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Willmann M, Vehreschild MJGT, Biehl LM, Vogel W, Dörfel D, Hamprecht A, Seifert H, Autenrieth IB, Peter S. Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study. BMC Biol 2019; 17:76. [PMID: 31533707 PMCID: PMC6749691 DOI: 10.1186/s12915-019-0692-y] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 08/27/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The selection pressure exercised by antibiotic drugs is an important consideration for the wise stewardship of antimicrobial treatment programs. Treatment decisions are currently based on crude assumptions, and there is an urgent need to develop a more quantitative knowledge base that can enable predictions of the impact of individual antibiotics on the human gut microbiome and resistome. RESULTS Using shotgun metagenomics, we quantified changes in the gut microbiome in two cohorts of hematological patients receiving prophylactic antibiotics; one cohort was treated with ciprofloxacin in a hospital in Tübingen and the other with cotrimoxazole in a hospital in Cologne. Analyzing this rich longitudinal dataset, we found that gut microbiome diversity was reduced in both treatment cohorts to a similar extent, while effects on the gut resistome differed. We observed a sharp increase in the relative abundance of sulfonamide antibiotic resistance genes (ARGs) by 148.1% per cumulative defined daily dose of cotrimoxazole in the Cologne cohort, but not in the Tübingen cohort treated with ciprofloxacin. Through multivariate modeling, we found that factors such as individual baseline microbiome, resistome, and plasmid diversity; liver/kidney function; and concurrent medication, especially virostatic agents, influence resistome alterations. Strikingly, we observed different effects on the plasmidome in the two treatment groups. There was a substantial increase in the abundance of ARG-carrying plasmids in the cohort treated with cotrimoxazole, but not in the cohort treated with ciprofloxacin, indicating that cotrimoxazole might contribute more efficiently to the spread of resistance. CONCLUSIONS Our study represents a step forward in developing the capability to predict the effect of individual antimicrobials on the human microbiome and resistome. Our results indicate that to achieve this, integration of the individual baseline microbiome, resistome, and mobilome status as well as additional individual patient factors will be required. Such personalized predictions may in the future increase patient safety and reduce the spread of resistance. TRIAL REGISTRATION ClinicalTrials.gov, NCT02058888 . Registered February 10 2014.
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Affiliation(s)
- Matthias Willmann
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany.
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Maria J G T Vehreschild
- 1st Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Lena M Biehl
- 1st Department of Internal Medicine, University Hospital of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Wichard Vogel
- Medical Center, Department of Hematology, Oncology, Immunology, Rheumatology & Pulmonology, University of Tübingen, Tübingen, Germany
| | - Daniela Dörfel
- Medical Center, Department of Hematology, Oncology, Immunology, Rheumatology & Pulmonology, University of Tübingen, Tübingen, Germany
| | - Axel Hamprecht
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Harald Seifert
- German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Ingo B Autenrieth
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
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252
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Yassine I, Rafei R, Osman M, Mallat H, Dabboussi F, Hamze M. Plasmid-mediated quinolone resistance: Mechanisms, detection, and epidemiology in the Arab countries. INFECTION GENETICS AND EVOLUTION 2019; 76:104020. [PMID: 31493557 DOI: 10.1016/j.meegid.2019.104020] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/24/2019] [Accepted: 08/28/2019] [Indexed: 01/19/2023]
Abstract
Quinolones are an important antimicrobial class used widely in the treatment of enterobacterial infections. Although there are multiple mechanisms of quinolone resistance, attention should be paid to plasmid-mediated genes due to their ability to facilitate the spread of quinolone resistance, the selection of mutants with a higher-level of quinolone resistance, and the promotion of treatment failure. Since their discovery in 1998, plasmid-mediated quinolone resistance (PMQR) mechanisms have been reported more frequently worldwide especially with the extensive use of quinolones in humans and animals. Nevertheless, data from the Arab countries are rare and often scattered. Understanding the prevalence and distribution of PMQR is essential to stop the irrational use of quinolone in these countries. This manuscript describes the quinolone resistance mechanisms and particularly PMQR among Enterobacteriaceae as well as their methods of detection. Then the available data on the epidemiology of PMQR in clinical and environmental isolates from the Arab countries are extensively reviewed along with the other associated resistance genes. These data shows a wide dissemination of PMQR genes among Enterobacteriaceae isolates from humans, animals, and environments in these countries with increasing rates over the years and a common association with other antibiotic resistance genes as blaCTX-M-15. The incontrovertible emergence of PMQR in the Arab countries highlights the pressing need for effective stewardship efforts to prevent the selection of a higher rate of quinolone resistance and to preserve these crucial antibiotics.
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Affiliation(s)
- Iman Yassine
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Hassan Mallat
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon.
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253
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Magesh S, Jonsson V, Bengtsson-Palme J. Mumame: a software tool for quantifying gene-specific point-mutations in shotgun metagenomic data. METABARCODING AND METAGENOMICS 2019. [DOI: 10.3897/mbmg.3.36236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Metagenomics has emerged as a central technique for studying the structure and function of microbial communities. Often the functional analysis is restricted to classification into broad functional categories. However, important phenotypic differences, such as resistance to antibiotics, are often the result of just one or a few point mutations in otherwise identical sequences. Bioinformatic methods for metagenomic analysis have generally been poor at accounting for this fact, resulting in a somewhat limited picture of important aspects of microbial communities. Here, we address this problem by providing a software tool called Mumame, which can distinguish between wildtype and mutated sequences in shotgun metagenomic data and quantify their relative abundances. We demonstrate the utility of the tool by quantifying antibiotic resistance mutations in several publicly available metagenomic data sets. We also identified that sequencing depth is a key factor to detect rare mutations. Therefore, much larger numbers of sequences may be required for reliable detection of mutations than for most other applications of shotgun metagenomics. Mumame is freely available online (http://microbiology.se/software/mumame).
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254
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DNA double-strand break formation and repair as targets for novel antibiotic combination chemotherapy. Future Sci OA 2019; 5:FSO411. [PMID: 31534779 PMCID: PMC6745595 DOI: 10.2144/fsoa-2019-0034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
An unrepaired DNA double-strand break (DSB) is lethal to cells. In bacteria, DSBs are usually repaired either via an error-prone pathway, which ligates the ends of the break or an accurate recombination pathway. Due to this lethality, drugs that induce persistent DSBs have been successful in bacterial infection treatment. However, recurrent usage of these drugs has led to emergence of resistant strains. Several articles have thoroughly reviewed the causes, mechanisms and effects of bacterial drug resistance while others have also discussed approaches for facilitating drug discovery and development. Here, we focus on a hypothetical chemotherapeutic strategy that can be explored for minimizing development of resistance to novel DSB-inducing compounds. We also highlight the possibility of utilizing bacterial DSB repair pathways as targets for the discovery and development of novel antibiotics. Our health systems face a huge challenge in the form of antimicrobial resistance, which may result in many common infections becoming untreatable. The same antibiotics that gave modern medicine its power are fast losing their hold on the germs that cause disease. Many options are being developed to restore the control that antibiotics have on the microbes that cause many diseases. In this perspective, we outline a concept that is built around the way and manner in which bacteria mend their DNA whenever there is a break in the DNA chain. We discuss the merits of finding a new class of drugs that obstruct bacterial ability to mend their broken DNA. In this scenario, a combination of these new drugs with existing drugs or other new drugs that cause breaks in bacterial DNA would become a powerful therapeutic regimen. This concept, when fully developed, will offer hope in our effort to combat antimicrobial-resistant infections.
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255
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Korang SK, Maagaard M, Feinberg J, Perner A, Gluud C, Jakobsen JC. Quinolones for sepsis. A protocol for a systematic review of randomised clinical trials with meta-analysis and trial sequential analysis. Acta Anaesthesiol Scand 2019; 63:1113-1123. [PMID: 31251397 DOI: 10.1111/aas.13418] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 05/12/2019] [Indexed: 12/29/2022]
Abstract
BACKGROUND Sepsis is a relatively common and deadly condition that constitutes a major challenge to the modern health care system. Quinolones are sometimes used in combination with beta-lactam antibiotics for sepsis, but no former systematic review has assessed the benefits and harms of quinolones in patients with sepsis. METHODS We will perform a systematic review with meta-analysis and trial sequential analysis including randomised clinical trials assessing the effects of quinolones as add on therapy to usual care in children and adults with sepsis. For the assessment of harms, we will also include quasi-randomised studies and observational studies identified during our searches for randomised clinical trials. DISCUSSION This systematic review will clarify if there is evidence to support quinolones being part of the standard treatment for sepsis.
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Affiliation(s)
- Steven Kwasi Korang
- Copenhagen Trial Unit, Centre for Clinical Intervention Research Department 7812, Rigshospitalet, Copenhagen University Hospital Copenhagen Denmark
- Paediatric Department Holbæk Hospital Holbæk Denmark
| | - Mathias Maagaard
- Copenhagen Trial Unit, Centre for Clinical Intervention Research Department 7812, Rigshospitalet, Copenhagen University Hospital Copenhagen Denmark
| | - Joshua Feinberg
- Copenhagen Trial Unit, Centre for Clinical Intervention Research Department 7812, Rigshospitalet, Copenhagen University Hospital Copenhagen Denmark
| | - Anders Perner
- Centre for Research in Intensive Care, Department 7831 Rigshospitalet, Copenhagen University Hospital Copenhagen Denmark
| | - Christian Gluud
- Copenhagen Trial Unit, Centre for Clinical Intervention Research Department 7812, Rigshospitalet, Copenhagen University Hospital Copenhagen Denmark
| | - Janus C. Jakobsen
- Copenhagen Trial Unit, Centre for Clinical Intervention Research Department 7812, Rigshospitalet, Copenhagen University Hospital Copenhagen Denmark
- The Faculty of Heath Sciences, Department of Regional Health Research University of Southern Denmark Sønderborg Denmark
- Department of Cardiology Holbæk Hospital Holbæk Denmark
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256
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Seo KW, Lee YJ. Prevalence and Characterization of Plasmid Mediated Quinolone Resistance Genes and Class 1 Integrons Among Multidrug-Resistant Escherichia coli Isolates from Chicken Meat. J APPL POULTRY RES 2019. [DOI: 10.3382/japr/pfz016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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257
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Rapid Evolution of Reduced Susceptibility against a Balanced Dual-Targeting Antibiotic through Stepping-Stone Mutations. Antimicrob Agents Chemother 2019; 63:AAC.00207-19. [PMID: 31235632 DOI: 10.1128/aac.00207-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/14/2019] [Indexed: 11/20/2022] Open
Abstract
Multitargeting antibiotics, i.e., single compounds capable of inhibiting two or more bacterial targets, are generally considered to be a promising therapeutic strategy against resistance evolution. The rationale for this theory is that multitargeting antibiotics demand the simultaneous acquisition of multiple mutations at their respective target genes to achieve significant resistance. The theory presumes that individual mutations provide little or no benefit to the bacterial host. Here, we propose that such individual stepping-stone mutations can be prevalent in clinical bacterial isolates, as they provide significant resistance to other antimicrobial agents. To test this possibility, we focused on gepotidacin, an antibiotic candidate that selectively inhibits both bacterial DNA gyrase and topoisomerase IV. In a susceptible organism, Klebsiella pneumoniae, a combination of two specific mutations in these target proteins provide an >2,000-fold reduction in susceptibility, while individually, none of these mutations affect resistance significantly. Alarmingly, strains with decreased susceptibility against gepotidacin are found to be as virulent as the wild-type Klebsiella pneumoniae strain in a murine model. Moreover, numerous pathogenic isolates carry mutations which could promote the evolution of clinically significant reduction of susceptibility against gepotidacin in the future. As might be expected, prolonged exposure to ciprofloxacin, a clinically widely employed gyrase inhibitor, coselected for reduced susceptibility against gepotidacin. We conclude that extensive antibiotic usage could select for mutations that serve as stepping-stones toward resistance against antimicrobial compounds still under development. Our research indicates that even balanced multitargeting antibiotics are prone to resistance evolution.
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258
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Hashempour-Baltork F, Hosseini H, Shojaee-Aliabadi S, Torbati M, Alizadeh AM, Alizadeh M. Drug Resistance and the Prevention Strategies in Food Borne Bacteria: An Update Review. Adv Pharm Bull 2019; 9:335-347. [PMID: 31592430 PMCID: PMC6773942 DOI: 10.15171/apb.2019.041] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 05/13/2019] [Accepted: 05/13/2019] [Indexed: 01/10/2023] Open
Abstract
Antibiotic therapy is among the most important treatments against infectious diseases and has tremendously improved effects on public health. Nowadays, development in using this treatment has led us to the emergence and enhancement of drug-resistant pathogens which can result in some problems including treatment failure, increased mortality as well as treatment costs, reduced infection control efficiency, and spread of resistant pathogens from hospital to community. Therefore, many researches have tried to find new alternative approaches to control and prevent this problem. This study, has been revealed some possible and effective approaches such as using farming practice, natural antibiotics, nano-antibiotics, lactic acid bacteria, bacteriocin, cyclopeptid, bacteriophage, synthetic biology and predatory bacteria as alternatives for traditional antibiotics to prevent or reduce the emergence of drug resistant bacteria.
