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Borgio JF, AlJindan R, Alghourab LH, Alquwaie R, Aldahhan R, Alhur NF, AlEraky DM, Mahmoud N, Almandil NB, AbdulAzeez S. Genomic Landscape of Multidrug Resistance and Virulence in Enterococcus faecalis IRMC827A from a Long-Term Patient. BIOLOGY 2023; 12:1296. [PMID: 37887006 PMCID: PMC10604365 DOI: 10.3390/biology12101296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 09/25/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023]
Abstract
We report on a highly virulent, multidrug-resistant strain of Enterococcus faecalis IRMC827A that was found colonizing a long-term male patient at a tertiary hospital in Khobar, Saudi Arabia. The E. faecalis IRMC827A strain carries several antimicrobial drug resistance genes and harbours mobile genetic elements such as Tn6009, which is an integrative conjugative element that can transfer resistance genes between bacteria and ISS1N via an insertion sequence. Whole-genome-sequencing-based antimicrobial susceptibility testing on strains from faecal samples revealed that the isolate E. faecalis IRMC827A is highly resistant to a variety of antibiotics, including tetracycline, doxycycline, minocycline, dalfopristin, virginiamycin, pristinamycin, chloramphenicol, streptomycin, clindamycin, lincomycin, trimethoprim, nalidixic acid and ciprofloxacin. The isolate IRMC827A carries several virulence factors that are significantly associated with adherence, biofilm formation, sortase-assembled pili, manganese uptake, antiphagocytosis, and spreading factor of multidrug resistance. The isolate also encompasses two mutations (G2576T and G2505A) in the 23S rRNA gene associated with linezolid resistance and three more mutations (gyrA p.S83Y, gyrA p.D759N and parC p.S80I) of the antimicrobial resistance phenotype. The findings through next-generation sequencing on the resistome, mobilome and virulome of the isolate in the study highlight the significance of monitoring multidrug-resistant E. faecalis colonization and infection in hospitalized patients. As multidrug-resistant E. faecalis is a serious pathogen, it is particularly difficult to treat and can cause fatal infections. It is important to have quick and accurate diagnostic tests for multidrug-resistant E. faecalis, to track the spread of multidrug-resistant E. faecalis in healthcare settings, and to improve targeted interventions to stop its spread. Further research is necessary to develop novel antibiotics and treatment strategies for multidrug-resistant E. faecalis infections.
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Affiliation(s)
- J. Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
| | - Reem AlJindan
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Lujeen H. Alghourab
- Summer Research Program, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Rahaf Alquwaie
- Master Program of Biotechnology, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Razan Aldahhan
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
| | - Norah F. Alhur
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
| | - Doaa M. AlEraky
- Department of Biomedical Dental Science, Microbiology and Immunology Division, Collage of Dentistry, Dammam 31441, Saudi Arabia
| | - Nehal Mahmoud
- Department of Microbiology, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Noor B. Almandil
- Department of Clinical Pharmacy Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia; (J.F.B.); (R.A.); (N.F.A.)
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Shobo CO, Amoako DG, Allam M, Ismail A, Essack SY, Bester LA. A Genomic Snapshot of Antibiotic-Resistant Enterococcus faecalis within Public Hospital Environments in South Africa. Glob Health Epidemiol Genom 2023; 2023:6639983. [PMID: 37342729 PMCID: PMC10279497 DOI: 10.1155/2023/6639983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023] Open
Abstract
Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship of Enterococcus faecalis isolated from hospital environments in South Africa. This study was carried out from September to November 2017. Isolates were recovered from 11 frequently touched sites by patients and healthcare workers in different wards at 4 levels of healthcare (A, B, C, and D) in Durban, South Africa. Out of the 245 identified E. faecalis isolates, 38 isolates underwent whole-genome sequencing (WGS) on the Illumina MiSeq platform, following microbial identification and antibiotic susceptibility tests. The tet(M) (31/38, 82%) and erm(C) (16/38, 42%) genes were the most common antibiotic-resistant genes found in isolates originating from different hospital environments which corroborated with their antibiotic resistance phenotypes. The isolates harboured mobile genetic elements consisting of plasmids (n = 11) and prophages (n = 14) that were mostly clone-specific. Of note, a large number of insertion sequence (IS) families were found on the IS3 (55%), IS5 (42%), IS1595 (40%), and Tn3 transposons the most predominant. Microbial typing using WGS data revealed 15 clones with 6 major sequence types (ST) belonging to ST16 (n = 7), ST40 (n = 6), ST21 (n = 5), ST126 (n = 3), ST23 (n = 3), and ST386 (n = 3). Phylogenomic analysis showed that the major clones were mostly conserved within specific hospital environments. However, further metadata insights revealed the complex intraclonal spread of these E. faecalis major clones between the sampling sites within each specific hospital setting. The results of these genomic analyses will offer insights into antibiotic-resistantE. faecalis in hospital environments relevant to the design of optimal infection prevention strategies in hospital settings.
