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Evidence of Linezolid Resistance and Virulence Factors in Enterococcus spp. Isolates from Wild and Domestic Ruminants, Italy. Antibiotics (Basel) 2022; 11:antibiotics11020223. [PMID: 35203825 PMCID: PMC8868082 DOI: 10.3390/antibiotics11020223] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 02/01/2023] Open
Abstract
The aim of this study was to evaluate the resistance patterns against selected critically and highly important antibiotics (quinupristin/dalfopristin, vancomycin, and linezolid) in 48 Enterococcus isolates obtained from wild (red deer and Apennine chamois) and domestic (cattle, sheep, and goats) ruminants living with varying degrees of sympatry in the protected area of Maiella National Park (central Italy). According to CLSI breakpoints, 9 out of 48 isolates (18.8%) showed resistance to at least one antibiotic. One Apennine chamois isolate was resistant to all tested antibiotics. The PCR screening of related resistance genes highlighted the occurrence of msrC or cfrD in seven Enterococcus resistant isolates. In addition, msrC and vanC genes were amplified in susceptible isolates. Specific sequences of virulence genes (gelE, ace, efa, asa1, and esp) related to pathogenic enterococci in humans were amplified in 21/48 isolates (43.75%), belonging mostly to wild animals (15/21; 71.42%). This is the first report of linezolid-resistant enterococci harboring virulence genes in Italian wildlife with special regard to the red deer and Apennine chamois species. The results allow us to evaluate the potential role of wild animals as indicators of antibiotic resistance in environments with different levels of anthropic pressure.
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52
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López C, Delmonti J, Bonomo RA, Vila AJ. Deciphering the evolution of metallo-β-lactamases: a journey from the test tube to the bacterial periplasm. J Biol Chem 2022; 298:101665. [PMID: 35120928 DOI: 10.1016/j.jbc.2022.101665] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 01/13/2022] [Accepted: 01/16/2022] [Indexed: 12/20/2022] Open
Abstract
Understanding the evolution of metallo-β-lactamases (MBLs) is fundamental to deciphering the mechanistic basis of resistance to carbapenems in pathogenic and opportunistic bacteria. Presently, these MBL producing pathogens are linked to high rates of morbidity and mortality worldwide. However, the study of the biochemical and biophysical features of MBLs in vitro provides an incomplete picture of their evolutionary potential, since this limited and artificial environment disregards the physiological context where evolution and selection take place. Herein, we describe recent efforts aimed to address the evolutionary traits acquired by different clinical variants of MBLs in conditions mimicking their native environment (the bacterial periplasm) and considering whether they are soluble or membrane-bound proteins. This includes addressing the metal content of MBLs within the cell under zinc starvation conditions, and the context provided by different bacterial hosts that result in particular resistance phenotypes. Our analysis highlights recent progress bridging the gap between in vitro and in-cell studies.
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Affiliation(s)
- Carolina López
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Juliana Delmonti
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina
| | - Robert A Bonomo
- Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; Departments of Medicine, Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA; Medical Service and GRECC, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, Ohio, USA; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), S2000EXF Rosario, Argentina; CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA; Area Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, S2002LRK Rosario, Argentina.
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Aslam B, Khurshid M, Arshad MI, Muzammil S, Rasool M, Yasmeen N, Shah T, Chaudhry TH, Rasool MH, Shahid A, Xueshan X, Baloch Z. Antibiotic Resistance: One Health One World Outlook. Front Cell Infect Microbiol 2021; 11:771510. [PMID: 34900756 PMCID: PMC8656695 DOI: 10.3389/fcimb.2021.771510] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 10/29/2021] [Indexed: 01/07/2023] Open
Abstract
Antibiotic resistance (ABR) is a growing public health concern worldwide, and it is now regarded as a critical One Health issue. One Health’s interconnected domains contribute to the emergence, evolution, and spread of antibiotic-resistant microorganisms on a local and global scale, which is a significant risk factor for global health. The persistence and spread of resistant microbial species, and the association of determinants at the human-animal-environment interface can alter microbial genomes, resulting in resistant superbugs in various niches. ABR is motivated by a well-established link between three domains: human, animal, and environmental health. As a result, addressing ABR through the One Health approach makes sense. Several countries have implemented national action plans based on the One Health approach to combat antibiotic-resistant microbes, following the Tripartite’s Commitment Food and Agriculture Organization (FAO)-World Organization for Animal Health (OIE)-World Health Organization (WHO) guidelines. The ABR has been identified as a global health concern, and efforts are being made to mitigate this global health threat. To summarize, global interdisciplinary and unified approaches based on One Health principles are required to limit the ABR dissemination cycle, raise awareness and education about antibiotic use, and promote policy, advocacy, and antimicrobial stewardship.
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Affiliation(s)
- Bilal Aslam
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mohsin Khurshid
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | | | - Saima Muzammil
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Maria Rasool
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Nafeesa Yasmeen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Taif Shah
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
| | - Tamoor Hamid Chaudhry
- Department of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan.,Public Health Laboratories Division, National Institute of Health, Islamabad, Pakistan
| | | | - Aqsa Shahid
- Faculty of Rehabilitation and Allied Health Sciences, Riphah International University, Faisalabad, Pakistan
| | - Xia Xueshan
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
| | - Zulqarnain Baloch
- Faculty of Life Science and Technology, Kunming University of Life Science and Technology, Kunming, China
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54
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Cave R, Cole J, Mkrtchyan HV. Surveillance and prevalence of antimicrobial resistant bacteria from public settings within urban built environments: Challenges and opportunities for hygiene and infection control. ENVIRONMENT INTERNATIONAL 2021; 157:106836. [PMID: 34479136 PMCID: PMC8443212 DOI: 10.1016/j.envint.2021.106836] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/12/2021] [Accepted: 08/15/2021] [Indexed: 05/09/2023]
Abstract
Antimicrobial resistant (AMR) bacteria present one of the biggest threats to public health; this must not be forgotten while global attention is focussed on the COVID-19 pandemic. Resistant bacteria have been demonstrated to be transmittable to humans in many different environments, including public settings in urban built environments where high-density human activity can be found, including public transport, sports arenas and schools. However, in comparison to healthcare settings and agriculture, there is very little surveillance of AMR in the built environment outside of healthcare settings and wastewater. In this review, we analyse the existing literature to aid our understanding of what surveillance has been conducted within different public settings and identify what this tells us about the prevalence of AMR. We highlight the challenges that have been reported; and make recommendations for future studies that will help to fill knowledge gaps present in the literature.
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Affiliation(s)
- Rory Cave
- School of Biomedical Sciences, University of West London, United Kingdom
| | - Jennifer Cole
- Royal Holloway University of London, Department of Health Studies, United Kingdom
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55
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Chaplin AV, Korzhanova M, Korostin DO. Identification of bacterial antibiotic resistance genes in next-generation sequencing data (review of literature). Klin Lab Diagn 2021; 66:684-688. [PMID: 34882354 DOI: 10.51620/0869-2084-2021-66-11-684-688] [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: 11/06/2022]
Abstract
The spread of antibiotic-resistant human bacterial pathogens is a serious threat to modern medicine. Antibiotic susceptibility testing is essential for treatment regimens optimization and preventing dissemination of antibiotic resistance. Therefore, development of antibiotic susceptibility testing methods is a priority challenge of laboratory medicine. The aim of this review is to analyze the capabilities of the bioinformatics tools for bacterial whole genome sequence data processing. The PubMed database, Russian scientific electronic library eLIBRARY, information networks of World health organization and European Society of Clinical Microbiology and Infectious Diseases (ESCMID) were used during the analysis. In this review, the platforms for whole genome sequencing, which are suitable for detection of bacterial genetic resistance determinants, are described. The classic step of genetic resistance determinants searching is an alignment between the query nucleotide/protein sequence and the subject (database) nucleotide/protein sequence, which is performed using the nucleotide and protein sequence databases. The most commonly used databases are Resfinder, CARD, Bacterial Antimicrobial Resistance Reference Gene Database. The results of the resistance determinants searching in genome assemblies is more correct in comparison to results of the searching in contigs. The new resistance genes searching bioinformatics tools, such as neural networks and machine learning, are discussed in the review. After critical appraisal of the current antibiotic resistance databases we designed a protocol for predicting antibiotic resistance using whole genome sequence data. The designed protocol can be used as a basis of the algorithm for qualitative and quantitative antimicrobial susceptibility testing based on whole genome sequence data.
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Affiliation(s)
- A V Chaplin
- Pirogov Russian National Research Medical University
| | - M Korzhanova
- Pirogov Russian National Research Medical University
| | - D O Korostin
- Pirogov Russian National Research Medical University
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56
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Survey on phenotypic resistance in Enterococcus faecalis: comparison between the expression of biofilm-associated genes in Enterococcus faecalis persister and non-persister cells. Mol Biol Rep 2021; 49:971-979. [PMID: 34751916 DOI: 10.1007/s11033-021-06915-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 10/28/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Phenotypic resistance is considered as a serious therapeutic challenge for which a definitive remedy has not been discovered yet. Biofilm and persister cell formation are two well-studied phenotypic resistance phenomena, leading to the recalcitrance and relapse of different types of chronic infections. The presence of persister cells in biofilm structures seems to be one of the main factors contributing to the relapse of infections and treatment failure. Given the dormant and inert nature of persister cells, they can be easy targets for the immune system factors. Biofilm formation can be a survival strategy for the defenseless persister cells. Thus, this study was aimed to evaluate the expression of biofilm-associated genes in Enterococcus faecalis persister and non-persister cells. METHODS Vancomycin susceptibility and biofilm formation ability were investigated among 95 E. faecalis clinical isolates using microtiter broth dilution and microtiter plate assays, respectively. PCR was used to determine the presence of biofilm-related genes (gelE, esp, and agg) among the vancomycin-susceptible, biofilm producer E. faecalis isolates (91 isolates). Minimum bactericidal concentration for biofilms (MBCB) were determined for vancomycin using the MTP assay. Bacterial persister assay was performed using an enzymatic lysis assay. Finally, the expression of biofilm-related genes was compared between the persister and non-persister isolates of E. faecalis using real-time qPCR. RESULTS E. faecalis isolates showed a high level of susceptibility (95.8%) to vancomycin (MIC < 1 µg/mL). The gelE, esp, and agg genes were found in 91 (100%), 72 (79.12), and 74 (81.32) of the isolates, respectively. All the E. faecalis isolates were tolerant to vancomycin in the biofilm condition, showing a MBCB of > 2500 µg/mL. Based on the enzymatic lysis assay, only 3 isolates, out of the 91, had the ability to form persister cells. The expression of biofilm-associated genes was higher among the persister compared to non-persister E. faecalis isolates. CONCLUSIONS Biofilm-associated persister cells indicated a high vancomycin tolerance compared to non-persister cells. Moreover, persister isolates showed a higher tendency for biofilm formation and a higher expression level of the biofilm-associated genes, compared to non-persister isolates.
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Králová S, Busse HJ, Bezdíček M, Sandoval-Powers M, Nykrýnová M, Staňková E, Krsek D, Sedláček I. Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., Two Multidrug-Resistant Psychrotrophic Species Isolated From Antarctica. Front Microbiol 2021; 12:729977. [PMID: 34745033 PMCID: PMC8570120 DOI: 10.3389/fmicb.2021.729977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/27/2021] [Indexed: 11/13/2022] Open
Abstract
Despite unfavorable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using a polyphasic taxonomic approach to determine their taxonomic position. Phylogenetic analyses based on the 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90% between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed the presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harbored multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic gene clusters in type strain genomes with a majority not matching any known clusters which supports further exploratory research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed a pattern of multidrug-resistant phenotypes that were correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed a multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which the names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed.
