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Hochstedler-Kramer BR, Ene A, Putonti C, Wolfe AJ. Comparative genomic analysis of clinical Enterococcus faecalis distinguishes strains isolated from the bladder. BMC Genomics 2023; 24:752. [PMID: 38062354 PMCID: PMC10701997 DOI: 10.1186/s12864-023-09818-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Enterococcus faecalis is the most commonly isolated enterococcal species in clinical infection. This bacterium is notorious for its ability to share genetic content within and outside of its species. With this increased proficiency for horizontal gene transfer, tremendous genomic diversity within this species has been identified. Many researchers have hypothesized E. faecalis exhibits niche adaptation to establish infections or colonize various parts of the human body. Here, we hypothesize that E. faecalis strains isolated from the human bladder will carry unique genomic content compared to clinical strains isolated from other sources. RESULTS This analysis includes comparison of 111 E. faecalis genomes isolated from bladder, urogenital, blood, and fecal samples. Phylogenomic comparison shows no association between isolation source and lineage; however, accessory genome comparison differentiates blood and bladder genomes. Further gene enrichment analysis identifies gene functions, virulence factors, antibiotic resistance genes, and plasmid-associated genes that are enriched or rare in bladder genomes compared to urogenital, blood, and fecal genomes. Using these findings as training data and 682 publicly available genomes as test data, machine learning classifiers successfully distinguished between bladder and non-bladder strains with high accuracy. Genes identified as important for this differentiation were often related to transposable elements and phage, including 3 prophage species found almost exclusively in bladder and urogenital genomes. CONCLUSIONS E. faecalis strains isolated from the bladder contain unique genomic content when compared to strains isolated from other body sites. This genomic diversity is most likely due to horizontal gene transfer, as evidenced by lack of phylogenomic clustering and enrichment of transposable elements and prophages. Investigation into how these enriched genes influence host-microbe interactions may elucidate gene functions required for successful bladder colonization and disease establishment.
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Affiliation(s)
- Baylie R Hochstedler-Kramer
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, 60153, IL, USA
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, 60660, IL, USA
| | - Catherine Putonti
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, 60153, IL, USA
- Bioinformatics Program, Loyola University Chicago, Chicago, 60660, IL, USA
- Department of Biology, Loyola University Chicago, Chicago, 60660, IL, USA
| | - Alan J Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, 60153, IL, USA.
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Pauter-Iwicka K, Railean V, Złoch M, Pomastowski P, Szultka-Młyńska M, Błońska D, Kupczyk W, Buszewski B. Characterization of the salivary microbiome before and after antibiotic therapy via separation technique. Appl Microbiol Biotechnol 2023; 107:2515-2531. [PMID: 36843196 PMCID: PMC10033590 DOI: 10.1007/s00253-023-12371-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 02/28/2023]
Abstract
In the present research, the MALDI-TOF MS technique was applied as a tool to rapidly identify the salivary microbiome. In this fact, it has been monitored the changes occurred in molecular profiles under different antibiotic therapy. Significant changes in the composition of the salivary microbiota were noticed not only in relation to the non antibiotic (non-AT) and antibiotic treatment (AT) groups, but also to the used media, the antibiotic therapy and co-existed microbiota. Each antibiotic generates specific changes in molecular profiles. The highest number of bacterial species was isolated in the universal culture medium (72%) followed by the selective medium (48% and 38%). In the case of non-AT patients, the prevalence of Streptococcus salivarius (25%), Streptococcus vestibularis (19%), Streptococcus oralis (13%), and Staphylococcus aureus (6%) was identified while in the case of AT, Streptococcus salivarius (11%), Streptococcus parasanguinis (11%), Staphylococcus epidermidis (12%), Enterococcus faecalis (9%), Staphylococcus hominis (8%), and Candida albicans (6%) were identified. Notable to specified that the Candida albicans was noticed only in AT samples, indicating a negative impact on the antibiotic therapy. The accuracy of the MALDI-TOF MS technique was performed by the 16S rRNA gene sequencing analysis-as a reference method. Conclusively, such an approach highlighted in the present study can help in developing the methods enabling a faster diagnosis of disease changes at the cellular level before clinical changes occur. Once the MALDI tool allows for the distinguishing of the microbiota of non-AT and AT, it may enable to monitor the diseases treatment and develop a treatment regimen for individual patients in relation to each antibiotic. KEY POINTS: The salivary microbiota of antibiotic-treated patients was more bacteria variety MALDI-TOF MS is a promising tool for recording of reproducible molecular profiles Our data can allow to monitor the treatment of bacterial diseases for patients.
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Affiliation(s)
- Katarzyna Pauter-Iwicka
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Viorica Railean
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
- Department of Infectious, Invasive Diseases and Veterinary Administration, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Toruń, Poland
| | - Michał Złoch
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
| | - Dominika Błońska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Wojciech Kupczyk
- Department of General, Gastroenterological&Oncological Surgery Collegium Medicum, Nicolaus Copernicus University, Torun, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland.
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland.
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3
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Li G, Walker MJ, De Oliveira DMP. Vancomycin Resistance in Enterococcus and Staphylococcus aureus. Microorganisms 2022; 11:microorganisms11010024. [PMID: 36677316 PMCID: PMC9866002 DOI: 10.3390/microorganisms11010024] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Enterococcus faecalis, Enterococcus faecium and Staphylococcus aureus are both common commensals and major opportunistic human pathogens. In recent decades, these bacteria have acquired broad resistance to several major classes of antibiotics, including commonly employed glycopeptides. Exemplified by resistance to vancomycin, glycopeptide resistance is mediated through intrinsic gene mutations, and/or transferrable van resistance gene cassette-carrying mobile genetic elements. Here, this review will discuss the epidemiology of vancomycin-resistant Enterococcus and S. aureus in healthcare, community, and agricultural settings, explore vancomycin resistance in the context of van and non-van mediated resistance development and provide insights into alternative therapeutic approaches aimed at treating drug-resistant Enterococcus and S. aureus infections.
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Davis BC, Keenum I, Calarco J, Liguori K, Milligan E, Pruden A, Harwood VJ. Towards the standardization of Enterococcus culture methods for waterborne antibiotic resistance monitoring: A critical review of trends across studies. WATER RESEARCH X 2022; 17:100161. [PMID: 36466738 PMCID: PMC9712764 DOI: 10.1016/j.wroa.2022.100161] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 11/15/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Antibiotic resistance is a major 21st century One Health (humans, animals, environment) challenge whose spread limits options to treat bacterial infections. There is growing interest in monitoring water environments, including surface water and wastewater, which have been identified as key recipients, pathways, and sources of antibiotic resistant bacteria (ARB). Aquatic environments also facilitate the transmission and amplification of ARB. Enterococcus spp. often carry clinically-important antibiotic resistance genes and are of interest as environmental monitoring targets. Enterococcus spp. are Gram-positive bacteria that are typically of fecal origin; however, they are also found in relevant environmental niches, with various species and strains that are opportunistic human pathogens. Although the value of environmental monitoring of antibiotic-resistant Enterococcus has been recognized by both national and international organizations, lack of procedural standardization has hindered generation of comparable data needed to implement integrated surveillance programs. Here we provide a comprehensive methodological review to assess the techniques used for the culturing and characterization of antibiotic-resistant Enterococcus across water matrices for the purpose of environmental monitoring. We analyzed 117 peer-reviewed articles from 33 countries across six continents. The goal of this review is to provide a critical analysis of (i) the various methods applied globally for isolation, confirmation, and speciation of Enterococcus isolates, (ii) the different methods for profiling antibiotic resistance among enterococci, and (iii) the current prevalence of resistance to clinically-relevant antibiotics among Enterococcus spp. isolated from various environments. Finally, we provide advice regarding a path forward for standardizing culturing of Enterococcus spp. for the purpose of antibiotic resistance monitoring in wastewater and wastewater-influenced waters within a global surveillance framework.
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Affiliation(s)
- Benjamin C. Davis
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Ishi Keenum
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Jeannette Calarco
- Department of Integrative Biology, University of South Florida, Tampa, Florida
| | - Krista Liguori
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Erin Milligan
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering, Virginia Tech, Blacksburg, Virginia
| | - Valerie J. Harwood
- Department of Integrative Biology, University of South Florida, Tampa, Florida
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Wardal E, Żabicka D, Hryniewicz W, Sadowy E. VanA-Enterococcus faecalis in Poland: hospital population clonal structure and vanA mobilome. Eur J Clin Microbiol Infect Dis 2022; 41:1245-1261. [PMID: 36057762 PMCID: PMC9489580 DOI: 10.1007/s10096-022-04479-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 07/18/2022] [Indexed: 11/03/2022]
Abstract
The aim of our study was to characterize the epidemiological situation concerning nosocomial vancomycin-resistant Enterococcus faecalis of VanA-phenotype (VREfs-VanA) in Poland by investigating their clonal relationships and the vanA-associated mobilome. One-hundred twenty-five clinical isolates of VREfs-VanA collected between 2004 and 2016 were studied by phenotypic assays, multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), PCR detection of plasmid-specific genes, and Tn1546 structure and localization mapping. Selected isolates were subjected to PFGE-S1, Southern hybridization, genomic sequencing and conjugation experiments. The majority of isolates (97.6%) belonged to clonal complexes CC2 and CC87 of E. faecalis. All isolates were resistant to vancomycin and teicoplanin, and resistance to ciprofloxacin and aminoglycosides (high level) was very prevalent in this group. VanA phenotype was associated with 16 types of Tn1546, carrying insertion sequences IS1216, ISEfa4, IS1251 and IS1542, located on repUS1pVEF1, rep1pIP501, rep2pRE25, rep9pAD1/pTEF2/pCF10 and rep6pS86 replicons. The most common Tn1546 B- and BB-type transposons, harbouring one or two copies of IS1216, were inserted between rep18ap200B and repUS1pVEF1 genes and located on ~ 20 kb and 150-200 kb plasmids. VREfs-VanA in Poland represent a polyclonal group, indicating a number of acquisitions of the vanA determinant. The repUS1pVEF1-vanA plasmids, unique for Poland, were the main factor beyond the acquisition of vancomycin resistance by E. faecalis, circulating in Polish hospitals.