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Affiliation(s)
- Christiana O. Shobo
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- School of Laboratory Medicine and Medical Science, Department of Medical Microbiology, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Daniel G. Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, UAE
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Linda A. Bester
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Department of Biochemistry and Microbiology, Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
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Chen W, Huang Y, Jiao X, Ye J, Lin Y, Yao F. Loss of erm(B)-Mediated rRNA Dimethylation and Restoration of Erythromycin Susceptibility in Erythromycin-Resistant Enterococci Following Induced Linezolid Resistance. Microb Drug Resist 2023; 29:51-58. [PMID: 36577022 DOI: 10.1089/mdr.2022.0140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Linezolid has been reported to restore erythromycin susceptibility in erythromycin-resistant Staphylococcus aureus. This phenomenon has not been reported in enterococci and the mechanisms involved therein are still unknown. The purpose of this study was to investigate the mechanisms involved and the effect of combining linezolid with erythromycin on erythromycin-resistant enterococci. Checkerboard techniques were used to determine drug interactions, and 12 of 14 isolates showed a synergistic effect between erythromycin and linezolid (fractional inhibitory concentration <0.5). We observed that the erm(B) gene, which encodes a dimethyltransferase responsible for erythromycin resistance, was expressed from transposon Tn1545 in the tested erythromycin-resistant enterococci. After exposure to linezolid, erm(B)-mediated rRNA dimethylation at A2071 could not be detected, and the erm(B) gene was lost following acquisition of erythromycin susceptibility. Thus, in conclusion, linezolid combined with erythromycin exerts a synergistic effect against erythromycin-resistant enterococci. Linezolid treatment suppressed erm(B)-mediated rRNA dimethylation at A2071, which could lead to loss of the erm(B) gene.
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Affiliation(s)
- Weidong Chen
- Department of Pharmacy, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Yuanchun Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xiaoyang Jiao
- Department of Cell Biology, Shantou University Medical College, Shantou, China
| | - Jiahui Ye
- Department of Pharmacology, Shantou University Medical College, Shantou, China
| | - Yanling Lin
- Affiliated Jiangmen Traditional Chinese Medical Hospital of Jinan University, Jiangmen, China
| | - Fen Yao
- Department of Pharmacology, Shantou University Medical College, Shantou, China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, China
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Cho S, McMillan EA, Barrett JB, Hiott LM, Woodley TA, House SL, Frye JG, Jackson CR. Distribution and Transfer of Plasmid Replicon Families among Multidrug-Resistant Enterococcus faecalis and Enterococcus faecium from Poultry. Microorganisms 2022; 10:microorganisms10061244. [PMID: 35744761 PMCID: PMC9228330 DOI: 10.3390/microorganisms10061244] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022] Open
Abstract
The presence and transfer of plasmids from commensal bacteria to more pathogenic bacteria may contribute to the dissemination of antimicrobial resistance. However, the prevalence of plasmids from commensal bacteria, such as the enterococci, in food animals remains largely unknown. In this study, the diversity and prevalence of plasmid families from multidrug-resistant (MDR; resistance to three or more antimicrobials) enterococci from poultry carcasses were determined. Plasmid-positive MDR enterococci were also tested for the ability to transfer plasmids to other enterococci using conjugation. MDR Enterococcus faecalis (n = 98) and Enterococcus faecium (n = 696) that were isolated from poultry carcass rinsates between 2004 and 2011 were tested for the presence of 21 plasmid replicon (rep) families using multiplex PCR. Approximately 48% of E. faecalis (47/98) and 16% of E. faecium (110/696) were positive for at least one rep-family. Fourteen rep-families were detected overall, and ten rep-families were shared between E. faecalis and E. faecium. The rep7 and rep17 families were unique to E. faecalis, while the rep5 and rep8 families were unique to E. faecium. The rep9 family was predominant in both E. faecalis and E. faecium for all the years tested. The greatest number of rep-families detected was in 2005 (n = 10), and the least was in 2009 (n = 1). Eight rep-families were transferred from E. faecalis donors to the E. faecalis JH2-2 recipient using conjugation. Results from this study showed that E. faecalis and E. faecium from poultry carcasses contain numerous and diverse rep-families that are capable of conjugal transfer.
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Affiliation(s)
- Sohyun Cho
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
- Oak Ridge Institute for Science and Education, Oak Ridge, TN 37830, USA
| | - Elizabeth A. McMillan
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - John B. Barrett
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Lari M. Hiott
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Tiffanie A. Woodley
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Sandra L. House
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Jonathan G. Frye
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
| | - Charlene R. Jackson
- Bacterial Epidemiology and Antimicrobial Resistance Research Unit, USDA-ARS, U.S. National Poultry Research Center, Athens, GA 30605, USA; (S.C.); (E.A.M.); (J.B.B.); (L.M.H.); (T.A.W.); (S.L.H.); (J.G.F.)