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Affiliation(s)
- Stanislava Králová
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hans-Jürgen Busse
- Institut für Mikrobiologie, Veterinärmedizinische Universität Wien, Vienna, Austria
| | - Matěj Bezdíček
- Department of Internal Medicine - Hematology and Oncology, University Hospital Brno, Brno, Czechia.,Department of Internal Medicine - Hematology and Oncology, Masaryk University, Brno, Czechia
| | | | - Markéta Nykrýnová
- Department of Biomedical Engineering, Faculty of Electrical Engineering and Communication, Brno University of Technology, Brno, Czechia
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
| | - Daniel Krsek
- NRL for Diagnostic Electron Microscopy of Infectious Agents, National Institute of Public Health, Prague, Czechia
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czechia
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The role of chemotaxis and efflux pumps on nitrate reduction in the toxic regions of a ciprofloxacin concentration gradient. THE ISME JOURNAL 2021; 15:2920-2932. [PMID: 33927341 PMCID: PMC8443623 DOI: 10.1038/s41396-021-00975-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 03/17/2021] [Accepted: 04/06/2021] [Indexed: 02/03/2023]
Abstract
Spatial concentration gradients of antibiotics are prevalent in the natural environment. Yet, the microbial response in these heterogeneous systems remains poorly understood. We used a microfluidic reactor to create an artificial microscopic ecosystem that generates diffusive gradients of solutes across interconnected microenvironments. With this reactor, we showed that chemotaxis toward a soluble electron acceptor (nitrate) allowed Shewanella oneidensis MR-1 to inhabit and sustain metabolic activity in highly toxic regions of the antibiotic ciprofloxacin (>80× minimum inhibitory concentration, MIC). Acquired antibiotic resistance was not observed for cells extracted from the reactor, so we explored the role of transient adaptive resistance by probing multidrug resistance (MDR) efflux pumps, ancient elements that are important for bacterial physiology and virulence. Accordingly, we constructed an efflux pump deficient mutant (∆mexF) and used resistance-nodulation-division (RND) efflux pump inhibitors (EPIs). While batch results showed the importance of RND efflux pumps for microbial survival, microfluidic studies indicated that these pumps were not necessary for survival in antibiotic gradients. Our work contributes to an emerging body of knowledge deciphering the effects of antibiotic spatial heterogeneity on microorganisms and highlights differences of microbial response in these systems versus well-mixed batch conditions.
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59
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Band VI, Weiss DS. Heteroresistance to beta-lactam antibiotics may often be a stage in the progression to antibiotic resistance. PLoS Biol 2021; 19:e3001346. [PMID: 34283833 PMCID: PMC8351966 DOI: 10.1371/journal.pbio.3001346] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 08/09/2021] [Accepted: 07/02/2021] [Indexed: 11/23/2022] Open
Abstract
Antibiotic resistance is a growing crisis that threatens many aspects of modern healthcare. Dogma is that resistance often develops due to acquisition of a resistance gene or mutation and that when this occurs, all the cells in the bacterial population are phenotypically resistant. In contrast, heteroresistance (HR) is a form of antibiotic resistance where only a subset of cells within a bacterial population are resistant to a given drug. These resistant cells can rapidly replicate in the presence of the antibiotic and cause treatment failures. If and how HR and resistance are related is unclear. Using carbapenem-resistant Enterobacterales (CRE), we provide evidence that HR to beta-lactams develops over years of antibiotic usage and that it is gradually supplanted by resistance. This suggests the possibility that HR may often develop before resistance and frequently be a stage in its progression, potentially representing a major shift in our understanding of the evolution of antibiotic resistance. A study of heteroresistance to broad range of beta-lactam antibiotics in clinical isolates of E. coli suggests that it may be an intermediate stage in the development of full antibiotic resistance, representing a shift in our understanding of the evolution of antibiotic resistance.
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Affiliation(s)
- Victor I. Band
- Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Atlanta, Georgia, United States of America
| | - David S. Weiss
- Emory Antibiotic Resistance Center, Atlanta, Georgia, United States of America
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Emory Vaccine Center, Atlanta, Georgia, United States of America
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
- Research Service, Atlanta VA Medical Center, Decatur, Georgia, United States of America
- * E-mail:
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60
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Rehman A, Jeukens J, Levesque RC, Lamont IL. Gene-Gene Interactions Dictate Ciprofloxacin Resistance in Pseudomonas aeruginosa and Facilitate Prediction of Resistance Phenotype from Genome Sequence Data. Antimicrob Agents Chemother 2021; 65:e0269620. [PMID: 33875431 PMCID: PMC8218647 DOI: 10.1128/aac.02696-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 04/10/2021] [Indexed: 12/12/2022] Open
Abstract
Ciprofloxacin is one of the most widely used antibiotics for treating Pseudomonas aeruginosa infections. However, P. aeruginosa acquires mutations that confer ciprofloxacin resistance, making treatment more difficult. Resistance is multifactorial, with mutations in multiple genes influencing the resistance phenotype. However, the contributions of individual mutations and mutation combinations to the amounts of ciprofloxacin that P. aeruginosa can tolerate are not well understood. Engineering P. aeruginosa strain PAO1 to contain mutations in any one of the resistance-associated genes gyrA, nfxB, rnfC, parC, and parE showed that only gyrA mutations increased the MIC for ciprofloxacin. Mutations in parC and parE increased the MIC of a gyrA mutant, making the bacteria ciprofloxacin resistant. Mutations in nfxB and rnfC increased the MIC, conferring resistance, only if both were mutated in a gyrA background. Mutations in all of gyrA, nfxB, rnfC, and parC/E further increased the MIC. These findings reveal an epistatic network of gene-gene interactions in ciprofloxacin resistance. We used this information to predict ciprofloxacin resistance/susceptibility for 274 isolates of P. aeruginosa from their genome sequences. Antibiotic susceptibility profiles were predicted correctly for 84% of the isolates. The majority of isolates for which prediction was unsuccessful were ciprofloxacin resistant, demonstrating the involvement of additional as yet unidentified genes and mutations in resistance. Our data show that gene-gene interactions can play an important role in antibiotic resistance and can be successfully incorporated into models predicting resistance phenotype.
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Affiliation(s)
- Attika Rehman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Julie Jeukens
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Québec, Canada
| | - Roger C. Levesque
- Institut de biologie intégrative et des systèmes (IBIS), Université Laval, Quebec City, Québec, Canada
| | - Iain L. Lamont
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
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Cilia G, Turchi B, Fratini F, Ebani VV, Turini L, Cerri D, Bertelloni F. Phenotypic and genotypic resistance to colistin in E. coli isolated from wild boar (Sus scrofa) hunted in Italy. EUR J WILDLIFE RES 2021. [DOI: 10.1007/s10344-021-01501-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
AbstractThe One Health approach is not only focused on diseases and zoonosis control but also on antimicrobial resistance. As concern this important issue, the problem of plasmid-mediated colistin resistance recently emerged. Few studies reported data about colistin resistance and mcr genes in bacteria from wildlife. In this manuscript, 168 Escherichia coli isolated from hunted wild boar were tested; colistin resistance was evaluated by MIC microdilution method, and the presence of mcr-1 and mcr-2 genes was evaluated by PCR. Overall, 27.9% of isolates resulted resistant to colistin, and most of them showed a MIC value > 256 μg/mL. A percentage of 44.6% of tested E. coli scored positive for one or both genes. In details, 13.6% of isolated harbored mcr-1 and mcr-2 in combination; most of them exhibiting the highest MIC values. Interestingly, 19.6% of mcr-positive E. coli resulted phenotypically susceptible to colistin. Wild boar could be considered a potential reservoir of colistin-resistant bacteria. In the light of the possible contacts with domestic animals and humans, this wild species could play an important role in the diffusion of colistin resistance. Thus, the monitoring programs on wildlife should include this aspect.
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The highly dynamic nature of bacterial heteroresistance impairs its clinical detection. Commun Biol 2021; 4:521. [PMID: 33953333 PMCID: PMC8099907 DOI: 10.1038/s42003-021-02052-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/26/2021] [Indexed: 11/23/2022] Open
Abstract
Many bacterial species and antibiotic classes exhibit heteroresistance, a phenomenon in which a susceptible bacterial isolate harbors a resistant subpopulation that can grow in the presence of an antibiotic and cause treatment failure. The resistant phenotype is often unstable and without antibiotic selection it reverts back to susceptibility. Here we studied the dynamics by which these resistant subpopulations are enriched in the presence of antibiotic and recede back to their baseline frequency in the absence of selection. An increasing understanding of this instability will allow more effective diagnostics and treatment of infections caused by heteroresistant bacteria. We show for clinical isolates of Escherichia coli and Salmonella enterica that different antibiotics at levels below the MIC of the susceptible main population can cause rapid enrichment of resistant subpopulations with increased copy number of genes that cause resistance. Modelling and growth rate measurements of bacteria with increased gene copy number in cultures and by microscopy of single-cells in a microfluidic chip show that the fitness cost of gene amplifications and their intrinsic instability drives their rapid loss in the absence of selection. Using a common antibiotic susceptibility test, we demonstrate that this test strongly underestimates the occurrence of heteroresistance in clinical isolates. Bacterial populations can show heteroresistance, where an antibiotic resistant subpopulation is part of a susceptible one. Pereira et al. show in Escherichia coli and Salmonella enterica that disk diffusion, a common antibiotic susceptibility test, underestimates the occurrence of heteroresistance in clinical isolates.
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Rodríguez-Sánchez S, Ramos IM, Seseña S, Poveda JM, Palop ML. Potential of Lactobacillus strains for health-promotion and flavouring of fermented dairy foods. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Virulence and Antimicrobial Resistance in Canine Staphylococcus spp. Isolates. Microorganisms 2021; 9:microorganisms9030515. [PMID: 33801518 PMCID: PMC7998746 DOI: 10.3390/microorganisms9030515] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/12/2021] [Accepted: 02/26/2021] [Indexed: 11/24/2022] Open
Abstract
Dogs are reservoirs of different Staphylococcus species, but at the same time, they could develop several clinical forms caused by these bacteria. The aim of the present investigation was to characterize 50 clinical Staphylococcus isolates cultured from sick dogs. Bacterial species determination, hemolysins, protease, lipase, gelatinase, slime, and biofilm production, presence of virulence genes (lukS/F-PV, eta, etb, tsst, icaA, and icaD), methicillin resistance, and antimicrobial resistance were investigated. Most isolates (52%) were Staphylococcus pseudointermedius, but 20% and 8% belonged to Staphylococcusxylosus and Staphylococcus chromogenes, respectively. Gelatinase, biofilm, and slime production were very common characters among the investigated strains with 80%, 86%, and 76% positive isolates, respectively. Virulence genes were detected in a very small number of the tested strains. A percentage of 14% of isolates were mecA-positive and phenotypically-resistant to methicillin. Multi-drug resistance was detected in 76% of tested staphylococci; in particular, high levels of resistance were detected for ampicillin, amoxicillin, clindamycin, and erythromycin. In conclusion, although staphylococci are considered to be opportunistic bacteria, the obtained data showed that dogs may be infected by Staphylococcus strains with important virulence characteristics and a high antimicrobial resistance.
