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Qi Y, Ji P, Yin K, Zheng Y, Niu J, Jia A, Zhou J, Li J. Phloretin Inhibits Quorum Sensing and Biofilm Formation in Serratia marcescens. Molecules 2023; 28:8067. [PMID: 38138556 PMCID: PMC10746122 DOI: 10.3390/molecules28248067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/28/2023] [Accepted: 12/03/2023] [Indexed: 12/24/2023] Open
Abstract
This study investigated the antivirulence capacity and mechanism of apple-skin-derived phloretin against Serratia marcescens NJ01, a vegetable spoilage bacterium. At 0.5 to 2 mg/mL doses, phloretin considerably inhibited the secretion of acyl homoserine lactones (AHLs), indicating that phloretin disrupted quorum sensing (QS) in S. marcescens NJ01. The dysfunction of QS resulted in reduced biofilms and the decreased production of protease, prodigiosin, extracellular polysaccharides (EPSs), and swimming and swarming motilities. Dysfunctional QS also weakened the activity of antioxidant enzymes and improved oxidative injury. The improved oxidative injury changed the composition of the membrane, improved membrane permeability, and eventually increased the susceptibility of biofilm cells to amikacin, netilmicin, and imipenem. The disrupted QS and enhanced oxidative stress also caused disorders of amino acid metabolism, energy metabolism, and nucleic acid metabolism, and ultimately attenuated the ability of S. marcescens NJ01 to induce spoilage. Our results indicated that phloretin can act as a potent drug to defend against spoilage by S. marcescens.
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Affiliation(s)
- Yueheng Qi
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 477150, China
- Luoyang Key Laboratory of Organic Functional Molecules, College of Food and Drug, Luoyang Normal University, Luoyang 471934, China
| | - Pengcheng Ji
- School of Food and Biological Engineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Kunyuan Yin
- School of Food and Biological Engineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Yi Zheng
- School of Food and Biological Engineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Jiangxiu Niu
- Luoyang Key Laboratory of Organic Functional Molecules, College of Food and Drug, Luoyang Normal University, Luoyang 471934, China
| | - Aiqun Jia
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 477150, China
| | - Jinwei Zhou
- School of Food and Biological Engineering, Xuzhou University of Technology, Xuzhou 221018, China
| | - Jingguo Li
- Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, Zhengzhou 477150, China
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Matteoli FP, Pedrosa-Silva F, Dutra-Silva L, Giachini AJ. The global population structure and beta-lactamase repertoire of the opportunistic pathogen Serratia marcescens. Genomics 2021; 113:3523-3532. [PMID: 34400240 DOI: 10.1016/j.ygeno.2021.08.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 07/15/2021] [Accepted: 08/11/2021] [Indexed: 11/26/2022]
Abstract
Serratia marcescens is a global spread nosocomial pathogen. This rod-shaped bacterium displays a broad host range and worldwide geographical distribution. Here we analyze an international collection of this multidrug-resistant, opportunistic pathogen from 35 countries to infer its population structure. We show that S. marcescens comprises 12 lineages; Sm1, Sm4, and Sm10 harbor 78.3% of the known environmental strains. Sm5, Sm6, and Sm7 comprise only human-associated strains which harbor smallest pangenomes, genomic fluidity and lowest levels of core recombination, indicating niche specialization. Sm7 and Sm9 lineages exhibit the most concerning resistome; blaKPC-2 plasmid is widespread in Sm7, whereas Sm9, also an anthropogenic-exclusive lineage, presents highest plasmid/lineage size ratio and plasmid-diversity encoding metallo-beta-lactamases comprising blaNDM-1. The heterogeneity of resistance patterns of S. marcescens lineages elucidated herein highlights the relevance of surveillance programs, using whole-genome sequencing, to provide insights into the molecular epidemiology of carbapenemase producing strains of this species.