- Correspondence: ; Tel.: +1-(706)-546-3604; Fax: +1-(706)-546-3616
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Antimicrobial Resistance, Biofilm Formation, and Virulence Genes in Enterococcus Species from Small Backyard Chicken Flocks. Antibiotics (Basel) 2022; 11:antibiotics11030380. [PMID: 35326843 PMCID: PMC8944505 DOI: 10.3390/antibiotics11030380] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 02/07/2023] Open
Abstract
Backyard birds are small flocks that are more common in developing countries. They are used for poultry meat and egg production. However, they are also implicated in the maintenance and transmission of several zoonotic diseases, including multidrug-resistant bacteria. Enterococci are one of the most common zoonotic bacteria. They colonize numerous body sites and cause a wide range of serious nosocomial infections in humans. Therefore, the objective of the present study was to investigate the diversity in Enterococcus spp. in healthy birds and to determine the occurrence of multidrug resistance (MDR), multi-locus sequence types, and virulence genes and biofilm formation. From March 2019 to December 2020, cloacal swabs were collected from 15 healthy backyard broiler flocks. A total of 90 enterococci strains were recovered and classified according to the 16S rRNA sequence into Enterococcus faecalis (50%); Enterococcus faecium (33.33%), Enterococcus hirae (13.33%), and Enterococcus avium (3.33%). The isolates exhibited high resistance to tetracycline (55.6%), erythromycin (31.1%), and ampicillin (30%). However, all of the isolates were susceptible to linezolid. Multidrug resistance (MDR) was identified in 30 (33.3%) isolates. The enterococci AMR-associated genes ermB, ermA, tetM, tetL, vanA, cat, and pbp5 were identified in 24 (26.6%), 11 (12.2%), 39 (43.3%), 34 (37.7%), 1 (1.1%), 4 (4.4%), and 23 (25.5%) isolates, respectively. Of the 90 enterococci, 21 (23.3%), 27 (30%), and 36 (40%) isolates showed the presence of cylA, gelE, and agg virulence-associated genes, respectively. Seventy-three (81.1%) isolates exhibited biofilm formation. A statistically significant correlation was obtained for biofilm formation versus the MAR index and MDR. Multi-locus sequence typing (MLST) identified eleven and eight different STs for E. faecalis and E. faecium, respectively. Seven different rep-family plasmid genes (rep1–2, rep3, rep5–6, rep9, and rep11) were detected in the MDR enterococci. Two-thirds (20/30; 66.6%) of the enterococci were positive for one or two rep-families. In conclusion, the results show that healthy backyard chickens could act as a reservoir for MDR and virulent Enterococcus spp. Thus, an effective antimicrobial stewardship program and further studies using a One Health approach are required to investigate the role of backyard chickens as vectors for AMR transmission to humans.
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Lertsuphotvanit N, Santimaleeworagun W, Narakornwit W, Chuenbarn T, Mahadlek J, Chantadee T, Phaechamud T. Borneol-based antisolvent-induced in situ forming matrix for crevicular pocket delivery of vancomycin hydrochloride. Int J Pharm 2022; 617:121603. [DOI: 10.1016/j.ijpharm.2022.121603] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 01/23/2022] [Accepted: 02/16/2022] [Indexed: 01/31/2023]
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Espíndola LCP, do Nascimento MVMR, do Souto RM, Colombo APV. Antimicrobial susceptibility and virulence of Enterococcus spp. isolated from periodontitis-associated subgingival biofilm. J Periodontol 2021; 92:1588-1600. [PMID: 33650677 DOI: 10.1002/jper.20-0815] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 01/19/2021] [Accepted: 02/12/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND This study evaluated the prevalence, virulence and antimicrobial susceptibility of enterococci isolated from the subgingival microbiota of patients with different periodontal status. METHODS Subgingival biofilm was obtained from individuals with periodontal health (PH) (n = 139), gingivitis (n = 103), and periodontitis (n = 305) and cultivated on selective media. Isolated strains were identified by mass spectrometry. Antimicrobial sensitivity was determined by disk diffusion, virulence genes by polymerase chain reaction, and the subgingival microbiota by checkerboard. Differences among groups were assessed by Kruskal-Wallis, Mann-Whitney, and Chi-square tests. RESULTS Enterococcus spp. were isolated from 7.4% of all samples; 53.7% were Enterococcus faecalis. They were more prevalent in periodontitis (9.8%) and gingivitis (7.8%) than PH (2.2%; P <0.05), but no differences among stages of disease severity were observed. High rates of low susceptibility/resistance (>64%) to at least one antimicrobial were observed. Predominant virulence factors included ace (64.3%), asa (39.3%), and esp (35.7%). Fusobacterium nucleatum was prevalent in the subgingival microbiota of enterococci+ individuals, whereas Dialister pneumosintes was found in low frequency in patients with bopD+ enterococci. Oral streptococci were prevalent (>70%) in patients carrying enterococci susceptible to doxycycline (P <0.05), usually bopD- and esp- (P <0.01). CONCLUSIONS E. faecalis is increased in periodontitis-associated biofilm. Oral enterococci carry virulence genes and express resistance to some antibiotics commonly used in dentistry, such as ciprofloxacin and erythromycin. Specific subgingival taxa are associated with oral enterococci, suggesting they may interact with species of the dysbiotic periodontitis biofilm, constituting a potential source of factors to tissue destruction, antibiotic resistance dissemination, and poor response to periodontal therapy.