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65
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Enterococci isolated from plant-derived food - Analysis of antibiotic resistance and the occurrence of resistance genes. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Lebeaux D, Merabishvili M, Caudron E, Lannoy D, Van Simaey L, Duyvejonck H, Guillemain R, Thumerelle C, Podglajen I, Compain F, Kassis N, Mainardi JL, Wittmann J, Rohde C, Pirnay JP, Dufour N, Vermeulen S, Gansemans Y, Van Nieuwerburgh F, Vaneechoutte M. A Case of Phage Therapy against Pandrug-Resistant Achromobacter xylosoxidans in a 12-Year-Old Lung-Transplanted Cystic Fibrosis Patient. Viruses 2021; 13:v13010060. [PMID: 33466377 PMCID: PMC7824836 DOI: 10.3390/v13010060] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022] Open
Abstract
Bacteriophages are a promising therapeutic strategy among cystic fibrosis and lung-transplanted patients, considering the high frequency of colonization/infection caused by pandrug-resistant bacteria. However, little clinical data are available regarding the use of phages for infections with Achromobacter xylosoxidans. A 12-year-old lung-transplanted cystic fibrosis patient received two rounds of phage therapy because of persistent lung infection with pandrug-resistant A. xylosoxidans. Clinical tolerance was perfect, but initial bronchoalveolar lavage (BAL) still grew A. xylosoxidans. The patient's respiratory condition slowly improved and oxygen therapy was stopped. Low-grade airway colonization by A. xylosoxidans persisted for months before samples turned negative. No re-colonisation occurred more than two years after phage therapy was performed and imipenem treatment was stopped. Whole genome sequencing indicated that the eight A. xylosoxidans isolates, collected during phage therapy, belonged to four delineated strains, whereby one had a stop mutation in a gene for a phage receptor. The dynamics of lung colonisation were documented by means of strain-specific qPCRs on different BALs. We report the first case of phage therapy for A. xylosoxidans lung infection in a lung-transplanted patient. The dynamics of airway colonization was more complex than deduced from bacterial culture, involving phage susceptible as well as phage resistant strains.
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Affiliation(s)
- David Lebeaux
- Université de Paris, F-75006 Paris, France; (I.P.); (F.C.); (J.-L.M.)
- Service de Microbiologie, Unité Mobile d’Infectiologie, AP-HP, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-56-09-29-69; Fax: +33-1-56-09-24-46
| | - Maia Merabishvili
- Laboratory Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, B-1120 Brussels, Belgium; (M.M.); (J.-P.P.)
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (L.V.S.); (H.D.); (M.V.)
| | - Eric Caudron
- Service de Pharmacie, Hôpital européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris Centre Université-Paris, 20 rue Leblanc, 75015 Paris, France;
- Lipides, Systèmes Analytiques et Biologiques, Université Paris-Saclay, 92296 Châtenay-Malabry, France
| | - Damien Lannoy
- CHU Lille, Institut de Pharmacie, F-59000 Lille, France;
- ULR7365—GRITA—Groupe de Recherche Sur Les Formes Injectables et Les Technologies Associées, Universit Lille, F-59000 Lille, France
| | - Leen Van Simaey
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (L.V.S.); (H.D.); (M.V.)
| | - Hans Duyvejonck
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (L.V.S.); (H.D.); (M.V.)
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium;
| | - Romain Guillemain
- Service d’Anesthésie-Réanimation, Hôpital Européen Georges Pompidou, 75015 Paris, France;
| | - Caroline Thumerelle
- Pediatric Pulmonology and Allergy Unit, Hôpital Jeanne de Flandre, University Lille, CHU Lille, F-59000 Lille, France;
| | - Isabelle Podglajen
- Université de Paris, F-75006 Paris, France; (I.P.); (F.C.); (J.-L.M.)
- Service de Microbiologie, AP-HP, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75015 Paris, France
| | - Fabrice Compain
- Université de Paris, F-75006 Paris, France; (I.P.); (F.C.); (J.-L.M.)
- Service de Microbiologie, AP-HP, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75015 Paris, France
| | - Najiby Kassis
- Unité d'Hygiène Hospitalière, Service de Microbiologie, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France;
| | - Jean-Luc Mainardi
- Université de Paris, F-75006 Paris, France; (I.P.); (F.C.); (J.-L.M.)
- Service de Microbiologie, AP-HP, Hôpital Européen Georges Pompidou, 20 rue Leblanc, 75015 Paris, France
| | - Johannes Wittmann
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (J.W.); (C.R.)
| | - Christine Rohde
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstraße 7B, 38124 Braunschweig, Germany; (J.W.); (C.R.)
| | - Jean-Paul Pirnay
- Laboratory Molecular and Cellular Technology, Queen Astrid Military Hospital, Bruynstraat 1, B-1120 Brussels, Belgium; (M.M.); (J.-P.P.)
| | - Nicolas Dufour
- Service de Réanimation Médico-Chirurgicale, Centre Hospitalier René Dubos, 95300 Pontoise, France;
| | - Stefan Vermeulen
- Research Center Health & Water Technology, University College Ghent, Keramiekstraat 80, B-9000 Gent, Belgium;
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium; (Y.G.); (F.V.N.)
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium; (Y.G.); (F.V.N.)
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, C. Heymanslaan 10, B-9000 Gent, Belgium; (L.V.S.); (H.D.); (M.V.)
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67
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Andersson DI, Balaban NQ, Baquero F, Courvalin P, Glaser P, Gophna U, Kishony R, Molin S, Tønjum T. Antibiotic resistance: turning evolutionary principles into clinical reality. FEMS Microbiol Rev 2020; 44:171-188. [PMID: 31981358 DOI: 10.1093/femsre/fuaa001] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
Antibiotic resistance is one of the major challenges facing modern medicine worldwide. The past few decades have witnessed rapid progress in our understanding of the multiple factors that affect the emergence and spread of antibiotic resistance at the population level and the level of the individual patient. However, the process of translating this progress into health policy and clinical practice has been slow. Here, we attempt to consolidate current knowledge about the evolution and ecology of antibiotic resistance into a roadmap for future research as well as clinical and environmental control of antibiotic resistance. At the population level, we examine emergence, transmission and dissemination of antibiotic resistance, and at the patient level, we examine adaptation involving bacterial physiology and host resilience. Finally, we describe new approaches and technologies for improving diagnosis and treatment and minimizing the spread of resistance.
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Affiliation(s)
- Dan I Andersson
- Department of Medical Biochemistry and Microbiology, University of Uppsala, BMC, Husargatan 3, 75237, Uppsala, Sweden
| | - Nathalie Q Balaban
- The Racah Institute of Physics, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Jerusalem, Israel
| | - Fernando Baquero
- Department of Microbiology, Ramón y Cajal Health Research Institute, Ctra. Colmenar Viejo Km 9,100 28034 - Madrid, Madrid, Spain
| | - Patrice Courvalin
- French National Reference Center for Antibiotics, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, Paris, France
| | - Philippe Glaser
- Ecology and Evolution of Antibiotic Resistance, Institut Pasteur, 25-28 Rue du Dr Roux, 75015 Paris, Paris, France
| | - Uri Gophna
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University, 121 Jack Green building, Tel-Aviv University, Ramat-Aviv, 6997801, Tel Aviv, Israel
| | - Roy Kishony
- Faculty of Biology, The Technion, Technion City, Haifa 3200003, Haifa, Israel
| | - Søren Molin
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet Building 220 2800 Kgs.Lyngby, Lyngby, Denmark
| | - Tone Tønjum
- Department of Microbiology, University of Oslo, OUS HF Rikshospitalet Postboks 4950 Nydalen 0424 Oslo, Oslo, Norway.,Oslo University Hospital, P. O. Box 4950 Nydalen N-0424 Oslo, Oslo, Norway
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68
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Gjini E, Paupério FFS, Ganusov VV. Treatment timing shifts the benefits of short and long antibiotic treatment over infection. Evol Med Public Health 2020; 2020:249-263. [PMID: 33376597 PMCID: PMC7750949 DOI: 10.1093/emph/eoaa033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/19/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotics are the major tool for treating bacterial infections. Rising antibiotic resistance, however, calls for a better use of antibiotics. While classical recommendations favor long and aggressive treatments, more recent clinical trials advocate for moderate regimens. In this debate, two axes of 'aggression' have typically been conflated: treatment intensity (dose) and treatment duration. The third dimension of treatment timing along each individual's infection course has rarely been addressed. By using a generic mathematical model of bacterial infection controlled by immune response, we examine how the relative effectiveness of antibiotic treatment varies with its timing, duration and antibiotic kill rate. We show that short or long treatments may both be beneficial depending on treatment onset, the target criterion for success and on antibiotic efficacy. This results from the dynamic trade-off between immune response build-up and resistance risk in acute, self-limiting infections, and uncertainty relating symptoms to infection variables. We show that in our model early optimal treatments tend to be 'short and strong', while late optimal treatments tend to be 'mild and long'. This suggests a shift in the aggression axis depending on the timing of treatment. We find that any specific optimal treatment schedule may perform more poorly if evaluated by other criteria, or under different host-specific conditions. Our results suggest that major advances in antibiotic stewardship must come from a deeper empirical understanding of bacterial infection processes in individual hosts. To guide rational therapy, mathematical models need to be constrained by data, including a better quantification of personal disease trajectory in humans. Lay summary: Bacterial infections are becoming more difficult to treat worldwide because bacteria are becoming resistant to the antibiotics used. Addressing this problem requires a better understanding of how treatment along with other host factors impact antibiotic resistance. Until recently, most theoretical research has focused on the importance of antibiotic dosing on antibiotic resistance, however, duration and timing of treatment remain less explored. Here, we use a mathematical model of a generic bacterial infection to study three aspects of treatment: treatment dose/efficacy (defined by the antibiotic kill rate), duration, and timing, and their impact on several infection endpoints. We show that short and long treatment success strongly depends on when treatment begins (defined by the symptom threshold), the target criterion to optimize, and on antibiotic efficacy. We find that if administered early in an infection, "strong and short" therapy performs better, while if treatment begins at higher bacterial densities, a "mild and long" course of antibiotics is favored. In the model host immune defenses are key in preventing relapses, controlling antibiotic resistant bacteria and increasing the effectiveness of moderate intervention. In order to improve rational treatments of human infections, we call for a better quantification of individual disease trajectories in bacteria-immunity space.
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Affiliation(s)
- Erida Gjini
- Mathematical Modeling of Biological Processes Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, 2780-156, Portugal
| | - Francisco F S Paupério
- Mathematical Modeling of Biological Processes Laboratory, Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, Oeiras, 2780-156, Portugal
- Departamento de Informática, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, 1749-016, Portugal
| | - Vitaly V Ganusov
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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69
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Genotypic antimicrobial resistance characterization of E. coli from dairy calves at high risk of respiratory disease administered enrofloxacin or tulathromycin. Sci Rep 2020; 10:19327. [PMID: 33168881 PMCID: PMC7653923 DOI: 10.1038/s41598-020-76232-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 10/26/2020] [Indexed: 01/15/2023] Open
Abstract
The objective of this study was to evaluate the longitudinal effect of enrofloxacin or tulathromycin use in calves at high risk of bovine respiratory disease (BRD) on antimicrobial resistance genes and mutation in quinolone resistance-determining regions (QRDR) in fecal E. coli. Calves at high risk of developing BRD were randomly enrolled in one of three groups receiving: (1) enrofloxacin (ENR; n = 22); (2) tulathromycin (TUL; n = 24); or (3) no treatment (CTL; n = 21). Fecal samples were collected at enrollment and at 7, 28, and 56 days after beginning treatment, cultured for Escherichiacoli (EC) and DNA extracted. Isolates were screened for cephalosporin, quinolone and tetracycline resistance genes using PCR. QRDR screening was conducted using Sanger sequencing. The only resistance genes detected were aac(6′)Ib-cr (n = 13), bla-CTX-M (n = 51), bla-TEM (n = 117), tetA (n = 142) and tetB (n = 101). A significantly higher detection of gyrA mutated at position 248 at time points 7 (OR = 11.5; P value = 0.03) and 28 (OR = 9.0; P value = 0.05) was observed in the ENR group when compared to calves in the control group. Our findings support a better understanding of the potential impacts from the use of enrofloxacin in calves on the selection and persistence of resistance.