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3
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Sandner-Miranda L, Vinuesa P, Cravioto A, Morales-Espinosa R. The Genomic Basis of Intrinsic and Acquired Antibiotic Resistance in the Genus Serratia. Front Microbiol 2018; 9:828. [PMID: 29867787 PMCID: PMC5958200 DOI: 10.3389/fmicb.2018.00828] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/11/2018] [Indexed: 12/18/2022] Open
Abstract
Serratia marcescens, a member of the Enterobacteriaceae family, was long thought to be a non-pathogenic bacterium prevalent in environmental habitats. Together with other members of this genus, it has emerged in recent years as an opportunistic nosocomial pathogen causing various types of infections. One important feature of pathogens belonging to this genus is their intrinsic and acquired resistance to a variety of antibiotic families, including β-lactam, aminoglycosides, quinolones and polypeptide antibiotics. The aim of this study was to elucidate which genes participate in the intrinsic and acquired antibiotic resistance of this genus in order to determine the Serratia genus resistome. We performed phylogenomic and comparative genomic analyses using 32 Serratia spp. genomes deposited in the NCBI GenBank from strains isolated from different ecological niches and different lifestyles. S. marcescens strain SmUNAM836, which was previously isolated from a Mexican adult with obstructive pulmonary disease, was included in this study. The results show that most of the antibiotic resistance genes (ARGs) were found on the chromosome, and to a lesser degree, on plasmids and transposons acquired through horizontal gene transfer. Four strains contained the gyrA point mutation in codon Ser83 that confers quinolone resistance. Pathogenic and environmental isolates presented a high number of ARGs, especially genes associated with efflux systems. Pathogenic strains, specifically nosocomial strains, presented more acquired resistance genes than environmental isolates. We may conclude that the environment provides a natural reservoir for antibiotic resistance, which has been underestimated in the medical field.
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Affiliation(s)
- Luisa Sandner-Miranda
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alejandro Cravioto
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Huang YT, Cheng JF, Liu YT, Mao YC, Wu MS, Liu PY. Genome-based analysis of virulence determinants of a Serratia marcescens strain from soft tissues following a snake bite. Future Microbiol 2017; 13:331-343. [PMID: 29105506 DOI: 10.2217/fmb-2017-0202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Serratia marcescens wound infection after snakebite is often associated with aggressive presentations. However, the virulence determinants remain understudied. MATERIALS & METHODS Whole-genome sequencing was performed on S. marcescens VGH107, an isolate from wound infection secondary to Trimeresurus mucrosquamatus bite. Comparative genomics approach coupled with multivirulent-locus sequencing typing was applied to systematically predict potential virulence factors. RESULTS Multivirulent-locus sequencing typing indicated VGH107 falls within the cluster of high pathogenic strains. Comparative analysis identified virulence genes unique in VGH107, including ecpD and ecpE genes for periplasmic chaperone-pilus subunit complex and cdiA and cdiB genes for contact-dependent growth inhibition system. CONCLUSION The data established here provide foundation for further research regarding the virulence and resistance of S. marcescens.
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Affiliation(s)
- Yao-Ting Huang
- Department of Computer Science & Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Jan-Fang Cheng
- Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Yi-Ting Liu
- Department of Computer Science & Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Yan-Chiao Mao
- Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Meng-San Wu
- Division of Infection & Immunity, University College London, London, UK
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,Rong Hsing Research Center for Translational Medicine, College of Life Sciences, National Chung Hsing University, Taichung, Taiwan
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5
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Boulund F, Berglund F, Flach CF, Bengtsson-Palme J, Marathe NP, Larsson DGJ, Kristiansson E. Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets. BMC Genomics 2017; 18:682. [PMID: 28865446 PMCID: PMC5581476 DOI: 10.1186/s12864-017-4064-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 08/15/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fluoroquinolones are broad-spectrum antibiotics used to prevent and treat a wide range of bacterial infections. Plasmid-mediated qnr genes provide resistance to fluoroquinolones in many bacterial species and are increasingly encountered in clinical settings. Over the last decade, several families of qnr genes have been discovered and characterized, but their true prevalence and diversity still remain unclear. In particular, environmental and host-associated bacterial communities have been hypothesized to maintain a large and unknown collection of qnr genes that could be mobilized into pathogens. RESULTS In this study we used computational methods to screen genomes and metagenomes for novel qnr genes. In contrast to previous studies, we analyzed an almost 20-fold larger dataset comprising almost 13 terabases of sequence data. In total, 362,843 potential qnr gene fragments were identified, from which 611 putative qnr genes were reconstructed. These gene sequences included all previously described plasmid-mediated qnr gene families. Fifty-two of the 611 identified qnr genes were reconstructed from metagenomes, and 20 of these were previously undescribed. All of the novel qnr genes were assembled from metagenomes associated with aquatic environments. Nine of the novel genes were selected for validation, and six of the tested genes conferred consistently decreased susceptibility to ciprofloxacin when expressed in Escherichia coli. CONCLUSIONS The results presented in this study provide additional evidence for the ubiquitous presence of qnr genes in environmental microbial communities, expand the number of known qnr gene variants and further elucidate the diversity of this class of resistance genes. This study also strengthens the hypothesis that environmental bacterial communities act as sources of previously uncharacterized qnr genes.