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Affiliation(s)
- Ewa Wardal
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Dorota Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
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Descriptive Analysis of Circulating Antimicrobial Resistance Genes in Vancomycin-Resistant Enterococcus (VRE) during the COVID-19 Pandemic. Biomedicines 2022; 10:biomedicines10051122. [PMID: 35625861 PMCID: PMC9138224 DOI: 10.3390/biomedicines10051122] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/25/2022] [Accepted: 05/09/2022] [Indexed: 01/07/2023] Open
Abstract
COVID-19 offers ideal premises for bacteria to develop antimicrobial resistance. In this study, we evaluated the presence of several antimicrobial resistance genes (ARG) in vancomycin-resistant Enterococcus (VRE) isolated from rectal swabs from patients at a hospital in Cluj-Napoca, Romania. Rectal swabs were cultivated on CHROMID® VRE (bioMérieux, Marcy—l’ Étoile, France) and positive isolates were identified using MALDI-TOF Mass Spectrometry (Bruker Daltonics, Bremen, Germany) and further analyzed using the PCR technique for the presence of the following ARGs: van A, van B, tet(M), tet(L), ermB, msrA, mefA, aac(6′)-Im, aph(2)-Ib, ant(4′)-Ia, sul1, sul2, sul3, and NDM1. We isolated and identified 68 isolates of Enterococcus faecium and 11 isolates of Enterococcus faecalis. The molecular analysis showed 66 isolates positive for the vanA gene and eight positive for vanB. The most frequent association of ARG in VRE was vanA-tet(M)-ermB. There was no statistically significant difference between Enterococcus faecium and Enterococcus faecalis regarding ARGs. Our work proves that during the COVID-19 pandemic, highly resistant isolates of Enterococcus were present in patients in the intensive care unit; thus, better healthcare policies should be implemented for the management and control of these highly resistant isolates in the future.
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7
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Scardaci R, Bietto F, Racine PJ, Boukerb AM, Lesouhaitier O, Feuilloley MGJ, Scutera S, Musso T, Connil N, Pessione E. Norepinephrine and Serotonin Can Modulate the Behavior of the Probiotic Enterococcus faecium NCIMB10415 towards the Host: Is a Putative Surface Sensor Involved? Microorganisms 2022; 10:microorganisms10030487. [PMID: 35336063 PMCID: PMC8954575 DOI: 10.3390/microorganisms10030487] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/12/2022] [Accepted: 02/16/2022] [Indexed: 01/27/2023] Open
Abstract
The human gut microbiota has co-evolved with humans by exchanging bidirectional signals. This study aims at deepening the knowledge of this crucial relationship by analyzing phenotypic and interactive responses of the probiotic Enterococcus faecium NCIMB10415 (E. faecium SF68) to the top-down signals norepinephrine (NE) and serotonin (5HT), two neuroactive molecules abundant in the gut. We treated E. faecium NCIMB10415 with 100 µM NE and 50 µM 5HT and tested its ability to form static biofilm (Confocal Laser Scanning Microscopy), adhere to the Caco-2/TC7 monolayer, affect the epithelial barrier function (Transepithelial Electrical Resistance) and human dendritic cells (DC) maturation, differentiation, and cytokines production. Finally, we evaluated the presence of a putative hormone sensor through in silico (whole genome sequence and protein modelling) and in vitro (Micro-Scale Thermophoresis) analyses. The hormone treatments increase biofilm formation and adhesion on Caco-2/TC7, as well as the epithelial barrier function. No differences concerning DC differentiation and maturation between stimulated and control bacteria were detected, while an enhanced TNF-α production was observed in NE-treated bacteria. Investigations on the sensor support the hypothesis that a two-component system on the bacterial surface can sense 5HT and NE. Overall, the data demonstrate that E. faecium NCIMB10415 can sense both NE and 5HT and respond accordingly.
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Affiliation(s)
- Rossella Scardaci
- Laboratory of Microbial Biochemistry and Proteomics, Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy; (F.B.); (E.P.)
- Correspondence:
| | - Francesca Bietto
- Laboratory of Microbial Biochemistry and Proteomics, Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy; (F.B.); (E.P.)
| | - Pierre-Jean Racine
- Laboratory of Microbiology—Bacterial Communication and Anti-infectious Strategies, University of Rouen Normandy, 27000 Evreux, France; (P.-J.R.); (A.M.B.); (O.L.); (M.G.J.F.); (N.C.)
| | - Amine M. Boukerb
- Laboratory of Microbiology—Bacterial Communication and Anti-infectious Strategies, University of Rouen Normandy, 27000 Evreux, France; (P.-J.R.); (A.M.B.); (O.L.); (M.G.J.F.); (N.C.)
| | - Olivier Lesouhaitier
- Laboratory of Microbiology—Bacterial Communication and Anti-infectious Strategies, University of Rouen Normandy, 27000 Evreux, France; (P.-J.R.); (A.M.B.); (O.L.); (M.G.J.F.); (N.C.)
| | - Marc G. J. Feuilloley
- Laboratory of Microbiology—Bacterial Communication and Anti-infectious Strategies, University of Rouen Normandy, 27000 Evreux, France; (P.-J.R.); (A.M.B.); (O.L.); (M.G.J.F.); (N.C.)
| | - Sara Scutera
- Laboratory of Immunology, Department of Public Health and Pediatric Sciences, University of Turin, Via Santena 9, 10126 Torino, Italy; (S.S.); (T.M.)
| | - Tiziana Musso
- Laboratory of Immunology, Department of Public Health and Pediatric Sciences, University of Turin, Via Santena 9, 10126 Torino, Italy; (S.S.); (T.M.)
| | - Nathalie Connil
- Laboratory of Microbiology—Bacterial Communication and Anti-infectious Strategies, University of Rouen Normandy, 27000 Evreux, France; (P.-J.R.); (A.M.B.); (O.L.); (M.G.J.F.); (N.C.)
| | - Enrica Pessione
- Laboratory of Microbial Biochemistry and Proteomics, Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123 Torino, Italy; (F.B.); (E.P.)
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8
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Conwell M, Dooley J, Naughton PJ. Enterococcal biofilm - a nidus for antibiotic resistance transfer? J Appl Microbiol 2022; 132:3444-3460. [PMID: 34990042 PMCID: PMC9306868 DOI: 10.1111/jam.15441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 08/03/2021] [Accepted: 01/03/2022] [Indexed: 11/30/2022]
Abstract
Enterococci, important agents of hospital acquired infection, are listed on the WHO list of multi-drug resistant pathogens commonly encountered in hospital acquired infections are now of increasing importance, due to the development of strains resistant to multiple antibiotics. Enterococci are also important microorganisms in the environment and their presence is frequently used as an indicator of faecal pollution. Their success is related to their ability to survive within a broad range of habitats and the ease by which they acquire mobile genetic elements, including plasmids, from other bacteria. The enterococci are frequently present within a bacterial biofilm which provides stability and protection to the bacterial population along with an opportunity for a variety of bacterial interactions. Enterococci can accept extrachromosomal DNA both from within its own species and from other bacterial species and this is enhanced by the proximity of the donor and recipient strains. It is this exchange of genetic material that makes the role of biofilm such an important aspect of the success of enterococci. There remain many questions regarding the most suitable model systems to study enterococci in biofilm and regarding the transfer of genetic material including antibiotic resistance in these biofilms. This review focuses on some important aspects of biofilm in the context of horizontal gene transfer (HGT) in enterococci.
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Affiliation(s)
- M Conwell
- The Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA
| | - Jsg Dooley
- The Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA
| | - P J Naughton
- The Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Cromore Road, Coleraine, Co. Londonderry, BT52 1SA
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Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let Me Upgrade You: Impact of Mobile Genetic Elements on Enterococcal Adaptation and Evolution. J Bacteriol 2021; 203:e0017721. [PMID: 34370561 PMCID: PMC8508098 DOI: 10.1128/jb.00177-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enterococci are Gram-positive bacteria that have evolved to thrive as both commensals and pathogens, largely due to their accumulation of mobile genetic elements via horizontal gene transfer (HGT). Common agents of HGT include plasmids, transposable elements, and temperate bacteriophages. These vehicles of HGT have facilitated the evolution of the enterococci, specifically Enterococcus faecalis and Enterococcus faecium, into multidrug-resistant hospital-acquired pathogens. On the other hand, commensal strains of Enterococcus harbor CRISPR-Cas systems that prevent the acquisition of foreign DNA, restricting the accumulation of mobile genetic elements. In this review, we discuss enterococcal mobile genetic elements by highlighting their contributions to bacterial fitness, examine the impact of CRISPR-Cas on their acquisition, and identify key areas of research that can improve our understanding of enterococcal evolution and ecology.
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Affiliation(s)
- Cydney N. Johnson
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Emma K. Sheriff
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Breck A. Duerkop
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Anushila Chatterjee
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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10
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Li W, Wang A. Genomic islands mediate environmental adaptation and the spread of antibiotic resistance in multiresistant Enterococci - evidence from genomic sequences. BMC Microbiol 2021; 21:55. [PMID: 33602143 PMCID: PMC7893910 DOI: 10.1186/s12866-021-02114-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/02/2021] [Indexed: 11/10/2022] Open
Abstract
Background Genomic islands (GIs) play an important role in the chromosome diversity of Enterococcus. In the current study, we aimed to investigate the spread of GIs between Enterococcus strains and their correlation with antibiotic resistance genes (ARGs). Bitsliced Genomic Signature Indexes (BIGSI) were used to screen the NCBI Sequence Read Archive (SRA) for multiple resistant Enterococcus. A total of 37 pairs of raw reads were screened from 457,000 whole-genome sequences (WGS) in the SRA database, which come from 37 Enterococci distributed in eight countries. These raw reads were assembled for the prediction and analysis of GIs, ARGs, plasmids and prophages. Results The results showed that GIs were universal in Enterococcus, with an average of 3.2 GIs in each strain. Network analysis showed that frequent genetic information exchanges mediated by GIs occurred between Enterococcus strains. Seven antibiotic-resistant genomic islands (ARGIs) were found to carry one to three ARGs, mdtG, tetM, dfrG, lnuG, and fexA, in six strains. These ARGIs were involved in the spread of antibiotic resistance in 45.9% of the 37 strains, although there was no significant positive correlation between the frequency of GI exchanges and the number of ARGs each strain harboured (r = 0. 287, p = 0.085). After comprehensively analysing the genome data, we found that partial GIs were associated with multiple mobile genetic elements (transposons, integrons, prophages and plasmids) and had potential natural transformation characteristics. Conclusions All of these results based on genomic sequencing suggest that GIs might mediate the acquisition of some ARGs and might be involved in the high genome plasticity of Enterococcus through transformation, transduction and conjugation, thus providing a fitness advantage for Enterococcus hosts under complex environmental factors. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02114-4.