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70
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Swain SS, Paidesetty SK, Padhy RN. Phytochemical conjugation as a potential semisynthetic approach toward reactive and reuse of obsolete sulfonamides against pathogenic bacteria. Drug Dev Res 2020; 82:149-166. [PMID: 33025605 DOI: 10.1002/ddr.21746] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 09/16/2020] [Accepted: 09/20/2020] [Indexed: 12/20/2022]
Abstract
The emergence and reemergence of multidrug-resistant (MDR) bacteria and mycobacteria in community and hospital periphery have directly enhanced the hospitalization costs, morbidity and mortality, globally. The appearance of MDR pathogens, the currently used antibiotics, remains insufficient, and the development of potent antibacterial(s) is merely slow. Thus, the development of active antibacterials is the call of the day. The sulfonamides class of antibacterials was the most successful synthesized drug in the 19th century. Mechanically, sulfonamides were targeting bacterial folic acid biosynthesis and today, those are obsolete or clinically inactive. Nevertheless, the magic sulfonamide pharmacophore has been used continuously in several mainstream antibacterial, antidiabetic, antiviral drugs. Concomitantly, thousands of phytochemicals with antimicrobial potencies have been recorded and were commanded as alternate antibacterials toward control of MDR pathogens. However, none/very few isolated phytochemicals have gone up to the pure-drug stage due to the lack of the desired drug-likeness values and the required pharmacokinetic properties. Thus, chemical modification of parent drug remains as the versatile approach in antibacterial drug development. Improvement of clinically inactive sulfa drugs with suitable phytochemicals to develop active, low-toxic drug molecules followed by medicinal chemistry could be prudent. This review highlights such "sulfonamide-phytochemical" hybrid drug development research works for utilizing inactive sulfonamides and phytochemicals; the ingenious cost-effective and resource-saving hybrid drug concept could be a new trend in current antibacterial drug discovery to reactive the obsolete antibacterials.
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Affiliation(s)
- Shasank S Swain
- Central Research Laboratory, Institute of Medical Sciences and Sum Hospital, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | - Sudhir K Paidesetty
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
| | - Rabindra N Padhy
- Central Research Laboratory, Institute of Medical Sciences and Sum Hospital, Siksha 'O' Anusandhan Deemed to be University, Bhubaneswar, Odisha, India
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71
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Nadeem SF, Gohar UF, Tahir SF, Mukhtar H, Pornpukdeewattana S, Nukthamna P, Moula Ali AM, Bavisetty SCB, Massa S. Antimicrobial resistance: more than 70 years of war between humans and bacteria. Crit Rev Microbiol 2020; 46:578-599. [PMID: 32954887 DOI: 10.1080/1040841x.2020.1813687] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Development of antibiotic resistance in bacteria is one of the major issues in the present world and one of the greatest threats faced by mankind. Resistance is spread through both vertical gene transfer (parent to offspring) as well as by horizontal gene transfer like transformation, transduction and conjugation. The main mechanisms of resistance are limiting uptake of a drug, modification of a drug target, inactivation of a drug, and active efflux of a drug. The highest quantities of antibiotic concentrations are usually found in areas with strong anthropogenic pressures, for example medical source (e.g., hospitals) effluents, pharmaceutical industries, wastewater influents, soils treated with manure, animal husbandry and aquaculture (where antibiotics are generally used as in-feed preparations). Hence, the strong selective pressure applied by antimicrobial use has forced microorganisms to evolve for survival. The guts of animals and humans, wastewater treatment plants, hospital and community effluents, animal husbandry and aquaculture runoffs have been designated as "hotspots for AMR genes" because the high density of bacteria, phages, and plasmids in these settings allows significant genetic exchange and recombination. Evidence from the literature suggests that the knowledge of antibiotic resistance in the population is still scarce. Tackling antimicrobial resistance requires a wide range of strategies, for example, more research in antibiotic production, the need of educating patients and the general public, as well as developing alternatives to antibiotics (briefly discussed in the conclusions of this article).
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Affiliation(s)
- Syeda Fatima Nadeem
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Umar Farooq Gohar
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Syed Fahad Tahir
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore, Pakistan
| | | | - Pikunthong Nukthamna
- Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,College of Research Methodology and Cognitive Science, Burapha University, Chonburi, Thailand
| | - Ali Muhammed Moula Ali
- Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand
| | | | - Salvatore Massa
- Faculty of Food Industry, King Mongkut's Institute of Technology Ladkrabang, Bangkok, Thailand.,Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
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72
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Saak CC, Dinh CB, Dutton RJ. Experimental approaches to tracking mobile genetic elements in microbial communities. FEMS Microbiol Rev 2020; 44:606-630. [PMID: 32672812 PMCID: PMC7476777 DOI: 10.1093/femsre/fuaa025] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 06/29/2020] [Indexed: 12/19/2022] Open
Abstract
Horizontal gene transfer is an important mechanism of microbial evolution and is often driven by the movement of mobile genetic elements between cells. Due to the fact that microbes live within communities, various mechanisms of horizontal gene transfer and types of mobile elements can co-occur. However, the ways in which horizontal gene transfer impacts and is impacted by communities containing diverse mobile elements has been challenging to address. Thus, the field would benefit from incorporating community-level information and novel approaches alongside existing methods. Emerging technologies for tracking mobile elements and assigning them to host organisms provide promise for understanding the web of potential DNA transfers in diverse microbial communities more comprehensively. Compared to existing experimental approaches, chromosome conformation capture and methylome analyses have the potential to simultaneously study various types of mobile elements and their associated hosts. We also briefly discuss how fermented food microbiomes, given their experimental tractability and moderate species complexity, make ideal models to which to apply the techniques discussed herein and how they can be used to address outstanding questions in the field of horizontal gene transfer in microbial communities.
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Affiliation(s)
- Christina C Saak
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Cong B Dinh
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Rachel J Dutton
- Division of Biological Sciences, Section of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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73
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Urmi UL, Nahar S, Rana M, Sultana F, Jahan N, Hossain B, Alam MS, Mosaddek ASM, McKimm J, Rahman NAA, Islam S, Haque M. Genotypic to Phenotypic Resistance Discrepancies Identified Involving β-Lactamase Genes, blaKPC, blaIMP, blaNDM-1, and blaVIM in Uropathogenic Klebsiella pneumoniae. Infect Drug Resist 2020; 13:2863-2875. [PMID: 32903880 PMCID: PMC7445497 DOI: 10.2147/idr.s262493] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/16/2020] [Indexed: 12/13/2022] Open
Abstract
Introduction Klebsiella pneumoniae carbapenemase (KPC) belongs to the Group-A β-lactamases that incorporate serine at their active site and hydrolyze various penicillins, cephalosporins, and carbapenems. Metallo-beta-lactamases (MBLs) are group-B enzymes that contain one or two essential zinc ions in the active sites and hydrolyze almost all clinically available β-lactam antibiotics. Klebsiella pneumoniae remains the pathogen with the most antimicrobial resistance to KPC and MBLs. Methods This research investigated the blaKPC, and MBL genes, namely, blaIMP, blaVIM, and blaNDM-1 and their phenotypic resistance to K. pneumoniae isolated from urinary tract infections (UTI) in Bangladesh. Isolated UTI K. pneumoniae were identified by API-20E and 16s rDNA gene analysis. Their phenotypic antimicrobial resistance was examined by the Kirby-Bauer disc diffusion method, followed by minimal inhibitory concentration (MIC) determination. blaKPC, blaIMP, blaNDM-1, and blaVIM genes were evaluated by polymerase chain reactions (PCR) and confirmed by sequencing. Results Fifty-eight K. pneumoniae were identified from 142 acute UTI cases. Their phenotypic resistance to amoxycillin-clavulanic acid, cephalexin, cefuroxime, ceftriaxone, and imipenem were 98.3%, 100%, 96.5%, 91.4%, 75.1%, respectively. Over half (31/58) of the isolates contained either blaKPC or one of the MBL genes. Individual prevalence of blaKPC, blaIMP, blaNDM-1, and blaVIM were 15.5% (9), 10.3% (6), 22.4% (13), and 19% (11), respectively. Of these, eight isolates (25.8%, 8/31) were found to have two genes in four different combinations. The co-existence of the ESBL genes generated more resistance than each one individually. Some isolates appeared phenotypically susceptible to imipenem in the presence of blaKPC, blaIMP, blaVIM, and blaNDM-1 genes, singly or in combination. Conclusion The discrepancy of genotype and phenotype resistance has significant consequences for clinical bacteriology, precision in diagnosis, the prudent selection of antimicrobials, and rational prescribing. Heterogeneous phenotypes of antimicrobial susceptibility testing should be taken seriously to avoid inappropriate diagnostic and therapeutic decisions.
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Affiliation(s)
- Umme Laila Urmi
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Shamsun Nahar
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Masud Rana
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Fahmida Sultana
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Nusrat Jahan
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Billal Hossain
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Mohammed Shah Alam
- Department of Microbiology, Gono Bishwabidyalay, Savar, Dhaka 1342, Bangladesh
| | - Abu Syed Md Mosaddek
- Department of Pharmacology, Uttara Adhunik Medical College, Uttara, Dhaka, Bangladesh
| | - Judy McKimm
- Medical Education, Strategic Educational Development, Leadership for the Health Professions, Swansea University Medical School, Swansea University, Swansea, Wales SA2 8PP, UK
| | - Nor Azlina A Rahman
- Department of Physical Rehabilitation Sciences, Kulliyyah of Allied Health Sciences, International Islamic University Malaysia, Kuantan 25200, Malaysia
| | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Dhaka 1342, Bangladesh
| | - Mainul Haque
- Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur 57000, Malaysia
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74
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Friberg C, Haaber JK, Vestergaard M, Fait A, Perrot V, Levin BR, Ingmer H. Human antimicrobial peptide, LL-37, induces non-inheritable reduced susceptibility to vancomycin in Staphylococcus aureus. Sci Rep 2020; 10:13121. [PMID: 32753585 PMCID: PMC7403302 DOI: 10.1038/s41598-020-69962-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 06/08/2020] [Indexed: 11/09/2022] Open
Abstract
Antimicrobial peptides (AMPs) are central components of the innate immune system providing protection against pathogens. Yet, serum and tissue concentrations vary between individuals and with disease conditions. We demonstrate that the human AMP LL-37 lowers the susceptibility to vancomycin in the community-associated methicillin-resistant S. aureus (CA-MRSA) strain FPR3757 (USA300). Vancomycin is used to treat serious MRSA infections, but treatment failures occur despite MRSA strains being tested susceptible according to standard susceptibility methods. Exposure to physiologically relevant concentrations of LL-37 increased the minimum inhibitory concentration (MIC) of S. aureus towards vancomycin by 75%, and resulted in shortened lag-phase and increased colony formation at sub-inhibitory concentrations of vancomycin. Computer simulations using a mathematical antibiotic treatment model indicated that a small increase in MIC might decrease the efficacy of vancomycin in clearing a S. aureus infection. This prediction was supported in a Galleria mellonella infection model, where exposure of S. aureus to LL-37 abolished the antimicrobial effect of vancomycin. Thus, physiological relevant concentrations of LL-37 reduce susceptibility to vancomycin, indicating that tissue and host specific variations in LL-37 concentrations may influence vancomycin susceptibility in vivo.
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Affiliation(s)
- Cathrine Friberg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
- Novo Nordisk, Hagedornsvej 1, 2820, Gentofte, Denmark
| | - Jakob Krause Haaber
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
- SNIPRbiome, Lerso Parkallé 44, 2100, Copenhagen, Denmark
| | - Martin Vestergaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | - Anaëlle Fait
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark
| | | | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, University of Copenhagen, Stigbøjlen 4, 1870, Frederiksberg C, Denmark.