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Affiliation(s)
- Fredrik Boulund
- Department of Mathematical sciences, Chalmers university of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Fanny Berglund
- Department of Mathematical sciences, Chalmers university of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Johan Bengtsson-Palme
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Nachiket P. Marathe
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - DG Joakim Larsson
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Erik Kristiansson
- Department of Mathematical sciences, Chalmers university of Technology and University of Gothenburg, Gothenburg, Sweden
- Centre for Antibiotic Resistance Research, University of Gothenburg, Gothenburg, Sweden
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Albornoz E, Lucero C, Romero G, Quiroga MP, Rapoport M, Guerriero L, Andres P, Rodriguez C, Galas M, Centrón D, Corso A, Petroni A. Prevalence of Plasmid-Mediated Quinolone Resistance Genes in Clinical Enterobacteria from Argentina. Microb Drug Resist 2016; 23:177-187. [PMID: 27728774 DOI: 10.1089/mdr.2016.0033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This first nationwide study was conducted to analyze the prevalence of plasmid-mediated quinolone resistance (PMQR) genes in phenotypically unselected (consecutive) clinical enterobacteria. We studied 1,058 isolates that had been consecutively collected in 66 hospitals of the WHONET-Argentina Resistance Surveillance Network. Overall, 26% of isolates were nonsusceptible to at least one of the three quinolones tested (nalidixic acid, ciprofloxacin, and levofloxacin). The overall prevalence of PMQR genes was 8.1% (4.6% for aac(6')-Ib-cr; 3.9% for qnr genes; and 0.4% for oqxA and oqxB, which were not previously reported in enterobacteria other than Klebsiella spp. from Argentina). The PMQR prevalence was highly variable among the enterobacterial species or when the different genes were considered. The prevalent PMQR genes were located in class 1 integrons [qnrB2, qnrB10, and aac(6')-Ib-cr]; in the ColE1-type plasmid pPAB19-1 or Tn2012-like transposons (qnrB19); and in Tn6238 or bracketed by IS26 and blaOXA-1 [aac(6')-Ib-cr]. The mutations associated with quinolone resistance that were located in the quinolone resistance-determining region (QRDR mutations) of gyrA, parC, and gyrB were also investigated. The occurrence of QRDR mutations was significantly associated with the presence of PMQR genes: At least one QRDR mutation was present in 82% of the PMQR-harboring isolates but in only 23% of those without PMQR genes (p < 0.0001, Fisher's Test). To the best of our knowledge, this is the first report on the prevalence of PMQR genes in consecutive clinical enterobacteria where all the genes currently known have been screened.
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Affiliation(s)
- Ezequiel Albornoz
- 1 Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Celeste Lucero
- 1 Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Genara Romero
- 1 Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - María Paula Quiroga
- 2 Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET) , Ciudad Autónoma de Buenos Aires, Argentina
| | - Melina Rapoport
- 1 Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Leonor Guerriero
- 1 Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Patricia Andres
- 1 Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Cecilia Rodriguez
- 2 Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET) , Ciudad Autónoma de Buenos Aires, Argentina
| | - Marcelo Galas
- 3 Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Centrón
- 2 Instituto de Investigaciones en Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET) , Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandra Corso
- 1 Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro Petroni
- 1 Servicio Antimicrobianos, Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas-ANLIS "Dr. Carlos G. Malbrán," Ciudad Autónoma de Buenos Aires, Argentina
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7
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Plasmid-mediated quinolone resistance: Two decades on. Drug Resist Updat 2016; 29:13-29. [PMID: 27912841 DOI: 10.1016/j.drup.2016.09.001] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/03/2016] [Accepted: 08/29/2016] [Indexed: 11/21/2022]
Abstract
After two decades of the discovery of plasmid-mediated quinolone resistance (PMQR), three different mechanisms have been associated to this phenomenon: target protection (Qnr proteins, including several families with multiple alleles), active efflux pumps (mainly QepA and OqxAB pumps) and drug modification [AAC(6')-Ib-cr acetyltransferase]. PMQR genes are usually associated with mobile or transposable elements on plasmids, and, in the case of qnr genes, are often incorporated into sul1-type integrons. PMQR has been found in clinical and environmental isolates around the world and appears to be spreading. Although the three PMQR mechanisms alone cause only low-level resistance to quinolones, they can complement other mechanisms of chromosomal resistance to reach clinical resistance level and facilitate the selection of higher-level resistance, raising a threat to the treatment of infections by microorganisms that host these mechanisms.
