulting, LLC, Dresher, Pennsylvania, USA
| | - Barbara Zimmer
- Beckman Coulter Microbiology, Sacramento, California, USA
| | | | - Janet A. Hindler
- Los Angeles County Department of Public Health, Public Health Laboratory, Los Angeles, California, USA
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Atassi G, Medernach R, Scheetz M, Nozick S, Rhodes NJ, Murphy-Belcaster M, Murphy KR, Alisoltani A, Ozer EA, Hauser AR. Genomics of Aminoglycoside Resistance in Pseudomonas aeruginosa Bloodstream Infections at a United States Academic Hospital. Microbiol Spectr 2023; 11:e0508722. [PMID: 37191517 PMCID: PMC10269721 DOI: 10.1128/spectrum.05087-22] [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: 12/12/2022] [Accepted: 04/22/2023] [Indexed: 05/17/2023] Open
Abstract
Pseudomonas aeruginosa frequently becomes resistant to aminoglycosides by the acquisition of aminoglycoside modifying enzyme (AME) genes and the occurrence of mutations in the mexZ, fusA1, parRS, and armZ genes. We examined resistance to aminoglycosides in a collection of 227 P. aeruginosa bloodstream isolates collected over 2 decades from a single United States academic medical institution. Resistance rates of tobramycin and amikacin were relatively stable over this time, while the resistance rates of gentamicin were somewhat more variable. For comparison, we examined resistance rates to piperacillin-tazobactam, cefepime, meropenem, ciprofloxacin, and colistin. Resistance rates to the first four antibiotics were also stable, although uniformly higher for ciprofloxacin. Colistin resistance rates were initially quite low, rose substantially, and then began to decrease at the end of the study. Clinically relevant AME genes were identified in 14% of isolates, and mutations predicted to cause resistance were relatively common in the mexZ and armZ genes. In a regression analysis, resistance to gentamicin was associated with the presence of at least one gentamicin-active AME gene and significant mutations in mexZ, parS, and fusA1. Resistance to tobramycin was associated with the presence of at least one tobramycin-active AME gene. An extensively drug-resistant strain, PS1871, was examined further and found to contain five AME genes, most of which were within clusters of antibiotic resistance genes embedded in transposable elements. These findings demonstrate the relative contributions of aminoglycoside resistance determinants to P. aeruginosa susceptibilities at a United States medical center. IMPORTANCE Pseudomonas aeruginosa is frequently resistant to multiple antibiotics, including aminoglycosides. The rates of resistance to aminoglycosides in bloodstream isolates collected over 2 decades at a United States hospital remained constant, suggesting that antibiotic stewardship programs may be effective in countering an increase in resistance. Mutations in the mexZ, fusA1, parR, pasS, and armZ genes were more common than acquisition of genes encoding aminoglycoside modifying enzymes. The whole-genome sequence of an extensively drug resistant isolate indicates that resistance mechanisms can accumulate in a single strain. Together, these results suggest that aminoglycoside resistance in P. aeruginosa remains problematic and confirm known resistance mechanisms that can be targeted for the development of novel therapeutics.
