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Yadav P. Challenges & Solutions for Recent Advancements in Multi-Drugs Resistance Tuberculosis: A Review. Microbiol Insights 2023; 16:11786361231152438. [PMID: 36741475 PMCID: PMC9893349 DOI: 10.1177/11786361231152438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/05/2023] [Indexed: 01/31/2023] Open
Abstract
In MDR-TB, mycobacterium is resistant to battlefront drugs like rifampicin and isoniazid. Now it's an urgent global challenge for treatment & diagnosis because more than 50% of drugs are resistant. Till today's information, 5 reasons are liable for MDR: (1) Errors of physicians/patients in therapy management, (2) Complexity and poor vascularization of granulomatous lesions, which obstruct drug distribution to some sites, leading to resistance development, (3) Intrinsic drug resistance of tubercle bacilli, (4) Formation of non-replicating, drug-tolerant bacilli inside the granulomas, (5) Development of mutations in Mtb genes, which are the foremost important molecular mechanisms of resistance. the most contribution of this work is a brief & clear explanation of things chargeable for resistant development, and recent diagnostic & treatment methods for MDR-TB. This study shall help researchers & scientists to develop replacement rapid diagnostic tools, drugs, and treatment protocols.
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Affiliation(s)
- Pramod Yadav
- Pramod Yadav, Department of AFAF, Amity
University Noida, J-1 Block, Noida, Uttar Pradesh 201313, India. Emails:
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Bassetti M, Kanj SS, Kiratisin P, Rodrigues C, Van Duin D, Villegas MV, Yu Y. Early appropriate diagnostics and treatment of MDR Gram-negative infections. JAC Antimicrob Resist 2022; 4:dlac089. [PMID: 36111208 PMCID: PMC9469888 DOI: 10.1093/jacamr/dlac089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The term difficult-to-treat resistance has been recently coined to identify Gram-negative bacteria exhibiting resistance to all fluoroquinolones and all β-lactam categories, including carbapenems. Such bacteria are posing serious challenges to clinicians trying to identify the best therapeutic option for any given patient. Delayed appropriate therapy has been associated with worse outcomes including increase in length of stay, increase in total in-hospital costs and ∼20% increase in the risk of in-hospital mortality. In addition, time to appropriate antibiotic therapy has been shown to be an independent predictor of 30 day mortality in patients with resistant organisms. Improving and anticipating aetiological diagnosis through optimizing not only the identification of phenotypic resistance to antibiotic classes/agents, but also the identification of specific resistance mechanisms, would have a major impact on reducing the frequency and duration of inappropriate early antibiotic therapy. In light of these considerations, the present paper reviews the increasing need for rapid diagnosis of bacterial infections and efficient laboratory workflows to confirm diagnoses and facilitate prompt de-escalation to targeted therapy, in line with antimicrobial stewardship principles. Rapid diagnostic tests currently available and future perspectives for their use are discussed. Early appropriate diagnostics and treatment of MDR Gram-negative infections require a multidisciplinary approach that includes multiple different diagnostic methods and further consensus of algorithms, protocols and guidelines to select the optimal antibiotic therapy.
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Affiliation(s)
- Matteo Bassetti
- Department of Health Science, University of Genoa , Italy
- Infectious Diseases Clinic, Ospedale Policlinico San Martino Hospital – IRCCS , Genoa , Italy
| | - Souha S Kanj
- Division of Infectious Diseases, American University of Beirut Medical Center , Beirut , Lebanon
| | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University , Bangkok , Thailand
| | - Camilla Rodrigues
- Department of Microbiology, P. D. Hinduja Hospital and Medical Research Centre , Mumbai, Maharashtra , India
| | - David Van Duin
- Department of Medicine, University of North Carolina School of Medicine , Chapel Hill, NC , USA
| | - María Virginia Villegas
- Grupo de Investigaciones en Resistencia Antimicrobiana y Epidemiología Hospitalaria (RAEH), Universidad El Bosque , Bogotá DC , Colombia
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine , Hangzhou, Zhejiang , China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province , Hangzhou, Zhejiang , China
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3
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Jacobs MR, Colson JD, Rhoads DD. Recent advances in rapid antimicrobial susceptibility testing systems. Expert Rev Mol Diagn 2021; 21:563-578. [PMID: 33926351 DOI: 10.1080/14737159.2021.1924679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
INTRODUCTION Until recently antimicrobial susceptibility testing (AST) methods based on the demonstration of phenotypic susceptibility in 16-24 h remained largely unchanged. AREAS COVERED Advances in rapid phenotypic and molecular-based AST systems. EXPERT OPINION AST has changed over the past decade, with many rapid phenotypic and molecular methods developed to demonstrate phenotypic or genotypic resistance, or biochemical markers of resistance such as β-lactamases associated with carbapenem resistance. Most methods still require isolation of bacteria from specimens before both legacy and newer methods can be used. Bacterial identification by MALDI-TOF mass spectroscopy is now widely used and is often key to the interpretation of rapid AST results. Several PCR arrays are available to detect the most frequent pathogens associated with bloodstream infections and their major antimicrobial resistance genes. Many advances in whole-genome sequencing of bacteria and fungi isolated by culture as well as directly from clinical specimens have been made but are not yet widely available. High cost and limited throughput are the major obstacles to uptake of rapid methods, but targeted use, continued development and decreasing costs are expected to result in more extensive use of these increasingly useful methods.