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Pourcher AM, Jadas-Hécart A, Cotinet P, Dabert P, Ziebal C, Le Roux S, Moraru R, Heddadj D, Kempf I. Effect of land application of manure from enrofloxacin-treated chickens on ciprofloxacin resistance of Enterobacteriaceae in soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 482-483:269-275. [PMID: 24657372 DOI: 10.1016/j.scitotenv.2014.02.136] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 02/26/2014] [Accepted: 02/28/2014] [Indexed: 06/03/2023]
Abstract
A field plot experiment was carried out to evaluate the impact of spreading chicken manure containing enrofloxacin (ENR) and its metabolite ciprofloxacin (CIP), on the levels of CIP-resistant Enterobacteriaceae in soil. The manures from chickens treated with ENR and from untreated control chickens were applied on six plots. Total and CIP-resistant Enterobacteriaceae were counted on Violet Red Bile Glucose medium containing 0 to 16mg L(-1) of CIP. A total of 145 isolates were genotyped by enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). The minimum inhibitory concentration (MIC) of CIP for the isolates of each ERIC-PCR profile was determined. The most frequently isolated Enterobacteriaceae included Escherichia coli, and to a lesser extent, Enterobacter and 5 other genera from environmental origin. The composition of the E. coli community differed between manure and manured soil suggesting that the E. coli genotypes determined by ERIC-PCR varied significantly in their ability to survive in soil. One of these genotypes, including both susceptible and resistant isolates, was detected up to 89 days after the manure was applied. Most of the E. coli isolated in soil amended with manure from treated chickens was resistant to CIP (with a MIC ranging between 2 and 32mg L(-1)). In contrast, despite the presence of ENR in soil at concentrations ranging from 13-518μg kg(-1), the environmental Enterobacteriaceae isolates had a CIP MIC≤0.064mg L(-1), except one isolate which had a MIC of 0.25mg L(-1), These results showed that spreading manure from ENR-treated chickens enabled CIP-resistant E. coli to persist for at least three months in the soil. However, neither the presence of fluoroquinolones, nor the persistence of CIP-resistant E. coli, increased the CIP-susceptibility of environmental Enterobacteriaceae.
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Affiliation(s)
- A-M Pourcher
- IRSTEA, 17 Avenue de Cucillé, 35044 Rennes, France; Université Européenne de Bretagne, France.
| | - A Jadas-Hécart
- Université d'Angers, LETG-Angers LEESA UMR CNRS 6554, UFR Sciences, 2 Boulevard Lavoisier, 49045 Angers, France
| | - P Cotinet
- Chambre Régionale d'Agriculture de Bretagne, ZAC Atalante Champeaux, 35042 Rennes, France
| | - P Dabert
- IRSTEA, 17 Avenue de Cucillé, 35044 Rennes, France; Université Européenne de Bretagne, France
| | - C Ziebal
- IRSTEA, 17 Avenue de Cucillé, 35044 Rennes, France; Université Européenne de Bretagne, France
| | - S Le Roux
- IRSTEA, 17 Avenue de Cucillé, 35044 Rennes, France; Université Européenne de Bretagne, France
| | - R Moraru
- University of Agricultural Sciences and Veterinary Medicine, Aleea Mihail Sadoveanu no. 8, 700489 Iaşi, Romania
| | - D Heddadj
- Chambre Régionale d'Agriculture de Bretagne, ZAC Atalante Champeaux, 35042 Rennes, France
| | - I Kempf
- Université Européenne de Bretagne, France; ANSES Laboratoire de Ploufragan/Plouzané, BP 53, 22440 Ploufragan, France
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Phylogenetic analysis of chromosomally determined qnr and related proteins. Antimicrob Agents Chemother 2013; 57:1930-4. [PMID: 23318805 DOI: 10.1128/aac.02080-12] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
qnr genes were discovered on plasmids by their ability to reduce quinolone susceptibility, but homologs can be found in the genomes of at least 92 Gram-negative, Gram-positive, and strictly anaerobic bacterial species. The related pentapeptide repeat protein-encoding mfpA gene is present in the genome of at least 19 species of Mycobacterium and 10 other Actinobacteria species. The native function of these genes is not yet known.