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All-electrical monitoring of bacterial antibiotic susceptibility in a microfluidic device. Proc Natl Acad Sci U S A 2020; 117:10639-10644. [PMID: 32350139 DOI: 10.1073/pnas.1922172117] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lack of rapid antibiotic susceptibility tests adversely affects the treatment of bacterial infections and contributes to increased prevalence of multidrug-resistant bacteria. Here, we describe an all-electrical approach that allows for ultrasensitive measurement of growth signals from only tens of bacteria in a microfluidic device. Our device is essentially a set of microfluidic channels, each with a nanoconstriction at one end and cross-sectional dimensions close to that of a single bacterium. Flowing a liquid bacteria sample (e.g., urine) through the microchannels rapidly traps the bacteria in the device, allowing for subsequent incubation in drugs. We measure the electrical resistance of the microchannels, which increases (or decreases) in proportion to the number of bacteria in the microchannels. The method and device allow for rapid antibiotic susceptibility tests in about 2 h. Further, the short-time fluctuations in the electrical resistance during an antibiotic susceptibility test are correlated with the morphological changes of bacteria caused by the antibiotic. In contrast to other electrical approaches, the underlying geometric blockage effect provides a robust and sensitive signal, which is straightforward to interpret without electrical models. The approach also obviates the need for a high-resolution microscope and other complex equipment, making it potentially usable in resource-limited settings.
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76
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Genetic Determinants Enabling Medium-Dependent Adaptation to Nafcillin in Methicillin-Resistant Staphylococcus aureus. mSystems 2020; 5:5/2/e00828-19. [PMID: 32234776 PMCID: PMC7112963 DOI: 10.1128/msystems.00828-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial susceptibility testing standards driving clinical decision-making have centered around the use of cation-adjusted Mueller-Hinton broth (CA-MHB) as the medium with the notion of supporting bacterial growth, without consideration of recapitulating the in vivo environment. However, it is increasingly recognized that various medium conditions have tremendous influence on antimicrobial activity, which in turn may have major implications on the ability of in vitro susceptibility assays to predict antibiotic activity in vivo. To elucidate differential growth optimization and antibiotic resistance mechanisms, adaptive laboratory evolution was performed in the presence or absence of the antibiotic nafcillin with methicillin-resistant Staphylococcus aureus (MRSA) TCH1516 in either (i) CA-MHB, a traditional bacteriological nutritionally rich medium, or (ii) Roswell Park Memorial Institute (RPMI), a medium more reflective of the in vivo host environment. Medium adaptation analysis showed an increase in growth rate in RPMI, but not CA-MHB, with mutations in apt, adenine phosphoribosyltransferase, and the manganese transporter subunit, mntA, occurring reproducibly in parallel replicate evolutions. The medium-adapted strains showed no virulence attenuation. Continuous exposure of medium-adapted strains to increasing concentrations of nafcillin led to medium-specific evolutionary strategies. Key reproducibly occurring mutations were specific for nafcillin adaptation in each medium type and did not confer resistance in the other medium environment. Only the vraRST operon, a regulator of membrane- and cell wall-related genes, showed mutations in both CA-MHB- and RPMI-evolved strains. Collectively, these results demonstrate the medium-specific genetic adaptive responses of MRSA and establish adaptive laboratory evolution as a platform to study clinically relevant resistance mechanisms.IMPORTANCE The ability of pathogens such as Staphylococcus aureus to evolve resistance to antibiotics used in the treatment of infections has been an important concern in the last decades. Resistant acquisition usually translates into treatment failure and puts patients at risk of unfavorable outcomes. Furthermore, the laboratory testing of antibiotic resistance does not account for the different environment the bacteria experiences within the human body, leading to results that do not translate into the clinic. In this study, we forced methicillin-resistant S. aureus to develop nafcillin resistance in two different environments, a laboratory environment and a physiologically more relevant environment. This allowed us to identify genetic changes that led to nafcillin resistance under both conditions. We concluded that not only does the environment dictate the evolutionary strategy of S. aureus to nafcillin but also that the evolutionary strategy is specific to that given environment.
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77
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Bacci C, Barilli E, Frascolla V, Rega M, Torreggiani C, Vismarra A. Antibiotic Treatment Administered to Pigs and Antibiotic Resistance of Escherichia coli Isolated from Their Feces and Carcasses. Microb Drug Resist 2020; 26:1081-1089. [PMID: 32240057 DOI: 10.1089/mdr.2019.0247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Antimicrobial resistance (AMR) in bacteria is a frequent and widespread phenomenon. The European Food Safety Authority (EFSA) reports that multidrug resistant (MDR) Escherichia coli is considered an important hazard to public health. The lack of data on the correlation between the administration of antibiotics to pigs and the diffusion of MDR E. coli necessitates an in-depth study. The aims of our study were first of all to determine the presence of MDR and/or extended spectrum β-lactamase (ESβL) E. coli isolated from feces and carcasses of pigs; and second, to evaluate the correlation between antibiotic resistance and the antibiotic treatment administrated to the animals considered. The examined E. coli was isolated from 100 fecal swabs and 100 carcass sponges taken from farms and slaughterhouses located in Reggio Emilia province in Italy. The MDR isolates were tested following the protocol defined by EUCAST (2015). Subsequently, a real-time PCR and an endpoint-PCR were used for the genomic analysis. Data highlighted 76.5% of MDR E. coli with a marked presence of the ampicillin (AMP)-streptomycin (STRE)-tetracycline (TETRA) pattern. Moreover, 13 isolates were ESβL producers, and the blaCTXM gene was the most frequently observed in genomic analysis. Results confirm the complexity of the AMR phenomenon showing a partial correlation between the administration of antibiotics and the resistance observed. Pigs destined to the production of Protected Designation of Origin items are colonized by bacteria resistant to a wide range of antibiotic classes even if data are encouraging for colistin and third generation cephalosporin. Furthermore, in-depth study focused on food production could be useful in a view of high safety standards for consumers.
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Affiliation(s)
- Cristina Bacci
- Department of Veterinary Sciences, University of Parma, Parma, Italy
| | | | - Viviana Frascolla
- Department of Veterinary Sciences, University of Parma, Parma, Italy
| | - Martina Rega
- Department of Veterinary Sciences, University of Parma, Parma, Italy
| | | | - Alice Vismarra
- Department of Veterinary Sciences, University of Parma, Parma, Italy
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78
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Saranathan R, Levi MH, Wattam AR, Malek A, Asare E, Behin DS, Pan DH, Jacobs WR, Szymczak WA. Helicobacter pylori Infections in the Bronx, New York: Surveying Antibiotic Susceptibility and Strain Lineage by Whole-Genome Sequencing. J Clin Microbiol 2020; 58:e01591-19. [PMID: 31801839 PMCID: PMC7041580 DOI: 10.1128/jcm.01591-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022] Open
Abstract
The emergence of drug resistance in Helicobacter pylori has resulted in a greater need for susceptibility-guided treatment. While the alleles associated with resistance to clarithromycin and levofloxacin have been defined, there are limited data regarding the molecular mechanisms underlying resistance to other antimicrobials. Using H. pylori isolates from 42 clinical specimens, we compared phenotypic and whole-genome sequencing (WGS)-based detection of resistance. Phenotypic resistance correlated with the presence of alleles of 23S rRNA (A2142G/A2143G) for clarithromycin (kappa coefficient, 0.84; 95% confidence interval [CI], 0.67 to 1.0) and gyrA (N87I/N87K/D91Y/D91N/D91G/D99N) for levofloxacin (kappa coefficient, 0.90; 95% CI, 0.77 to 1.0). Phenotypic resistance to amoxicillin in three isolates correlated with mutations in pbp1, pbp2, and/or pbp3 within coding regions near known amoxicillin binding motifs. All isolates were phenotypically susceptible to tetracycline, although four bore a mutation in 16S rRNA (A926G). For metronidazole, nonsense mutations and R16H substitutions in rdxA correlated with phenotypic resistance (kappa coefficient, 0.76; 95% CI, 0.56 to 0.96). Previously identified mutations in the rpoB rifampin resistance-determining region (RRDR) were not present, but 14 novel mutations outside the RRDR were found in rifampin-resistant isolates. WGS also allowed for strain lineage determination, which may be important for future studies in associating precise MICs with specific resistance alleles. In summary, WGS allows for broad analyses of H. pylori isolates, and our findings support the use of WGS for the detection of clarithromycin and levofloxacin resistance. Additional studies are warranted to better define mutations conferring resistance to amoxicillin, tetracycline, and rifampin, but combinatorial analyses for rdxA gene truncations and R16H mutations have utility for determining metronidazole resistance.
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Affiliation(s)
- Rajagopalan Saranathan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Michael H Levi
- Department of Pathology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Alice R Wattam
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, Virginia, USA
| | - Adel Malek
- Provincial Public Health Laboratory, Eastern Health Microbiology Services, St. John's, New Foundland and Labrador, Canada
| | - Emmanuel Asare
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
- Department of Pathology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Daniel S Behin
- Department of Medicine, Division of Gastroenterology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - Debra H Pan
- Department of Pediatrics, Division of Gastroenterology and Nutrition, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
| | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Wendy A Szymczak
- Department of Pathology, Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, USA
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79
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Bioinformatics Approaches to the Understanding of Molecular Mechanisms in Antimicrobial Resistance. Int J Mol Sci 2020; 21:ijms21041363. [PMID: 32085478 PMCID: PMC7072858 DOI: 10.3390/ijms21041363] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 12/30/2022] Open
Abstract
Antimicrobial resistance (AMR) is a major health concern worldwide. A better understanding of the underlying molecular mechanisms is needed. Advances in whole genome sequencing and other high-throughput unbiased instrumental technologies to study the molecular pathogenicity of infectious diseases enable the accumulation of large amounts of data that are amenable to bioinformatic analysis and the discovery of new signatures of AMR. In this work, we review representative methods published in the past five years to define major approaches developed to-date in the understanding of AMR mechanisms. Advantages and limitations for applications of these methods in clinical laboratory testing and basic research are discussed.
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80
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Antibiotic Resistance and Epigenetics: More to It than Meets the Eye. Antimicrob Agents Chemother 2020; 64:AAC.02225-19. [PMID: 31740560 DOI: 10.1128/aac.02225-19] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The discovery of antibiotics in the last century is considered one of the most important achievements in the history of medicine. Antibiotic usage has significantly reduced morbidity and mortality associated with bacterial infections. However, inappropriate use of antibiotics has led to emergence of antibiotic resistance at an alarming rate. Antibiotic resistance is regarded as a major health care challenge of this century. Despite extensive research, well-documented biochemical mechanisms and genetic changes fail to fully explain mechanisms underlying antibiotic resistance. Several recent reports suggest a key role for epigenetics in the development of antibiotic resistance in bacteria. The intrinsic heterogeneity as well as transient nature of epigenetic inheritance provides a plausible backdrop for high-paced emergence of drug resistance in bacteria. The methylation of adenines and cytosines can influence mutation rates in bacterial genomes, thus modulating antibiotic susceptibility. In this review, we discuss a plethora of recently discovered epigenetic mechanisms and their emerging roles in antibiotic resistance. We also highlight specific epigenetic mechanisms that merit further investigation for their role in antibiotic resistance.
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81
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Ben Maamar S, Glawe AJ, Brown TK, Hellgeth N, Hu J, Wang JP, Huttenhower C, Hartmann EM. Mobilizable antibiotic resistance genes are present in dust microbial communities. PLoS Pathog 2020; 16:e1008211. [PMID: 31971995 PMCID: PMC6977718 DOI: 10.1371/journal.ppat.1008211] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/13/2019] [Indexed: 11/23/2022] Open
Abstract
The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.
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Affiliation(s)
- Sarah Ben Maamar
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Adam J. Glawe
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Taylor K. Brown
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Nancy Hellgeth
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Jinglin Hu
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
| | - Ji-Ping Wang
- Department of Statistics, Northwestern University, Evanston, Illinois, United States of America
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Erica M. Hartmann
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, Illinois, United States of America
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82
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Evidence of mutations conferring resistance to clarithromycin in wastewater and activated sludge. 3 Biotech 2020; 10:7. [PMID: 31832295 DOI: 10.1007/s13205-019-1989-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 11/10/2019] [Indexed: 10/25/2022] Open
Abstract
The occurrence of clarithromycin in wastewater samples and of the activated sludge bacteria possibly resistant to this pharmaceutical was the object of the study. Samples of wastewater or activated sludge were taken from a municipal wastewater treatment plant in summer and winter and characterised regarding their clarithromycin concentrations and the presence of nucleic acid fragments (Cla-sequences) known to be responsible for clarithromycin resistance in Helicobacter pylori. The concentrations of clarithromycin in raw wastewater were about 1086-2271 ng/L. Around 50-60% less of the pharmaceutical was found in treated wastewater. The concentrations were much higher in winter samples, as compared to summer samples. The clarithromycin resistance markers in H. pylori were detected by fluorescence in situ hybridisation in activated sludge bacterial cells. Cla-sequences were found in all the detected Proteobacteria, independently of the sampling season. Among nitrifying or phosphate or glycogen accumulating bacteria only Nitrosomonas spp. revealed presence of the clarithromycin sequences.