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Affiliation(s)
- Giancarlo Atassi
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rachel Medernach
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Marc Scheetz
- Department of Pharmacy Practice, Pharmacometrics Center of Excellence, Chicago College of Pharmacy, Midwestern University, Downers Grove, Illinois, USA
| | - Sophia Nozick
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Nathaniel J. Rhodes
- Pharmacometrics Center of Excellence, College of Graduate Studies, Department of Pharmacology, Midwestern University, Downers Grove, Illinois, USA
| | - Megan Murphy-Belcaster
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Katherine R. Murphy
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Arghavan Alisoltani
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A. Ozer
- Department of Medicine (Division of Infectious Diseases), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alan R. Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine (Division of Infectious Diseases), Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Neuenschwander FR, Groß B, Schubert S. Rapid Antibiotic Susceptibility Testing of Gram-Negative Bacteria Directly from Urine Samples of UTI Patients Using MALDI-TOF MS. Antibiotics (Basel) 2023; 12:1042. [PMID: 37370361 DOI: 10.3390/antibiotics12061042] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Urinary tract infections (UTIs) are one of the most common human infections and are most often caused by Gram-negative bacteria such as Escherichia coli. In view of the increasing number of antibiotic-resistant isolates, rapidly initiating effective antibiotic therapy is essential. Therefore, a faster antibiotic susceptibility test (AST) is desirable. The MALDI-TOF MS-based phenotypic antibiotic susceptibility test (MALDI AST) has been used in blood culture diagnostics to rapidly detect antibiotic susceptibility. This study demonstrates for the first time that MALDI AST can be used to rapidly determine antibiotic susceptibility in UTIs directly from patients' urine samples. MALDI-TOF MS enables the rapid identification and AST of Gram-negative UTIs within 4.5 h of receiving urine samples. Six urinary tract infection antibiotics, including ciprofloxacin, cotrimoxazole, fosfomycin, meropenem, cefuroxime, and nitrofurantoin, were analyzed and compared with conventional culture-based AST methods. A total of 105 urine samples from UTI patients contained bacterial isolates for MALDI AST. The combination of ID and AST by MALDI-TOF allowed us to interpret the result according to EUCAST guidelines. An overall agreement of 94.7% was found between MALDI AST and conventional AST for the urinary tract pathogens tested.
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Affiliation(s)
- Felix R Neuenschwander
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
| | - Birgit Groß
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
| | - Sören Schubert
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
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Katzenstein TL, Faurholt-Jepsen D, Qvist T, Jensen PØ, Pressler T, Johansen HK, Kolpen M. Antimicrobial resistance of Pseudomonas aeruginosa in a cystic fibrosis population after introduction of a novel cephalosporin/β-lactamase inhibitor combination. APMIS 2023. [PMID: 37294911 DOI: 10.1111/apm.13331] [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: 06/06/2023] [Accepted: 06/06/2023] [Indexed: 06/11/2023]
Abstract
Ceftolozane-tazobactam is a new β-lactam/β-lactamase inhibitor combination approved by the U.S. Food and Drug Administration in 2019 for the treatment of hospital-acquired and ventilator-associated pneumonia. The combination is a particularly potent inhibitor of penicillin-binding proteins with higher affinity than other β-lactam agents. Persons with cystic fibrosis (pwCF) often harbour resistant Gram-negative bacteria in the airways and need antibiotics to prevent declining lung function. To test whether the introduction of ceftolozane-tazobactam in the period 2015-2020 led to a bacterial population level increase in cephalosporin resistance in a Danish CF population. In vitro, activity of ceftolozane-tazobactam was evaluated by susceptibility testing of clinical Pseudomonas aeruginosa isolated from pwCF from January 1, 2015, to June 1, 2020. Six thousand three hundred thirty two isolates collected from 210 adult pwCF were included. Thirty pwCF were treated with ceftolozane-tazobactam at least once. Ceftolozane-tazobactam exposure did not increase cephalosporin resistance on an individual or population level. However, resistance to ceftolozane-tazobactam was recorded despite no prior exposure in four pwCF. Compared to ceftazidime, ceftolozane-tazobactam had a better in vitro activity on P. aeruginosa. The percentage of non-mucoid P. aeruginosa isolates susceptible to ceftolozane-tazobactam were higher or equal to 5 other β-lactams. Ceftolozane-tazobactam expands the armamentaria against P. aeruginosa with acceptable levels for a selection of drug resistance.
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Affiliation(s)
| | | | - Tavs Qvist
- Department of Infectious Diseases, Rigshospitalet, Copenhagen, Denmark
| | - Peter Østrup Jensen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | | | - Helle Krogh Johansen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen, Denmark
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Marutescu LG. Current and Future Flow Cytometry Applications Contributing to Antimicrobial Resistance Control. Microorganisms 2023; 11:1300. [PMID: 37317273 DOI: 10.3390/microorganisms11051300] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/16/2023] Open
Abstract
Antimicrobial resistance is a global threat to human health and welfare, food safety, and environmental health. The rapid detection and quantification of antimicrobial resistance are important for both infectious disease control and public health threat assessment. Technologies such as flow cytometry can provide clinicians with the early information, they need for appropriate antibiotic treatment. At the same time, cytometry platforms facilitate the measurement of antibiotic-resistant bacteria in environments impacted by human activities, enabling assessment of their impact on watersheds and soils. This review focuses on the latest applications of flow cytometry for the detection of pathogens and antibiotic-resistant bacteria in both clinical and environmental samples. Novel antimicrobial susceptibility testing frameworks embedding flow cytometry assays can contribute to the implementation of global antimicrobial resistance surveillance systems that are needed for science-based decisions and actions.