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Affiliation(s)
- Weiwei Li
- School of Life Science,
- Ludong University, Yantai, 264025, China.
| | - Ailan Wang
- School of Life Science,
- Ludong University, Yantai, 264025, China
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11
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Suryaletha K, Chandrika SK, Thomas S. Comprehensive genomics depict accessory genes encoding pathogenicity and biofilm determinants in Enterococcus faecalis. Future Microbiol 2021; 16:175-184. [PMID: 33528277 DOI: 10.2217/fmb-2020-0111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: Enterococcus faecalis is a leading nosocomial pathogen in biofilm-associated polymicrobial infections. The study aims to understand pathogenicity and biofilm determinants of the pathogen by genome analysis. Methodology: Genome sequencing of a strong biofilm forming clinical isolate Enterococcus faecalis SK460 devoid of Fsr quorum-signaling system, was performed and comparative genomics was carried out among a set of pathogenic biofilm formers and nonpathogenic weak biofilm formers. Results: Analysis revealed a pool of virulence and adhesion related factors associated with pathogenicity. Absence of CRISPR-Cas system facilitated acquisition of pheromone responsive plasmid, pathogenicity island and phages. Comprehensive analysis identified a subset of accessory genes encoding polysaccharide lyase, sugar phosphotransferase system, phage proteins and transcriptional regulators exclusively in pathogenic biofilm formers. Conclusion: The study identified a set of genes specific to pathogenic biofilm formers and these can act as targets which in turn help to develop future treatment endeavors against enterococcal infections.
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Affiliation(s)
- Karthika Suryaletha
- Cholera & Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695 014, Kerala, India
| | - Sivakumar K Chandrika
- Distributed Information Sub-Centre, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695 014, Kerala, India
| | - Sabu Thomas
- Cholera & Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram 695 014, Kerala, India
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12
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A GC-Rich Prophage-Like Genomic Region of Mycoplasma bovirhinis HAZ141_2 Carries a Gene Cluster Encoding Resistance to Kanamycin and Neomycin. Antimicrob Agents Chemother 2021; 65:AAC.01010-20. [PMID: 33257452 DOI: 10.1128/aac.01010-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/20/2020] [Indexed: 12/23/2022] Open
Abstract
Recently, a complete genome sequence of Mycoplasma bovirhinis HAZ141_2 was published showing the presence of a 54-kB prophage-like region. Bioinformatic analysis revealed that this region has a more than 40% GC content and a chimeric organization with three structural elements-a prophage continuous region, a restriction-modification cassette, and a highly transmittable aadE-sat4-aphA-3 gene cluster found in both Gram-positive and Gram-negative bacteria. It is known that aadE confers resistance to streptomycin, sat4 governs resistance to streptothricin/nourseothricin, and aphA-3 is responsible for resistance to kanamycin and structurally related antibiotics. An aadE-like (aadE*) gene of strain HAZ141_2 encodes a 228-amino acid (aa) polypeptide whose carboxy-terminal domain (positions 44 to 206) is almost identical to that of a functional 302-aa AadE (positions 140 to 302). Transcription analysis of the aadE*-sat4-aphA-3 genes showed their cotranscription in M. bovirhinis HAZ141_2. Moreover, a common promoter for aadE*-sat4-aphA-3 was mapped upstream of aadE* using 5' rapid amplification of cDNA ends analysis. Determination of MICs to aminoglycosides and nourseothricin revealed that M. bovirhinis HAZ141_2 is highly resistant to kanamycin and neomycin (≥512 μg/ml). However, MICs to streptomycin (64 μg/ml) and nourseothricin (16 to 32 μg/ml) were similar to those identified in the prophageless M. bovirhinis type strain PG43 and Israeli field isolate 316981. We cloned the aadE*-sat4-aphA-3 genes into a low-copy-number vector and transferred them into antibiotic-sensitive Escherichia coli cells. While the obtained E. coli transformants were highly resistant to kanamycin, neomycin, and nourseothricin (MICs, ≥256 μg/ml), there were no changes in MICs to streptomycin, suggesting a functional defect of the aadE*.
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Schmitt A, Hirt H, Järvå MA, Sun WS, Ter Beek J, Dunny GM, Berntsson RPA. Enterococcal PrgA Extends Far Outside the Cell and Provides Surface Exclusion to Protect against Unwanted Conjugation. J Mol Biol 2020; 432:5681-5695. [PMID: 32860774 DOI: 10.1016/j.jmb.2020.08.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 01/09/2023]
Abstract
Horizontal gene transfer between Gram-positive bacteria leads to a rapid spread of virulence factors and antibiotic resistance. This transfer is often facilitated via type 4 secretion systems (T4SS), which frequently are encoded on conjugative plasmids. However, donor cells that already contain a particular conjugative plasmid resist acquisition of a second copy of said plasmid. They utilize different mechanisms, including surface exclusion for this purpose. Enterococcus faecalis PrgA, encoded by the conjugative plasmid pCF10, is a surface protein that has been implicated to play a role in both virulence and surface exclusion, but the mechanism by which this is achieved has not been fully explained. Here, we report the structure of full-length PrgA, which shows that PrgA protrudes far out from the cell wall (approximately 40 nm), where it presents a protease domain. In vivo experiments show that PrgA provides a physical barrier to cellular adhesion, thereby reducing cellular aggregation. This function of PrgA contributes to surface exclusion, reducing the uptake of its cognate plasmid by approximately one order of magnitude. Using variants of PrgA with mutations in the catalytic site we show that the surface exclusion effect is dependent on the activity of the protease domain of PrgA. In silico analysis suggests that PrgA can interact with another enterococcal adhesin, PrgB, and that these two proteins have co-evolved. PrgB is a strong virulence factor, and PrgA is involved in post-translational processing of PrgB. Finally, competition mating experiments show that PrgA provides a significant fitness advantage to plasmid-carrying cells.
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Affiliation(s)
- Andreas Schmitt
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Helmut Hirt
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, 55455 MN, USA
| | - Michael A Järvå
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Wei-Sheng Sun
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Gary M Dunny
- Department of Microbiology and Immunology, University of Minnesota, Minneapolis, 55455 MN, USA.
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden; Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.
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14
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Detection of a Novel, and Likely Ancestral, Tn 916-Like Element from a Human Saliva Metagenomic Library. Genes (Basel) 2020; 11:genes11050548. [PMID: 32422869 PMCID: PMC7288454 DOI: 10.3390/genes11050548] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/01/2020] [Accepted: 05/12/2020] [Indexed: 01/22/2023] Open
Abstract
Tn916 is a conjugative transposon (CTn) and the first reported and most well characterised of the Tn916/Tn1545 family of CTns. Tn916-like elements have a characteristic modular structure and different members of this family have been identified based on similarities and variations in these modules. In addition to carrying genes encoding proteins required for their conjugation, Tn916-like elements also carry accessory, antimicrobial resistance genes; most commonly the tetracycline resistance gene, tet(M). Our study aimed to identify and characterise tetracycline resistance genes from the human saliva metagenome using a functional metagenomic approach. We identified a tetracycline-resistant clone, TT31, the sequencing of which revealed it to encode both tet(M) and tet(L). Comparison of the TT31 sequence with the accessory, regulation, and recombination modules of other Tn916-like elements indicated that a partial Tn916-like element encoding a truncated orf9 was cloned in TT31. Analysis indicated that a previous insertion within the truncated orf9 created the full length orf9 found in most Tn916-like transposons; demonstrating that orf9 is, in fact, the result of a gene fusion event. Thus, we hypothesise that the Tn916-like element cloned in TT31 likely represents an ancestral Tn916.
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15
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Christley S, Shogan B, Levine Z, Koo H, Guyton K, Owens S, Gilbert J, Zaborina O, Alverdy JC. Comparative genetics of Enterococcus faecalis intestinal tissue isolates before and after surgery in a rat model of colon anastomosis. PLoS One 2020; 15:e0232165. [PMID: 32343730 PMCID: PMC7188289 DOI: 10.1371/journal.pone.0232165] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
Abstract
We have recently demonstrated that collagenolytic Enterococcus faecalis plays a key and causative role in the pathogenesis of anastomotic leak, an uncommon but potentially lethal complication characterized by disruption of the intestinal wound following segmental removal of the colon (resection) and its reconnection (anastomosis). Here we hypothesized that comparative genetic analysis of E. faecalis isolates present at the anastomotic wound site before and after surgery would shed insight into the mechanisms by which collagenolytic strains are selected for and predominate at sites of anastomotic disruption. Whole genome optical mapping of four pairs of isolates from rat colonic tissue obtained following surgical resection (herein named “pre-op” isolates) and then 6 days later from the anastomotic site (herein named “post-op” isolates) demonstrated that the isolates with higher collagenolytic activity formed a distinct cluster. In order to perform analysis at a deeper level, a single pair of E. faecalis isolates (16A pre-op and 16A post-op) was selected for whole genome sequencing and assembled using a hybrid assembly algorithm. Comparative genomics demonstrated absence of multiple gene clusters, notably a pathogenicity island in the post-op isolate. No differences were found in the fsr-gelE-sprE genes (EF1817-1822) responsible for regulation and production of collagenolytic activity. Analysis of unique genes among the 16A pre-op and post-op isolates revealed the predominance of transporter systems-related genes in the pre-op isolate and phage-related and hydrolytic enzyme-encoding genes in the post-op isolate. Despite genetic differences observed between pre-op and post-op isolates, the precise genetic determinants responsible for their differential expression of collagenolytic activity remains unknown.
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Affiliation(s)
- Scott Christley
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Benjamin Shogan
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Zoe Levine
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Hyun Koo
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Kristina Guyton
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - Sarah Owens
- Argonne National Laboratory, Argonne, IL, United States of America
| | - Jack Gilbert
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
- Argonne National Laboratory, Argonne, IL, United States of America
| | - Olga Zaborina
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
| | - John C. Alverdy
- Department of Surgery, University of Chicago, Chicago, IL, United States of America
- * E-mail:
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16
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Sterling AJ, Snelling WJ, Naughton PJ, Ternan NG, Dooley JSG. Competent but complex communication: The phenomena of pheromone-responsive plasmids. PLoS Pathog 2020; 16:e1008310. [PMID: 32240270 PMCID: PMC7117660 DOI: 10.1371/journal.ppat.1008310] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Enterococci are robust gram-positive bacteria that are found in a variety of surroundings and that cause a significant number of healthcare-associated infections. The genus possesses a high-efficiency pheromone-responsive plasmid (PRP) transfer system for genetic exchange that allows antimicrobial-resistance determinants to spread within bacterial populations. The pCF10 plasmid system is the best characterised, and although other PRP systems are structurally similar, they lack exact functional homologues of pCF10-encoded genes. In this review, we provide an overview of the enterococcal PRP systems, incorporating functional details for the less-well-defined systems. We catalogue the virulence-associated elements of the PRPs that have been identified to date, and we argue that this reinforces the requirement for elucidation of the less studied systems.