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Affiliation(s)
- Fataneh Hashempour-Baltork
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hedayat Hosseini
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Food Safety Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Saeedeh Shojaee-Aliabadi
- Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadali Torbati
- Department of Food Science and Technology, Faculty of Nutrition, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Adel Mirza Alizadeh
- Student Research Committee, Department of Food Science and Technology, National Nutrition and Food Technology Research Institute, Faculty of Nutrition Science and Food Technology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Matin Alizadeh
- Department of Clinical Sciences (Surgery), Faculty of Specialized Veterinary Sciences, Science and Research Branch, Islamic Azad University, Tehran, Iran
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259
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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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260
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Liao J, Orsi RH, Carroll LM, Kovac J, Ou H, Zhang H, Wiedmann M. Serotype-specific evolutionary patterns of antimicrobial-resistant Salmonella enterica. BMC Evol Biol 2019; 19:132. [PMID: 31226931 PMCID: PMC6588947 DOI: 10.1186/s12862-019-1457-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 06/11/2019] [Indexed: 12/28/2022] Open
Abstract
Background The emergence of antimicrobial-resistant (AMR) strains of the important human and animal pathogen Salmonella enterica poses a growing threat to public health. Here, we studied the genome-wide evolution of 90 S. enterica AMR isolates, representing one host adapted serotype (S. Dublin) and two broad host range serotypes (S. Newport and S. Typhimurium). Results AMR S. Typhimurium had a large effective population size, a large and diverse genome, AMR profiles with high diversity, and frequent positive selection and homologous recombination. AMR S. Newport showed a relatively low level of diversity and a relatively clonal population structure. AMR S. Dublin showed evidence for a recent population bottleneck, and the genomes were characterized by a larger number of genes and gene ontology terms specifically absent from this serotype and a significantly higher number of pseudogenes as compared to other two serotypes. Approximately 50% of accessory genes, including specific AMR and putative prophage genes, were significantly over- or under-represented in a given serotype. Approximately 65% of the core genes showed phylogenetic clustering by serotype, including the AMR gene aac (6′)-Iaa. While cell surface proteins were shown to be the main target of positive selection, some proteins with possible functions in AMR and virulence also showed evidence for positive selection. Homologous recombination mainly acted on prophage-associated proteins. Conclusions Our data indicates a strong association between genome content of S. enterica and serotype. Evolutionary patterns observed in S. Typhimurium are consistent with multiple emergence events of AMR strains and/or ecological success of this serotype in different hosts or habitats. Evolutionary patterns of S. Newport suggested that antimicrobial resistance emerged in one single lineage, Lineage IIC. A recent population bottleneck and genome decay observed in AMR S. Dublin are congruent with its narrow host range. Finally, our results suggest the potentially important role of positive selection in the evolution of antimicrobial resistance, host adaptation and serotype diversification in S. enterica. Electronic supplementary material The online version of this article (10.1186/s12862-019-1457-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jingqiu Liao
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA.,Graduate Field of Microbiology, Cornell University, Ithaca, NY, 14853, USA
| | - Renato Hohl Orsi
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Laura M Carroll
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hongyu Ou
- School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hailong Zhang
- Department of Computer Science & Engineering, Ohio State University, Columbus, OH, 43210, USA
| | - Martin Wiedmann
- Department of Food Science, 341 Stocking Hall, Cornell University, Ithaca, NY, 14853, USA.
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261
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Markovska R, Stoeva T, Dimitrova D, Boyanova L, Stankova P, Mihova K, Mitov I. Quinolone resistance mechanisms among third-generation cephalosporin resistant isolates of Enterobacter spp. in a Bulgarian university hospital. Infect Drug Resist 2019; 12:1445-1455. [PMID: 31213860 PMCID: PMC6549396 DOI: 10.2147/idr.s204199] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 04/07/2019] [Indexed: 01/27/2023] Open
Abstract
Background: There have been no reports in Bulgaria about quinolone resistance determinants among Enterobacter spp. Aims: To investigate plasmid and chromosomal quinolone resistance rates among 175 third-generation cephalosporin resistant Enterobacter spp. isolates (167 Enterobacter cloacae complex and eight Enterobacter aerogenes isolates) collected at a university hospital in Varna, Bulgaria, as well as to reveal their association with ESBL/AmpC production and a carriage of specific plasmid replicon types. Methods: PCR, isoelectric focusing, replicon typing, sequencing, and epidemiology typing were carried out. Results: A high level of combined third-generation cephalosporin and quinolone resistant Enterobacter spp. was found - 79.4%. The ESBL production rate was 87%, consisting mainly of CTX-M-15 among E. cloacae complex (in 76%) and CTX-M-3 among E. aerogenes (in 88%). Plasmid mediated quinolone resistance (PMQR) determinants were identified in 57% of the isolates. The most commonly detected PMQR determinants were qnrB (90%), consisting mainly of qnrB1 (in 61%), and qnrB9 (in 27%) of the isolates. Both alleles were transferred with CTX-M-15 genes; transconjugants showed HI2 replicons (for qnrB1 positive transconjugants) and were non-typeable (for qnrB9). One Enterobacter spp. isolate produced qnrB4. QnrA1, qnrS1, and aac(6')-Ib-cr were detected in single isolates only. QnrC, qnrD, qepA, and oqxAB genes were not found. QnrB was associated with CTX-M-15 production, and qnrS1 was linked to CTX-M-3. Alterations in 83 and 87 positions of gyrB in quinolone-resistance determining regions, and 80 position of parC were detected in high level quinolone resistant isolates. Among all the Enterobacter spp. isolates tested, one predominant clone A was identified (53%). Conclusion: Our data showed the necessity of more prudent use of quinolones and third-generation cephalosporins, because of the risk of promoting dissemination, and selection of multiple resistance determinants (ESBL, PMQR) among Enterobacter spp. isolates in Bulgaria.
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Affiliation(s)
- Rumyana Markovska
- Department of Medical Microbiology, Medical University of Sofia, Sofia, Bulgaria
| | - Temenuga Stoeva
- Department of Microbiology, University Hospital “Saint Marina”, Medical University, Varna, Bulgaria
| | - Dobromira Dimitrova
- Department of Microbiology, University Hospital “Saint Marina”, Medical University, Varna, Bulgaria
| | - Lyudmila Boyanova
- Department of Medical Microbiology, Medical University of Sofia, Sofia, Bulgaria
| | - Petya Stankova
- Department of Medical Microbiology, Medical University of Sofia, Sofia, Bulgaria
| | - Kalina Mihova
- Molecular Medicine Center, Medical University of Sofia, Sofia, Bulgaria
| | - Ivan Mitov
- Department of Medical Microbiology, Medical University of Sofia, Sofia, Bulgaria
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262
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Resistance and Virulence Mechanisms of Escherichia coli Selected by Enrofloxacin in Chicken. Antimicrob Agents Chemother 2019; 63:AAC.01824-18. [PMID: 30803968 DOI: 10.1128/aac.01824-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 02/04/2019] [Indexed: 11/20/2022] Open
Abstract
This study aimed to investigate the genetic characteristics, antibiotic resistance patterns, and novel mechanisms involved in fluoroquinolone (FQ) resistance in commensal Escherichia coli isolates. The E. coli isolates were recovered from a previous clinical study and subjected to antimicrobial susceptibility testing and molecular typing. Known mechanisms of FQ resistance (target site mutations, plasmid-mediated quinolone resistance [PMQR] genes, relative expression levels of efflux pumps and porins) were detected using DNA sequencing of PCR products and real-time quantitative PCR. Whole-genome shotgun sequencing was performed on 11 representative strains to screen for single nucleotide polymorphisms (SNPs). The function of a key SNP (A1541G) was investigated by site-directed mutagenesis and allelic exchange. The results showed that long-term enrofloxacin treatment selected multidrug-resistant (MDR) E. coli isolates in the chicken gut and that these E. coli isolates had diverse genetic backgrounds. Multiple genetic alterations, including double mutations on GyrA (S83L and D87N), a single mutation on ParC (S80I) and ParE (S458E), activation of efflux pumps, and the presence of the QnrS1 protein, contributed to the high-level FQ resistance (enrofloxacin MIC [MICENR] ≥ 128 μg/ml), while the relatively low-level FQ resistance (MICENR = 8 or 16 μg/ml) was commonly mediated by decreased expression of the porin OmpF, besides enhancement of the efflux pumps. No significant relationship was observed between resistance mechanisms and virulence genes. Introduction of the A1541G mutation on aegA was able to increase FQ susceptibility by 2-fold. This study contributes to a better understanding of the development of MDR and the differences underlying the mechanisms of high-level and low-level FQ resistance in E. coli.
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263
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Harris PNA, Ben Zakour NL, Roberts LW, Wailan AM, Zowawi HM, Tambyah PA, Lye DC, Jureen R, Lee TH, Yin M, Izharuddin E, Looke D, Runnegar N, Rogers B, Bhally H, Crowe A, Schembri MA, Beatson SA, Paterson DL. Whole genome analysis of cephalosporin-resistant Escherichia coli from bloodstream infections in Australia, New Zealand and Singapore: high prevalence of CMY-2 producers and ST131 carrying blaCTX-M-15 and blaCTX-M-27. J Antimicrob Chemother 2019; 73:634-642. [PMID: 29253152 DOI: 10.1093/jac/dkx466] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Accepted: 11/09/2017] [Indexed: 12/11/2022] Open
Abstract
Objectives To characterize MDR Escherichia coli from bloodstream infections (BSIs) in Australia, New Zealand and Singapore. Methods We collected third-generation cephalosporin-resistant (3GC-R) E. coli from blood cultures in patients enrolled in a randomized controlled trial from February 2014 to August 2015. WGS was used to characterize antibiotic resistance genes, MLST, plasmids and phylogenetic relationships. Antibiotic susceptibility was determined using disc diffusion and Etest. Results A total of 70 3GC-R E. coli were included, of which the majority were ST131 (61.4%). BSI was most frequently from a urinary source (69.6%), community associated (62.9%) and in older patients (median age 71 years). The median Pitt score was 1 and ICU admission was infrequent (3.1%). ST131 possessed more acquired resistance genes than non-ST131 (P = 0.003). Clade C1/C2 ST131 predominated (30.2% and 53.5% of ST131, respectively) and these were all ciprofloxacin resistant. All clade A ST131 (n = 6) were community associated. The predominant ESBL types were blaCTX-M (80.0%) and were strongly associated with ST131 (95% carried blaCTX-M), with the majority blaCTX-M-15. Clade C1 was associated with blaCTX-M-14 and blaCTX-M-27, whereas blaCTX-M-15 predominated in clade C2. Plasmid-mediated AmpC genes (mainly blaCMY-2) were frequent (17.1%) but were more common in non-ST131 (P < 0.001) isolates from Singapore and Brisbane. Two strains carried both blaCMY-2 and blaCTX-M. The majority of plasmid replicon types were IncF. Conclusions In a prospective collection of 3GC-R E. coli causing BSI, community-associated Clade C1/C2 ST131 predominate in association with blaCTX-M ESBLs, although a significant proportion of non-ST131 strains carried blaCMY-2.