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Affiliation(s)
- Laís Christina P Espíndola
- Department of Clinics, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Department of Medical Microbiology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Marcus Vinícius M R do Nascimento
- Department of Clinics, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Department of Medical Microbiology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Renata M do Souto
- Department of Medical Microbiology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Ana Paula V Colombo
- Department of Clinics, School of Dentistry, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Department of Medical Microbiology, Institute of Microbiology, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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Antimicrobial Resistance Gene Detection and Plasmid Typing Among Multidrug Resistant Enterococci Isolated from Freshwater Environment. Microorganisms 2020; 8:microorganisms8091338. [PMID: 32887339 PMCID: PMC7563215 DOI: 10.3390/microorganisms8091338] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 08/27/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
In this study, mechanisms of antimicrobial resistance (AR) as well as the abundance and diversity of plasmids were determined among multidrug resistant (MDR) enterococci from surface water in GA, USA. A total of 51 enterococci isolates were screened for the presence of 27 AR genes conferring resistance to ciprofloxacin, erythromycin, tylosin, kanamycin, streptomycin, lincomycin, Quinupristin/Dalfopristin (Q/D), and tetracycline. A plasmid classification system based on replication genes was used to detect 19 defined Gram-positive plasmid replicon families. Twelve genes were identified as conferring resistance to erythromycin and tylosin (erm(B) and erm(C)), kanamycin (aph(3′)-IIIa), streptomycin (ant(6)-Ia), lincomycin (lnu(B)), Q/D (vat(E)), ciprofloxacin (qnrE. faecalis), and tetracycline (tet(K), tet(L), tet(M), tet(O) and tet(S)). Twelve different rep-families were identified in two-thirds of the isolates. While AR genes commonly found in human and animals were detected in this study among environmental enterococci, resistance genes could not be determined for many of the isolates, which indicates that diverse AR mechanisms exist among enterococci, and the understanding of AR mechanisms for environmental enterococci is limited. Diverse rep-families were identified among the enterococci recovered from the aquatic environment, and these rep-families appear to be quite different from those recovered from other sources. This work expands knowledge of AR gene reservoirs and enterococcal plasmids across a wider range of environments.
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Iurovschi R, Joaquim CR, de Faveri M, de Miranda TS, Feres M, de Figueiredo LC. Evaluation of the Microbiological Profile of Alveolar Residual Screws and Cleft-Adjacent Teeth in Individuals With Complete Unilateral Fissures. Cleft Palate Craniofac J 2020; 57:1182-1189. [PMID: 32748644 DOI: 10.1177/1055665620945568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE To evaluate the microbiota profile of residual alveolar slits and teeth adjacent to the cleft in fissured individuals. DESIGNS This study used a cross-sectional design. PARTICIPANTS Twenty individuals, aged 14 to 24 years, who had a residual fissure in the maxillary alveolar ridge region were selected. MAIN OUTCOME MEASURES Three sites per individual were selected for microbiological collection (the site of the residual cleft and the 2 nearest teeth). The samples were analyzed using the Checkerboard DNA-DNA hybridization technique for 73 species of bacteria. RESULTS All the species analyzed were found in the 2 niches (slits and teeth). The bacterial species present in the largest number in the residual cracks were Prevotella melaninogenica, Prevotella nigrescens, and Streptococcus mitis. With regard to the bacterial profiles in the mesial and distal faces, the most prevalent species were P nigrescens, Veillonella parvula, and Fusobacterium nucleatum sp vicentii. The analysis of all the collected samples demonstrated very similar profiles for the mesial and distal faces, with these 2 sites even presenting the same species in greater frequencies. Higher counts of 20 bacterial species (Wilcoxon test) were observed in the dental niche, in relation to the fissure, particularly, P nigrescens, V parvula, F nucleatum sp vicentii, and Neisseria mucosa. CONCLUSION Some species were significantly more prevalent in the residual alveolar fissures and in adjacent teeth. The comparison between the profiles of the 2 niches demonstrated large differences in the most frequent species in the teeth, and no qualitative differences with regard to specific pathogens.
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Affiliation(s)
- Ronaldo Iurovschi
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, São Paulo, Brazil
| | - Claudia Regina Joaquim
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, São Paulo, Brazil
| | - Marcelo de Faveri
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, São Paulo, Brazil
| | | | - Magda Feres
- Department of Periodontology, Dental Research Division, Guarulhos University, Guarulhos, São Paulo, Brazil
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Prevalence of an Intestinal ST40 Enterococcus faecalis over Other E. faecalis Strains in the Gut Environment of Mice Fed Different High Fat Diets. Int J Mol Sci 2020; 21:ijms21124330. [PMID: 32570702 PMCID: PMC7352901 DOI: 10.3390/ijms21124330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 12/16/2022] Open
Abstract
E. faecalis is a commensal bacterium with specific strains involved in opportunistic and nosocomial infections. Therefore, it is important to know how the strains of this species are selected in the gut. In this study, fifteen E. faecalis strains, isolated over twelve weeks from the faeces of mice fed standard chow or one of three high fat diets enriched with extra virgin olive oil, refined olive oil or butter were subjected to a genetic “Multilocus Sequence Typing” study that revealed the presence of mainly two genotypes, ST9 and ST40, the latter one prevailing at the end of the research. A V3–V5 sequence comparison of the predominant ST40 strain (12B3-5) in a metagenomic study showed that this sequence was the only E. faecalis present in the mouse cohort after twelve weeks. The strain was subjected to a comparative proteomic study with a ST9 strain by 2D electrophoresis and mass spectrometry. After comparing the results with a E. faecalis database, unshared entries were compared and 12B3-5 showed higher antimicrobial production as well as greater protection from environmental factors such as xenobiotics, oxidative stress and metabolite accumulation, which could be the reason for its ability to outcompete other possible rivals in an intestinal niche.