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Affiliation(s)
- Amy J. Sterling
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
- * E-mail:
| | - William J. Snelling
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| | - Patrick J. Naughton
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| | - Nigel G. Ternan
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
| | - James S. G. Dooley
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Londonderry, Northern Ireland
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17
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Dos Santos BA, de Oliveira JDS, Parmanhani-da-Silva BM, Ribeiro RL, Teixeira LM, Neves FPG. CRISPR elements and their association with antimicrobial resistance and virulence genes among vancomycin-resistant and vancomycin-susceptible enterococci recovered from human and food sources. INFECTION GENETICS AND EVOLUTION 2020; 80:104183. [PMID: 31923727 DOI: 10.1016/j.meegid.2020.104183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 12/23/2019] [Accepted: 01/06/2020] [Indexed: 11/26/2022]
Abstract
We aimed to investigate the occurrence of CRISPR elements in the genomes of vancomycin-resistant (VRE) and vancomycin-susceptible (VSE) enterococci and their association with the presence of antimicrobial resistance and virulence genes. We analyzed 180 isolates, including 91 VRE and 89 VSE. Isolates were identified by PCR or MALDI-TOF. Antimicrobial susceptibility and MICs for vancomycin were determined by the disk-diffusion method and E-test®, respectively. The presence of resistance and virulence genes, as well as CRISPR elements, was investigated by PCR. We identified 95 (53%) E. faecalis, 78 (43%) E. faecium, five (2.8%) E. gallinarum, and one (0.6% each) E. casseliflavus and E. durans. The highest and the lowest non-susceptibility frequencies were observed for erythromycin (n = 152; 84.4%) and fosfomycin (n = 5; 2.8%), respectively. Most erythromycin-resistant isolates had the erm(B) gene (106/152; 69.7%). Of 118 (65.6%) isolates with high-level resistance to aminoglycoside, 69 (58.5%) had at least one aminoglycoside resistance gene, mostly ant(6)-Ia and aac(6')-Ie + aph(2″)-Ia. We found at least one virulence gene among 135 (75%) isolates, mostly gelE (79/180; 43.9%). Ninety-two (51.1%) isolates had at least one CRISPR element, especially CRISPR3 (62/92; 67.4%). CRISPR elements were more common among E. faecalis, in which we observed a relationship between the absence of CRISPR and the presence of the vanA resistance gene, and the hyl and esp virulence genes. Among VRE. faecium, a relationship was found between the absence of CRISPR and the hyl gene. In conclusion, we found evident associations between the lack of CRISPR elements with species, multidrug resistance, and major resistance- and virulence-associated genes.
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Affiliation(s)
- Barbara Araújo Dos Santos
- Instituto Biomédico, Universidade Federal Fluminense. Rua Professor Hernani Melo, 101. São Domingos, Niterói, RJ 24210-130, Brazil
| | - Jessica da Silva de Oliveira
- Instituto Biomédico, Universidade Federal Fluminense. Rua Professor Hernani Melo, 101. São Domingos, Niterói, RJ 24210-130, Brazil
| | | | - Rachel Leite Ribeiro
- Hospital Universitário Antônio Pedro, Universidade Federal Fluminense, Av. Marquês do Paraná, 303. Centro, Niterói, RJ 24033-900, Brazil.
| | - Lúcia Martins Teixeira
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373. Cidade Universitária, Rio de Janeiro, RJ 21941-902, Brazil.
| | - Felipe Piedade Gonçalves Neves
- Instituto Biomédico, Universidade Federal Fluminense. Rua Professor Hernani Melo, 101. São Domingos, Niterói, RJ 24210-130, Brazil.
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18
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León-Sampedro R, Del Campo R, Rodriguez-Baños M, Lanza VF, Pozuelo MJ, Francés-Cuesta C, Tedim AP, Freitas AR, Novais C, Peixe L, Willems RJL, Corander J, González Candelas F, Baquero F, Coque TM. Phylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species. Environ Microbiol 2019; 21:3046-3062. [PMID: 31162871 DOI: 10.1111/1462-2920.14702] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 05/20/2019] [Accepted: 06/01/2019] [Indexed: 11/29/2022]
Abstract
Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone-responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.
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Affiliation(s)
- Ricardo León-Sampedro
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - Rosa Del Campo
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Spanish Network for Research in Infectious Diseases (REIPI), Health Institute Carlos III, Madrid, Spain
| | - Mercedes Rodriguez-Baños
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Val F Lanza
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain
| | - María José Pozuelo
- Department of Biology, Pharmacy Faculty, University San Pablo-CEU, Boadilla del Monte, Spain
| | - Carlos Francés-Cuesta
- Infection and Public Health Unit, FISABIO/University of Valencia, Spain.,Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain
| | - Ana P Tedim
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain
| | - Ana R Freitas
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Carla Novais
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO/REQUIMTE, Department of Biological Sciences, Microbiology Laboratory, Pharmacy Faculty, University of Porto, Porto, Portugal
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Fernando González Candelas
- Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Infection and Public Health Unit, FISABIO/University of Valencia, Spain.,Institute for Integrative Systems Biology, I2SysBio, CSIC-University of Valencia, Valencia, Spain
| | - Fernando Baquero
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain
| | - Teresa M Coque
- Department of Microbiology, University Hospital Ramón y Cajal, Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.,Biomedical Research Networking Center for Epidemiology and Public Health (CIBER-ESP), Madrid, Spain.,Antibiotic Resistance and Bacterial Virulence Unit Associated with the Superior Council of Scientific Investigations (CSIC), Madrid, Spain
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19
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Taji A, Heidari H, Ebrahim-Saraie HS, Sarvari J, Motamedifar M. High prevalence of vancomycin and high-level gentamicin resistance in Enterococcus faecalis isolates. Acta Microbiol Immunol Hung 2019; 66:203-217. [PMID: 30465449 DOI: 10.1556/030.65.2018.046] [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] [Indexed: 11/19/2022]
Abstract
Multiple drug-resistant enterococci are major cause of healthcare-associated infections due to their antibiotic resistance traits. Among them, Enterococcus faecalis is an important opportunistic pathogen causing various hospital-acquired infections. A total of 53 E. faecalis isolates were obtained from various infections. They were identified by phenotypic and genotypic methods. Determination of antimicrobial resistance patterns was done according to CLSI guidelines. The isolates that were non-susceptible to at least one agent in ≥3 antimicrobial categories were defined as multidrug-resistant (MDR). Detection of antimicrobial resistance genes was performed using standard procedures. According to MDR definition, all of the isolates were MDR (100%). High-level gentamicin resistance was observed among 50.9% of them (MIC ≥ 500 μg/ml). The distributions of aac(6')-Ie-aph(2'')-Ia and aph(3')-IIIa genes were 47.2% and 69.8%, respectively. The aph(2'')-Ib, aph(2'')-Ic, aph(2'')-Id, and ant(4')-Ia genes were not detected. Vancomycin resistance was found in 45.3% of strains. The vanA gene was detected in 37.7% of isolates, whereas vanB and vanC1 genes were not observed in any strain. Erythromycin resistance rate was 79.2% and the frequencies of ermB and ermC genes were 88.6% and 69.8%, respectively. The ermA and msrA genes were not present in any of the isolates. Our data indicate a high rate of MDR E. faecalis strains. All of high-level gentamicin-resistant isolates carried at least one of aac(6')-Ie-aph(2'')-Ia or aph(3')-IIIa genes. Distribution of vanA was notable among the isolates. In addition, ermB and ermC were accountable for resistance to erythromycin.
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Affiliation(s)
- Asieh Taji
- 1 Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hamid Heidari
- 1 Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hadi Sedigh Ebrahim-Saraie
- 1 Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jamal Sarvari
- 1 Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Motamedifar
- 1 Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
- 2 Shiraz HIV/AIDS Research Center, Institute of Health, Shiraz University of Medical Sciences, Shiraz, Iran
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20
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Cirrincione S, Neumann B, Zühlke D, Riedel K, Pessione E. Detailed Soluble Proteome Analyses of a Dairy-Isolated Enterococcus faecalis: A Possible Approach to Assess Food Safety and Potential Probiotic Value. Front Nutr 2019; 6:71. [PMID: 31157229 PMCID: PMC6533484 DOI: 10.3389/fnut.2019.00071] [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: 11/26/2018] [Accepted: 04/26/2019] [Indexed: 12/18/2022] Open
Abstract
Enterococci are common inhabitants of the gastrointestinal tracts of humans and animals and thanks to their capability to tolerate different environmental conditions and their high rates of gene transfer, they are able to colonize various ecological niches, as food matrices. Enterococcus faecalis bacteria are defined as controversial microorganisms. From one side they are used as food starters, bio-control agents and probiotics to improve human or animal health. From the other side, in the last two decades enterococci have emerged as important nosocomial pathogens, because bearing high-level of resistance to antibiotics and several putative virulence factors. In this study, the soluble proteome quantitation data (LC-MS/MS) of the food-isolated strain E. faecalis D27 (dairy-isolate) was compared with the soluble proteome quantitation data of the pathogenic E. faecalis UW3114 (urinary tract infection isolate) and with the one of the health promoting strain E. faecalis Symbioflor1, respectively. The comparison of cytosolic protein expression profiles highlighted statistically significant changes in the abundance of proteins mainly involved in specific metabolic pathways, nutrient transport, stress response, and cell wall modulation. Moreover, especially in the dairy isolate and the clinical isolate, several proteins with potential pathogenic implications were found, such as serine proteases, von Willebrand factor, serine hydrolase with beta lactamase activity, efflux transporter, and proteins involved in horizontal gene transfer. The analysis of the extracellular proteome provided interesting results concerning proteins involved in bacterial communication, such as pheromones and conjugative elements and also proteins able to interact with human components. The phenotypic characterization evaluating (i) biofilm formation (ii) hemolytic activity on blood agar plates (iii) protease activity (iv) gelatinase (v) antibiotic resistance pattern, enabled us to elucidate the risks associated with the poor characterized foodborne E. faecalis D27.