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Affiliation(s)
- Patrick N A Harris
- University of Queensland, UQ Centre for Clinical Research, Royal Brisbane & Women's Hospital, Queensland, Australia.,Microbiology Department, Central Laboratory, Pathology Queensland, Royal Brisbane & Women's Hospital, Queensland, Australia
| | - Nouri L Ben Zakour
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Leah W Roberts
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alexander M Wailan
- University of Queensland, UQ Centre for Clinical Research, Royal Brisbane & Women's Hospital, Queensland, Australia.,Infection Genomics, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Hosam M Zowawi
- University of Queensland, UQ Centre for Clinical Research, Royal Brisbane & Women's Hospital, Queensland, Australia.,College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Centre for Infection Control, Riyadh, Saudi Arabia
| | - Paul A Tambyah
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Infectious Diseases, Department of Medicine, National University Hospital, Singapore
| | - David C Lye
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Communicable Disease Centre, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Roland Jureen
- Department of Laboratory Medicine, Division of Microbiology, National University Hospital, Singapore
| | - Tau H Lee
- Communicable Disease Centre, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Mo Yin
- Division of Infectious Diseases, Department of Medicine, National University Hospital, Singapore
| | - Ezlyn Izharuddin
- Communicable Disease Centre, Institute of Infectious Diseases and Epidemiology, Tan Tock Seng Hospital, Singapore
| | - David Looke
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia.,The University of Queensland, School of Medicine, Brisbane, Queensland, Australia
| | - Naomi Runnegar
- Infection Management Services, Princess Alexandra Hospital, Brisbane, Queensland, Australia.,The University of Queensland, School of Medicine, Brisbane, Queensland, Australia
| | - Benjamin Rogers
- Centre for Inflammatory Disease, Monash University, Clayton, Victoria, Australia.,Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia
| | - Hasan Bhally
- Department of Medicine, North Shore Hospital, Milford, Auckland, New Zealand
| | - Amy Crowe
- Department of Infectious Diseases, St Vincent's Hospital, Melbourne, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - David L Paterson
- University of Queensland, UQ Centre for Clinical Research, Royal Brisbane & Women's Hospital, Queensland, Australia.,Wesley Medical Research, Wesley Hospital, Toowong, Queensland, Australia
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264
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Wu CJ, Lu HF, Lin YT, Zhang MS, Li LH, Yang TC. Substantial Contribution of SmeDEF, SmeVWX, SmQnr, and Heat Shock Response to Fluoroquinolone Resistance in Clinical Isolates of Stenotrophomonas maltophilia. Front Microbiol 2019; 10:822. [PMID: 31057523 PMCID: PMC6479208 DOI: 10.3389/fmicb.2019.00822] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022] Open
Abstract
Stenotrophomonas maltophilia is an emerging multi-drug resistant opportunistic pathogen. Although fluoroquinolones (FQ) are still clinically valuable for the treatment of S. maltophilia infection, an increasing prevalence in FQ resistance has been reported. Overexpression of SmeDEF, SmeVWX, and SmQnr, and de-repressed expression of heat shock response are reported mechanisms responsible for FQ resistance in S. maltophilia; nevertheless, some of these mechanisms are identified from laboratory-constructed mutants, and it remains unclear whether they occur in clinical setting. In this study, we aimed to assess whether these mechanisms contribute substantially to FQ resistance in clinical isolates. Eighteen ciprofloxacin- and levofloxacin-resistant isolates were selected from 125 clinical isolates of S. maltophilia. The expression of smeE, smeW, and Smqnr genes of these isolates was investigated by RT-qPCR. The de-repressed heat shock response was assessed by rpoE expression at 37°C and bacterial viability at 40°C. The contribution of SmeDEF, SmeVWX, and SmQnr, and heat shock response to FQ resistance was evaluated by mutants construction and susceptibility testing. The results demonstrated that simply assessing the overexpression of SmeDEF, SmeVWX, and SmQnr by RT-qPCR may overestimate their contribution to FQ resistance. Simultaneous overexpression of SmeDEF and SmeVWX did not increase the resistance level to their common substrates, but extended the resistance spectrum. Moreover, the de-repressed expression of heat shock response was not observed to contribute to FQ resistance in the clinical isolates of S. maltophilia.
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Affiliation(s)
- Chao-Jung Wu
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Hsu-Feng Lu
- Department of Clinical Pathology, Cheng Hsin General Hospital, Taipei, Taiwan.,Department of Restaurant, Hotel and Institutional Management, Fu-Jen Catholic University, New Taipei City, Taiwan
| | - Yi-Tsung Lin
- Division of Infectious Diseases, Department of Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Man-San Zhang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Li-Hua Li
- Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.,School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Tsuey-Ching Yang
- Department of Biotechnology and Laboratory Science in Medicine, National Yang-Ming University, Taipei, Taiwan
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265
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Gibson EG, Bax B, Chan PF, Osheroff N. Mechanistic and Structural Basis for the Actions of the Antibacterial Gepotidacin against Staphylococcus aureus Gyrase. ACS Infect Dis 2019; 5:570-581. [PMID: 30757898 DOI: 10.1021/acsinfecdis.8b00315] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gepotidacin is a first-in-class triazaacenaphthylene novel bacterial topoisomerase inhibitor (NBTI). The compound has successfully completed phase II trials for the treatment of acute bacterial skin/skin structure infections and for the treatment of uncomplicated urogenital gonorrhea. It also displays robust in vitro activity against a range of wild-type and fluoroquinolone-resistant bacteria. Due to the clinical promise of gepotidacin, a detailed understanding of its interactions with its antibacterial targets is essential. Thus, we characterized the mechanism of action of gepotidacin against Staphylococcus aureus gyrase. Gepotidacin was a potent inhibitor of gyrase-catalyzed DNA supercoiling (IC50 ≈ 0.047 μM) and relaxation of positively supercoiled substrates (IC50 ≈ 0.6 μM). Unlike fluoroquinolones, which induce primarily double-stranded DNA breaks, gepotidacin induced high levels of gyrase-mediated single-stranded breaks. No double-stranded breaks were observed even at high gepotidacin concentration, long cleavage times, or in the presence of ATP. Moreover, gepotidacin suppressed the formation of double-stranded breaks. Gepotidacin formed gyrase-DNA cleavage complexes that were stable for >4 h. In vitro competition suggests that gyrase binding by gepotidacin and fluoroquinolones are mutually exclusive. Finally, we determined crystal structures of gepotidacin with the S. aureus gyrase core fusion truncate with nicked (2.31 Å resolution) or intact (uncleaved) DNA (2.37 Å resolution). In both cases, a single gepotidacin molecule was bound midway between the two scissile DNA bonds and in a pocket between the two GyrA subunits. A comparison of the two structures demonstrates conformational flexibility within the central linker of gepotidacin, which may contribute to the activity of the compound.
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Affiliation(s)
| | - Ben Bax
- Medicines Discovery Institute, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Pan F. Chan
- Infectious Diseases Discovery, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States
| | - Neil Osheroff
- VA Tennessee Valley Healthcare System, 1310 24th Avenue S., Nashville, Tennessee 37212, United States
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266
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Vidovic S, An R, Rendahl A. Molecular and Physiological Characterization of Fluoroquinolone-Highly Resistant Salmonella Enteritidis Strains. Front Microbiol 2019; 10:729. [PMID: 31024504 PMCID: PMC6465633 DOI: 10.3389/fmicb.2019.00729] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 03/25/2019] [Indexed: 01/11/2023] Open
Abstract
Four clinical isolates of Salmonella Enteritidis, susceptible to ciprofloxacin, and their spontaneous ciprofloxacin resistant (MICs from 8 to 16 μg/mL) and highly resistant (MIC 2048 μg/mL) mutants were used to gain an insight into the dynamics of development of fluoroquinolone (FQs) resistance in S. Enteritidis serovar. The first two high-frequency (i.e., mutations that occurred in each tested strain) mutations occurred in the gyrA, resulting in amino acid substitutions S83Y and S83F as well as D87G. Amino acid substitution D87G was significantly associated with the highly resistant mutants. Another high-frequency mutation, deletion in the ramRA intergenic region, was determined among the same group of highly resistant mutants. More importantly, each of these deletion mutations affected the RamR binding site. The effect of one 41 bp deletion mutation was empirically tested. The results showed that the deletion was responsible for resistance to ceftiofur and amoxicillin/clavulanic acid and decreased susceptibility to azithromycin and tetracycline. Performing gene expression assays across all ciprofloxacin susceptible groups, we found a consistent and significant upregulation of the ramA, acrB, and tolC (efflux pump associated genes) and downregulation of ompF (porin), clearly illustrating the importance of not only efflux but also porin-mediated permeability in the development of FQs resistance. Our data also showed that S. Enteritidis could acquire multiple mutations in QRDR region, further resulting in no up regulation of the ramA, acrB and tolC genes. These QRDR mutations and no activation of the AcrAB efflux pump seem to preserve the fitness of this organism compared to the S. Enteritidis strains that did not acquire multiple QRDR mutations. This report describes the dynamics of FQ-associated mutations in the highly resistant in FQ mutants in S. Enteritidis. In addition, we characterized a deletion in the ramRA integenic region, demonstrating that this frequent mutation in the highly resistant FQ mutants provide resistance or reduce susceptibility to multiple families of antibiotics.
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Affiliation(s)
- Sinisa Vidovic
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Ran An
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Aaron Rendahl
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, United States
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267
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Giordano PA, Pogue JM, Cammarata S. Analysis of Pooled Phase III Efficacy Data for Delafloxacin in Acute Bacterial Skin and Skin Structure Infections. Clin Infect Dis 2019; 68:S223-S232. [PMID: 30957167 PMCID: PMC6452004 DOI: 10.1093/cid/ciz006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Delafloxacin is an oral or intravenous (IV) antibiotic indicated for the treatment of acute bacterial skin and skin structure infections (ABSSSI), including both gram-positive (including methicillin-resistant Staphylococcus aureus [MRSA]) and gram-negative organisms. Chemically distinct from other quinolones, delafloxacin exhibits enhanced potency, particularly against gram-positive pathogens. The integration of efficacy data across the Phase III ABSSSI studies is presented here and allows for additional examination of results across subgroups. METHODS Results of 2 multicenter, randomized, double-blind trials of 1510 adults with ABSSSI were pooled for this analysis. Subjects in the vancomycin arm received 15 mg/kg, plus 1-2 g of aztreonam every 12 hours. Delafloxacin was dosed at 300 mg IV every 12 hours in Study 302; dosing in Study 303 was 300 mg IV every 12 hours for 3 days, with a mandatory, blinded switch to delafloxacin at 450 mg orally every 12 hours. The primary endpoint was objective response (OR), defined as a ≥20% reduction of lesion spread of erythema area at the primary infection site at 48 to 72 hours (±2 hours), in the absence of clinical failure. Investigator-assessed response, based on the resolution of signs and symptoms at follow-up (FU; Day 14 ± 1) and late follow-up (LFU; Day 21- 28), were secondary endpoints. RESULTS In the intent-to-treat analysis set, the OR was 81.3% in the delafloxacin arm and 80.7% in the comparator arm (mean treatment difference 0.8%, 95% confidence interval -3.2% to 4.7). Results for OR in the defined subgroups showed delafloxacin to be comparable to vancomycin/aztreonam. Investigator-assessed success was similar at FU (84.7% versus 84.1%) and LFU (82.0% versus 81.7%). Delafloxacin was comparable to vancomycin/aztreonam in the eradication of MRSA, at 98.1% versus 98.0%, respectively, at FU. The frequencies of treatment-emergent adverse events between the groups were similar. CONCLUSIONS Overall, IV/oral delafloxacin fixed-dose monotherapy was non-inferior to IV vancomycin/aztreonam combination therapy and was well tolerated in each Phase III study, as well as in the pooled analysis, regardless of endpoint or analysis population.
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Affiliation(s)
| | - Jason M Pogue
- Division of Infectious Diseases, Detroit Medical Center, Wayne State University, Michigan
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268
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Vanden Broeck A, McEwen AG, Chebaro Y, Potier N, Lamour V. Structural Basis for DNA Gyrase Interaction with Coumermycin A1. J Med Chem 2019; 62:4225-4231. [PMID: 30920824 DOI: 10.1021/acs.jmedchem.8b01928] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Coumermycin A1 is a natural aminocoumarin that inhibits bacterial DNA gyrase, a member of the GHKL proteins superfamily. We report here the first cocrystal structures of gyrase B bound to coumermycin A1, revealing that one coumermycin A1 molecule traps simultaneously two ATP-binding sites. The inhibited dimers from different species adopt distinct sequence-dependent conformations, alternative to the ATP-bound form. These structures provide a basis for the rational development of coumermycin A1 derivatives for antibiotherapy and biotechnology applications.
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Affiliation(s)
- Arnaud Vanden Broeck
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Alastair G McEwen
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Yassmine Chebaro
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France
| | - Noëlle Potier
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes, UMR 7140 CNRS, University of Strasbourg, Strasbourg 67000 , France
| | - Valérie Lamour
- Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France.,Hôpitaux Universitaires de Strasbourg , Strasbourg 67000 , France
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269
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Li X, Zhang Y, Zhou X, Hu X, Zhou Y, Liu D, Maxwell A, Mi K. The plasmid-borne quinolone resistance protein QnrB, a novel DnaA-binding protein, increases the bacterial mutation rate by triggering DNA replication stress. Mol Microbiol 2019; 111:1529-1543. [PMID: 30838726 PMCID: PMC6617969 DOI: 10.1111/mmi.14235] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2019] [Indexed: 02/02/2023]
Abstract
Bacterial antibiotic resistance, a global health threat, is caused by plasmid transfer or genetic mutations. Quinolones are important antibiotics, partially because they are fully synthetic and resistance genes are unlikely to exist in nature; nonetheless, quinolone resistance proteins have been identified. The mechanism by which plasmid-borne quinolone resistance proteins promotes the selection of quinolone-resistant mutants is unclear. Here, we show that QnrB increases the bacterial mutation rate. Transcriptomic and genome sequencing analyses showed that QnrB promoted gene abundance near the origin of replication (oriC). In addition, the QnrB expression level correlated with the replication origin to terminus (oriC/ter) ratio, indicating QnrB-induced DNA replication stress. Our results also show that QnrB is a DnaA-binding protein that may act as an activator of DNA replication initiation. Interaction of QnrB with DnaA promoted the formation of the DnaA-oriC open complex, which leads to DNA replication over-initiation. Our data indicate that plasmid-borne QnrB increases bacterial mutation rates and that genetic changes can alleviate the fitness cost imposed by transmitted plasmids. Derivative mutations may impair antibiotic efficacy and threaten the value of antibiotic treatments. Enhanced understanding of how bacteria adapt to the antibiotic environment will lead to new therapeutic strategies for antibiotic-resistant infections.