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Vickerman MM, Mansfield JM. Streptococcal peptides that signal Enterococcus faecalis cells carrying the pheromone-responsive conjugative plasmid pAM373. Mol Oral Microbiol 2019; 34:254-262. [PMID: 31610092 DOI: 10.1111/omi.12271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/11/2019] [Accepted: 10/09/2019] [Indexed: 01/30/2023]
Abstract
Pheromone-mediated conjugative transfer of enterococcal plasmids can contribute to the dissemination of genes involved in antibiotic resistance, fitness, and virulence among co-residents of mixed microbial communities. We have previously shown that intergeneric signaling by the Streptococcus gordonii strain Challis heptapeptide s.g.cAM373 (SVFILAA) induces an aggregation substance-mediated mating response and facilitates plasmid transfer from Enterococcus faecalis cells carrying the pheromone-responsive plasmid pAM373 to both pheromone-producing and non-pheromone-producing oral streptococcal recipients. To further investigate the streptococcal pheromone-like peptides, s.g.cAM373-like sequences were identified in the signal sequences of streptococcal CamG lipoproteins and their abilities to induce a mating response in E. faecalis/pAM373 cells were examined. Synthetic heptamers with the consensus sequence (A/S)-(I/V)-F-I-L-(A/V/T)-(S/A) induced AS-mediated clumping. The conserved pheromone ABC transporter encoded by S. gordonii genome loci SGO_RS02660 and SGO_RS02665 was identified and confirmed to be required for s.g.cAM373 activity. Functional assays of culture supernatants from representative oral and blood isolates of S. gordonii showed that in addition to strains encoding s.g.cAM373, strain SK120, encoding the newly identified pheromone s.g.cAM373-V (SVFILVA), was able to induce enterococcal clumping, whereas strains SK6, SK8, SK9, and SK86 which encoded s.g.cAM373-T (SVFILTA) did not elicit a detectable mating response. Absence of pheromone activity in supernatants of heterologous hosts encoding its CamG precursor suggested that s.g.cAM373-T was not effectively processed and/or transported. Overall, these studies demonstrated the distribution of active pheromone peptides among strains of S. gordonii, and support a potential role for enterococcal-streptococcal communication in contributing to genetic plasticity in the oral metagenome.
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Affiliation(s)
- M Margaret Vickerman
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY, USA
| | - Jillian M Mansfield
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY, USA
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12
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Dabul ANG, Avaca-Crusca JS, Navais RB, Merlo TP, Van Tyne D, Gilmore MS, Camargo ILBDC. Molecular basis for the emergence of a new hospital endemic tigecycline-resistant Enterococcus faecalis ST103 lineage. INFECTION GENETICS AND EVOLUTION 2018; 67:23-32. [PMID: 30393188 DOI: 10.1016/j.meegid.2018.10.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/22/2018] [Accepted: 10/23/2018] [Indexed: 11/25/2022]
Abstract
Enterococcus faecalis are a major cause of nosocomial infection worldwide, and the spread of vancomycin resistant strains (VRE) limits treatment options. Tigecycline-resistant VRE began to be isolated from inpatients at a Brazilian hospital within months following the addition of tigecycline to the hospital formulary. This was found to be the result of a spread of an ST103 E. faecalis clone. Our objective was to identify the basis for tigecycline resistance in this lineage. The genomes of two closely related tigecycline-susceptible (MIC = 0.06 mg/L), and three representative tigecycline-resistant (MIC = 1 mg/L) ST103 isolates were sequenced and compared. Further, efforts were undertaken to recapitulate the emergence of resistant strains in vitro. The specific mutations identified in clinical isolates in several cases were within the same genes identified in laboratory-evolved strains. The contribution of various polymorphisms to the resistance phenotype was assessed by trans-complementation of the wild type or mutant alleles, by testing for differences in mRNA abundance, and/or by examining the phenotype of transposon insertion mutants. Among tigecycline-resistant clinical isolates, five genes contained non-synonymous mutations, including two genes known to be related to enterococcal tigecycline resistance (tetM and rpsJ). Finally, within the in vitro-selected resistant variants, mutation in the gene for a MarR-family response regulator was associated with tigecycline resistance. This study shows that E. faecalis mutates to attain tigecycline resistance through the complex interplay of multiple mechanisms, along multiple evolutionary trajectories.