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Affiliation(s)
- Simona Cirrincione
- Department of Life Sciences and Systems Biology, Univerity of Torino, Turin, Italy
| | - Bernd Neumann
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Daniela Zühlke
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, University of Greifswald, Greifswald, Germany
| | - Enrica Pessione
- Department of Life Sciences and Systems Biology, Univerity of Torino, Turin, Italy
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Abstract
The study of the genetics of enterococci has focused heavily on mobile genetic elements present in these organisms, the complex regulatory circuits used to control their mobility, and the antibiotic resistance genes they frequently carry. Recently, more focus has been placed on the regulation of genes involved in the virulence of the opportunistic pathogenic species Enterococcus faecalis and Enterococcus faecium. Little information is available concerning fundamental aspects of DNA replication, partition, and division; this article begins with a brief overview of what little is known about these issues, primarily by comparison with better-studied model organisms. A variety of transcriptional and posttranscriptional mechanisms of regulation of gene expression are then discussed, including a section on the genetics and regulation of vancomycin resistance in enterococci. The article then provides extensive coverage of the pheromone-responsive conjugation plasmids, including sections on regulation of the pheromone response, the conjugative apparatus, and replication and stable inheritance. The article then focuses on conjugative transposons, now referred to as integrated, conjugative elements, or ICEs, and concludes with several smaller sections covering emerging areas of interest concerning the enterococcal mobilome, including nonpheromone plasmids of particular interest, toxin-antitoxin systems, pathogenicity islands, bacteriophages, and genome defense.
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22
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Morroni G, Brenciani A, Litta-Mulondo A, Vignaroli C, Mangiaterra G, Fioriti S, Citterio B, Cirioni O, Giovanetti E, Biavasco F. Characterization of a new transferable MDR plasmid carrying thepbp5gene from a clade B commensalEnterococcus faecium. J Antimicrob Chemother 2019; 74:843-850. [DOI: 10.1093/jac/dky549] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 11/16/2018] [Accepted: 11/28/2018] [Indexed: 01/01/2023] Open
Affiliation(s)
- Gianluca Morroni
- Infectious Disease Clinic, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Alice Litta-Mulondo
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Carla Vignaroli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Gianmarco Mangiaterra
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Simona Fioriti
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Barbara Citterio
- Department of Biomolecular Science, Biotechnology Section, University of Urbino ‘Carlo Bo’, Urbino, Italy
| | - Oscar Cirioni
- Infectious Disease Clinic, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche, Ancona, Italy
| | - Eleonora Giovanetti
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Francesca Biavasco
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Schmitt A, Jiang K, Camacho MI, Jonna VR, Hofer A, Westerlund F, Christie PJ, Berntsson RPA. PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction. Mol Microbiol 2018; 109:291-305. [PMID: 29723434 DOI: 10.1111/mmi.13980] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/30/2018] [Indexed: 12/28/2022]
Abstract
Gram-positive bacteria deploy type IV secretion systems (T4SSs) to facilitate horizontal gene transfer. The T4SSs of Gram-positive bacteria rely on surface adhesins as opposed to conjugative pili to facilitate mating. Enterococcus faecalis PrgB is a surface adhesin that promotes mating pair formation and robust biofilm development in an extracellular DNA (eDNA) dependent manner. Here, we report the structure of the adhesin domain of PrgB. The adhesin domain binds and compacts DNA in vitro. In vivo PrgB deleted of its adhesin domain does not support cellular aggregation, biofilm development and conjugative DNA transfer. PrgB also binds lipoteichoic acid (LTA), which competes with DNA binding. We propose that PrgB binding and compaction of eDNA facilitates cell aggregation and plays an important role in establishment of early biofilms in mono- or polyspecies settings. Within these biofilms, PrgB mediates formation and stabilization of direct cell-cell contacts through alternative binding of cell-bound LTA, which in turn promotes establishment of productive mating junctions and efficient intra- or inter-species T4SS-mediated gene transfer.
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Affiliation(s)
- Andreas Schmitt
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Kai Jiang
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Martha I Camacho
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, Texas 77030, USA
| | - Venkateswara Rao Jonna
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Peter J Christie
- Department of Microbiology and Molecular Genetics, McGovern Medical School, 6431 Fannin St, Houston, Texas 77030, USA
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
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24
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Di Sante L, Morroni G, Brenciani A, Vignaroli C, Antonelli A, D'Andrea MM, Di Cesare A, Giovanetti E, Varaldo PE, Rossolini GM, Biavasco F. pHTβ-promoted mobilization of non-conjugative resistance plasmids from Enterococcus faecium to Enterococcus faecalis. J Antimicrob Chemother 2018. [PMID: 28645197 DOI: 10.1093/jac/dkx197] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Objectives To analyse the recombination events associated with conjugal mobilization of two multiresistance plasmids, pRUM17i48 and pLAG (formerly named pDO1-like), from Enterococcus faecium 17i48 to Enterococcus faecalis JH2-2. Methods The plasmids from two E. faecalis transconjugants (JH-4T, tetracycline resistant, and JH-8E, erythromycin resistant) and from the E. faecium donor (also carrying a pHTβ-like conjugative plasmid, named pHTβ17i48) were investigated by several methods, including PCR mapping and sequencing, S1-PFGE followed by Southern blotting and hybridization, and WGS. Results Two locations of repApHTβ were detected in both transconjugants, one on a ∼50 kb plasmid (as in the donor) and the other on plasmids of larger sizes. In JH-4T, WGS disclosed an 88.6 kb plasmid resulting from the recombination of pHTβ17i48 (∼50 kb) and a new plasmid, named pLAG (35.3 kb), carrying the tet(M), tet(L), lsa(E), lnu(B), spw and aadE resistance genes. In JH-8E, a 75 kb plasmid resulting from the recombination of pHTβ17i48 and pRUM17i48 was observed. In both cases, the cointegrates were apparently derived from replicative transposition of an IS1216 present in each of the multiresistance plasmids into pHTβ17i48. The cointegrates could resolve to yield the multiresistance plasmids and a pHTβ17i48 derivative carrying an IS1216 (unlike the pHTβ17i48 of the donor). Conclusions Our results completed the characterization of the multiresistance plasmids carried by the E. faecium 17i48, confirming the role of pHT plasmids in the mobilization of non-conjugative antibiotic resistance elements among enterococci. Results also revealed that mobilization to E. faecalis was associated with the generation of cointegrate plasmids promoted by IS1216-mediated transposition.
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Affiliation(s)
- Laura Di Sante
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Gianluca Morroni
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Carla Vignaroli
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Alberto Antonelli
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marco Maria D'Andrea
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Andrea Di Cesare
- Microbial Ecology Group, CNR - Institute of Ecosystem Study, Verbania, Italy
| | - Eleonora Giovanetti
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Pietro E Varaldo
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, Ancona, Italy
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.,Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Francesca Biavasco
- Unit of Microbiology, Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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25
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Bello Gonzalez TDJ, Pham P, Top J, Willems RJL, van Schaik W, van Passel MWJ, Smidt H. Characterization of Enterococcus Isolates Colonizing the Intestinal Tract of Intensive Care Unit Patients Receiving Selective Digestive Decontamination. Front Microbiol 2017; 8:1596. [PMID: 28894438 PMCID: PMC5581364 DOI: 10.3389/fmicb.2017.01596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 08/07/2017] [Indexed: 12/11/2022] Open
Abstract
Enterococci have emerged as important opportunistic pathogens in intensive care units (ICUs). In this study, enterococcal population size and Enterococcus isolates colonizing the intestinal tract of ICU patients receiving Selective Digestive Decontamination (SDD) were investigated. All nine patients included in the study showed substantial shifts in the enterococcal 16S rRNA gene copy number in the gut microbiota during the hospitalization period. Furthermore, 41 Enterococcus spp. strains were isolated and characterized from these patients at different time points during and after ICU hospitalization, including E. faecalis (n = 13), E. faecium (n = 23), and five isolates that could not unequivocally assigned to a specific species (E. sp. n = 5) Multi locus sequence typing revealed a high prevalence of ST 6 in E. faecalis isolates (46%) and ST 117 in E. faecium (52%). Furthermore, antibiotic resistance phenotypes, including macrolide and vancomycin resistance, as well as virulence factor-encoding genes [asa1, esp-fm, esp-fs, hyl, and cyl (B)] were investigated in all isolates. Resistance to ampicillin and tetracycline was observed in 25 (61%) and 19 (46%) isolates, respectively. Furthermore, 30 out of 41 isolates harbored the erm (B) gene, mainly present in E. faecium isolates (78%). The most prevalent virulence genes were asa1 in E. faecalis (54%) and esp (esp-fm, 74%; esp-fs, 39%). Six out of nine patients developed nosocomial enterococcal infections, however, corresponding clinical isolates were unfortunately not available for further analysis. Our results show that multiple Enterococcus species, carrying several antibiotic resistance and virulence genes, occurred simultaneously in patients receiving SDD therapy, with varying prevalence dynamics over time. Furthermore, simultaneous presence and/or replacement of E. faecium STs was observed-, reinforcing the importance of screening multiple isolates to comprehensively characterize enterococcal diversity in ICU patients.