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Affiliation(s)
- Xiaojing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yujiao Zhang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xintong Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xinling Hu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yixuan Zhou
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Di Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing, 101408, China
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270
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Circulation of Plasmids Harboring Resistance Genes to Quinolones and/or Extended-Spectrum Cephalosporins in Multiple Salmonella enterica Serotypes from Swine in the United States. Antimicrob Agents Chemother 2019; 63:AAC.02602-18. [PMID: 30745386 DOI: 10.1128/aac.02602-18] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 01/30/2019] [Indexed: 11/20/2022] Open
Abstract
Nontyphoidal Salmonella enterica (NTS) poses a major public health risk worldwide that is amplified by the existence of antimicrobial-resistant strains, especially those resistant to quinolones and extended-spectrum cephalosporins (ESC). Little is known on the dissemination of plasmids harboring the acquired genetic determinants that confer resistance to these antimicrobials across NTS serotypes from livestock in the United States. NTS isolates (n = 183) from U.S. swine clinical cases retrieved during 2014 to 2016 were selected for sequencing based on their phenotypic resistance to enrofloxacin (quinolone) or ceftiofur (3rd-generation cephalosporin). De novo assemblies were used to identify chromosomal mutations and acquired antimicrobial resistance genes (AARGs). In addition, plasmids harboring AARGs were identified using short-read assemblies and characterized using a multistep approach that was validated by long-read sequencing. AARGs to quinolones [qnrB15, qnrB19, qnrB2, qnrD, qnrS1, qnrS2, and aac(6')Ib-cr] and ESC (bla CMY-2, bla CTX-M-1, bla CTX-M-27, and bla SHV-12) were distributed across serotypes and were harbored by several plasmids. In addition, chromosomal mutations associated with resistance to quinolones were identified in the target enzyme and efflux pump regulation genes. The predominant plasmid harboring the prevalent qnrB19 gene was distributed across serotypes. It was identical to a plasmid previously reported in S. enterica serovar Anatum from swine in the United States (GenBank accession number KY991369.1) and similar to Escherichia coli plasmids from humans in South America (GenBank accession numbers GQ374157.1 and JN979787.1). Our findings suggest that plasmids harboring AARGs encoding mechanisms of resistance to critically important antimicrobials are present in multiple NTS serotypes circulating in swine in the United States and can contribute to resistance expansion through horizontal transmission.
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271
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Alcántar-Curiel MD, Fernández-Vázquez JL, Toledano-Tableros JE, Gayosso-Vázquez C, Jarillo-Quijada MD, López-Álvarez MDR, Giono-Cerezo S, Santos-Preciado JI. Emergence of IncFIA Plasmid-Carrying blaNDM-1 Among Klebsiella pneumoniae and Enterobacter cloacae Isolates in a Tertiary Referral Hospital in Mexico. Microb Drug Resist 2019; 25:830-838. [PMID: 30835632 DOI: 10.1089/mdr.2018.0306] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The emergence of New Delhi metallo-β-lactamase 1 on carbapenemase-producing bacteria has raised a major worldwide public health concern. This study reports the dissemination of blaNDM-1 in carbapenem-resistant isolates that caused nosocomial infections in a tertiary hospital in Mexico City. Seven Enterobacter cloacae and three Klebsiella pneumoniae nosocomial isolates from the same time period harbored the blaNDM-1 gene. The resistance phenotype and the blaNDM-1 gene were transferred through conjugative plasmids belonging to the incompatibility group IncFIA of 85, 101, and 195 kb in E. cloacae and 95 and 101 kb in K. pneumoniae isolates. Restriction fragment length polymorphism analysis showed that blaNDM-1 was carried in similar plasmids with molecular sizes of 101 and 85 kb, each one in three isolates of E. cloacae and one of 101 kb on two isolates of K. pneumoniae. During a 9-month period, six of the seven isolates of E. cloacae analyzed harbored blaNDM-1 and belonged to clone E1. Similarly, over a 5-month period, two of the three K. pneumoniae isolates that harbored blaNDM-1 belonged to clone K1. These results demonstrate the horizontal transfer of blaNDM-1 between different bacterial species, dissemination of clones with high levels of resistance to carbapenems, and underscore the need for heightened measures to control their further spread.
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Affiliation(s)
- María Dolores Alcántar-Curiel
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - José Luis Fernández-Vázquez
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - José Eduardo Toledano-Tableros
- 2 Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Catalina Gayosso-Vázquez
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Ma Dolores Jarillo-Quijada
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | | | - Silvia Giono-Cerezo
- 2 Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - José Ignacio Santos-Preciado
- 1 Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
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272
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Jian MJ, Cheng YH, Chung HY, Cheng YH, Yang HY, Hsu CS, Perng CL, Shang HS. Fluoroquinolone resistance in carbapenem-resistant Elizabethkingia anophelis: phenotypic and genotypic characteristics of clinical isolates with topoisomerase mutations and comparative genomic analysis. J Antimicrob Chemother 2019; 74:1503-1510. [DOI: 10.1093/jac/dkz045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 12/15/2018] [Accepted: 01/11/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
MDR Elizabethkingia anophelis strains are implicated in an increasing number of healthcare-associated infections worldwide, including a recent cluster of E. anophelis infections in the Midwestern USA associated with significant morbidity and mortality. However, there is minimal information on the antimicrobial susceptibilities of E. anophelis strains or their antimicrobial resistance to carbapenems and fluoroquinolones.
Objectives
Our aim was to examine the susceptibilities and genetic profiles of clinical isolates of E. anophelis from our hospital, characterize their carbapenemase genes and production of MBLs, and determine the mechanism of fluoroquinolone resistance.
Methods
A total of 115 non-duplicated isolates of E. anophelis were examined. MICs of antimicrobial agents were determined using the Sensititre 96-well broth microdilution panel method. QRDR mutations and MBL genes were identified using PCR. MBL production was screened for using a combined disc test.
Results
All E. anophelis isolates harboured the blaGOB and blaB genes with resistance to carbapenems. Antibiotic susceptibility testing indicated different resistance patterns to ciprofloxacin and levofloxacin in most isolates. Sequencing analysis confirmed that a concurrent GyrA amino acid substitution (Ser83Ile or Ser83Arg) in the hotspots of respective QRDRs was primarily responsible for high-level ciprofloxacin/levofloxacin resistance. Only one isolate had no mutation but a high fluoroquinolone MIC.
Conclusions
Our study identified a strong correlation between antibiotic susceptibility profiles and mechanisms of fluoroquinolone resistance among carbapenem-resistant E. anophelis isolates, providing an important foundation for continued surveillance and epidemiological analyses of emerging E. anophelis opportunistic infections. Minocycline or ciprofloxacin has the potential for treatment of severe E. anophelis infections.
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Affiliation(s)
- Ming-Jr Jian
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yun-Hsiang Cheng
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hsing-Yi Chung
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yu-Hsuan Cheng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Yi Yang
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Sin Hsu
- Center for Precision Medicine and Genomics, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cherng-Lih Perng
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Sheng Shang
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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273
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The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2017. EFSA J 2019; 17:e05598. [PMID: 32626224 PMCID: PMC7009238 DOI: 10.2903/j.efsa.2019.5598] [Citation(s) in RCA: 157] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The data on antimicrobial resistance in zoonotic and indicator bacteria in 2017, submitted by 28 EU Member States (MSs), were jointly analysed by EFSA and ECDC. Resistance in zoonotic Salmonella and Campylobacter from humans, animals and food, and resistance in indicator Escherichia coli as well as meticillin‐resistant Staphylococcus aureus in animals and food were addressed, and temporal trends assessed. ‘Microbiological’ resistance was assessed using epidemiological cut‐off (ECOFF) values; for some countries, qualitative data on human isolates were interpreted in a way which corresponds closely to the ECOFF‐defined ‘microbiological’ resistance. In Salmonella from humans, as well as in Salmonella and E. coli isolates from fattening pigs and calves of less than 1 year of age, high proportions of isolates were resistant to ampicillin, sulfonamides and tetracyclines, whereas resistance to third‐generation cephalosporins was uncommon. Varying occurrence/prevalence rates of presumptive extended‐spectrum beta‐lactamase (ESBL)/AmpC producers in Salmonella and E. coli monitored in meat (pork and beef), fattening pigs and calves, and Salmonella monitored in humans, were observed between countries. Carbapenemase‐producing E. coli were detected in one single
sample from fattening pigs in one MS. Resistance to colistin was observed at low levels in Salmonella and E. coli from fattening pigs and calves and meat thereof and in Salmonella from humans. In Campylobacter from humans, high to extremely high proportions of isolates were resistant to ciprofloxacin and tetracyclines, particularly in Campylobacter coli. In five countries, high to very high proportions of C. coli from humans were resistant also to erythromycin, leaving few options for treatment of severe Campylobacter infections. High resistance to ciprofloxacin and tetracyclines was observed in C. coli isolates from fattening pigs, whereas much lower levels were recorded for erythromycin. Combined resistance to critically important antimicrobials in both human and animal isolates was generally uncommon but very high to extremely high multidrug resistance levels were observed in S. Typhimurium and its monophasic variant in both humans and animals. S. Kentucky from humans exhibited high‐level resistance to ciprofloxacin, in addition to a high prevalence of ESBL.
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274
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Garoff L, Yadav K, Hughes D. Increased expression of Qnr is sufficient to confer clinical resistance to ciprofloxacin in Escherichia coli. J Antimicrob Chemother 2019; 73:348-352. [PMID: 29106520 PMCID: PMC5890660 DOI: 10.1093/jac/dkx375] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 09/15/2017] [Indexed: 02/05/2023] Open
Abstract
Background Ciprofloxacin, a fluoroquinolone, targets two essential bacterial enzymes, DNA gyrase and topoisomerase IV. Plasmid-borne qnr genes, encoding proteins that protect DNA gyrase and topoisomerase IV from inhibition by fluoroquinolones, contribute to resistance development. However, the presence of a plasmid-borne qnr gene alone is insufficient to confer clinical resistance. Objectives We asked whether the level of expression of qnr was a limiting factor in its ability to confer clinical resistance and whether expression could be increased without reducing fitness or viability. Methods qnrB and qnrS were recombineered onto the chromosome of Escherichia coli under the control of constitutive promoters of various strengths. Expression was measured by qPCR, MIC and relative fitness as a function of expression level were determined. Results For both qnr genes there was a positive relationship between the level of qnr mRNA and the MIC of ciprofloxacin. The highest MICs achieved with qnrB or qnrS as the sole resistance determinant were 0.375 and 1 mg/L, respectively, and were reached at expression levels that did not affect growth rate or viability. The qnrS-mediated MIC is above the EUCAST clinical breakpoint for resistance to ciprofloxacin. In the absence of Lon protease activity, overexpression of qnr genes was associated with high fitness cost, possibly explaining observations of toxicity in other genetic backgrounds. Conclusions The ability to generate a high MIC without incurring a fitness cost shows that, in an appropriate genetic context, qnrS has the potential to generate clinical resistance to ciprofloxacin in one step.
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Affiliation(s)
- Linnéa Garoff
- Department of Medical Biochemistry and Microbiology, Biomedical Centre (Box 582), Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Kavita Yadav
- Department of Medical Biochemistry and Microbiology, Biomedical Centre (Box 582), Uppsala University, Husargatan 3, Uppsala 75123, Sweden
| | - Diarmaid Hughes
- Department of Medical Biochemistry and Microbiology, Biomedical Centre (Box 582), Uppsala University, Husargatan 3, Uppsala 75123, Sweden
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275
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Miftahussurur M, Aftab H, Shrestha PK, Sharma RP, Subsomwong P, Waskito LA, Doohan D, Fauzia KA, Yamaoka Y. Effective therapeutic regimens in two South Asian countries with high resistance to major Helicobacter pylori antibiotics. Antimicrob Resist Infect Control 2019; 8:40. [PMID: 30815255 PMCID: PMC6377755 DOI: 10.1186/s13756-019-0482-x] [Citation(s) in RCA: 15] [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: 11/27/2018] [Accepted: 01/30/2019] [Indexed: 12/17/2022] Open
Abstract
Background Nepal and Bangladesh have a high prevalence of Helicobacter pylori with high resistance rates to clarithromycin, metronidazole, and levofloxacin. Here, we evaluated the susceptibility and genetic mutations of 5 alternative antibiotics against isolates from both countries to obtain an effective treatment regimen for H. pylori eradication. Methods We used the agar dilution method to determine the minimal inhibitory concentration of 5 alternative antibiotics against 42 strains from Nepal and 56 from Bangladesh and performed whole genome mutation analysis. Results No resistance to furazolidone or rifabutin and a high susceptibility of sitafloxacin (95.2% in Nepal and 98.2% in Bangladesh) were observed. In contrast, resistance to rifaximin (52.4% in Nepal and 64.3% in Bangladesh) was high. Moreover, resistance to garenoxacin was higher in Bangladesh (51.6%) than in Nepal (28.6%, P = 0.041), most likely due to its correlation with levofloxacin resistance (P = 0.03). Garenoxacin and rifaximin were significantly correlated in Bangladesh (P = 0.014) and occurred together with all sitafloxacin-resistant strains. Mutations of gyrA could play a significant role in garenoxacin resistance, and double mutations of A87 and D91 were associated with sitafloxacin resistance. Analysis of the rpoB gene demonstrated well-known mutations, such as V657I, and several novel mutations, including I2619V, V2592 L, T2537A, and F2538 L. Conclusions Rifabutin can be cautiously implemented as therapy for H. pylori infection due to its interaction with the tuberculosis endemic in Bangladesh. The high susceptibility of furazolidone and sitafloxacin suggests their possible future application in Nepal and Bangladesh.