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Affiliation(s)
- Luminita Gabriela Marutescu
- Department of Botany and Microbiology, Faculty of Biology, University of Bucharest, 91-95 Spl. Independentei, 050095 Bucharest, Romania
- Research Institute of the University of Bucharest, 050095 Bucharest, Romania
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Reiber C, Bodendoerfer E, Brugger SD, Eberhard N, Hitz E, Hofmaenner DA, Herren S, Kolesnik-Goldmann N, Manicini S, Zbinden R, Zinkernagel AS, Hasse B. Rapid antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales: an implementation study. Swiss Med Wkly 2023; 153:40066. [PMID: 37190876 DOI: 10.57187/smw.2023.40066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
AIMS OF THE STUDY The goal of this descriptive study was to assess the performance as well as the extent of the clinical impact of rapid automated antimicrobial susceptibility testing in patients with bacteraemia due to Enterobacterales. We also aimed to analyse how rapid automated antimicrobial susceptibility testing influences clinical decision-making. METHODS This single-centre study conducted at the University Hospital of Zurich included data from all consecutive patients with Enterobacterales bacteraemia from November 2019 to October 2020. There was no control group. The primary outcome was the effect of rapid automated antimicrobial susceptibility testing on antibiotic therapy (no adjustment, escalation to a broader-spectrum antibiotic or de-escalation to a narrower-spectrum antibiotic). Rapid automated antimicrobial susceptibility testing results were further compared to susceptibility tests using European Committee on Antimicrobial Susceptibility Testing (EUCAST) standard methods and erroneous results were noted. Additionally, we investigated turnaround times for rapid automated antimicrobial susceptibility testing and routine diagnostic testing. RESULTS We analysed 106 patients with 116 episodes of bacteraemia due to Enterobacterales, with Escherichia coli and Klebsiella pneumoniae being the most frequent isolates. Almost 8% of pathogens were multidrug resistant. Rapid automated antimicrobial susceptibility testing showed category agreement in 98.4% of all interpretable cases. A significant reduction of more than 20 h in turnaround times could be achieved with rapid automated antimicrobial susceptibility testing compared to the routine diagnostic workflow. In the majority of cases, rapid automated antimicrobial susceptibility testing had no effect, given that the empirical therapy was already correct or circumstances did not allow for de-escalation. In 38.8% of cases, antimicrobial therapy was adjusted, whereas eight cases were de-escalated based on rapid automated antimicrobial susceptibility testing alone. CONCLUSIONS Rapid automated antimicrobial susceptibility testing may be a valuable and safe way to accelerate diagnosis. In particular, time to suitable therapy can be shortened in cases of incorrect therapy. However, physicians are reluctant to de-escalate antibiotic therapy based on rapid automated antimicrobial susceptibility testing alone, limiting its impact in everyday clinics. To further explore the potential of rapid automated antimicrobial susceptibility testing, a stringent/compulsory antibiotic stewardship programme would be a valuable next step.