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Affiliation(s)
| | - Phu Pham
- Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
| | - Janetta Top
- Department of Medical Microbiology, University Medical Center UtrechtUtrecht, Netherlands
| | - Rob J L Willems
- Department of Medical Microbiology, University Medical Center UtrechtUtrecht, Netherlands
| | - Willem van Schaik
- Department of Medical Microbiology, University Medical Center UtrechtUtrecht, Netherlands
| | - Mark W J van Passel
- Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands.,Centre for Zoonoses and Environmental Microbiology, National Institute for Public Health and the EnvironmentBilthoven, Netherlands
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University & ResearchWageningen, Netherlands
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26
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Correia Santos S, Fraqueza MJ, Elias M, Salvador Barreto A, Semedo-Lemsaddek T. Traditional dry smoked fermented meat sausages: Characterization of autochthonous enterococci. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.01.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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27
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Hung WC, Wan TW, Kuo YC, Yamamoto T, Tsai JC, Lin YT, Hsueh PR, Teng LJ. Molecular Evolutionary Pathways toward Two Successful Community-Associated but Multidrug-Resistant ST59 Methicillin-Resistant Staphylococcus aureus Lineages in Taiwan: Dynamic Modes of Mobile Genetic Element Salvages. PLoS One 2016; 11:e0162526. [PMID: 27606427 PMCID: PMC5015870 DOI: 10.1371/journal.pone.0162526] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 08/24/2016] [Indexed: 12/04/2022] Open
Abstract
Clonal complex 59 (CC59) Staphylococcus aureus in Taiwan includes both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). As the most prominent community-associated MRSA (CA-MRSA) in Taiwan, CC59 has two major clones characterized as PVL-negative SCCmec IV (carrying the staphylococcal cassette chromosome mec IV but Panton-Valentine leukocidin-negative) and PVL-positive SCCmec V (5C2&5). We investigated the drug resistance, phylogeny and the distribution and sequence variation of SCCmec, staphylococcal bacteriophage φSA3, genomic island νSaβ and MES (an enterococcal mobile genetic element conferring multidrug resistance) in 195 CC59 S. aureus. Sequencing and PCR mapping revealed that all of the CC59/SCCmec V (5C2&5) MRSA strains had acquired MESPM1 or its segregants, and obtained a φSA3-related fragment in νSaβ. In contrast, MES6272-2 and MES4578, which showed gentamicin resistance that was not encoded by MESPM1, were dominant in SCCmec IVg MRSA. Translocation of a whole φSA3 into νSaβ instead of only a φSA3-related fragment was common in SCCmec IVg MRSA. However, the non-subtype-g SCCmec IV MRSA (SCCmec IVa is the major) still carried MES and νSaβ structures similar to those in SCCmec V (5C2&5) MRSA. A minimum spanning tree constructed by multiple-locus variable-number tandem repeat analysis revealed that SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA grouped respectively in two major clades. The CC59 MSSA was equally distributed among the two clades, while the non-subtype-g SCCmec IV MRSA mostly clustered with SCCmec V (5C2&5) MRSA. Our findings strongly suggest that CC59 MSSA acquired divergent mobile genetic elements and evolved to SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA/non-subtype-g SCCmec IV MRSA independently. The evolutionary history of CC59 S. aureus explains how mobile genetic elements increase the antimicrobial resistance and virulence and contribute to the success of CA-MRSA in Taiwan.
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Affiliation(s)
- Wei-Chun Hung
- Department of Microbiology and Immunology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Tsai-Wen Wan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Yu-Chia Kuo
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tatsuo Yamamoto
- Department of Epidemiology, Genomics, and Evolution, International Medical Education and Research Center, Niigata, Japan
| | - Jui-Chang Tsai
- Institute of Medical Device and Imaging, National Taiwan University College of Medicine, Taipei, Taiwan
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Yu-Tzu Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
- * E-mail:
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28
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Hammad AM, Hassan HA, Shimamoto T. Prevalence, antibiotic resistance and virulence of Enterococcus spp. in Egyptian fresh raw milk cheese. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.10.020] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Zischka M, Künne CT, Blom J, Wobser D, Sakιnç T, Schmidt-Hohagen K, Dabrowski PW, Nitsche A, Hübner J, Hain T, Chakraborty T, Linke B, Goesmann A, Voget S, Daniel R, Schomburg D, Hauck R, Hafez HM, Tielen P, Jahn D, Solheim M, Sadowy E, Larsen J, Jensen LB, Ruiz-Garbajosa P, Quiñones Pérez D, Mikalsen T, Bender J, Steglich M, Nübel U, Witte W, Werner G. Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40. BMC Genomics 2015; 16:175. [PMID: 25887115 PMCID: PMC4374294 DOI: 10.1186/s12864-015-1367-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Accepted: 02/20/2015] [Indexed: 11/28/2022] Open
Abstract
Background Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is also a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Since enterococci are known to be highly recombinogenic we determined to analyse the microevolution and niche adaptation of this highly distributed clonal type. Results We compared a set of 42 ST40 isolates by assessing key molecular determinants, performing whole genome sequencing (WGS) and a number of phenotypic assays including resistance profiling, formation of biofilm and utilisation of carbon sources. We generated the first circular closed reference genome of an E. faecalis isolate D32 of animal origin and compared it with the genomes of other reference strains. D32 was used as a template for detailed WGS comparisons of high-quality draft genomes of 14 ST40 isolates. Genomic and phylogenetic analyses suggest a high level of similarity regarding the core genome, also demonstrated by similar carbon utilisation patterns. Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source. Further analyses of mobile genetic elements (MGE) revealed genomic diversity owed to: (1) a modularly structured pathogenicity island; (2) a site-specifically integrated and previously unknown genomic island of 138 kb in two strains putatively involved in exopolysaccharide synthesis; and (3) isolate-specific plasmid and phage patterns. Moreover, we used different cell-biological and animal experiments to compare the isolate D32 with a closely related ST40 endocarditis isolate whose draft genome sequence was also generated. D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro). Conclusion Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1367-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Melanie Zischka
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855, Wernigerode, Germany. .,Present address: Institute for Pathology, Hannover Medical School (MHH), Hannover, Germany.
| | - Carsten T Künne
- Functional Genomics of Bacterial Pathogens, Institute for Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany. .,Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany.
| | - Jochen Blom
- Center for Biotechnology (CeBiTec)/University of Bielefeld, Bielefeld, Germany. .,Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany.
| | - Dominique Wobser
- Division of Infectious Diseases, Department of Medicine, University Hospital Freiburg, Freiburg, Germany.
| | - Türkân Sakιnç
- Division of Infectious Diseases, Department of Medicine, University Hospital Freiburg, Freiburg, Germany.
| | - Kerstin Schmidt-Hohagen
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany.
| | - P Wojtek Dabrowski
- Robert Koch Institute, ZBS 1 Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, Berlin, Germany.
| | - Andreas Nitsche
- Robert Koch Institute, ZBS 1 Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, Berlin, Germany.
| | - Johannes Hübner
- Division of Infectious Diseases, Department of Medicine, University Hospital Freiburg, Freiburg, Germany. .,Division of Pediatric Infectious Diseases, Hauner Children's Hospital, Ludwig-Maximilians University Munich, Munich, Germany.
| | - Torsten Hain
- Functional Genomics of Bacterial Pathogens, Institute for Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany.
| | - Trinad Chakraborty
- Functional Genomics of Bacterial Pathogens, Institute for Medical Microbiology, Justus Liebig University Giessen and German Center for Infection Research (DZIF), Partner site Giessen-Marburg-Langen, Campus Giessen, Giessen, Germany.
| | - Burkhard Linke
- Center for Biotechnology (CeBiTec)/University of Bielefeld, Bielefeld, Germany. .,Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany.
| | - Alexander Goesmann
- Center for Biotechnology (CeBiTec)/University of Bielefeld, Bielefeld, Germany. .,Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany.
| | - Sonja Voget
- Goettingen Genomics Laboratory, Georg August University, Goettingen, Germany.
| | - Rolf Daniel
- Goettingen Genomics Laboratory, Georg August University, Goettingen, Germany.
| | - Dietmar Schomburg
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany.
| | - Rüdiger Hauck
- Department of Veterinary Medicine, Institute for Poultry Diseases, Free University Berlin, Berlin, Germany.
| | - Hafez M Hafez
- Department of Veterinary Medicine, Institute for Poultry Diseases, Free University Berlin, Berlin, Germany.
| | - Petra Tielen
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.
| | - Dieter Jahn
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany.
| | - Margrete Solheim
- Laboratory of Microbial Gene Technology and Food Microbiology, The Norwegian University of Life Sciences, Ås, Norway.
| | - Ewa Sadowy
- National Medicines Institute, Warsaw, Poland.
| | | | - Lars B Jensen
- Division of Microbiology, National Food Institute, Danish Technical University, Copenhagen, Denmark.
| | | | - Dianelys Quiñones Pérez
- Instituto de Medicina Tropical Pedro Kourí, Servicio de Bacteriología-Micología, La Habana, Cuba.
| | - Theresa Mikalsen
- Department of Medical Biology, Faculty of Health Sciences, Research Group for Host Microbe Interactions, University of Tromsø, Tromsø, Norway.
| | - Jennifer Bender
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855, Wernigerode, Germany.
| | - Matthias Steglich
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855, Wernigerode, Germany.
| | - Ulrich Nübel
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855, Wernigerode, Germany. .,Leibniz-Institut DSMZ - Deutsche Sammlung von Mikrorganismen und Zellkulturen GmbH, Braunschweig, Germany.
| | - Wolfgang Witte
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855, Wernigerode, Germany.
| | - Guido Werner
- Division of Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, D-38855, Wernigerode, Germany.
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30
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Population biology of intestinal enterococcus isolates from hospitalized and nonhospitalized individuals in different age groups. Appl Environ Microbiol 2014; 81:1820-31. [PMID: 25548052 DOI: 10.1128/aem.03661-14] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The diversity of enterococcal populations from fecal samples from hospitalized (n = 133) and nonhospitalized individuals (n = 173) of different age groups (group I, ages 0 to 19 years; group II, ages 20 to 59 years; group III, ages ≥60 years) was analyzed. Enterococci were recovered at similar rates from hospitalized and nonhospitalized persons (77.44% to 79.77%) of all age groups (75.0% to 82.61%). Enterococcus faecalis and Enterococcus faecium were predominant, although seven other Enterococcus species were identified. E. faecalis and E. faecium (including ampicillin-resistant E. faecium) colonization rates in nonhospitalized persons were age independent. For inpatients, E. faecalis colonization rates were age independent, but E. faecium colonization rates (particularly the rates of ampicillin-resistant E. faecium colonization) significantly increased with age. The population structure of E. faecium and E. faecalis was determined by superimposing goeBURST and Bayesian analysis of the population structure (BAPS). Most E. faecium sequence types (STs; 150 isolates belonging to 75 STs) were linked to BAPS groups 1 (22.0%), 2 (31.3%), and 3 (36.7%). A positive association between hospital isolates and BAPS subgroups 2.1a and 3.3a (which included major ampicillin-resistant E. faecium human lineages) and between community-based ampicillin-resistant E. faecium isolates and BAPS subgroups 1.2 and 3.3b was found. Most E. faecalis isolates (130 isolates belonging to 58 STs) were grouped into 3 BAPS groups, BAPS groups 1 (36.9%), 2 (40.0%), and 3 (23.1%), with each one comprising widespread lineages. No positive associations with age or hospitalization were established. The diversity and dynamics of enterococcal populations in the fecal microbiota of healthy humans are largely unexplored, with the available knowledge being fragmented and contradictory. The study offers a novel and comprehensive analysis of enterococcal population landscapes and suggests that E. faecium populations from hospitalized patients and from community-based individuals differ, with a predominance of certain clonal lineages, often in association with elderly individuals, occurring in the hospital setting.