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Affiliation(s)
- Muhammad Miftahussurur
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, 60131 Indonesia
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115 Indonesia
| | - Hafeza Aftab
- Department of Gastroenterology, Dhaka Medical College and Hospital, Dhaka, Bangladesh
| | - Pradeep Krishna Shrestha
- Department of Gastroenterology, Maharajgunj Medical Campus, Tribhuvan University Teaching Hospital, Kathmandu, 44600 Nepal
| | - Rabi Prakash Sharma
- Department of Gastroenterology, Maharajgunj Medical Campus, Tribhuvan University Teaching Hospital, Kathmandu, 44600 Nepal
| | - Phawinee Subsomwong
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593 Japan
| | - Langgeng Agung Waskito
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115 Indonesia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593 Japan
| | - Dalla Doohan
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115 Indonesia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593 Japan
| | - Kartika Afrida Fauzia
- Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115 Indonesia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593 Japan
| | - Yoshio Yamaoka
- Division of Gastroentero-Hepatology, Department of Internal Medicine, Faculty of Medicine-Dr. Soetomo Teaching Hospital, Universitas Airlangga, Surabaya, 60131 Indonesia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593 Japan
- Global Oita Medical Advanced Research Center for Health, Oita University, Oita, 870-1192 Japan
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX 77030 USA
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276
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Yamada K, Saito R, Muto S, Sasaki M, Murakami H, Aoki K, Ishii Y, Tateda K. Long-term observation of antimicrobial susceptibility and molecular characterisation of Campylobacter jejuni isolated in a Japanese general hospital 2000-2017. J Glob Antimicrob Resist 2019; 18:59-63. [PMID: 30753906 DOI: 10.1016/j.jgar.2019.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 02/01/2019] [Accepted: 02/01/2019] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES Campylobacter jejuni (C. jejuni) is one of the most common pathogens that causes gastroenteritis. Because there is currently insufficient epidemiological information about the antimicrobial susceptibility and molecular characterisation of clinical isolates of C. jejuni in Japan, this study carried out antimicrobial susceptibility testing and multilocus sequence typing (MLST) of clinical C. jejuni isolates in Tokyo between 2000-2017. METHODS Antimicrobial susceptibility to erythromycin and ciprofloxacin was tested using the broth microdilution method in 430 C. jejuni clinical isolates collected over 18 years, between 2000-2017, at a Tokyo general hospital. To observe the sequence type (ST) evolution, 82 isolates were chosen from three non-consecutive years (16 isolates from 2000, 25 isolates from 2008, and 41 isolates from 2017) and analysed by MLST as a molecular characterisation test. Mutations in the quinolone resistance-determining region of the gyrA and gyrB genes were identified. RESULTS The rate of resistance to erythromycin was low, but that of ciprofloxacin resistance was 34.9% in 2000-2008 and 41.9% in 2009-2017. The most common clonal complex (CC) identified during the entire period was CC21; ST4526 with ciprofloxacin resistance was highly prevalent in 2017 (6 of 11; 54.5%). CONCLUSION The results indicate that the rate of resistance to quinolone has gradually increased. Since ST4526 was not isolated in 2000 and 2008, it is likely that ST4526 is rapidly increasing in Japan.
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Affiliation(s)
- Kageto Yamada
- Department of Clinical Laboratory, Toho University Medical center Omori Hospital, Tokyo, Japan.
| | - Ryoichi Saito
- Department of Microbiology and Immunology, Graduate School of Health Care Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Saori Muto
- Department of Clinical Laboratory, Tokyo Metropolitan Health and Medical Treatment Corporation Toshima Hospital, Tokyo, Japan
| | - Masakazu Sasaki
- Department of Clinical Laboratory, Toho University Medical center Omori Hospital, Tokyo, Japan
| | - Hinako Murakami
- Department of Clinical Laboratory, Toho University Medical center Omori Hospital, Tokyo, Japan
| | - Kotaro Aoki
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Disease, Toho University School of Medicine, Tokyo, Japan
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277
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Faucher M, Nouvel LX, Dordet-Frisoni E, Sagné E, Baranowski E, Hygonenq MC, Marenda MS, Tardy F, Citti C. Mycoplasmas under experimental antimicrobial selection: The unpredicted contribution of horizontal chromosomal transfer. PLoS Genet 2019; 15:e1007910. [PMID: 30668569 PMCID: PMC6358093 DOI: 10.1371/journal.pgen.1007910] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 02/01/2019] [Accepted: 12/19/2018] [Indexed: 11/18/2022] Open
Abstract
Horizontal Gene Transfer was long thought to be marginal in Mycoplasma a large group of wall-less bacteria often portrayed as minimal cells because of their reduced genomes (ca. 0.5 to 2.0 Mb) and their limited metabolic pathways. This view was recently challenged by the discovery of conjugative exchanges of large chromosomal fragments that equally affected all parts of the chromosome via an unconventional mechanism, so that the whole mycoplasma genome is potentially mobile. By combining next generation sequencing to classical mating and evolutionary experiments, the current study further explored the contribution and impact of this phenomenon on mycoplasma evolution and adaptation using the fluoroquinolone enrofloxacin (Enro), for selective pressure and the ruminant pathogen Mycoplasma agalactiae, as a model organism. For this purpose, we generated isogenic lineages that displayed different combination of spontaneous mutations in Enro target genes (gyrA, gyrB, parC and parE) in association to gradual level of resistance to Enro. We then tested whether these mutations can be acquired by a susceptible population via conjugative chromosomal transfer knowing that, in our model organism, the 4 target genes are scattered in three distinct and distant loci. Our data show that under antibiotic selective pressure, the time scale of the mutational pathway leading to high-level of Enro resistance can be readily compressed into a single conjugative step, in which several EnroR alleles were transferred from resistant to susceptible mycoplasma cells. In addition to acting as an accelerator for antimicrobial dissemination, mycoplasma chromosomal transfer reshuffled genomes beyond expectations and created a mosaic of resistant sub-populations with unpredicted and unrelated features. Our findings provide insights into the process that may drive evolution and adaptability of several pathogenic Mycoplasma spp. via an unconventional conjugative mechanism.
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Affiliation(s)
- Marion Faucher
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- UMR Mycoplasmoses of ruminants, ANSES, VetAgro Sup, University of Lyon, Lyon, France
| | | | | | - Eveline Sagné
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
| | | | | | - Marc-Serge Marenda
- Asia-Pacific Centre for Animal Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Florence Tardy
- UMR Mycoplasmoses of ruminants, ANSES, VetAgro Sup, University of Lyon, Lyon, France
| | - Christine Citti
- IHAP, Université de Toulouse, INRA, ENVT, Toulouse, France
- * E-mail: (LXN); (CC)
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278
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El-Badawy MF, Alrobaian MM, Shohayeb MM, Abdelwahab SF. Investigation of six plasmid-mediated quinolone resistance genes among clinical isolates of pseudomonas: a genotypic study in Saudi Arabia. Infect Drug Resist 2019; 12:915-923. [PMID: 31118699 PMCID: PMC6499481 DOI: 10.2147/idr.s203288] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 03/05/2019] [Indexed: 02/05/2023] Open
Abstract
Background: Quinolones are among the most effective antibiotics against Pseudomonas spp. Several chromosomal and/or plasmid-mediated quinolone-resistance mechanisms have been found in Pseudomonas. Plasmid-mediated quinolone-resistance (PMQR) is mediated by quinolone-resistance (QNR) proteins, modifying enzymes or efflux pumps. Only a few previous studies examined the prevalence of quinolone-resistance in the Kingdom of Saudi Arabia (KSA) and showed it is increasing. Mechanisms of quinolone-resistance among Pseudomonas spp. in the KSA; examined herein; have not been extensively studied. Methods: Ninety-two Pseudomonas isolates were collected and their resistance to seven different types of quinolones was determined by the microbroth dilution method. PMQR mechanisms were examined using a PCR screen to identify six PMQR genes including qnrA, qnrB, qnrD, qnrS, aac(6´)-Ib-cr, and qepA. Clonal relatedness of the quinolone-resistant isolates was determined by ERIC-PCR. Results: Of the isolates, 42.4% (39/92) were resistant to 1-7 of the tested quinolones. Gemifloxacin resistance was the lowest (28.3%) while resistance to the other six quinolones were ≥ 35%. The most common biotype among the 39 quinolone-resistant isolates was resistance to the seven tested quinolones (26/39; 66.7%). qnrD, qnrS, and aac(6´)-Ib-cr were found in 31 (79.5%), 31 (79.5%) and 28 (71.8%) of the 39 isolates, respectively, and all three genes together were found in 22 of the 39 isolates (56.4%). qnrA, qnrB, and qepA were not detected in any of the isolates and two isolates did not harbor any of the six tested genes. The isolates showed 38 different ERIC profiles and only two isolates (Pa16 and Pa17) had an identical profile. Conclusion: This is the first description of PMQR mechanisms among clinical Pseudomonas isolates from the KSA, which appears to be mainly mediated by qnrD, qnrS, and aac(6´)-Ib-cr.
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Affiliation(s)
- Mohamed F El-Badawy
- Division of Pharmaceutical Microbiology, Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif21974, Kingdom of Saudi Arabia
- Department of Microbiology and Immunology, Faculty of Pharmacy, Misr University for Science and Technology, Al-Motamayez District12568, Egypt
| | - Majed M Alrobaian
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif21974, Kingdom of Saudi Arabia
| | - Mohamed M Shohayeb
- Division of Pharmaceutical Microbiology, Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif21974, Kingdom of Saudi Arabia
- Department of Microbiology and Biotechnology, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa35712, Egypt
| | - Sayed F Abdelwahab
- Division of Pharmaceutical Microbiology, Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif21974, Kingdom of Saudi Arabia
- Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511, Egypt
- Correspondence: Sayed F AbdelwahabDivision of Pharmaceutical Microbiology, Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif21974, Kingdom of Saudi Arabia and Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia 61511,Egypt Tel +966 54 122 1361; +20 109 000 8885Fax +20 86 234 2813Email
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Pattabiraman V, Katz LS, Chen JC, McCullough AE, Trees E. Genome wide characterization of enterotoxigenic Escherichia coli serogroup O6 isolates from multiple outbreaks and sporadic infections from 1975-2016. PLoS One 2018; 13:e0208735. [PMID: 30596673 PMCID: PMC6312315 DOI: 10.1371/journal.pone.0208735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 11/22/2018] [Indexed: 02/07/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) are an important cause of diarrhea globally, particularly among children under the age of five in developing countries. ETEC O6 is the most common ETEC serogroup, yet the genome wide population structure of isolates of this serogroup is yet to be determined. In this study, we have characterized 40 ETEC O6 isolates collected between 1975–2016 by whole genome sequencing (WGS) and by phenotypic antimicrobial susceptibility testing. To determine the relatedness of isolates, we evaluated two methods—whole genome high-quality single nucleotide polymorphism (whole genome-hqSNP) and core genome SNP analyses using Lyve-SET and Parsnp respectively. All isolates were tested for antimicrobial susceptibility using a panel of 14 antibiotics. ResFinder 2.1 and a custom quinolone resistance determinants workflow were used for resistance determinant detection. VirulenceFinder 1.5 was used for prediction of the virulence genes. Thirty-seven isolates clustered into three major clades (I, II, III) by whole genome-hqSNP and core genome SNP analyses, while three isolates included in the whole genome-hqSNP analysis only did not cluster with clades I-III by both analyses and formed a distantly related outgroup, designated clade IV. Median number of pairwise whole genome-hqSNPs in clonal ETEC O6 outbreaks ranged from 0 to 5. Of the 40 isolates tested for antimicrobial susceptibility, 18 isolates were pansusceptible. Twenty-two isolates were resistant to at least one antibiotic, nine of which were multidrug resistant. Phenotypic antimicrobial resistance (AR) correlated with AR determinants in 22 isolates. Thirty-two isolates harbored both enterotoxin virulence genes while the remaining 8 isolates had only one of the two virulence genes. In summary, whole genome-hqSNP and core genome SNP analyses from this study revealed similar evolutionary relationships and an overall diversity of ETEC O6 isolates independent of time of isolation. Less than 5 pairwise hqSNPs between ETEC O6 isolates is circumstantially indicative of an outbreak cluster. Findings from this study will be a basis for quicker outbreak detection and control by efficient subtyping by WGS.