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Affiliation(s)
- Michael R Jacobs
- Emeritus Professor of Pathology and Emeritus Medical Director, Clinical Microbiology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jordan D Colson
- Microbiology Fellow, Department of Pathology, Cleveland Clinic, Cleveland, OH, USA
| | - Daniel D Rhoads
- Section Head of Microbiology, Robert J. Tomsich Pathology & Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
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The Evolving Role of the Clinical Microbiology Laboratory in Identifying Resistance in Gram-Negative Bacteria: An Update. Infect Dis Clin North Am 2020; 34:659-676. [PMID: 33011047 DOI: 10.1016/j.idc.2020.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The evolution of resistance to antimicrobial agents in gram-negatives has challenged the role of the clinical microbiology laboratory to implement new methods for their timely detection. Recent development has enabled the use of novel methods for more rapid pathogen identification, antimicrobial susceptibility testing, and detection of resistance markers. Commonly used methods improve the rapidity of resistance detection from both cultured bacteria and specimens. This review focuses on the commercially available systems available together with their technical performance and possible clinical impact.
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Abram TJ, Cherukury H, Ou CY, Vu T, Toledano M, Li Y, Grunwald JT, Toosky MN, Tifrea DF, Slepenkin A, Chong J, Kong L, Del Pozo DV, La KT, Labanieh L, Zimak J, Shen B, Huang SS, Gratton E, Peterson EM, Zhao W. Rapid bacterial detection and antibiotic susceptibility testing in whole blood using one-step, high throughput blood digital PCR. LAB ON A CHIP 2020; 20:477-489. [PMID: 31872202 PMCID: PMC7250044 DOI: 10.1039/c9lc01212e] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Sepsis due to antimicrobial resistant pathogens is a major health problem worldwide. The inability to rapidly detect and thus treat bacteria with appropriate agents in the early stages of infections leads to excess morbidity, mortality, and healthcare costs. Here we report a rapid diagnostic platform that integrates a novel one-step blood droplet digital PCR assay and a high throughput 3D particle counter system with potential to perform bacterial identification and antibiotic susceptibility profiling directly from whole blood specimens, without requiring culture and sample processing steps. Using CTX-M-9 family ESBLs as a model system, we demonstrated that our technology can simultaneously achieve unprecedented high sensitivity (10 CFU per ml) and rapid sample-to-answer assay time (one hour). In head-to-head studies, by contrast, real time PCR and BioRad ddPCR only exhibited a limit of detection of 1000 CFU per ml and 50-100 CFU per ml, respectively. In a blinded test inoculating clinical isolates into whole blood, we demonstrated 100% sensitivity and specificity in identifying pathogens carrying a particular resistance gene. We further demonstrated that our technology can be broadly applicable for targeted detection of a wide range of antibiotic resistant genes found in both Gram-positive (vanA, nuc, and mecA) and Gram-negative bacteria, including ESBLs (blaCTX-M-1 and blaCTX-M-2 families) and CREs (blaOXA-48 and blaKPC), as well as bacterial speciation (E. coli and Klebsiella spp.) and pan-bacterial detection, without requiring blood culture or sample processing. Our rapid diagnostic technology holds great potential in directing early, appropriate therapy and improved antibiotic stewardship in combating bloodstream infections and antibiotic resistance.