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31
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Rossi F, Rizzotti L, Felis GE, Torriani S. Horizontal gene transfer among microorganisms in food: Current knowledge and future perspectives. Food Microbiol 2014; 42:232-43. [DOI: 10.1016/j.fm.2014.04.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 04/10/2014] [Indexed: 01/01/2023]
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32
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Bellanger X, Payot S, Leblond-Bourget N, Guédon G. Conjugative and mobilizable genomic islands in bacteria: evolution and diversity. FEMS Microbiol Rev 2014; 38:720-60. [DOI: 10.1111/1574-6976.12058] [Citation(s) in RCA: 223] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/15/2013] [Accepted: 12/19/2013] [Indexed: 11/28/2022] Open
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Gradual pediocin PA-1 resistance in Enterococcus faecalis confers cross-protection to diverse pore-forming cationic antimicrobial peptides displaying changes in cell wall and mannose PTS expression. ANN MICROBIOL 2014. [DOI: 10.1007/s13213-014-0912-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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34
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35
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Gyles C, Boerlin P. Horizontally Transferred Genetic Elements and Their Role in Pathogenesis of Bacterial Disease. Vet Pathol 2013; 51:328-40. [DOI: 10.1177/0300985813511131] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
This article reviews the roles that laterally transferred genes (LTG) play in the virulence of bacterial pathogens. The features of LTG that allow them to be recognized in bacterial genomes are described, and the mechanisms by which LTG are transferred between and within bacteria are reviewed. Genes on plasmids, integrative and conjugative elements, prophages, and pathogenicity islands are highlighted. Virulence genes that are frequently laterally transferred include genes for bacterial adherence to host cells, type 3 secretion systems, toxins, iron acquisition, and antimicrobial resistance. The specific roles of LTG in pathogenesis are illustrated by specific reference to Escherichia coli, Salmonella, pyogenic streptococci, and Clostridium perfringens.
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Affiliation(s)
- C. Gyles
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - P. Boerlin
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
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36
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Tremblay CL, Archambault M. Interference in pheromone-responsive conjugation of a high-level bacitracin resistant Enterococcus faecalis plasmid of poultry origin. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2013; 10:4245-60. [PMID: 24030654 PMCID: PMC3799527 DOI: 10.3390/ijerph10094245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/29/2013] [Accepted: 09/03/2013] [Indexed: 12/13/2022]
Abstract
The current study reports on contact interference of a high-level bacitracin- resistant pheromone-responsive plasmid of Enterococcus faecalis strain 543 of poultry origin during conjugative transfer of bcr antimicrobial resistance genes using a polyclonal antiserum aggregation substance44–560 (AS). After induction with pheromones produced by the recipient strain E. faecalis JH2-2, clumping of the donor E. faecalis strain 543 was observed as well as high transfer frequencies of bcr in short time broth mating. Filter mating assays from donor strain E. faecalis 543 to the recipient strain E. faecalis JH2-2 revealed conjugative transfer of asa1 (AS), bcrRAB and traB (negative regulator pheromone response) genes. The presence of these genes in transconjugants was confirmed by antimicrobial susceptibility testing, PCR, Southern hybridization and sequencing. A significant reduction in formation of aggregates was observed when the polyclonal anti-AS44–560 was added in the pheromone-responsive conjugation experiments as compared to the induced state. Moreover, interference of anti-AS44–560 antibodies in pheromone-responsive conjugation was demonstrated by a reduction in horizontal transfer of asa1 and bcr genes between E. faecalis strain 543 and E. faecalis JH2-2. Reducing the pheromone-responsive conjugation of E. faecalis is of interest because of its clinical importance in the horizontal transfer of antimicrobial resistance.
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Affiliation(s)
- Cindy-Love Tremblay
- GREMIP research group, Department of Pathology and Microbiology, Faculty of Veterinary Medicine, University of Montreal, 3200 Sicotte Street, Saint-Hyacinthe, QC J2S 7C6, Canada.
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Hammad AM, Shimamoto T, Shimamoto T. Genetic characterization of antibiotic resistance and virulence factors in Enterococcus spp. from Japanese retail ready-to-eat raw fish. Food Microbiol 2013; 38:62-6. [PMID: 24290627 DOI: 10.1016/j.fm.2013.08.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/17/2013] [Accepted: 08/15/2013] [Indexed: 10/26/2022]
Abstract
Little information is available on the diversity and distribution of resistance and virulence factors in enterococci isolated from retail fish. In this study, 200 samples of retail ready-to-eat raw fish (sashimi) collected from the Japanese prefecture of Hiroshima were analyzed for incidence of Enterococcus spp. We recovered 96 enterococcal isolates from 90 (45%, 90/200) samples. Fifty-six strains were identified at the species level: E. faecalis (n = 31), E. faecium (n = 7), E. casseliflavus (n = 7), E. gallinarum (n = 3), E. phoeniculicola (n = 4), E. raffinosus (n = 2), E. saccharolyticus (n = 1), and E. gilvus (n = 1). Twenty-five (26%, 25/96) strains carried antibiotic resistance genes. These included the tet(M), tet(L), tet(K), erm(B), msr(A/B), aph(3'), and blaZ genes, which were detected in 12.5%, 9.3%, 2%, 14.5%, 1%, 1%, and 2% of isolates, respectively. The virulence genes gelE and asa1 were detected in 31 and 24 E. faecalis strains, respectively. Both genes were detected in one E. faecium strain. In conclusion, this is the first study to underscore the importance of sashimi as not only a reservoir of Enterococcus spp. carrying resistance and virulence genes, but also a reservoir for unusual Enterococcus spp.
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Affiliation(s)
- Ahmed M Hammad
- Laboratory of Food Microbiology and Hygiene, Faculty of Veterinary Medicine, University of Sadat City, Sadat City 32897, Egypt.
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Huys G, Botteldoorn N, Delvigne F, De Vuyst L, Heyndrickx M, Pot B, Dubois JJ, Daube G. Microbial characterization of probiotics--advisory report of the Working Group "8651 Probiotics" of the Belgian Superior Health Council (SHC). Mol Nutr Food Res 2013; 57:1479-504. [PMID: 23801655 PMCID: PMC3910143 DOI: 10.1002/mnfr.201300065] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 01/22/2013] [Accepted: 02/20/2013] [Indexed: 12/17/2022]
Abstract
When ingested in sufficient numbers, probiotics are expected to confer one or more proven health benefits on the consumer. Theoretically, the effectiveness of a probiotic food product is the sum of its microbial quality and its functional potential. Whereas the latter may vary much with the body (target) site, delivery mode, human target population, and health benefit envisaged microbial assessment of the probiotic product quality is more straightforward. The range of stakeholders that need to be informed on probiotic quality assessments is extremely broad, including academics, food and biotherapeutic industries, healthcare professionals, competent authorities, consumers, and professional press. In view of the rapidly expanding knowledge on this subject, the Belgian Superior Health Council installed Working Group "8651 Probiotics" to review the state of knowledge regarding the methodologies that make it possible to characterize strains and products with purported probiotic activity. This advisory report covers three main steps in the microbial quality assessment process, i.e. (i) correct species identification and strain-specific typing of bacterial and yeast strains used in probiotic applications, (ii) safety assessment of probiotic strains used for human consumption, and (iii) quality of the final probiotic product in terms of its microbial composition, concentration, stability, authenticity, and labeling.
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Affiliation(s)
- Geert Huys
- Laboratory for Microbiology & BCCM/LMG Bacteria Collection, Faculty of Sciences, Ghent University, Ghent, Belgium.
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Starikova I, Al-Haroni M, Werner G, Roberts AP, Sørum V, Nielsen KM, Johnsen PJ. Fitness costs of various mobile genetic elements in Enterococcus faecium and Enterococcus faecalis. J Antimicrob Chemother 2013; 68:2755-65. [PMID: 23833178 PMCID: PMC3820106 DOI: 10.1093/jac/dkt270] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Objectives To determine the fitness effects of various mobile genetic elements (MGEs) in Enterococcus faecium and Enterococcus faecalis when newly acquired. We also tested the hypothesis that the biological cost of vancomycin resistance plasmids could be mitigated during continuous growth in the laboratory. Methods Different MGEs, including two conjugative transposons (CTns) of the Tn916 family (18 and 33 kb), a pathogenicity island (PAI) of 200 kb and vancomycin-resistance (vanA) plasmids (80–200 kb) of various origins and classes, were transferred into common ancestral E. faecium and E. faecalis strains by conjugation assays and experimentally evolved (vanA plasmids only). Transconjugants were characterized by PFGE, S1 nuclease assays and Southern blotting hybridization analyses. Single specific primer PCR was performed to determine the target sites for the insertion of the CTns. The fitness costs of various MGEs in E. faecium and E. faecalis were estimated in head-to-head competition experiments, and evolved populations were generated in serial transfer assays. Results The biological cost of a newly acquired PAI and two CTns were both host- and insertion-locus-dependent. Newly acquired vanA plasmids may severely reduce host fitness (25%–27%), but these costs were rapidly mitigated after only 400 generations of continuous growth in the absence of antibiotic selection. Conclusions Newly acquired MGEs may impose an immediate biological cost in E. faecium. However, as demonstrated for vanA plasmids, the initial costs of MGE carriage may be mitigated during growth and beneficial plasmid–host association can rapidly emerge.
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Affiliation(s)
- Irina Starikova
- Department of Pharmacy, Faculty of Health Sciences, University of Tromsø, Tromsø, Norway
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Aktan Y, Tan S, Icgen B. Characterization of lead-resistant river isolate Enterococcus faecalis and assessment of its multiple metal and antibiotic resistance. ENVIRONMENTAL MONITORING AND ASSESSMENT 2013; 185:5285-93. [PMID: 23079796 DOI: 10.1007/s10661-012-2945-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2012] [Accepted: 10/08/2012] [Indexed: 05/25/2023]
Abstract
Contamination of surface waters has a direct impact on the public health of entire communities. Microorganisms inhabiting contaminated surface waters have developed mechanisms of coping with a variety of toxic metals and drugs. Investigations were carried out to isolate and identify lead-resistant bacteria from the river Kızılırmak along the city of Kırıkkale, Turkey. Of the 33 lead-resistant isolates, one isolate with a minimal inhibitory concentration of 1,200 mg L(-1) was isolated and identified as Enterococcus faecalis by using biochemical tests and 16S rRNA sequencing. Lead-resistant E. faecalis isolate was found out to be resistant to other heavy metals like aluminum, lithium, barium, chromium, iron, silver, tin, nickel, zinc, and strontium and to drugs like amikacin, aztreonam, and gentamicin. E. faecalis harbored four plasmids with the molecular sizes of 1.58, 3.06, 22.76, and 28.95 kb. Plasmid profile analyses of cured derivatives revealed that the lead resistance ability of E. faecalis was still existing despite the elimination of all the plasmids. Moreover, the antibiotic resistance pattern of the cured derivatives did not demonstrate any change from the parental strain. Our findings indicated that the lead resistance genes of E. faecalis were located on the chromosomal DNA rather than the plasmid.