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83
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Qiu H, Gong J, Butaye P, Lu G, Huang K, Zhu G, Zhang J, Hathcock T, Cheng D, Wang C. CRISPR/Cas9/sgRNA-mediated targeted gene modification confirms the cause-effect relationship between gyrA mutation and quinolone resistance in Escherichia coli. FEMS Microbiol Lett 2019; 365:4995911. [PMID: 29767711 DOI: 10.1093/femsle/fny127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 05/11/2018] [Indexed: 12/24/2022] Open
Abstract
Quinolones are broad-spectrum antibiotics that have been used for decades in treating bacterial infections in humans and animals, and subsequently bacterial resistance to these agents has increased. While studies indicated the relationship between gyrA mutations and bacterial resistance to quinolones, CRISPR/Cas9 was used in this study to investigate causal role of gyrA mutation in the quinolone resistance. In this study, 818 clinical Escherichia coli isolates were analyzed for gyrA mutations and their resistance to quinolones. The CRISPR/Cas9 system was used to generate gyrA mutations in quinolone-susceptible E. coli ATCC 25922, and quinolone-resistant clinical E. coli. The antimicrobial resistance prevalence rate in E. coli against nalidixic acid, ciprofloxacin and enrofloxacin was 77.1% (631/818), 51.1% (418/818) and 49.8% (407/818), respectively. The gyrA mutations were identified in nucleotide positions 248, 255, 259, 260, 261, 273 and 300, and mutations at positions 248 and 259 resulting in amino acid changes at positions 83 and 87 were associated with quinolone resistance. Double-site amino acid mutations increase resistance to quinolones. The gyrA mutations causing changes at amino acids 83 and 87 reversed the features of quinolone resistance in ATCC and clinical strains, verifying the causal role of gyrA mutation in the quinolone resistance of E. coli.
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Affiliation(s)
- Haixiang Qiu
- Department of Basic Sciences, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, 225009, PR China
| | - Jiansen Gong
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, 221003, PR China
| | - Patrick Butaye
- Department of Biosciences, Ross University School of Veterinary Medicine, P.O. Box 334, Basseterre, St. Kitts, West Indies.,Department of Pathology, Bacteriology and Poultry Diseases, Faculty of Veterinary Medicine Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Guangwu Lu
- Department of Basic Sciences, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, 225009, PR China
| | - Ke Huang
- Department of Basic Sciences, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, 225009, PR China
| | - Guoqiang Zhu
- Department of Basic Sciences, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, 225009, PR China
| | - Jilei Zhang
- Department of Basic Sciences, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, 225009, PR China
| | - Terri Hathcock
- College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, USA
| | - Darong Cheng
- Department of Basic Sciences, Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, 225009, PR China
| | - Chengming Wang
- College of Veterinary Medicine, Auburn University, Auburn, AL, 36849, USA
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84
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Sang VT, Dat TTH, Vinh LB, Cuong LCV, Oanh PTT, Ha H, Kim YH, Anh HLT, Yang SY. Coral and Coral-Associated Microorganisms: A Prolific Source of Potential Bioactive Natural Products. Mar Drugs 2019; 17. [PMID: 31405226 DOI: 10.3390/md1708046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 05/20/2023] Open
Abstract
Marine invertebrates and their associated microorganisms are rich sources of bioactive compounds. Among them, coral and its associated microorganisms are promising providers of marine bioactive compounds. The present review provides an overview of bioactive compounds that are produced by corals and coral-associated microorganisms, covering the literature from 2010 to March 2019. Accordingly, 245 natural products that possess a wide range of potent bioactivities, such as anti-inflammatory, cytotoxic, antimicrobial, antivirus, and antifouling activities, among others, are described in this review.
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Affiliation(s)
- Vo Thanh Sang
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, District 5, Ho Chi Minh City 748000, Vietnam
| | - Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Le Ba Vinh
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 100000, Vietnam
| | - Le Canh Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Phung Thi Thuy Oanh
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Hoang Ha
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 122300, Vietnam
| | - Young Ho Kim
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea.
| | - Hoang Le Tuan Anh
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam.
- Graduated University of Science and Technology, VAST, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 122300, Vietnam.
| | - Seo Young Yang
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea.
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85
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Sang VT, Dat TTH, Vinh LB, Cuong LCV, Oanh PTT, Ha H, Kim YH, Anh HLT, Yang SY. Coral and Coral-Associated Microorganisms: A Prolific Source of Potential Bioactive Natural Products. Mar Drugs 2019; 17:E468. [PMID: 31405226 PMCID: PMC6723858 DOI: 10.3390/md17080468] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 08/05/2019] [Accepted: 08/07/2019] [Indexed: 02/06/2023] Open
Abstract
Marine invertebrates and their associated microorganisms are rich sources of bioactive compounds. Among them, coral and its associated microorganisms are promising providers of marine bioactive compounds. The present review provides an overview of bioactive compounds that are produced by corals and coral-associated microorganisms, covering the literature from 2010 to March 2019. Accordingly, 245 natural products that possess a wide range of potent bioactivities, such as anti-inflammatory, cytotoxic, antimicrobial, antivirus, and antifouling activities, among others, are described in this review.
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Affiliation(s)
- Vo Thanh Sang
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 300A Nguyen Tat Thanh, District 5, Ho Chi Minh City 748000, Vietnam
| | - Ton That Huu Dat
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Le Ba Vinh
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 100000, Vietnam
| | - Le Canh Viet Cuong
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Phung Thi Thuy Oanh
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam
| | - Hoang Ha
- Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 122300, Vietnam
| | - Young Ho Kim
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea.
| | - Hoang Le Tuan Anh
- Mientrung Institute for Scientific Research, Vietnam Academy of Science and Technology, 321 Huynh Thuc Khang, Hue City, Thua Thien Hue 531600, Vietnam.
- Graduated University of Science and Technology, VAST, 18 Hoang Quoc Viet, Cau Giay, Ha Noi 122300, Vietnam.
| | - Seo Young Yang
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea.
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86
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Song D, Liu H, Ji H, Lei Y. Whole Slide Imaging for High-Throughput Sensing Antibiotic Resistance at Single-Bacterium Level and Its Application to Rapid Antibiotic Susceptibility Testing. Molecules 2019; 24:molecules24132441. [PMID: 31277201 PMCID: PMC6651422 DOI: 10.3390/molecules24132441] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 01/01/2023] Open
Abstract
Since conventional culture-based antibiotic susceptibility testing (AST) methods are too time-consuming (typically 24–72 h), rapid AST is urgently needed for preventing the increasing emergence and spread of antibiotic resistant infections. Although several phenotypic antibiotic resistance sensing modalities are able to reduce the AST time to a few hours or less, concerning the biological heterogeneity, their accuracy or limit of detection are limited by low throughput. Here, we present a rapid AST method based on whole slide imaging (WSI)-enabled high-throughput sensing antibiotic resistance at single-bacterium level. The time for determining the minimum inhibitory concentration (MIC) was theoretically shortest, which ensures that the growth of each individual cell present in a large population is inhibited. As a demonstration, our technique was able to sense the growth of at least several thousand bacteria at single-cell level. Reliable MIC of Enterobacter cloacae against gentamicin was obtained within 1 h, while the gold standard broth dilution method required at least 16 h for the same result. In addition, the application of our method prevails over other imaging-based AST approaches in allowing rapid and accurate determination of antibiotic susceptibility for phenotypically heterogeneous samples, in which the number of antibiotic resistant cells was negligible compared to that of the susceptible cells. Hence, our method shows great promise for both rapid AST determination and point-of-care testing of complex clinical bacteria isolates.
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Affiliation(s)
- Donghui Song
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Haomin Liu
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Huayi Ji
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Yu Lei
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT 06269, USA.
- Department of Chemical and Biomolecular Engineering, University of Connecticut, Storrs, CT 06269, USA.
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87
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Giri S, Waschina S, Kaleta C, Kost C. Defining Division of Labor in Microbial Communities. J Mol Biol 2019; 431:4712-4731. [PMID: 31260694 DOI: 10.1016/j.jmb.2019.06.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 11/15/2022]
Abstract
In order to survive and reproduce, organisms must perform a multitude of tasks. However, trade-offs limit their ability to allocate energy and resources to all of these different processes. One strategy to solve this problem is to specialize in some traits and team up with other organisms that can help by providing additional, complementary functions. By reciprocally exchanging metabolites and/or services in this way, both parties benefit from the interaction. This phenomenon, which has been termed functional specialization or division of labor, is very common in nature and exists on all levels of biological organization. Also, microorganisms have evolved different types of synergistic interactions. However, very often, it remains unclear whether or not a given example represents a true case of division of labor. Here we aim at filling this gap by providing a list of criteria that clearly define division of labor in microbial communities. Furthermore, we propose a set of diagnostic experiments to verify whether a given interaction fulfills these conditions. In contrast to the common use of the term, our analysis reveals that both intraspecific and interspecific interactions meet the criteria defining division of labor. Moreover, our analysis identified non-cooperators of intraspecific public goods interactions as growth specialists that divide labor with conspecific producers, rather than being social parasites. By providing a conceptual toolkit, our work will help to unambiguously identify cases of division of labor and stimulate more detailed investigations of this important and widespread type of inter-microbial interaction.
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Affiliation(s)
- Samir Giri
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Silvio Waschina
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christian Kost
- Department of Ecology, School of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany.
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88
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Mechanisms and clinical relevance of bacterial heteroresistance. Nat Rev Microbiol 2019; 17:479-496. [DOI: 10.1038/s41579-019-0218-1] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2019] [Indexed: 02/08/2023]
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89
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Zhi S, Banting G, Stothard P, Ashbolt NJ, Checkley S, Meyer K, Otto S, Neumann NF. Evidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater. WATER RESEARCH 2019; 156:208-222. [PMID: 30921537 DOI: 10.1016/j.watres.2019.03.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 03/12/2019] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
We previously demonstrated the existence of naturalized strains of E. coli in wastewater and herein perform an in-depth comparative whole genome analysis of these strains (n = 17). Fourteen of the Canadian E. coli strains, isolated from geographically separated wastewater treatment plants, were virtually identical at the core genome and were ≥96% similar at the whole genome level, suggesting clonal-relatedness among these isolates. Remarkably, these strains were shown to be extremely similar to the genome of an E. coli isolated from wastewater in Switzerland, suggesting a global distribution of these strains. The genomes of three other Canadian wastewater strains were more diverse but very similar to the genomes of E. coli isolates collected from U.S. wastewater samples. Based on maximum likelihood phylogenetic analysis, wastewater strains from Canada, the U.S. and Switzerland formed a clade separate from other known enteric phylogroups (i.e., A, B1, B2, D, E) and the cryptic clades. All Canadian, Swiss and U.S. wastewater strains possessed a common SNP biomarker pattern across their genomes, and a sub-population (i.e., 14 Canadian and 1 Swiss strain) also possessed a previously identified wastewater-specific marker known as uspC-IS30-flhDC element. Biochemical heat mapping of 518 categories of genes recapitulated phylogeny, with wastewater strains phenotypically clustering separately from enteric and cryptic clades. Wastewater strains were enriched for stress-response genes (i.e., nutrient acquisition/deprivation, DNA repair, oxidative stress, and UV resistance) - elements reflective of their environmental survival challenges. Wastewater strains were shown to carry a plethora of known antibiotic resistance (AR) genes, the patterns of which were remarkably similar among all Canadian, U.S. and Swiss wastewater strains. Virulence gene composition was also similar among all the wastewater strains, with an abundant representation of virulence genes commonly associated with urinary pathogenic E. coli (UPEC) as well as enterohemorrhagic (EHEC) E. coli. The remarkable degree of similarity between all wastewater strains from Canada, Switzerland and the U.S. suggests the evolution and global-dissemination of water treatment-resistant clone of E. coli. These finding, along with others, raise some important concerns about the potential for emergence of E. coli pathotypes resistant to water-treatment.