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Affiliation(s)
- Timothy J Abram
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Hemanth Cherukury
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA
| | - Chen-Yin Ou
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Tam Vu
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA
| | - Michael Toledano
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Yiyan Li
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Physics and Engineering, Fort Lewis College, Durango, CO 81301, USA
| | | | - Melody N Toosky
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Delia F Tifrea
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Anatoly Slepenkin
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Jonathan Chong
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Lingshun Kong
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Domenica Vanessa Del Pozo
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Kieu Thai La
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Louai Labanieh
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Jan Zimak
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA.
| | - Byron Shen
- Velox Biosystems, 5 Mason, Suite 160, Irvine, CA 92618, USA.
| | - Susan S Huang
- Division of Infectious Diseases, UCI School of Medicine, Irvine, CA 92697, USA
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA and Laboratory for Fluorescence Dynamics, University of California, Irvine, CA 92697, USA
| | - Ellena M Peterson
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Weian Zhao
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, 845 Health Sciences Road, Suite 3027, Irvine, CA 92697, USA. and Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA and Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697, USA and Chao Family Comprehensive Cancer Center, University of California, Irvine, Irvine, CA 92697, USA and Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, Irvine, CA 92697, USA and Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697, USA
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Diaz A, Antonara S, Barton T. Prevention Strategies to Combat Antimicrobial Resistance in Children in Resource-Limited Settings. CURRENT TROPICAL MEDICINE REPORTS 2018. [DOI: 10.1007/s40475-018-0136-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Li Y, Yang X, Zhao W. Emerging Microtechnologies and Automated Systems for Rapid Bacterial Identification and Antibiotic Susceptibility Testing. SLAS Technol 2017; 22:585-608. [PMID: 28850804 DOI: 10.1177/2472630317727519] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Rapid bacterial identification (ID) and antibiotic susceptibility testing (AST) are in great demand due to the rise of drug-resistant bacteria. Conventional culture-based AST methods suffer from a long turnaround time. By necessity, physicians often have to treat patients empirically with antibiotics, which has led to an inappropriate use of antibiotics, an elevated mortality rate and healthcare costs, and antibiotic resistance. Recent advances in miniaturization and automation provide promising solutions for rapid bacterial ID/AST profiling, which will potentially make a significant impact in the clinical management of infectious diseases and antibiotic stewardship in the coming years. In this review, we summarize and analyze representative emerging micro- and nanotechnologies, as well as automated systems for bacterial ID/AST, including both phenotypic (e.g., microfluidic-based bacterial culture, and digital imaging of single cells) and molecular (e.g., multiplex PCR, hybridization probes, nanoparticles, synthetic biology tools, mass spectrometry, and sequencing technologies) methods. We also discuss representative point-of-care (POC) systems that integrate sample processing, fluid handling, and detection for rapid bacterial ID/AST. Finally, we highlight major remaining challenges and discuss potential future endeavors toward improving clinical outcomes with rapid bacterial ID/AST technologies.
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Affiliation(s)
- Yiyan Li
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,7 Department of Physics and Engineering, Fort Lewis College, Durango, Colorado, USA
| | | | - Weian Zhao
- 1 Sue and Bill Gross Stem Cell Research Center, University of California-Irvine, Irvine, CA, USA.,6 Department of Biological Chemistry, University of California-Irvine, Irvine, CA, USA
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Omulo S, Lofgren ET, Mugoh M, Alando M, Obiya J, Kipyegon K, Kikwai G, Gumbi W, Kariuki S, Call DR. The impact of fecal sample processing on prevalence estimates for antibiotic-resistant Escherichia coli. J Microbiol Methods 2017; 136:71-77. [PMID: 28323065 DOI: 10.1016/j.mimet.2017.03.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/15/2017] [Accepted: 03/15/2017] [Indexed: 10/19/2022]
Abstract
Investigators often rely on studies of Escherichia coli to characterize the burden of antibiotic resistance in a clinical or community setting. To determine if prevalence estimates for antibiotic resistance are sensitive to sample handling and interpretive criteria, we collected presumptive E. coli isolates (24 or 95 per stool sample) from a community in an urban informal settlement in Kenya. Isolates were tested for susceptibility to nine antibiotics using agar breakpoint assays and results were analyzed using generalized linear mixed models. We observed a <3-fold difference between prevalence estimates based on freshly isolated bacteria when compared to isolates collected from unprocessed fecal samples or fecal slurries that had been stored at 4°C for up to 7days. No time-dependence was evident (P>0.1). Prevalence estimates did not differ for five distinct E. coli colony morphologies on MacConkey agar plates (P>0.2). Successive re-plating of samples for up to five consecutive days had little to no impact on prevalence estimates. Finally, culturing E. coli under different conditions (with 5% CO2 or micro-aerobic) did not affect estimates of prevalence. For the conditions tested in these experiments, minor modifications in sample processing protocols are unlikely to bias estimates of the prevalence of antibiotic-resistance for fecal E. coli.