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10
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Boulund F, Johnning A, Pereira MB, Larsson DGJ, Kristiansson E. A novel method to discover fluoroquinolone antibiotic resistance (qnr) genes in fragmented nucleotide sequences. BMC Genomics 2012; 13:695. [PMID: 23231464 PMCID: PMC3543242 DOI: 10.1186/1471-2164-13-695] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 12/04/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Broad-spectrum fluoroquinolone antibiotics are central in modern health care and are used to treat and prevent a wide range of bacterial infections. The recently discovered qnr genes provide a mechanism of resistance with the potential to rapidly spread between bacteria using horizontal gene transfer. As for many antibiotic resistance genes present in pathogens today, qnr genes are hypothesized to originate from environmental bacteria. The vast amount of data generated by shotgun metagenomics can therefore be used to explore the diversity of qnr genes in more detail. RESULTS In this paper we describe a new method to identify qnr genes in nucleotide sequence data. We show, using cross-validation, that the method has a high statistical power of correctly classifying sequences from novel classes of qnr genes, even for fragments as short as 100 nucleotides. Based on sequences from public repositories, the method was able to identify all previously reported plasmid-mediated qnr genes. In addition, several fragments from novel putative qnr genes were identified in metagenomes. The method was also able to annotate 39 chromosomal variants of which 11 have previously not been reported in literature. CONCLUSIONS The method described in this paper significantly improves the sensitivity and specificity of identification and annotation of qnr genes in nucleotide sequence data. The predicted novel putative qnr genes in the metagenomic data support the hypothesis of a large and uncharacterized diversity within this family of resistance genes in environmental bacterial communities. An implementation of the method is freely available at http://bioinformatics.math.chalmers.se/qnr/.
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Affiliation(s)
- Fredrik Boulund
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Göteborg, SE-412 96, Sweden
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11
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Dalhoff A. Global fluoroquinolone resistance epidemiology and implictions for clinical use. Interdiscip Perspect Infect Dis 2012; 2012:976273. [PMID: 23097666 PMCID: PMC3477668 DOI: 10.1155/2012/976273] [Citation(s) in RCA: 212] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2012] [Accepted: 06/26/2012] [Indexed: 12/22/2022] Open
Abstract
This paper on the fluoroquinolone resistance epidemiology stratifies the data according to the different prescription patterns by either primary or tertiary caregivers and by indication. Global surveillance studies demonstrate that fluoroquinolone resistance rates increased in the past years in almost all bacterial species except S. pneumoniae and H. influenzae, causing community-acquired respiratory tract infections. However, 10 to 30% of these isolates harbored first-step mutations conferring low level fluoroquinolone resistance. Fluoroquinolone resistance increased in Enterobacteriaceae causing community acquired or healthcare associated urinary tract infections and intraabdominal infections, exceeding 50% in some parts of the world, particularly in Asia. One to two-thirds of Enterobacteriaceae producing extended spectrum β-lactamases were fluoroquinolone resistant too. Furthermore, fluoroquinolones select for methicillin resistance in Staphylococci. Neisseria gonorrhoeae acquired fluoroquinolone resistance rapidly; actual resistance rates are highly variable and can be as high as almost 100%, particularly in Asia, whereas resistance rates in Europe and North America range from <10% in rural areas to >30% in established sexual networks. In general, the continued increase in fluoroquinolone resistance affects patient management and necessitates changes in some guidelines, for example, treatment of urinary tract, intra-abdominal, skin and skin structure infections, and traveller's diarrhea, or even precludes the use in indications like sexually transmitted diseases and enteric fever.