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Affiliation(s)
- Shuai Zhi
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada
| | - Graham Banting
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada
| | - Paul Stothard
- Faculty of Agricultural, Life and Environmental Sciences, 1400 College Plaza, University of Alberta, Edmonton, Alberta, Canada
| | - Nicholas J Ashbolt
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada
| | - Sylvia Checkley
- Faculty of Veterinary Medicine, Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Kelsey Meyer
- Faculty of Veterinary Medicine, Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Simon Otto
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada
| | - Norman F Neumann
- School of Public Health, Room 3-57, South Academic Building, University of Alberta, Edmonton, Alberta, T6G 2G7, Canada.
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90
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Sekhon PK, Chander AM, Mayilraj S, Rishi P. Genomic analysis of Indian strains of Salmonella enterica subsp. enterica serovar Typhi indicates novel genetic repertoire for pathogenicity and adaptations. Mol Biol Rep 2019; 46:3967-3989. [DOI: 10.1007/s11033-019-04843-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 04/27/2019] [Indexed: 01/23/2023]
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91
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Abstract
Systemic Salmonella enterica infections are a major cause of mortality worldwide and are becoming increasingly untreatable. Recent single-cell data from a mouse model of typhoid fever show that the host immune system actually eradicates many Salmonella cells, while other Salmonella organisms thrive at the same time in the same tissue, causing lethal disease progression. The surviving Salmonella cells have highly heterogeneous metabolism, growth rates, and exposure to various stresses. Emerging evidence suggests that similarly heterogeneous host-pathogen encounters might be a key feature of many infectious diseases. This heterogeneity offers fascinating opportunities for research and application. If we understand the mechanisms that determine the disparate local outcomes, we might be able to develop entirely novel strategies for infection control by broadening successful host antimicrobial attacks and closing permissive niches in which pathogens can thrive. This review describes suitable technologies, a current working model of heterogeneous host-Salmonella interactions, the impact of diverse Salmonella subsets on antimicrobial chemotherapy, and major open questions and challenges.
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92
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Crabbé A, Ostyn L, Staelens S, Rigauts C, Risseeuw M, Dhaenens M, Daled S, Van Acker H, Deforce D, Van Calenbergh S, Coenye T. Host metabolites stimulate the bacterial proton motive force to enhance the activity of aminoglycoside antibiotics. PLoS Pathog 2019; 15:e1007697. [PMID: 31034512 PMCID: PMC6508747 DOI: 10.1371/journal.ppat.1007697] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 05/09/2019] [Accepted: 03/11/2019] [Indexed: 11/27/2022] Open
Abstract
Antibiotic susceptibility of bacterial pathogens is typically evaluated using in vitro assays that do not consider the complex host microenvironment. This may help explaining a significant discrepancy between antibiotic efficacy in vitro and in vivo, with some antibiotics being effective in vitro but not in vivo or vice versa. Nevertheless, it is well-known that antibiotic susceptibility of bacteria is driven by environmental factors. Lung epithelial cells enhance the activity of aminoglycoside antibiotics against the opportunistic pathogen Pseudomonas aeruginosa, yet the mechanism behind is unknown. The present study addresses this gap and provides mechanistic understanding on how lung epithelial cells stimulate aminoglycoside activity. To investigate the influence of the local host microenvironment on antibiotic activity, an in vivo-like three-dimensional (3-D) lung epithelial cell model was used. We report that conditioned medium of 3-D lung cells, containing secreted but not cellular components, potentiated the bactericidal activity of aminoglycosides against P. aeruginosa, including resistant clinical isolates, and several other pathogens. In contrast, conditioned medium obtained from the same cell type, but grown as conventional (2-D) monolayers did not influence antibiotic efficacy. We found that 3-D lung cells secreted endogenous metabolites (including succinate and glutamate) that enhanced aminoglycoside activity, and provide evidence that bacterial pyruvate metabolism is linked to the observed potentiation of antimicrobial activity. Biochemical and phenotypic assays indicated that 3-D cell conditioned medium stimulated the proton motive force (PMF), resulting in increased bacterial intracellular pH. The latter stimulated antibiotic uptake, as determined using fluorescently labelled tobramycin in combination with flow cytometry analysis. Our findings reveal a cross-talk between host and bacterial metabolic pathways, that influence downstream activity of antibiotics. Understanding the underlying basis of the discrepancy between the activity of antibiotics in vitro and in vivo may lead to improved diagnostic approaches and pave the way towards novel means to stimulate antibiotic activity. There is a poor correlation between the activity of antibiotics in the laboratory and in patients, including in several infectious diseases of the respiratory tract. What may help explaining differences between antibiotic activity in vitro and in vivo is that current antibiotic susceptibility tests do not consider the in vivo lung environment. The lung environment contains many factors that may influence bacterial susceptibility to antibiotics. This includes lung epithelial cells, which have been shown to improve the activity of aminoglycoside antibiotics. Yet, how lung epithelial cells increase aminoglycoside activity is currently unknown. Here, we cultured lung epithelial cells in an in vivo-like model and found that they secrete metabolites that enhance the activity of aminoglycoside antibiotics. We found that host cell secretions increased antibiotic uptake through stimulation of bacterial metabolism, which in turn resulted in enhanced activity. Our findings highlight that cross-talk between host and bacterial metabolisms contributes to the efficacy of antibiotic treatment. Understanding how the host metabolism influences antibiotic activity may open up therapeutic avenues to exploit host metabolism for improving antibiotic activity and help explaining discrepancies between antibiotic efficacy in vitro and in vivo.
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Affiliation(s)
- Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
- * E-mail:
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Sorien Staelens
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Charlotte Rigauts
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Martijn Risseeuw
- Laboratory for Medicinal Chemistry, Ghent University, Ghent, Belgium
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Simon Daled
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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93
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Rouhi S, Ramazanzadeh R. Phenotypic and Molecular Survey of Metallo-beta-lactamase-producing Pseudomonas aeruginosa Isolated from Patients with Nosocomial and Non- Nosocomial Infections. Infect Disord Drug Targets 2019; 20:56-64. [PMID: 30659550 DOI: 10.2174/1871526519666190119113328] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 08/08/2018] [Accepted: 01/04/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND Resistance to antimicrobial agents in Pseudomonas aeruginosa (P. aeruginosa) including carbapenems is a prominent problem in patients. The aim of this study is surveying Metallo-beta-lactamase (MBL)-producing P. aeruginosa isolated from patient specimens with nosocomial and non-nosocomial infections in Kurdistan province, Iran. METHODS In total, 146 Pseudomonas spp. were collected (December 2015 to August 2017). P. aeruginosa isolates were detected by phenotypic and polymerase chain reactions (PCR) of gyrB gene. Combination disk (CD) phenotypic test was used for the identification of MBL-producing strains and PCR was applied for identification of blaIMP and blaVIM genes in P. aeruginosa. Sensitivity and specificity of phenotypic tests were calculated as well. Fisher's exact test and logistic regression were used for data analysis (p≤0.05). RESULTS A total of 134 (91.78%) and 133 (91.09%) P. aeruginosa were detected using PCR and the phenotypic test, respectively. Fifty-six (41.79%) clinical isolates were isolated from patients with nosocomial infection. CD test proved that 67 out of 134 (50%) P. aeruginosa isolates were positive for MBL, of which 11 (8.20%) carried blaIMP gene. No significant relationship was found between MBL-producing P. aeruginosa and blaIMP genes; as well as between MBL-producing P. aeruginosa and blaIMP genes with age, sex, city of residence, inpatient/outpatient and specimen's type (p≥0.05). CONCLUSION Presence of MBL-producing P. aeruginosa strains and blaIMP genes were proved in this study; thus more precaution should be taken in the administration of carbapenem antibiotics to patients.
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Affiliation(s)
- Samaneh Rouhi
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran.,Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Rashid Ramazanzadeh
- Cellular and Molecular Research Center, Research Institute for Health Development, Kurdistan University of Medical Sciences, Sanandaj, Iran.,Microbiology Department, Kurdistan University of Medical Sciences, Sanandaj, Iran
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94
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Kabra R, Chauhan N, Kumar A, Ingale P, Singh S. Efflux pumps and antimicrobial resistance: Paradoxical components in systems genomics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 141:15-24. [PMID: 30031023 PMCID: PMC7173168 DOI: 10.1016/j.pbiomolbio.2018.07.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/10/2018] [Accepted: 07/15/2018] [Indexed: 01/01/2023]
Abstract
Efflux pumps play a major role in the increasing antimicrobial resistance rendering a large number of drugs of no use. Large numbers of pathogens are becoming multidrug resistant due to inadequate dosage and use of the existing antimicrobials. This leads to the need for identifying new efflux pump inhibitors. Design of novel targeted therapies using inherent complexity involved in the biological network modeling has gained increasing importance in recent times. The predictive approaches should be used to determine antimicrobial activities with high pathogen specificity and microbicidal potency. Antimicrobial peptides, which are part of our innate immune system, have the ability to respond to infections and have gained much attention in making resistant strain sensitive to existing drugs. In this review paper, we outline evidences linking host-directed therapy with the efflux pump activity to infectious disease.
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Affiliation(s)
- Ritika Kabra
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, India
| | - Nutan Chauhan
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, India
| | - Anurag Kumar
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, India
| | - Prajakta Ingale
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, India
| | - Shailza Singh
- National Centre for Cell Science, NCCS Complex, Ganeshkhind, SP Pune University Campus, Pune 411007, India.
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95
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Wajid M, Awan AB, Saleemi MK, Weinreich J, Schierack P, Sarwar Y, Ali A. Multiple Drug Resistance and Virulence Profiling ofSalmonella entericaSerovars Typhimurium and Enteritidis from Poultry Farms of Faisalabad, Pakistan. Microb Drug Resist 2019; 25:133-142. [DOI: 10.1089/mdr.2018.0121] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Muhammad Wajid
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Asad Bashir Awan
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Muhammad Kashif Saleemi
- Department of Pathology, Faculty of Veterinary Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Jörg Weinreich
- Institute for Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Peter Schierack
- Institute for Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Yasra Sarwar
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
| | - Aamir Ali
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Pakistan Institute of Engineering and Applied Sciences, Islamabad, Pakistan
- Institute for Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
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96
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Núñez-Montero K, Barrientos L. Advances in Antarctic Research for Antimicrobial Discovery: A Comprehensive Narrative Review of Bacteria from Antarctic Environments as Potential Sources of Novel Antibiotic Compounds Against Human Pathogens and Microorganisms of Industrial Importance. Antibiotics (Basel) 2018; 7:E90. [PMID: 30347637 PMCID: PMC6316688 DOI: 10.3390/antibiotics7040090] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/05/2018] [Accepted: 10/04/2018] [Indexed: 12/16/2022] Open
Abstract
The recent emergence of antibiotic-resistant bacteria has become a critical public health problem. It is also a concern for industries, since multidrug-resistant microorganisms affect the production of many agricultural and food products of economic importance. Therefore, discovering new antibiotics is crucial for controlling pathogens in both clinical and industrial spheres. Most antibiotics have resulted from bioprospecting in natural environments. Today, however, the chances of making novel discoveries of bioactive molecules from various well-known sources have dramatically diminished. Consequently, unexplored and unique environments have become more likely avenues for discovering novel antimicrobial metabolites from bacteria. Due to their extreme polar environment, Antarctic bacteria in particular have been reported as a potential source for new antimicrobial compounds. We conducted a narrative review of the literature about findings relating to the production of antimicrobial compounds by Antarctic bacteria, showing how bacterial adaptation to extreme Antarctic conditions confers the ability to produce these compounds. We highlighted the diversity of antibiotic-producing Antarctic microorganisms, including the phyla Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, and Bacteroidetes, which has led to the identification of new antibiotic molecules and supports the belief that research on Antarctic bacterial strains has important potential for biotechnology applications, while providing a better understanding of polar ecosystems.