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Affiliation(s)
- Sylvia Omulo
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Community Health Analytics Initiative, Washington State University, Pullman, WA, USA
| | - Eric T Lofgren
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Community Health Analytics Initiative, Washington State University, Pullman, WA, USA
| | - Maina Mugoh
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Moshe Alando
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Joshua Obiya
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Korir Kipyegon
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Gilbert Kikwai
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Wilson Gumbi
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Douglas R Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, USA; Community Health Analytics Initiative, Washington State University, Pullman, WA, USA; The Nelson Mandela African Institute for Science and Technology, Arusha, Tanzania.
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9
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Dimopoulos G, Akova M. An overview on severe infections in Europe. Intensive Care Med 2016; 43:686-689. [PMID: 27995284 PMCID: PMC7079918 DOI: 10.1007/s00134-016-4650-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/08/2016] [Indexed: 02/05/2023]
Affiliation(s)
- George Dimopoulos
- Department of Critical Care, University Hospital Attikon, National and Kapodistrian University of Athens, 1 Rimini Str, Haidari, 12462, Athens, Greece.
| | - Murat Akova
- Department of Infectious Diseases, Hacettepe University School of Medicine, Ankara, Turkey
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Pires J, Kuenzli E, Kasraian S, Tinguely R, Furrer H, Hilty M, Hatz C, Endimiani A. Polyclonal Intestinal Colonization with Extended-Spectrum Cephalosporin-Resistant Enterobacteriaceae upon Traveling to India. Front Microbiol 2016; 7:1069. [PMID: 27462305 PMCID: PMC4940376 DOI: 10.3389/fmicb.2016.01069] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/27/2016] [Indexed: 12/18/2022] Open
Abstract
We aimed to assess the intestinal colonization dynamics by multiple extended-spectrum cephalosporin-resistant Enterobacteriaceae (ESC-R-Ent) clones in Swiss travelers to India, a country with high prevalence of these multidrug-resistant pathogens. Fifteen healthy volunteers (HVs) colonized with ESC-R-Ent after traveling to India who provided stools before, after, and at 3- and 6-month follow-up are presented in this study. Stools were enriched in a LB broth containing 3 mg/L cefuroxime and plated in standard selective media (BLSE, ChromID ESBL, Supercarba) to detect carbapenem- and/or ESC-R-Ent. At least 5 Enterobacteriaceae colonies were analyzed for each stool provided. All strains underwent phenotypic tests (MICs in microdilution) and molecular typing to define bla genes (microarray, PCR/sequencing), clonality (MLST, rep-PCR), and plasmid content. While only three HVs were colonized before the trip, all participants had positive stools after returning, but the colonization rate decreased during the follow-up period (i.e., six HVs were still colonized at both 3 and 6 months). More importantly, polyclonal acquisition (median of 2 clones, range 1–5) was identified at return in all HVs. The majority of the Escherichia coli isolates belonged to phylogenetic groups A and B1 and to high diverse non-epidemic sequence types (STs); however, 15% of them belonged to clonal complex 10 and mainly possessed blaCTX−M−15 genes. F family plasmids were constantly found (~80%) in the recovered ESC-R-Ent. Our results indicate a possible polyclonal acquisition of the ESC-R-Ent via food-chain and/or through an environmental exposure. For some HVs, prolonged colonization in the follow-up period was observed due to clonal persistence or presence of the same plasmid replicon types in a new bacterial host. Travel medicine practitioners, clinicians, and clinical microbiologists who are facing the returning travelers and their samples for different reasons should be aware of this important phenomenon, so that better infection control measures, treatment strategies, and diagnostic tests can be adopted.
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Affiliation(s)
- João Pires
- Institute for Infectious Diseases, University of BernBern, Switzerland; Graduate School of Cellular and Biomedical Sciences, University of BernBern, Switzerland
| | - Esther Kuenzli
- Division for Infectious Diseases and Hospital Epidemiology, University Hospital BaselBasel, Switzerland; Swiss Tropical and Public Health InstituteBasel, Switzerland; Epidemiology, Biostatistics and Prevention Institute, University of ZurichZurich, Switzerland
| | - Sara Kasraian
- Institute for Infectious Diseases, University of Bern Bern, Switzerland
| | - Regula Tinguely
- Institute for Infectious Diseases, University of Bern Bern, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern Bern, Switzerland
| | - Markus Hilty
- Institute for Infectious Diseases, University of BernBern, Switzerland; Department of Infectious Diseases, Bern University Hospital, University of BernBern, Switzerland
| | - Christoph Hatz
- Swiss Tropical and Public Health InstituteBasel, Switzerland; Epidemiology, Biostatistics and Prevention Institute, University of ZurichZurich, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern Bern, Switzerland
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