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Affiliation(s)
- Yasin Aktan
- Department of Biology, Kırıkkale University, 71450 Kırıkkale, Turkey
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Di Cesare A, Luna GM, Vignaroli C, Pasquaroli S, Tota S, Paroncini P, Biavasco F. Aquaculture can promote the presence and spread of antibiotic-resistant Enterococci in marine sediments. PLoS One 2013; 8:e62838. [PMID: 23638152 PMCID: PMC3637307 DOI: 10.1371/journal.pone.0062838] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 03/27/2013] [Indexed: 12/20/2022] Open
Abstract
Aquaculture is an expanding activity worldwide. However its rapid growth can affect the aquatic environment through release of large amounts of chemicals, including antibiotics. Moreover, the presence of organic matter and bacteria of different origin can favor gene transfer and recombination. Whereas the consequences of such activities on environmental microbiota are well explored, little is known of their effects on allochthonous and potentially pathogenic bacteria, such as enterococci. Sediments from three sampling stations (two inside and one outside) collected in a fish farm in the Adriatic Sea were examined for enterococcal abundance and antibiotic resistance traits using the membrane filter technique and an improved quantitative PCR. Strains were tested for susceptibility to tetracycline, erythromycin, ampicillin and gentamicin; samples were directly screened for selected tetracycline [tet(M), tet(L), tet(O)] and macrolide [erm(A), erm(B) and mef] resistance genes by newly-developed multiplex PCRs. The abundance of benthic enterococci was higher inside than outside the farm. All isolates were susceptible to the four antimicrobials tested, although direct PCR evidenced tet(M) and tet(L) in sediment samples from all stations. Direct multiplex PCR of sediment samples cultured in rich broth supplemented with antibiotic (tetracycline, erythromycin, ampicillin or gentamicin) highlighted changes in resistance gene profiles, with amplification of previously undetected tet(O), erm(B) and mef genes and an increase in benthic enterococcal abundance after incubation in the presence of ampicillin and gentamicin. Despite being limited to a single farm, these data indicate that aquaculture may influence the abundance and spread of benthic enterococci and that farm sediments can be reservoirs of dormant antibiotic-resistant bacteria, including enterococci, which can rapidly revive in presence of new inputs of organic matter. This reservoir may constitute an underestimated health risk and deserves further investigation.
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Affiliation(s)
- Andrea Di Cesare
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.
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Werner G, Coque TM, Franz CMAP, Grohmann E, Hegstad K, Jensen L, van Schaik W, Weaver K. Antibiotic resistant enterococci-tales of a drug resistance gene trafficker. Int J Med Microbiol 2013; 303:360-79. [PMID: 23602510 DOI: 10.1016/j.ijmm.2013.03.001] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Enterococci have been recognized as important hospital-acquired pathogens in recent years, and isolates of E. faecalis and E. faecium are the third- to fourth-most prevalent nosocomial pathogen worldwide. Acquired resistances, especially against penicilin/ampicillin, aminoglycosides (high-level) and glycopeptides are therapeutically important and reported in increasing numbers. On the other hand, isolates of E. faecalis and E. faecium are commensals of the intestines of humans, many vertebrate and invertebrate animals and may also constitute an active part of the plant flora. Certain enterococcal isolates are used as starter cultures or supplements in food fermentation and food preservation. Due to their preferred intestinal habitat, their wide occurrence, robustness and ease of cultivation, enterococci are used as indicators for fecal pollution assessing hygiene standards for fresh- and bathing water and they serve as important key indicator bacteria for various veterinary and human resistance surveillance systems. Enterococci are widely prevalent and genetically capable of acquiring, conserving and disseminating genetic traits including resistance determinants among enterococci and related Gram-positive bacteria. In the present review we aimed at summarizing recent advances in the current understanding of the population biology of enterococci, the role mobile genetic elements including plasmids play in shaping the population structure and spreading resistance. We explain how these elements could be classified and discuss mechanisms of plasmid transfer and regulation and the role and cross-talk of enterococcal isolates from food and food animals to humans.
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Affiliation(s)
- Guido Werner
- National Reference Centre for Stapyhlococci and Enterococci, Division of Nosocomial Pathogens and Antibiotic Resistances, Robert Koch Institute, Wernigerode Branch, Burgstr. 37, 38855 Wernigerode, Germany.
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Hung WC, Takano T, Higuchi W, Iwao Y, Khokhlova O, Teng LJ, Yamamoto T. Comparative genomics of community-acquired ST59 methicillin-resistant Staphylococcus aureus in Taiwan: novel mobile resistance structures with IS1216V. PLoS One 2012; 7:e46987. [PMID: 23071689 PMCID: PMC3465296 DOI: 10.1371/journal.pone.0046987] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 09/07/2012] [Indexed: 12/20/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) with ST59/SCCmecV and Panton-Valentine leukocidin gene is a major community-acquired MRSA (CA-MRSA) lineage in Taiwan and has been multidrug-resistant since its initial isolation. In this study, we studied the acquisition mechanism of multidrug resistance in an ST59 CA-MRSA strain (PM1) by comparative genomics. PM1’s non-β-lactam resistance was encoded by two unique genetic traits. One was a 21,832-bp composite mobile element structure (MESPM1), which was flanked by direct repeats of enterococcal IS1216V and was inserted into the chromosomal sasK gene; the target sequence (att) was 8 bp long and was duplicated at both ends of MESPM1. MESPM1 consisted of two regions: the 5′-end side 12.4-kb region carrying Tn551 (with ermB) and Tn5405-like (with aph[3′]-IIIa and aadE), similar to an Enterococcus faecalis plasmid, and the 3′-end side 6,587-bp region (MEScat) that carries cat and is flanked by inverted repeats of IS1216V. MEScat possessed att duplication at both ends and additional two copies of IS1216V inside. MESPM1 represents the first enterococcal IS1216V-mediated composite transposon emerged in MRSA. IS1216V-mediated deletion likely occurred in IS1216V-rich MESPM1, resulting in distinct resistance patterns in PM1-derivative strains. Another structure was a 6,025-bp tet-carrying element (MEStet) on a 25,961-bp novel mosaic penicillinase plasmid (pPM1); MEStet was flanked by direct repeats of IS431, but with no target sequence repeats. Moreover, the PM1 genome was deficient in a copy of the restriction and modification genes (hsdM and hsdS), which might have contributed to the acquisition of enterococcal multidrug resistance.
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Affiliation(s)
- Wei-Chun Hung
- Division of Bacteriology, Department of Infectious Disease Control and International Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Tomomi Takano
- Division of Bacteriology, Department of Infectious Disease Control and International Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Wataru Higuchi
- Division of Bacteriology, Department of Infectious Disease Control and International Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yasuhisa Iwao
- Division of Bacteriology, Department of Infectious Disease Control and International Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Olga Khokhlova
- Division of Bacteriology, Department of Infectious Disease Control and International Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tatsuo Yamamoto
- Division of Bacteriology, Department of Infectious Disease Control and International Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
- * E-mail:
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Santagati M, Campanile F, Stefani S. Genomic diversification of enterococci in hosts: the role of the mobilome. Front Microbiol 2012; 3:95. [PMID: 22435066 PMCID: PMC3303144 DOI: 10.3389/fmicb.2012.00095] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2011] [Accepted: 02/27/2012] [Indexed: 12/11/2022] Open
Abstract
Enterococci are ubiquitous lactic acid bacteria, possessing a flexible nature that allows them to colonize various environments and hosts but also to be opportunistic pathogens. Many papers have contributed to a better understanding of: (i) the taxonomy of this complex group of microorganisms; (ii) intra-species variability; (iii) the role of different pathogenicity traits; and (iv) some markers related to the character of host-specificity, but the reasons of such incredible success of adaptability is still far from being fully explained. Recently, genomic-based studies have improved our understanding of the genome diversity of the most studied species, i.e., E. faecalis and E. faecium. From these studies, what is becoming evident is the role of the mobilome in adding new abilities to colonize new hosts and environments, and eventually in driving their evolution: specific clones associated with human infections or specific hosts can exist, but probably the consideration of these populations as strictly clonal groups is only partially correct. The variable presence of mobile genetic elements may, indeed, be one of the factors involved in the evolution of one specific group in a specific host and/or environment. Certainly more extensive studies using new high throughput technologies are mandatory to fully understand the evolution of predominant clones and species in different hosts and environments.
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Affiliation(s)
- Maria Santagati
- Molecular Microbiology and Antibiotic Resistance Lab, Department of Microbiology, University of Catania Catania, Italy
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Mendes RE, Woosley LN, Farrell DJ, Sader HS, Jones RN. Oritavancin activity against vancomycin-susceptible and vancomycin-resistant Enterococci with molecularly characterized glycopeptide resistance genes recovered from bacteremic patients, 2009-2010. Antimicrob Agents Chemother 2012; 56:1639-42. [PMID: 22183169 PMCID: PMC3294904 DOI: 10.1128/aac.06067-11] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 12/08/2011] [Indexed: 11/20/2022] Open
Abstract
Oritavancin exhibited potent activity against vancomycin-susceptible (MIC(50) and MIC(90), 0.015/0.03 μg/ml) and vanB-carrying E. faecalis isolates (MIC(50) and MIC(90), 0.015 and 0.015 μg/ml). Higher (16- to 32-fold) MIC(50)s and MIC(90)s for vanA-harboring E. faecalis were noted (MIC(50) and MIC(90), 0.25 and 0.5 μg/ml), although oritavancin inhibited all strains at ≤ 0.5 μg/ml. Vancomycin-susceptible and vanB-carrying E. faecium strains (MIC(50) and MIC(90), ≤ 0.008 and ≤ 0.008 μg/ml for both) were very susceptible to oritavancin, as were VanA-producing isolates (MIC(50) and MIC(90), 0.03 and 0.06 μg/ml). Oritavancin exhibited good in vitro potency against this collection of organisms, including vancomycin-resistant enterococci.
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