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Affiliation(s)
- Kattia Núñez-Montero
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Avenida Alemania 0458, 4810296 Temuco, Chile.
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, 481123 Temuco, Chile.
- Centro de Investigación en Biotecnología, Escuela de Biología, Instituto Tecnológico de Costa Rica, 30101 Cartago, Costa Rica.
| | - Leticia Barrientos
- Laboratorio de Biología Molecular Aplicada, Centro de Excelencia en Medicina Traslacional, Universidad de La Frontera, Avenida Alemania 0458, 4810296 Temuco, Chile.
- Núcleo Científico y Tecnológico en Biorecursos (BIOREN), Universidad de La Frontera, Avenida Francisco Salazar 01145, 481123 Temuco, Chile.
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97
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Wu F, Bethke JH, Wang M, You L. Quantitative and synthetic biology approaches to combat bacterial pathogens. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2018; 4:116-126. [PMID: 30263975 DOI: 10.1016/j.cobme.2017.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Antibiotic resistance is one of the biggest threats to public health. The rapid emergence of resistant bacterial pathogens endangers the efficacy of current antibiotics and has led to increasing mortality and economic burden. This crisis calls for more rapid and accurate diagnosis to detect and identify pathogens, as well as to characterize their response to antibiotics. Building on this foundation, treatment options also need to be improved to use current antibiotics more effectively and develop alternative strategies that complement the use of antibiotics. We here review recent developments in diagnosis and treatment of bacterial pathogens with a focus on quantitative biology and synthetic biology approaches.
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Affiliation(s)
- Feilun Wu
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Jonathan H Bethke
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA
| | - Meidi Wang
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, North Carolina, 27708, USA.,Department of Molecular Genetics and Microbiology, Duke University School of Medicine, NC 27710, USA.,Center for Genomic and Computational Biology, Duke University, Durham, North Carolina, 27708, USA
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98
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Aristimuño Ficoseco C, Mansilla FI, Maldonado NC, Miranda H, Fátima Nader-Macias ME, Vignolo GM. Safety and Growth Optimization of Lactic Acid Bacteria Isolated From Feedlot Cattle for Probiotic Formula Design. Front Microbiol 2018; 9:2220. [PMID: 30323790 PMCID: PMC6172481 DOI: 10.3389/fmicb.2018.02220] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/30/2018] [Indexed: 01/08/2023] Open
Abstract
In order to eliminate the widespread use of antibiotics in livestock production, the research for alternatives has increased lately. This study examined the safety of 40 lactic acid bacteria (LAB) isolated from bovine feedlot environment and previously selected as potential probiotics. A high sensitivity prevalence to ampicillin (AMP, 100%), gentamicin (GEN, 96.3%), kanamycin (KAN, 96.3%), clindamycin (CLI, 85.2%), chloramphenicol (CHL, 92.6%) and streptomycin (STR, 88.9%) while moderate and high resistance against erythromycin (ERY, 48%) and tetracycline (TET, 79%) respectively, were determined. Feedlot enterococci and pediococci displayed high resistance to CLI, ERY, GEN and TET (73, 100, 54.5, and 73%, respectively). Among fifteen resistance genes investigated, seven were identified in lactobacilli; their presence not always was correlated with phenotypic resistance. STR resistance genes, aadA and ant(6) were observed in 7.4 and 3.7% of isolates, respectively; genes responsible for aminoglycosides resistance, such as bla (7.4%), and aph(3”)-III (3.7%) were also recognized. In addition, resistance cat and tetS genes (3.7 and 7.4%, respectively) were harbored by feedlot lactobacilli strains. The presence of ermB gene in 22.3% of isolates, including two of the six strains phenotypically resistant to ERY, exhibited the highest prevalence among the assessed antibiotics. None of the feedlot lactobacilli harbored virulence factors genes, while positive PCR amplification for ace, agg, fsrA, and atpA genes was found for enterococci. With the objective of producing large cell biomass for probiotic delivery, growth media without peptone but containing glucose and skim milk powder (Mgl and Mlac) were selected as optimal. Lactobacillus acidophilus CRL2074, L. amylovorus CRL2115, L. mucosae CRL2069, and L. rhamnosus CRL2084 were strains selected as free of antibiotic resistance and virulence determinants, able to reach high cell numbers in non-expensive culture media and being compatible among them.
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Affiliation(s)
- Cecilia Aristimuño Ficoseco
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - Flavia I Mansilla
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - Natalia C Maldonado
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - Hortencia Miranda
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - María E Fátima Nader-Macias
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
| | - Graciela M Vignolo
- Centro de Referencia para Lactobacilos, Consejo Nacional de Investigaciones Científicas y Técnicas, San Miguel de Tucuman, Argentina
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99
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Scortti M, Han L, Alvarez S, Leclercq A, Moura A, Lecuit M, Vazquez-Boland J. Epistatic control of intrinsic resistance by virulence genes in Listeria. PLoS Genet 2018; 14:e1007525. [PMID: 30180166 PMCID: PMC6122793 DOI: 10.1371/journal.pgen.1007525] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 06/29/2018] [Indexed: 01/31/2023] Open
Abstract
Elucidating the relationships between antimicrobial resistance and virulence is key to understanding the evolution and population dynamics of resistant pathogens. Here, we show that the susceptibility of the gram-positive bacterium Listeria monocytogenes to the antibiotic fosfomycin is a complex trait involving interactions between resistance and virulence genes and the environment. We found that a FosX enzyme encoded in the listerial core genome confers intrinsic fosfomycin resistance to both pathogenic and non-pathogenic Listeria spp. However, in the genomic context of the pathogenic L. monocytogenes, FosX-mediated resistance is epistatically suppressed by two members of the PrfA virulence regulon, hpt and prfA, which upon activation by host signals induce increased fosfomycin influx into the bacterial cell. Consequently, in infection conditions, most L. monocytogenes isolates become susceptible to fosfomycin despite possessing a gene that confers high-level resistance to the drug. Our study establishes the molecular basis of an epistatic interaction between virulence and resistance genes controlling bacterial susceptibility to an antibiotic. The reported findings provide the rationale for the introduction of fosfomycin in the treatment of Listeria infections even though these bacteria are intrinsically resistant to the antibiotic in vitro.
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Affiliation(s)
- Mariela Scortti
- Microbial Pathogenesis Group, Division of Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Little France campus, Edinburgh, United Kingdom
- Division of Infection & Immunity, The Roslin Institute, University of Edinburgh, Easter Bush campus, Edinburgh, United Kingdom
| | - Lei Han
- Microbial Pathogenesis Group, Division of Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Little France campus, Edinburgh, United Kingdom
| | - Sonsiray Alvarez
- Microbial Pathogenesis Group, Division of Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Little France campus, Edinburgh, United Kingdom
| | - Alexandre Leclercq
- Institut Pasteur, Biology of Infection Unit, INSERM U111 and National Reference Centre / WHO Collaborating Centre for Listeria, Paris, France
| | - Alexandra Moura
- Institut Pasteur, Biology of Infection Unit, INSERM U111 and National Reference Centre / WHO Collaborating Centre for Listeria, Paris, France
| | - Marc Lecuit
- Institut Pasteur, Biology of Infection Unit, INSERM U111 and National Reference Centre / WHO Collaborating Centre for Listeria, Paris, France
- Paris Descartes University, Division of Infectious Diseases and Tropical Medicine, Necker-Enfants Malades University Hospital, Paris, France
| | - Jose Vazquez-Boland
- Microbial Pathogenesis Group, Division of Infection Medicine, Edinburgh Medical School (Biomedical Sciences), University of Edinburgh, Little France campus, Edinburgh, United Kingdom
- Division of Infection & Immunity, The Roslin Institute, University of Edinburgh, Easter Bush campus, Edinburgh, United Kingdom
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Dias C, Borges A, Oliveira D, Martinez-Murcia A, Saavedra MJ, Simões M. Biofilms and antibiotic susceptibility of multidrug-resistant bacteria from wild animals. PeerJ 2018; 6:e4974. [PMID: 29910986 PMCID: PMC6003395 DOI: 10.7717/peerj.4974] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/24/2018] [Indexed: 12/12/2022] Open
Abstract
Background The "One Health" concept recognizes that human health and animal health are interdependent and bound to the health of the ecosystem in which they (co)exist. This interconnection favors the transmission of bacteria and other infectious agents as well as the flow of genetic elements containing antibiotic resistance genes. This problem is worsened when pathogenic bacteria have the ability to establish as biofilms. Therefore, it is important to understand the characteristics and behaviour of microorganisms in both planktonic and biofilms states from the most diverse environmental niches to mitigate the emergence and dissemination of resistance. Methods The purpose of this work was to assess the antibiotic susceptibility of four bacteria (Acinetobacter spp., Klebsiella pneumoniae, Pseudomonas fluorescens and Shewanella putrefaciens) isolated from wild animals and their ability to form biofilms. The effect of two antibiotics, imipenem (IPM) and ciprofloxacin (CIP), on biofilm removal was also assessed. Screening of resistance genetic determinants was performed by PCR. Biofilm tests were performed by a modified microtiter plate method. Bacterial surface hydrophobicity was determined by sessile drop contact angles. Results The susceptibility profile classified the bacteria as multidrug-resistant. Three genes coding for β-lactamases were detected in K. pneumoniae (TEM, SHV, OXA-aer) and one in P. fluorescens (OXA-aer). K. pneumoniae was the microorganism that carried more β-lactamase genes and it was the most proficient biofilm producer, while P. fluorescens demonstrated the highest adhesion ability. Antibiotics at their MIC, 5 × MIC and 10 × MIC were ineffective in total biofilm removal. The highest biomass reductions were found with IPM (54% at 10 × MIC) against K. pneumoniae biofilms and with CIP (40% at 10 × MIC) against P. fluorescens biofilms. Discussion The results highlight wildlife as important host reservoirs and vectors for the spread of multidrug-resistant bacteria and genetic determinants of resistance. The ability of these bacteria to form biofilms should increase their persistence.
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Affiliation(s)
- Carla Dias
- LEPABE-Department of Chemical Engineering, Faculty of Engineering-University of Porto, Portugal.,CITAB, Centre for the Research and Technology of Agro-Environment and Biological Sciences, Universidade de Tras-os-Montes e Alto Douro, Portugal.,CECAV, Veterinary and Animal Science Research Center, Universidade de Tras-os-Montes e Alto Douro, Portugal
| | - Anabela Borges
- LEPABE-Department of Chemical Engineering, Faculty of Engineering-University of Porto, Portugal.,CECAV, Veterinary and Animal Science Research Center, Universidade de Tras-os-Montes e Alto Douro, Portugal.,CIQUP, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Portugal
| | - Diana Oliveira
- LEPABE-Department of Chemical Engineering, Faculty of Engineering-University of Porto, Portugal
| | | | - Maria José Saavedra
- CITAB, Centre for the Research and Technology of Agro-Environment and Biological Sciences, Universidade de Tras-os-Montes e Alto Douro, Portugal.,CECAV, Veterinary and Animal Science Research Center, Universidade de Tras-os-Montes e Alto Douro, Portugal
| | - Manuel Simões
- LEPABE-Department of Chemical Engineering, Faculty of Engineering-University of Porto, Portugal
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