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Affiliation(s)
- Vaishnavi Pattabiraman
- Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- * E-mail:
| | - Lee S. Katz
- Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Center for Food Safety, College of Agricultural and Environmental Sciences, University of Georgia, Griffin, GA, United States of America
| | - Jessica C. Chen
- Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | | | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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280
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Ostrer L, Khodursky RF, Johnson JR, Hiasa H, Khodursky A. Analysis of mutational patterns in quinolone resistance-determining regions of GyrA and ParC of clinical isolates. Int J Antimicrob Agents 2018; 53:318-324. [PMID: 30582984 DOI: 10.1016/j.ijantimicag.2018.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/15/2018] [Indexed: 01/03/2023]
Abstract
Fluoroquinolone (FQ)-resistant bacteria pose a major global health threat. Unanalysed genomic data from thousands of sequenced microbes likely contain important hints regarding the evolution of FQ resistance, yet this information lies fallow. Here we analysed the co-occurrence patterns of quinolone resistance mutations in genes encoding the FQ drug targets DNA gyrase (gyrase) and topoisomerase IV (topo-IV) from 36,402 bacterial genomes, representing 10 Gram-positive and 10 Gram-negative species. For 19 species, the likeliest routes toward resistance mutations in both targets were determined, and for 5 species those mutations necessary and sufficient to predict FQ resistance were also determined. Target mutation hierarchy was fixed in all examined Gram-negative species, with gyrase being the primary and topo-IV the secondary quinolone target, as well as in six of nine Gram-positive species, with topo-IV being the primary and gyrase the secondary target. By contrast, in three Gram-positive species (Staphylococcus haemolyticus, Streptococcus pneumoniae and Streptococcus suis), under some conditions gyrase became the primary and topo-IV the secondary target. The path through individual resistance mutations varied by species. Both linear and branched paths were identified in Gram-positive and Gram-negative organisms alike. Finally, FQ resistance could be predicted based solely on target gene quinolone resistance mutations for Acinetobacter baumannii, Escherichia coli and Staphylococcus aureus, but not Klebsiella pneumoniae or Pseudomonas aeruginosa. These findings have important implications both for sequence-based diagnostics and for understanding the emergence of FQ resistance.
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Affiliation(s)
- Lev Ostrer
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, St Paul, MN, USA
| | - Rachel F Khodursky
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, St Paul, MN, USA
| | | | - Hiroshi Hiasa
- Department of Pharmacology, University of Minnesota Medical School, 6-120 Jackson Hall, 321 Church Street SE, Minneapolis, MN, USA
| | - Arkady Khodursky
- Department of Biochemistry, Molecular Biology and Biophysics, Biotechnology Institute, University of Minnesota, St Paul, MN, USA.
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Peltier F, Choquet M, Decroix V, Adjidé CC, Castelain S, Guiheneuf R, Pluquet E. Characterization of a multidrug-resistant Klebsiella pneumoniae ST607-K25 clone responsible for a nosocomial outbreak in a neonatal intensive care unit. J Med Microbiol 2018; 68:67-76. [PMID: 30507374 DOI: 10.1099/jmm.0.000884] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Multidrug-resistant Klebsiella pneumoniae strains are regularly involved in hospital outbreaks. This study describes an ESBL-producing K. pneumoniae clone (ST607-K25) responsible for a nosocomial outbreak in a neonatal intensive care unit. METHODOLOGY Fourteen strains isolated from 13 patients were included. Antimicrobial susceptibility testing was performed by the agar diffusion method. A clonal link was first investigated by fingerprinting (ERIC-PCR and REP-PCR) then confirmed by MLST. Characterization was performed by molecular detection and identification of several drug resistance and virulence determinants. RESULTS All strains expressed the same antibiotype, combining ESBL production, fluoroquinolones and aminoglycoside resistance, except for one which remained susceptible to fluoroquinolones. Fingerprinting methods confirmed the clonal link and MLST identified a ST607 clone. Molecular investigations revealed: (I) genes encoding for two narrow-spectrum beta-lactamases (SHV-1 and TEM-1) and an ESBL (CTX-M-15); (II) absence of any chromosomal mutation in quinolone resistance-determining- regions (QRDR) of gyrA/gyrB and parC/parE genes; (III) genes encoding for three plasmid-mediated quinolone-resistance (PMQR) determinants: oqxAB (14/14), aac(6')-Ib-cr (14/14) and qnrB (13/14); (IV) production of a K25 capsule; and (V) carriage of three genes encoding for virulence factors: mrkD (type 3 fimbriae) (14/14), ybts (yersiniabactin) (12/14) and entB (enterobactin) (14/14). CONCLUSION We described a multidrug-resistant Kp ST607 clone responsible for a nosocomial outbreak in vulnerable and premature newborns. Molecular investigations allowed us to identify several resistance factors responsible for ESBL production (CTX-M-15) and quinolone resistance (three PMQR determinants). The detection of a gene (ybtS) belonging to the high-pathogenicity island yersiniabactin could partly explain its high colonization and diffusion potential.
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Affiliation(s)
- F Peltier
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - M Choquet
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - V Decroix
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - C C Adjidé
- 3Nosocomial Infection Department, Amiens-Picardie University Hospital, Amiens, France
| | - S Castelain
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - R Guiheneuf
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
| | - E Pluquet
- 1Department of Bacteriology, Amiens-Picardie University Hospital, Amiens, France.,2Microbiology Research Unit, AGIR -EA4294, Jules Verne University of Picardie, Amiens, France
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Jaidane N, Naas T, Oueslati S, Bernabeu S, Boujaafar N, Bouallegue O, Bonnin RA. Whole-genome sequencing of NDM-1-producing ST85 Acinetobacter baumannii isolates from Tunisia. Int J Antimicrob Agents 2018; 52:916-921. [DOI: 10.1016/j.ijantimicag.2018.05.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/16/2018] [Accepted: 05/23/2018] [Indexed: 12/30/2022]
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283
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Kocsis B, Szmolka A, Szabo O, Gulyas D, Kristóf K, Göcző I, Szabo D. Ciprofloxacin Promoted qnrD Expression and Phylogenetic Analysis of qnrD Harboring Plasmids. Microb Drug Resist 2018; 25:501-508. [PMID: 30461351 DOI: 10.1089/mdr.2018.0245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Morganella morganii SE10MM harboring quinolone resistance determinant qnrD was investigated in our study. An entirely sequenced novel 2,662 bp qnrD-plasmid pSE10MM was identified and deposited at GenBank under accession number KU160530. Nucleic acid sequence of pSE10MM showed 94-97% similarity to previously detected qnrD-plasmids of Proteus mirabilis strains. Phylogenetic analysis by Geneious 9.0.5 showed clusters of plasmids with possible common origin. Initial expression of qnrD gene was found 12.5 normalized to rpoB housekeeping gene. Subsequently, a sub-minimum inhibitory concentration (1 mg/L) ciprofloxacin exposure resulted in a fold change of 30.06 at 24 hours. In contrast, qnrD-plasmid pSE10MM copy number increased in time from 1.1 to 6.63. Chromosomal mutations of gyrA with S83I, gyrB with S463A, and parC with S80I amino acid substitutions were detected, but no other mutations have occurred as a consequence of ciprofloxacin exposure. Elevated expression of qnrD correlated with that of recA in M. morganii during ciprofloxacin exposure, which indicates SOS-dependent regulation of qnrD. Protective effect of QnrD plays a role in fluoroquinolone-resistant strain even in the presence of chromosomal mutations in gyrase and topoisomerase IV.
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Affiliation(s)
- Bela Kocsis
- 1 Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Ama Szmolka
- 2 Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, Hungary
| | - Orsolya Szabo
- 1 Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Daniel Gulyas
- 1 Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Katalin Kristóf
- 3 Institute of Laboratory Medicine, Diagnostic Laboratory of Clinical Microbiology, Semmelweis University, Budapest, Hungary
| | - Istvan Göcző
- 1 Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Dora Szabo
- 1 Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
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284
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Caruso G, Giammanco A, Cardamone C, Oliveri G, Mascarella C, Capra G, Fasciana T. Extra-Intestinal Fluoroquinolone-Resistant Escherichia coli Strains Isolated from Meat. BIOMED RESEARCH INTERNATIONAL 2018; 2018:8714975. [PMID: 30581870 PMCID: PMC6276482 DOI: 10.1155/2018/8714975] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/17/2018] [Accepted: 10/28/2018] [Indexed: 01/01/2023]
Abstract
Extra-intestinal E. coli are emerging as a global threat due to their diffusion as opportunistic pathogens and, above all, to their wide set of antibiotic resistance determinants. There are still many gaps in our knowledge of their origin and spread pathways, although food animals have been adjudicated vehicles for passing mult-drug resistant bacteria to humans. This study analyzed 46 samples of meat purchased from retail stores in Palermo in order to obtain quinolone-resistant E. coli isolates. Strains were screened for their phylogenetic groups, ST131-associated single nucleotide polymorphisms (SNPs), and then typed by ERIC-PCR. Their set of virulence factors, namely, kpsMII, papA, sfaS, focG, iutA, papC, hlyD, and afa genes, were investigated and their fluoroquinolone-resistance determinants evaluated. The data obtained show a dramatically high prevalence of multidrug resistance patterns in the Palermo area, with 28% of the isolates having virulence factor genes typical of ExPEC strains. No B2 group or ST131 strains were detected. Moreover, 20% of our isolates showed positivity to all the plasmid-mediated quinolone resistance (PMQR) determinants, showing a potential to transfer these genes among other bacteria. Therefore, these data underline the possibility that food animals and, specifically, poultry in particular may be a significant source of resistant bacterial strains, posing a potential zoonotic risk.
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Affiliation(s)
- Giorgia Caruso
- Department of Sciences for Health Promotion and Mother & Child Care, University of Palermo, Italy
| | - Anna Giammanco
- Department of Sciences for Health Promotion and Mother & Child Care, University of Palermo, Italy
| | - Cinzia Cardamone
- Institute for Experimental Veterinary Medicine of Sicily, Palermo, Italy
| | - Giuseppa Oliveri
- Institute for Experimental Veterinary Medicine of Sicily, Palermo, Italy
| | - Chiara Mascarella
- Department of Sciences for Health Promotion and Mother & Child Care, University of Palermo, Italy
| | - Giuseppina Capra
- Department of Sciences for Health Promotion and Mother & Child Care, University of Palermo, Italy
| | - Teresa Fasciana
- Department of Sciences for Health Promotion and Mother & Child Care, University of Palermo, Italy
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285
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Jaillard M, Lima L, Tournoud M, Mahé P, van Belkum A, Lacroix V, Jacob L. A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events. PLoS Genet 2018; 14:e1007758. [PMID: 30419019 PMCID: PMC6258240 DOI: 10.1371/journal.pgen.1007758] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/26/2018] [Accepted: 10/12/2018] [Indexed: 11/21/2022] Open
Abstract
Genome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or detailed assessment of marker effect. Recently, alignment-free methods based on k-mer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are sometimes hard to interpret. Here we introduce DBGWAS, an extended k-mer-based GWAS method producing interpretable genetic variants associated with distinct phenotypes. Relying on compacted De Bruijn graphs (cDBG), our method gathers cDBG nodes, identified by the association model, into subgraphs defined from their neighbourhood in the initial cDBG. DBGWAS is alignment-free and only requires a set of contigs and phenotypes. In particular, it does not require prior annotation or reference genomes. It produces subgraphs representing phenotype-associated genetic variants such as local polymorphisms and mobile genetic elements (MGE). It offers a graphical framework which helps interpret GWAS results. Importantly it is also computationally efficient-experiments took one hour and a half on average. We validated our method using antibiotic resistance phenotypes for three bacterial species. DBGWAS recovered known resistance determinants such as mutations in core genes in Mycobacterium tuberculosis, and genes acquired by horizontal transfer in Staphylococcus aureus and Pseudomonas aeruginosa-along with their MGE context. It also enabled us to formulate new hypotheses involving genetic variants not yet described in the antibiotic resistance literature. An open-source tool implementing DBGWAS is available at https://gitlab.com/leoisl/dbgwas.