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Affiliation(s)
| | | | - Roberto Barranco Navais
- São Carlos Institute of Physics, University of São Paulo, PO Box 369, 135560-970 São Carlos, SP, Brazil
| | - Thaís Panhan Merlo
- São Carlos Institute of Physics, University of São Paulo, PO Box 369, 135560-970 São Carlos, SP, Brazil
| | - Daria Van Tyne
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, USA; Department of Microbiology and Immunobiology, Harvard Medical School, 25 Shattuck Street, Boston, USA
| | - Michael S Gilmore
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, USA; Department of Microbiology and Immunobiology, Harvard Medical School, 25 Shattuck Street, Boston, USA
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Evaluation of Virulence Factors and Detection of vanA, vanB and esp Genes from Clinical Isolates of Vancomycin - Resistant Enterococcus faecalis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2018. [DOI: 10.22207/jpam.12.2.23] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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14
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Mansfield JM, Herrmann P, Jesionowski AM, Vickerman MM. Streptococcus gordonii pheromone s.g.cAM373 may influence the reservoir of antibiotic resistance determinants of Enterococcus faecalis origin in the oral metagenome. J Med Microbiol 2017; 66:1635-1639. [PMID: 29022550 DOI: 10.1099/jmm.0.000613] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Streptococcus gordonii produces a pheromone heptapeptide, s.g.cAM373, which induces a conjugative mating response in Enterococcus faecalis cells carrying the responsive plasmid, pAM373. We investigated the extent of this intergeneric signaling on DNA acquisition by streptococcal species likely to cohabit oral biofilms. E. faecalis/pAM373/pAMS470 cells were incubated with synthetic s.g.cAM373, reverse peptide s.g.cAM373-R, or peptide-free medium and examined for their abilities to transfer plasmid DNA to streptococcal species in the presence of DNase. Preinduction of E. faecalis donors with s.g.cAM373 resulted in transconjugation frequencies in non-pheromone producing strains of Streptococcus mutans, Streptococcus sanguinis, Streptococcus anginosus, and Streptococcus suis that were significantly higher than frequencies when donors were preincubated with s.g.cAM373-R or medium alone. Peptide-mediated communication between commensal streptococci and E. faecalis carrying pheromone-responsive plasmids may facilitate conjugative DNA transfer to bystander species, and influence the reservoir of antibiotic resistance determinants of enterococcal origin in the oral metagenome.
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Affiliation(s)
- Jillian M Mansfield
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY 14214, USA
| | - Paul Herrmann
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY 14214, USA
| | - Amy M Jesionowski
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY 14214, USA
| | - M Margaret Vickerman
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, NY 14214, USA
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15
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Jepsen K, Jepsen S. Antibiotics/antimicrobials: systemic and local administration in the therapy of mild to moderately advanced periodontitis. Periodontol 2000 2017; 71:82-112. [PMID: 27045432 DOI: 10.1111/prd.12121] [Citation(s) in RCA: 179] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2015] [Indexed: 02/06/2023]
Abstract
This review gives an update of the current scientific evidence on the efficacy of the adjunctive use of systemic and local antibiotics/antimicrobials in the treatment of periodontitis. In particular, it addresses whether their use can improve the results of nonsurgical mechanical therapy in mild-to-moderate forms of the disease. Large numbers of randomized clinical trials and systematic reviews with meta-analyses have clearly established that adjunctive systemic antibiotics, combined with mechanical debridement, offer clinical improvements additional to those obtained with scaling and root planing alone. These effects are more pronounced in aggressive periodontitis and in initially deep pockets, whereas more limited additional improvements, of 0.3 mm for additional pocket reduction and 0.2 mm for additional clinical attachment gain, have been documented for moderately deep sites (4-6 mm) in patients with chronic periodontitis. The marginal clinical benefit in patients with moderate disease has to be balanced against possible side effects. Notably, it has to be realized that an increasing number of warnings have been articulated against the unrestricted use of antibiotics in treating periodontal diseases because of the emerging global public health issue of bacterial resistance. The effects of the adjunctive local administration of antimicrobials have also been very well documented in several systematic reviews. Overall, in persistent or recurrent localized deep sites, the application of antimicrobials by sustained-delivery devices may offer a benefit of an additional 0.4 mm in pocket depth reduction and 0.3 mm in clinical attachment level gain. In conclusion, the slight additional benefits of adjunctive antimicrobials, which were shown for moderate forms of periodontitis, have to be balanced against their side effects and therefore their prescription should be limited as much as possible.
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16
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Bhardwaj SB, Mehta M, Sood S, Sharma J. Biofilm Formation by Drug Resistant Enterococci Isolates Obtained from Chronic Periodontitis Patients. J Clin Diagn Res 2017; 11:DC01-DC03. [PMID: 28273964 DOI: 10.7860/jcdr/2017/24472.9152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/10/2016] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Enterococci are an important cause of opportunistic nosocomial infections and several multidrug resistant strains have emerged. The severity of periodontal diseases is managed by reduction in the pathogenic bacteria. There is a need to assess the prevalence and antibiotic susceptibility of enterococci colonizing the periodontal pocket and correlate its biofilm formation ability because oral biofilms provide a protective environment and are a reservoir of bacterial colonization of the gingival crevice. AIM To investigate possible association between antibiotic susceptibility and biofilm formation in enterococci isolates from chronic periodontitis patients. MATERIALS AND METHODS This retrospective study was conducted at Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital, Punjab University, Chandigarh from January 2015 to October 2015. Sterile paper points were inserted in the periodontal pocket of 100 subjects and put in a transport media. Forty -six isolates were identified as enterococci. The isolates were further examined for their ability to form biofilm by microtitre plate assay and antimicrobial susceptibility testing was done by disc diffusion method for clinically relevant antibiotics. RESULTS Significant relationship (p<0.001) was found between biofilm production with antibiotic resistance to Vancomycin, Erythromycin, Ciprofloxacin, Tiecoplanin, Amoxycillin and Gentamycin. CONCLUSION The study demonstrates a high propensity among the isolates of Enterococci to form biofilm and a significant association of biofilm with multiple drug resistance.