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Affiliation(s)
- Claudine Reiber
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Elias Bodendoerfer
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Silvio D Brugger
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nadia Eberhard
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Eva Hitz
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Daniel A Hofmaenner
- Institute of Intensive Care Medicine, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Sebastian Herren
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | | | - Stefano Manicini
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Reinhard Zbinden
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Barbara Hasse
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
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Li C, McCrone S, Warrick JW, Andes DR, Hite Z, Volk CF, Rose WE, Beebe DJ. Under-oil open microfluidic systems for rapid phenotypic antimicrobial susceptibility testing. LAB ON A CHIP 2023; 23:2005-2015. [PMID: 36883560 PMCID: PMC10581760 DOI: 10.1039/d3lc00066d] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Antimicrobial susceptibility testing (AST) remains the cornerstone of effective antimicrobial selection and optimization in patients. Despite recent advances in rapid pathogen identification and resistance marker detection with molecular diagnostics (e.g., qPCR, MALDI-TOF MS), phenotypic (i.e., microbial culture-based) AST methods - the gold standard in hospitals/clinics - remain relatively unchanged over the last few decades. Microfluidics-based phenotypic AST has been growing fast in recent years, aiming for rapid (i.e., turnaround time <8 h), high-throughput, and automated species identification, resistance detection, and antibiotics screening. In this pilot study, we describe the application of a multi-liquid-phase open microfluidic system, named under-oil open microfluidic systems (UOMS), to achieve a rapid phenotypic AST. UOMS provides an open microfluidics-based solution for rapid phenotypic AST (UOMS-AST) by implementing and recording a pathogen's antimicrobial activity in micro-volume testing units under an oil overlay. UOMS-AST allows free physical access (e.g., by standard pipetting) to the system and label-free, single-cell resolution optical access. UOMS-AST can accurately and rapidly determine antimicrobial activities [including susceptibility/resistance breakpoint and minimum inhibitory concentration (MIC)] from nominal sample/bacterial cells in a system aligned with clinical laboratory standards where open systems and optical microscopy are predominantly adopted. Further, we combine UOMS-AST with a cloud lab data analytic technique for real-time image analysis and report generation to provide a rapid (<4 h) sample-to-report turnaround time, shedding light on its utility as a versatile (e.g., low-resource setting and manual laboratory operation, or high-throughput automated system) phenotypic AST platform for hospital/clinic use.
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Affiliation(s)
- Chao Li
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sue McCrone
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Jay W. Warrick
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David R. Andes
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Medical Microbiology & Immunology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Zachary Hite
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cecilia F. Volk
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Warren E. Rose
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David J. Beebe
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Pathology and Laboratory Medicine, University of Wisconsin-Madison, Madison, WI 53705, USA
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50
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Li S, Wan C, Wang B, Chen D, Zeng W, Hong X, Li L, Pang Z, Du W, Feng X, Chen P, Li Y, Liu BF. Handyfuge Microfluidic for On-Site Antibiotic Susceptibility Testing. Anal Chem 2023; 95:6145-6155. [PMID: 36996249 DOI: 10.1021/acs.analchem.3c00557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Low-cost, rapid, and accurate acquisition of minimum inhibitory concentrations (MICs) is key to limiting the development of antimicrobial resistance (AMR). Until now, conventional antibiotic susceptibility testing (AST) methods are typically time-consuming, high-cost, and labor-intensive, making them difficult to accomplish this task. Herein, an electricity-free, portable, and robust handyfuge microfluidic chip was developed for on-site AST, termed handyfuge-AST. With simply handheld centrifugation, the bacterial-antibiotic mixtures with accurate antibiotic concentration gradients could be generated in less than 5 min. The accurate MIC values of single antibiotics (including ampicillin, kanamycin, and chloramphenicol) or their combinations against Escherichia coli could be obtained within 5 h. To further meet the growing demands of point-of-care testing, we upgraded our handyfuge-AST with a pH-based colorimetric strategy, enabling naked eye recognition or intelligent recognition with a homemade mobile app. Through a comparative study of 60 clinical data (10 clinical samples corresponding to six commonly used antibiotics), the accurate MICs by handyfuge-AST with 100% categorical agreements were achieved compared to clinical standard methods (area under curves, AUCs = 1.00). The handyfuge-AST could be used as a low-cost, portable, and robust point-of-care device to rapidly obtain accurate MIC values, which significantly limit the progress of AMR.
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Affiliation(s)
- Shunji Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Chao Wan
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bangfeng Wang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dongjuan Chen
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430070, China
| | - Wenyi Zeng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xianzhe Hong
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lina Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zheng Pang
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Wei Du
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaojun Feng
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Peng Chen
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yiwei Li
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics-Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
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