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Affiliation(s)
- Magali Jaillard
- bioMérieux, Marcy l’Étoile, France
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
| | - Leandro Lima
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
- EPI ERABLE - Inria Grenoble, Rhône-Alpes, France
| | | | | | | | - Vincent Lacroix
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
- EPI ERABLE - Inria Grenoble, Rhône-Alpes, France
| | - Laurent Jacob
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
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286
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Lloyd NA, Nazaret S, Barkay T. Whole genome sequences to assess the link between antibiotic and metal resistance in three coastal marine bacteria isolated from the mummichog gastrointestinal tract. MARINE POLLUTION BULLETIN 2018; 135:514-520. [PMID: 30301067 DOI: 10.1016/j.marpolbul.2018.07.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 07/17/2018] [Accepted: 07/20/2018] [Indexed: 06/08/2023]
Abstract
Antibiotic resistance is a global public health issue and metal exposure can co-select for antibiotic resistance. We examined genome sequences of three multi-drug and metal resistant bacteria: one Shewanella sp., and two Vibrio spp., isolated from the gut of the mummichog fish (Fundulus heteroclitus). Our primary goal was to understand the mechanisms of co-selection. Phenotypically, the strains showed elevated resistance to arsenate, mercury, and various types of β-lactams. The genomes contained genes of public health concern including one carbapenemase (blaOXA-48). Our analyses indicate that the co-selection phenotype is mediated by chromosomal resistance genes and cross-resistance. No evidence of co-resistance was found; most resistance genes were chromosomally located. Moreover, the identification of many efflux pump gene homologs indicates that cross-resistance and/or co-regulation may further contribute to resistance. We suggest that the mummichog gut microbiota may be a source of clinically relevant antibiotic resistance genes.
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Affiliation(s)
- Nicole A Lloyd
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, USA.
| | - Sylvie Nazaret
- UMR 5557 Ecologie Microbienne, CNRS, INRA, VetagroSup, UCBL, Université de Lyon, 43 Boulevard du 11 Novembre, F-69622 Villeurbanne, France
| | - Tamar Barkay
- Department of Biochemistry and Microbiology, Rutgers University, 76 Lipman Drive, New Brunswick, NJ 08901, USA
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287
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Uechi K, Tada T, Shimada K, Nakasone I, Kirikae T, Fujita J. Emergence of a carbapenem-resistant and colistin-heteroresistant Enterobacter cloacae clinical isolate in Japan. J Infect Chemother 2018; 25:285-288. [PMID: 30279112 DOI: 10.1016/j.jiac.2018.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 08/08/2018] [Accepted: 09/04/2018] [Indexed: 10/28/2022]
Abstract
A carbapenem-resistant and colistin-heteroresistant clinical isolate of Enterobacter cloacae was obtained from an inpatient in Okinawa, Japan. The minimum inhibitory concentrations of both imipenem and meropenem were 32 μg/mL. The isolate showed heteroresistance to colistin using the Etest method and resistance to colistin using the broth microdilution method. It had a disrupted ompC and a mutation in the promoter region of blaACT-2, but did not harbor any genes encoding carbapenemase. The disruption of ompC and the mutation in blaACT-2 was associated with the carbapenem resistance of this isolate. This isolate also had mutations in pmrAB and phoPQ encoding two-component regulatory systems, which may be associated with colistin heteroresistance.
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Affiliation(s)
- Kohei Uechi
- Department of Infectious Diseases, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan; Division of Clinical Laboratory and Blood Transfusion, University Hospital of the Ryukyus, Okinawa, Japan
| | - Tatsuya Tada
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan; Department of Infectious Disease, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Kayo Shimada
- Department of Infectious Disease, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Isamu Nakasone
- Control and Prevention of Infectious Disease, University Hospital of the Ryukyus, Okinawa, Japan
| | - Teruo Kirikae
- Department of Microbiology, Juntendo University School of Medicine, Tokyo, Japan; Department of Infectious Disease, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan.
| | - Jiro Fujita
- Department of Infectious Diseases, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
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288
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Jiang X, Yu T, Xu P, Xu X, Ji S, Gao W, Shi L. Role of Efflux Pumps in the in vitro Development of Ciprofloxacin Resistance in Listeria monocytogenes. Front Microbiol 2018; 9:2350. [PMID: 30319598 PMCID: PMC6170607 DOI: 10.3389/fmicb.2018.02350] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/12/2018] [Indexed: 12/19/2022] Open
Abstract
Efflux is a primary fluoroquinolone resistance mechanism in Listeria monocytogenes. In the present study, ciprofloxacin resistant strains were selected by exposure of sensitive strain to progressively increasing concentrations of ciprofloxacin and then the roles of efflux pumps Lde and MdrL in the development of resistance to ciprofloxacin were also investigated in L. monocytogenes. Ciprofloxacin sensitive strain of L. monocytogenes exhibited reduced susceptibility to this antibiotic after induction. Cross-resistance to ethidium bromide (EtBr) was observed in ciprofloxacin-induced strains. However, cross-resistance to benzalkonium chloride (BC) did not occur in this study. Compared to the wild-type strain HL06, the expression levels of lde were increased in four ciprofloxacin-induced strains. The single-gene deletion mutants of lde and mdrL from the ciprofloxacin-induced resistant strain HL06CIP4 were constructed. However, decreased minimum inhibitory concentration (MIC) of ciprofloxacin was observed only in HL06CIP4Δlde compared to that of the parental strain HL06CIP4. Ciprofloxacin uptake appeared to be obviously increased in HL06CIP4Δlde in relative to HL06CIP4. These evidences suggested that efflux pump Lde is involved in ciprofloxacin resistance in L. monocytogenes HL06CIP4. The deletion of lexA had no effect on the expression levels of lde in HL06CIP4 in the absence or presence of ciprofloxacin, indicating that LexA was not involved in the regulation of efflux pump Lde in L. monocytogenes.
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Affiliation(s)
- Xiaobing Jiang
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Tao Yu
- College of Life Science and Technology, Xinxiang University, Xinxiang, China
| | - Ping Xu
- College of Life Science and Technology, Xinxiang University, Xinxiang, China
| | - Xiaobo Xu
- College of Life Science and Technology, Xinxiang University, Xinxiang, China
| | - Shengdong Ji
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, China
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289
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Pandey A, Aggarwal N, Adholeya A, Kochar M. Resurrection of Nalidixic Acid: Evaluation of Water-Based Nanoformulations as Potential Nanomedicine. NANOSCALE RESEARCH LETTERS 2018; 13:298. [PMID: 30251124 PMCID: PMC6153259 DOI: 10.1186/s11671-018-2718-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
Resistance to quinolone antibiotics has been a serious problem ever since nalidixic acid was introduced into clinical medicine. Over time, resistance of pathogenic microbes to nalidixic acid led to the design of novel variants to revive its potential application. In the present work, a series of eight nanoformulations of nalidixic acid-based diacyl and sulfonyl acyl hydrazine derivatives were prepared. All nanoformulations were found to be stable at different storage temperatures. Antibacterial and anticandida activity of the eight nanoformulations presented encouraging results when compared with their non-nano parent counterparts. The nanoformulations of chloro, furanyl, and sulfonyl acyl substituted derivatives of nalidixic acid displayed most promising results (MIC ranging from 50 to 100 μg mL-1) against the tested bacteria and yeast. Among the screened bacteria, Acinetobacter baumannii displayed maximum sensitivity to the above nanoformulations. Biosafety study on the mammalian model-wax moth, Galleria mellonella-showed that all eight prepared nanoformulations were absolutely nontoxic to the larvae and subsequent pupae and hence may likely have no or low toxicity against mammalian systems.
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Affiliation(s)
- Alka Pandey
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gwal Pahari, Gurugram, Haryana 122003 India
| | - Nisha Aggarwal
- Department of Chemistry, Sri Aurobindo College, University of Delhi, New Delhi, India
| | - Alok Adholeya
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gwal Pahari, Gurugram, Haryana 122003 India
| | - Mandira Kochar
- TERI-Deakin Nanobiotechnology Centre, TERI Gram, The Energy and Resources Institute, Gwal Pahari, Gurugram, Haryana 122003 India
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290
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Jian MJ, Cheng YH, Perng CL, Shang HS. Molecular typing and profiling of topoisomerase mutations causing resistance to ciprofloxacin and levofloxacin in Elizabethkingia species. PeerJ 2018; 6:e5608. [PMID: 30225179 PMCID: PMC6139017 DOI: 10.7717/peerj.5608] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 08/19/2018] [Indexed: 12/02/2022] Open
Abstract
Objectives Several Elizabethkingia species often exhibit extensive antibiotic resistance, causing infections associated with severe morbidity and high mortality rates worldwide. In this study, we determined fluoroquinolone susceptibility profiles of clinical Elizabethkingia spp. isolates and investigated the resistance mechanisms. Methods In 2017–2018, 131 Elizabethkingia spp. isolates were recovered from specimens collected at tertiary care centers in northern Taiwan. Initial species identification using the Vitek MS system and subsequent verification by 16S rRNA sequencing confirmed the presence of Elizabethkingia anophelis (n = 111), E. miricola (n = 11), and E. meningoseptica (n = 9). Fluoroquinolone susceptibility was determined using the microbroth dilution method, and fluoroquinolone resistance genes were analyzed by sequencing. Results Among Elizabethkingia spp. isolates, 91% and 77% were resistant to ciprofloxacin and levofloxacin, respectively. The most prevalent alterations were two single mutations in GyrA, Ser83Ile, and Ser83Arg, detected in 76% of the isolates exhibiting fluoroquinolone MIC between 8 and 128 μg/ml. Another GyrA single mutation, Asp87Asn, was identified in two quinolone-resistant E. miricola strains. None of the isolates had alterations in GyrB, ParC, or ParE. We developed a high-resolution melting assay for rapid identification of the prevalent gyrA gene mutations. The genetic relationship between the isolates was evaluated by random amplified polymorphic DNA PCR that yielded diverse pulsotypes, indicating the absence of any temporal or spatial overlap among the patients during hospitalization. Conclusion Our analysis of fluoroquinolone-resistant Elizabethkingia spp. isolates provides information for further research on the variations of the resistance mechanism and potential clinical guidance for infection management.
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Affiliation(s)
- Ming-Jr Jian
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Yun-Hsiang Cheng
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Cherng-Lih Perng
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Hung-Sheng Shang
- Graduate Institute of Medical Science, National Defense Medical Center, Taipei, Taiwan.,Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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291
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Kuang D, Zhang J, Xu X, Shi W, Chen S, Yang X, Su X, Shi X, Meng J. Emerging high-level ciprofloxacin resistance and molecular basis of resistance in Salmonella enterica from humans, food and animals. Int J Food Microbiol 2018; 280:1-9. [DOI: 10.1016/j.ijfoodmicro.2018.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/31/2018] [Accepted: 05/01/2018] [Indexed: 10/17/2022]
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292
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Genes and Proteins Involved in qnrS1 Induction. Antimicrob Agents Chemother 2018; 62:AAC.00806-18. [PMID: 29914953 DOI: 10.1128/aac.00806-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 06/05/2018] [Indexed: 11/20/2022] Open
Abstract
Expression of the quinolone resistance gene qnrS1 is increased by quinolones, but unlike induction of some other qnr genes, the bacterial SOS system is not involved and no lexA box is found upstream. Nonetheless, at least 205 bp of upstream sequence is required for induction to take place. An upstream sequence bound to beads trapped potential binding proteins from cell extracts that were identified by mass spectrometry as Dps, Fis, Ihf, Lrp, CysB, and YjhU. To further elucidate their role, a reporter plasmid linking the qnrS1 upstream sequence to lacZ was introduced into cells of the Keio collection with single-gene deletions and screened for lacZ expression. Mutants in ihfA and ihfB had decreased lacZ induction, while induction in a cysB mutant was increased and dps, fis, lrp, yjhU, and other mutants showed no change. The essential upstream sequence contains potential binding sites for Ihf and DnaA. A dnaA deletion could not be tested because it provides essential functions in cell replication; however, increased dnaA expression decreased qnrS1 induction while decreased dnaA expression enhanced it, implying a role for DnaA as a repressor. In a mobility shift assay, purified IhfA, IhfB, and DnaA proteins (but not CysB) were shown to bind to the upstream segment. Induction decreased in a gyrA quinolone-resistant mutant, indicating that GyrA also has a role. Thus, quinolones acting through proteins DnaA, GyrA, IhfA, and IhfB regulate expression of qnrS1.