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Affiliation(s)
- Sonia Bhonchal Bhardwaj
- Assistant Professor, Department of Microbiology, Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital , Chandigarh, India
| | - Manjula Mehta
- Associate Professor, Department of Microbiology, Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital , Chandigarh, India
| | - Shaveta Sood
- Assistant Professor, Department of Periodontics, Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital , Chandigarh, India
| | - Jyoti Sharma
- Assistant Professor, Department of Microbiology, Dr. Harvansh Singh Judge Institute of Dental Sciences and Hospital , Chandigarh, India
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Plasmid metagenomics reveals multiple antibiotic resistance gene classes among the gut microbiomes of hospitalised patients. J Glob Antimicrob Resist 2016; 6:57-66. [DOI: 10.1016/j.jgar.2016.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/29/2016] [Accepted: 03/05/2016] [Indexed: 01/09/2023] Open
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18
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Schkarpetkin D, Reise M, Wyrwa R, Völpel A, Berg A, Schweder M, Schnabelrauch M, Watts DC, Sigusch BW. Development of novel electrospun dual-drug fiber mats loaded with a combination of ampicillin and metronidazole. Dent Mater 2016; 32:951-60. [PMID: 27262200 DOI: 10.1016/j.dental.2016.05.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/08/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVE Our study was performed with the aim of preparing electrospun polylactide fibers with a combination of ampicillin (AMP) and metronidazole (MNZ) and investigating their drug release behavior and the antibacterial effect on Aggregatibacter actinomycetemcomitans and other oral pathogens. METHODS AMP and MNZ were integrated as a combination in two separate fibers (dual fiber mats - DFW mix) of electrospun PLA fiber mats by means of multijet electrospinning and in a single fiber (single fiber mats - SFW mix). HPLC (high-performance liquid chromatography) was used to measure the released drug quantities. Agar diffusion tests were used to determine the antibacterial effect of the eluates on A. actinomycetemcomitans, Fusobacterium nucleatum, Porphyromonas gingivalis and Enterococcus faecalis. The neutral red test was made to examine the cytocompatibility of the eluates with human gingival fibroblasts (hGFs). RESULTS The release of the active agents varied with the antibiotic concentrations initially used in the fiber mats, but also with the distribution of the active agents in one or two fibers. Of the total quantity of MNZ (AMP), the SFW mix fiber mats released >60% (>70%) within a span of 5min, and 76% (71%) after 96h. With these drug concentrations released by the fiber mats (≥5m%), an antibacterial effect was achieved on A. actinomycetemcomitans and on all other species tested. Fiber mats and their eluates have no cytotoxic influence on human gingival fibroblasts (hGFs). SIGNIFICANCE Electrospun AMP/MNZ-loaded polymer fibers are a potential drug delivery system for use in periodontal and endodontic infections.
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Affiliation(s)
- Dennis Schkarpetkin
- Department of Conservative Dentistry and Periodontology, Jena University Hospital, An der Alten Post 4, 07743 Jena, Germany
| | - Markus Reise
- Department of Conservative Dentistry and Periodontology, Jena University Hospital, An der Alten Post 4, 07743 Jena, Germany.
| | - Ralf Wyrwa
- Department of Biomaterials, INNOVENT e.V., Prüssingstrasse 27B, 07743 Jena, Germany
| | - Andrea Völpel
- Department of Conservative Dentistry and Periodontology, Jena University Hospital, An der Alten Post 4, 07743 Jena, Germany
| | - Albrecht Berg
- Department of Biomaterials, INNOVENT e.V., Prüssingstrasse 27B, 07743 Jena, Germany
| | - Martina Schweder
- Department of Biomaterials, INNOVENT e.V., Prüssingstrasse 27B, 07743 Jena, Germany
| | | | - David C Watts
- University of Manchester, School of Dentistry and Photon Science Institute, Manchester M13 9PL, UK
| | - Bernd W Sigusch
- Department of Conservative Dentistry and Periodontology, Jena University Hospital, An der Alten Post 4, 07743 Jena, Germany
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19
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Morroni G, Di Cesare A, Di Sante L, Brenciani A, Vignaroli C, Pasquaroli S, Giovanetti E, Sabatino R, Rossi L, Magnani M, Biavasco F. Enterococcus faecium ST17 from Coastal Marine Sediment Carrying Transferable Multidrug Resistance Plasmids. Microb Drug Resist 2016; 22:523-530. [PMID: 26982016 DOI: 10.1089/mdr.2015.0222] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The multidrug-resistant Enterococcus faecium 17i48, sequence type 17, from marine sediment, carrying erm(B), tet(M), and tet(L) genes, was analyzed for the presence of antibiotic resistance plasmids and for the ability to transfer resistance genes. The strain was found to harbor the replicon type (repA) of pRE25, pRUM, pHTβ, and the axe-txe toxin-antitoxin (TA) system. In mating experiments, tet(M) and tet(L) were cotransferred with the repApRE25, whereas erm(B) was consistently cotransferred with the axe-txe and repApRUM, suggesting that tetracycline and erythromycin resistance genes were carried on different elements both transferable by conjugation, likely via pHTβ-mediated mobilization. Hybridization and PCR mapping demonstrated that tet(M) and tet(L) were located in tandem on a pDO1-like plasmid that also carried the repApRE25, whereas erm(B) was carried by a pRUM-like plasmid. Sequencing of the latter plasmid showed a high nucleotide identity with pRUM and the presence of cat, aadE, sat4, and a complete aphA resistance genes. These findings show that the genetic features of E. faecium 17i48 are consistent with a hospital-adapted clone and suggest that antibiotic resistance may spread in the environment, also in the absence of antibiotic pressure, due to TA system plasmid maintenance.