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Affiliation(s)
- Axel Dalhoff
- Institute for Infection-Medicine, Christian-Albrechts Univerity of Kiel and University Medical Center Schleswig-Holstein, Brunswiker Straße 4, 24105 Kiel, Germany
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12
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Transferable mechanisms of quinolone resistance. Int J Antimicrob Agents 2012; 40:196-203. [DOI: 10.1016/j.ijantimicag.2012.02.011] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 02/20/2012] [Accepted: 02/21/2012] [Indexed: 11/20/2022]
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13
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Briales A, Rodriguez-Martinez JM, Velasco C, Machuca J, Diaz de Alba P, Blazquez J, Pascual A. Exposure to diverse antimicrobials induces the expression of qnrB1, qnrD and smaqnr genes by SOS-dependent regulation. J Antimicrob Chemother 2012; 67:2854-9. [DOI: 10.1093/jac/dks326] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
Serratia species, in particular Serratia marcescens, are significant human pathogens. S. marcescens has a long and interesting taxonomic, medical experimentation, military experimentation, and human clinical infection history. The organisms in this genus, particularly S. marcescens, were long thought to be nonpathogenic. Because S. marcescens was thought to be a nonpathogen and is usually red pigmented, the U.S. military conducted experiments that attempted to ascertain the spread of this organism released over large areas. In the process, members of both the public and the military were exposed to S. marcescens, and this was uncovered by the press in the 1970s, leading to U.S. congressional hearings. S. marcescens was found to be a certain human pathogen by the mid-1960s. S. marcescens and S. liquefaciens have been isolated as causative agents of numerous outbreaks and opportunistic infections, and the association of these organisms with point sources such as medical devices and various solutions given to hospitalized patients is striking. Serratia species appear to be common environmental organisms, and this helps to explain the large number of nosocomial infections due to these bacteria. Since many nosocomial infections are caused by multiply antibiotic-resistant strains of S. marcescens, this increases the danger to hospitalized patients, and hospital personnel should be vigilant in preventing nosocomial outbreaks due to this organism. S. marcescens, and probably other species in the genus, carries several antibiotic resistance determinants and is also capable of acquiring resistance genes. S. marcescens and S. liquefaciens are usually identified well in the clinical laboratory, but the other species are rare enough that laboratory technologists may not recognize them. 16S rRNA gene sequencing may enable better identification of some of the less common Serratia species.
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Lupo A, Coyne S, Berendonk TU. Origin and evolution of antibiotic resistance: the common mechanisms of emergence and spread in water bodies. Front Microbiol 2012; 3:18. [PMID: 22303296 PMCID: PMC3266646 DOI: 10.3389/fmicb.2012.00018] [Citation(s) in RCA: 221] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 01/10/2012] [Indexed: 11/25/2022] Open
Abstract
The environment, and especially freshwater, constitutes a reactor where the evolution and the rise of new resistances occur. In water bodies such as waste water effluents, lakes, and rivers or streams, bacteria from different sources, e.g., urban, industrial, and agricultural waste, probably selected by intensive antibiotic usage, are collected and mixed with environmental species. This may cause two effects on the development of antibiotic resistances: first, the contamination of water by antibiotics or other pollutants lead to the rise of resistances due to selection processes, for instance, of strains over-expressing broad range defensive mechanisms, such as efflux pumps. Second, since environmental species are provided with intrinsic antibiotic resistance mechanisms, the mixture with allochthonous species is likely to cause genetic exchange. In this context, the role of phages and integrons for the spread of resistance mechanisms appears significant. Allochthonous species could acquire new resistances from environmental donors and introduce the newly acquired resistance mechanisms into the clinics. This is illustrated by clinically relevant resistance mechanisms, such as the fluoroquinolones resistance genes qnr. Freshwater appears to play an important role in the emergence and in the spread of antibiotic resistances, highlighting the necessity for strategies of water quality improvement. We assume that further knowledge is needed to better understand the role of the environment as reservoir of antibiotic resistances and to elucidate the link between environmental pollution by anthropogenic pressures and emergence of antibiotic resistances. Only an integrated vision of these two aspects can provide elements to assess the risk of spread of antibiotic resistances via water bodies and suggest, in this context, solutions for this urgent health issue.