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293
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Gibson EG, Blower TR, Cacho M, Bax B, Berger JM, Osheroff N. Mechanism of Action of Mycobacterium tuberculosis Gyrase Inhibitors: A Novel Class of Gyrase Poisons. ACS Infect Dis 2018; 4:1211-1222. [PMID: 29746087 DOI: 10.1021/acsinfecdis.8b00035] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Tuberculosis is one of the leading causes of morbidity worldwide, and the incidences of drug resistance and intolerance are prevalent. Thus, there is a desperate need for the development of new antitubercular drugs. Mycobacterium tuberculosis gyrase inhibitors (MGIs) are napthyridone/aminopiperidine-based drugs that display activity against M. tuberculosis cells and tuberculosis in mouse models [Blanco, D., et al. (2015) Antimicrob. Agents Chemother. 59, 1868-1875]. Genetic and mutagenesis studies suggest that gyrase, which is the target for fluoroquinolone antibacterials, is also the target for MGIs. However, little is known regarding the interaction of these drugs with the bacterial type II enzyme. Therefore, we examined the effects of two MGIs, GSK000 and GSK325, on M. tuberculosis gyrase. MGIs greatly enhanced DNA cleavage mediated by the bacterial enzyme. In contrast to fluoroquinolones (which induce primarily double-stranded breaks), MGIs induced only single-stranded DNA breaks under a variety of conditions. MGIs work by stabilizing covalent gyrase-cleaved DNA complexes and appear to suppress the ability of the enzyme to induce double-stranded breaks. The drugs displayed little activity against type II topoisomerases from several other bacterial species, suggesting that these drugs display specificity for M. tuberculosis gyrase. Furthermore, MGIs maintained activity against M. tuberuclosis gyrase enzymes that contained the three most common fluoroquinolone resistance mutations seen in the clinic and displayed no activity against human topoisomerase IIα. These findings suggest that MGIs have potential as antitubercular drugs, especially in the case of fluoroquinolone-resistant disease.
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Affiliation(s)
| | - Tim R. Blower
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, United States
| | - Monica Cacho
- Department of Diseases of the Developing World, GlaxoSmithKline, Parque Tecnológico de Madrid, Calle de Severo Ochoa, 2, 28760 Tres Cantos, Madrid, Spain
| | - Ben Bax
- Medicines Discovery Institute, Cardiff University, Cardiff CF10 3AT, United Kingdom
| | - James M. Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205-2185, United States
| | - Neil Osheroff
- VA Tennessee Valley Healthcare System, Nashville, Tennessee 37212, United States
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294
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Duan J, Li M, Hao Z, Shen X, Liu L, Jin Y, Wang S, Guo Y, Yang L, Wang L, Yu F. Subinhibitory concentrations of resveratrol reduce alpha-hemolysin production in Staphylococcus aureus isolates by downregulating saeRS. Emerg Microbes Infect 2018; 7:136. [PMID: 30065273 PMCID: PMC6068196 DOI: 10.1038/s41426-018-0142-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 12/15/2022]
Abstract
Resveratrol is a natural phytoalexin. In recent studies, it has been shown to have beneficial effects on cardiovascular disease and cancer and has been deemed to have effective antiviral and immunomodulatory activities. Methicillin-resistant Staphylococcus aureus is a multidrug-resistant pathogen associated with skin and soft tissue infections. Alpha-hemolysin is known to play a key role in the symptoms caused by S. aureus, and the saeRS two-component system has been shown to be a major regulatory system of S. aureus virulence. The present study was designed to determine the effect of subinhibitory concentrations of resveratrol on the production of alpha-hemolysin in S. aureus. The effect of resveratrol on the transcription of S. aureus was studied by transcriptome sequencing. A total of 760 genes with >2-fold changes in expression were selected, including 479 upregulated genes and 281 downregulated genes. On the basis of transcriptome sequencing, the expression of alpha-hemolysin in the S. aureus strains of the resveratrol-treated group was downregulated. Our results showed that resveratrol weakly inhibited the growth of S. aureus strains, and subinhibitory concentration of resveratrol decreased the expression of hla and inhibited the regulation of saeRS. Hemolysis testing confirmed that resveratrol had an inhibitory effect on the hemolysis of rabbit erythrocytes infected with S. aureus strains in a dose-dependent manner. Resveratrol also decreased the hemolytic capacity by reducing the production of alpha-hemolysin. We found that resveratrol could decrease the expression of hla and reduce the secretion of alpha-hemolysin by downregulating saeRS. These findings have provided more evidence of the potential of resveratrol as a drug for resisting S. aureus infections.
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Affiliation(s)
- Jingjing Duan
- Department of Laboratory Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Meilan Li
- Emergency Intensive Care Unit, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200082, China
| | - Zhihao Hao
- Department of Laboratory Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Xiaofei Shen
- Department of Respiratory Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Li Liu
- Department of Laboratory Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Ye Jin
- Department of Laboratory Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Shanshan Wang
- Department of Laboratory Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Yinjuan Guo
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200082, China
| | - Lehe Yang
- Department of Respiratory Medicine, Affiliated Yueqing Hospital of Wenzhou Medical University, Wenzhou, 325600, China
| | - Liangxing Wang
- Department of Respiratory Medicine, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Fangyou Yu
- Department of Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200082, China.
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295
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Karp BE, Campbell D, Chen JC, Folster JP, Friedman CR. Plasmid-mediated quinolone resistance in human non-typhoidal Salmonella infections: An emerging public health problem in the United States. Zoonoses Public Health 2018; 65:838-849. [PMID: 30027554 DOI: 10.1111/zph.12507] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 06/24/2018] [Accepted: 06/25/2018] [Indexed: 11/30/2022]
Abstract
Invasive Salmonella infections in adults are commonly treated with fluoroquinolones, a critically important antimicrobial class. Historically, quinolone resistance was the result of chromosomal mutations, but plasmid-mediated quinolone resistance (PMQR) has emerged and is increasingly being reported in Enterobacteriaceae worldwide. PMQR may facilitate the spread of quinolone resistance, lead to higher-level quinolone resistance, and make infections harder to treat. To better understand the epidemiology of PMQR in non-typhoidal Salmonella causing human infections in the United States, we looked at trends in quinolone resistance among isolates submitted to the Centers for Disease Control and Prevention. We reviewed demographic, exposure and outcome information for patients with isolates having a PMQR-associated phenotype during 2008-2014 and tested isolates for quinolone resistance mechanisms. We found that PMQR is emerging among non-typhoidal Salmonella causing human infections in the United States and that international travel, reptile and amphibian exposure, and food are likely sources of human infection.
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Affiliation(s)
- Beth E Karp
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Davina Campbell
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee
| | | | - Jason P Folster
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Cindy R Friedman
- Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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296
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Antimicrobial resistance trends in fecal Salmonella isolates from northern California dairy cattle admitted to a veterinary teaching hospital, 2002-2016. PLoS One 2018; 13:e0199928. [PMID: 29953552 PMCID: PMC6023112 DOI: 10.1371/journal.pone.0199928] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/15/2018] [Indexed: 11/19/2022] Open
Abstract
Nontyphoidal Salmonella infections contribute to approximately 1.2 million annual illnesses in the United States. Historical and recent outbreaks have been associated with dairy products, ground beef, and direct contact with cattle. Salmonella antimicrobial resistance (AMR) is a serious concern that can reduce successful treatment of infections, increasing recovery time, medical costs, and mortality rates in humans and animals. This highlights the need to track AMR in Salmonella isolated from cattle to improve treatment plans, manage trends in AMR, and prevent future AMR development. A total of 242 Salmonella isolates were retrieved from 9,162 cattle fecal samples submitted to the University of California, Davis Veterinary Medical Teaching Hospital from 2002 to 2016. These isolates were tested for antimicrobial susceptibility using a standardized broth dilution panel. Multidrug resistance (MDR) to three or more classes of antimicrobials was observed in 50.8% of isolates, and the most common MDR pattern was amoxicillin-ampicillin-cefoxitin-ceftiofur-ceftriaxone-chloramphenicol-streptomycin-tetracycline (23.2%). There were significantly greater odds for antimicrobial resistance to aminoglycosides (OR: 2.03, 95% CI: 1.1–3.7), penicillins (OR: 1.87, 95% CI: 1.007–3.5), and tetracyclines (OR: 1.87, 95% CI: 1.017–3.4) for the 2002–2009 period when compared to the 2010–2016 period. The most prevalent MDR serotypes were Newport (100% MDR, n = 52), Typhimurium (100%, n = 20), and Dublin (71% MDR, n = 46). Risk factors associated with higher odds for isolating MDR Salmonella included isolates from calves when compared to adult cattle (OR: 22.0; 95% C.I.: 3.9–125.7), and isolates obtained from cattle suspect of having salmonellosis versus from the infectious disease control surveillance program (OR:13.7; 95%C.I.: 2.8–66.8). Despite a temporal trend for reduced AMR to most antimicrobial drug classes, a lack of this observed in the 2002–2009 period when compared to the 2010–2016 period for important drug classes such as cephalosporins (OR: 1.6, 95% CI: 0.87–3.1), and a trend for temporal increase in resistant to quinolones drugs (P value 0.004) highlight the relevance of AMR surveillance in cattle with Salmonella infections with the aim of targeting future prophylactic interventions.
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297
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Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance. Proc Natl Acad Sci U S A 2018; 115:E5726-E5735. [PMID: 29871954 PMCID: PMC6016788 DOI: 10.1073/pnas.1801646115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology.
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298
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CrpP Is a Novel Ciprofloxacin-Modifying Enzyme Encoded by the Pseudomonas aeruginosa pUM505 Plasmid. Antimicrob Agents Chemother 2018; 62:AAC.02629-17. [PMID: 29581123 DOI: 10.1128/aac.02629-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/13/2018] [Indexed: 12/27/2022] Open
Abstract
The pUM505 plasmid, isolated from a clinical Pseudomonas aeruginosa isolate, confers resistance to ciprofloxacin (CIP) when transferred into the standard P. aeruginosa strain PAO1. CIP is an antibiotic of the quinolone family that is used to treat P. aeruginosa infections. In silico analysis, performed to identify CIP resistance genes, revealed that the 65-amino-acid product encoded by the orf131 gene in pUM505 displays 40% amino acid identity to the Mycobacterium smegmatis aminoglycoside phosphotransferase (an enzyme that phosphorylates and inactivates aminoglycoside antibiotics). We cloned orf131 (renamed crpP, for ciprofloxacin resistance protein, plasmid encoded) into the pUCP20 shuttle vector. The resulting recombinant plasmid, pUC-crpP, conferred resistance to CIP on Escherichia coli strain J53-3, suggesting that this gene encodes a protein involved in CIP resistance. Using coupled enzymatic analysis, we determined that the activity of CrpP on CIP is ATP dependent, while little activity against norfloxacin was detected, suggesting that CIP may undergo phosphorylation. Using a recombinant His-tagged CrpP protein and liquid chromatography-tandem mass spectrometry, we also showed that CIP was phosphorylated prior to its degradation. Thus, our findings demonstrate that CrpP, encoded on the pUM505 plasmid, represents a new mechanism of CIP resistance in P. aeruginosa, which involves phosphorylation of the antibiotic.
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299
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Identification and Characterization of Salmonella enterica Serotype Newport Isolates with Decreased Susceptibility to Ciprofloxacin in the United States. Antimicrob Agents Chemother 2018; 62:AAC.00653-18. [PMID: 29760131 DOI: 10.1128/aac.00653-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/06/2018] [Indexed: 11/20/2022] Open
Abstract
Nontyphoidal Salmonella (NTS) causes an estimated 1.2 million illnesses, 23,000 hospitalizations, and 450 deaths each year in the United States. Decreased susceptibility to ciprofloxacin (DSC) has historically been associated with chromosomal mutations of the quinolone resistance determining region (QRDR), but plasmid-mediated quinolone resistance (PMQR) genes are increasing. To investigate DSC among Salmonella enterica serotype Newport strains, we examined 40 isolates from 1996 to 2016 with DSC. Thirty isolates (71%) contained the PMQR gene qnrB and eight isolates (19%) contained a QRDR.
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300
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Otarigho B, Falade MO. Analysis of antibiotics resistant genes in different strains of Staphylococcus aureus. Bioinformation 2018; 14:113-122. [PMID: 29785070 PMCID: PMC5953858 DOI: 10.6026/97320630014113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 02/21/2018] [Accepted: 02/21/2018] [Indexed: 12/20/2022] Open
Abstract
The control of Staphylococcus aureus infection is being hampered by methicillin and other resistant strains. The identification of the unique antibiotic resistant genes from the genomes of various strains of S. aureus is of interest. We analyzed 11 S. aureus genomes sequences for Antibiotics Resistance Genes (ARGs) using CARD 2017 platform. We identified 32 ARGs across 11 S. aureus strains. Tet(38), norB, lmrB, mepA and mepR were present across genomes except for S. aureus strain UTSW MRSA 55. The mepA and mepR were found across 11 different genomes. However, FosB3, vgaALC, mphC and SAT-4 were found in UTSW MRSA 55, S.a. strain ISU935 and S.a. strain FDAARGOS_159. The prevalent mode of mechanism of antibiotics resistant was efflux pump complex or subunit conferring antibiotic resistance as well as protein(s). Analysis of norB, ImrB, norA, ImrB, tet (38), sav1866 and mecA have 12 to 14 TMHs. The results help in the understanding of Staphylococcus aureus pathogenesis in the context of antibiotic resistance.
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Affiliation(s)
- Benson Otarigho
- Department of Biological Science, Edo University, Iyamho, Edo State, Nigeria
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health and Science University, Portland, OR USA
| | - Mofolusho O. Falade
- Cellular Parasitology Programme, Cell Biology and Genetics Unit, Department of Zoology, University of Ibadan, Ibadan, Nigeria
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