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Affiliation(s)
- Agnese Lupo
- Institute of Hydrobiology, Department of Hydrosciences, Technical University Dresden Dresden, Germany
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Ruiz E, Sáenz Y, Zarazaga M, Rocha-Gracia R, Martínez-Martínez L, Arlet G, Torres C. qnr, aac(6′)-Ib-cr and qepA genes in Escherichia coli and Klebsiella spp.: genetic environments and plasmid and chromosomal location. J Antimicrob Chemother 2012; 67:886-97. [DOI: 10.1093/jac/dkr548] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Samonis G, Vouloumanou EK, Christofaki M, Dimopoulou D, Maraki S, Triantafyllou E, Kofteridis DP, Falagas ME. Serratia infections in a general hospital: characteristics and outcomes. Eur J Clin Microbiol Infect Dis 2011; 30:653-60. [PMID: 21222011 DOI: 10.1007/s10096-010-1135-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Accepted: 12/17/2010] [Indexed: 02/06/2023]
Abstract
We aimed to present our experience regarding infections caused by Serratia spp. in a region with relatively high antimicrobial resistance rates. We retrospectively reviewed the databases of the microbiological laboratory of the University Hospital of Heraklion, Crete (2/2004-12/2009). A total of 77 patients [67.5% men, mean age ± standard deviation (SD) = 56.9 ± 24.5 years) were identified; 37.7% were outpatients. Sixty-five (84.4%) of the 77 included patients had a Serratia marcescens isolate; the remaining 12 patients had a non-marcescens Serratia spp. The most frequently observed infections were respiratory tract infection (32.5%) and keratitis/endophthalmitis (20.8%). Seventy-three (94.9%) patients were cured. Four deaths were observed; three of them were considered as attributed to the Serratia infection. No difference was found regarding the characteristics and outcomes between patients with Serratia marcescens and non-marcescens infections. In addition, antipseudomonal penicillins and their combinations with beta-lactamase inhibitors, as well as carbapenemes, and fluoroquinolones exhibited high antimicrobial activity against both the tested Serratia marcescens and non-marcescens isolates. Our study adds useful information regarding the characteristics and outcomes of patients with Serratia infection, as well as the susceptibilities of the respective Serratia marcescens and non-marcescens isolates, in a region with relatively high levels of antimicrobial resistance.
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Affiliation(s)
- G Samonis
- Department of Internal Medicine, University Hospital of Heraklion, Heraklion, Crete, Greece
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Rodríguez-Martínez JM, Velasco C, Pascual Á, Cano ME, Martínez-Martínez L, Martínez-Martínez L, Pascual Á. Plasmid-mediated quinolone resistance: an update. J Infect Chemother 2011; 17:149-82. [DOI: 10.1007/s10156-010-0120-2] [Citation(s) in RCA: 181] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2010] [Indexed: 01/27/2023]
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Structural and biochemical analysis of the pentapeptide repeat protein EfsQnr, a potent DNA gyrase inhibitor. Antimicrob Agents Chemother 2010; 55:110-7. [PMID: 20937785 DOI: 10.1128/aac.01158-10] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The chromosomally encoded Qnr homolog protein from Enterococcus faecalis (EfsQnr), when expressed, confers to its host a decreased susceptibility to quinolones and consists mainly of tandem repeats, which is consistent with belonging to the pentapeptide repeat family of proteins (PRPs). EfsQnr was cloned with an N-terminal 6× His tag and purified to homogeneity. EfsQnr partially protected DNA gyrase from fluoroquinolone inhibition at concentrations as low as 20 nM. EfsQnr inhibited the ATP-dependent supercoiling activity of DNA gyrase with a 50% inhibitory concentration (IC(50)) of 1.2 μM, while no significant inhibition of ATP-independent relaxation activity was observed. EfsQnr was cytotoxic when overexpressed in Escherichia coli, resulting in the clumping of cells and a loss of viability. The X-ray crystal structure of EfsQnr was determined to 1.6-Å resolution. EfsQnr exhibits the right-handed quadrilateral beta-helical fold typical of PRPs, with features more analogous to MfpA (mycobacterium fluoroquinolone resistance pentapeptide) than to the PRPs commonly found in cyanobacteria.
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