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Affiliation(s)
- Gianluca Morroni
- 1 Department of Biomedical Sciences and Public Health, Polytechnic University of Marche , Ancona, Italy
| | - Andrea Di Cesare
- 2 Department of Life and Environmental Sciences, Polytechnic University of Marche , Ancona, Italy
| | - Laura Di Sante
- 2 Department of Life and Environmental Sciences, Polytechnic University of Marche , Ancona, Italy
| | - Andrea Brenciani
- 1 Department of Biomedical Sciences and Public Health, Polytechnic University of Marche , Ancona, Italy
| | - Carla Vignaroli
- 2 Department of Life and Environmental Sciences, Polytechnic University of Marche , Ancona, Italy
| | - Sonia Pasquaroli
- 2 Department of Life and Environmental Sciences, Polytechnic University of Marche , Ancona, Italy
| | - Eleonora Giovanetti
- 2 Department of Life and Environmental Sciences, Polytechnic University of Marche , Ancona, Italy
| | - Raffaella Sabatino
- 3 Biochemistry and Molecular Biology Section, Department of Biomolecular Sciences, University of Urbino "Carlo Bo," Urbino, Italy
| | - Luigia Rossi
- 3 Biochemistry and Molecular Biology Section, Department of Biomolecular Sciences, University of Urbino "Carlo Bo," Urbino, Italy
| | - Mauro Magnani
- 3 Biochemistry and Molecular Biology Section, Department of Biomolecular Sciences, University of Urbino "Carlo Bo," Urbino, Italy
| | - Francesca Biavasco
- 2 Department of Life and Environmental Sciences, Polytechnic University of Marche , Ancona, Italy
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20
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Dib JR, Wagenknecht M, Farías ME, Meinhardt F. Strategies and approaches in plasmidome studies-uncovering plasmid diversity disregarding of linear elements? Front Microbiol 2015; 6:463. [PMID: 26074886 PMCID: PMC4443254 DOI: 10.3389/fmicb.2015.00463] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 04/28/2015] [Indexed: 01/01/2023] Open
Abstract
The term plasmid was originally coined for circular, extrachromosomal genetic elements. Today, plasmids are widely recognized not only as important factors facilitating genome restructuring but also as vehicles for the dissemination of beneficial characters within bacterial communities. Plasmid diversity has been uncovered by means of culture-dependent or -independent approaches, such as endogenous or exogenous plasmid isolation as well as PCR-based detection or transposon-aided capture, respectively. High-throughput-sequencing made possible to cover total plasmid populations in a given environment, i.e., the plasmidome, and allowed to address the quality and significance of self-replicating genetic elements. Since such efforts were and still are rather restricted to circular molecules, here we put equal emphasis on the linear plasmids which—despite their frequent occurrence in a large number of bacteria—are largely neglected in prevalent plasmidome conceptions.
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Affiliation(s)
- Julián R Dib
- Planta Piloto de Procesos Industriales Microbiológicos-Consejo Nacional de Investigaciones Científicas y Técnicas , Tucumán, Argentina ; Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster, Germany ; Instituto de Microbiología, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán , Tucumán, Argentina
| | - Martin Wagenknecht
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster, Germany ; Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität Münster , Münster, Germany
| | - María E Farías
- Planta Piloto de Procesos Industriales Microbiológicos-Consejo Nacional de Investigaciones Científicas y Técnicas , Tucumán, Argentina
| | - Friedhelm Meinhardt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster , Münster, Germany
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Shintani M, Sanchez ZK, Kimbara K. Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy. Front Microbiol 2015; 6:242. [PMID: 25873913 PMCID: PMC4379921 DOI: 10.3389/fmicb.2015.00242] [Citation(s) in RCA: 213] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 03/12/2015] [Indexed: 12/21/2022] Open
Abstract
Plasmids are important "vehicles" for the communication of genetic information between bacteria. The exchange of plasmids transmits pathogenically and environmentally relevant traits to the host bacteria, promoting their rapid evolution and adaptation to various environments. Over the past six decades, a large number of plasmids have been identified and isolated from different microbes. With the revolution of sequencing technology, more than 4600 complete sequences of plasmids found in bacteria, archaea, and eukaryotes have been determined. The classification of a wide variety of plasmids is not only important to understand their features, host ranges, and microbial evolution but is also necessary to effectively use them as genetic tools for microbial engineering. This review summarizes the current situation of the classification of fully sequenced plasmids based on their host taxonomy and their features of replication and conjugative transfer. The majority of the fully sequenced plasmids are found in bacteria in the Proteobacteria, Firmicutes, Spirochaetes, Actinobacteria, Cyanobacteria and Euryarcheota phyla, and key features of each phylum are included. Recent advances in the identification of novel types of plasmids and plasmid transfer by culture-independent methods using samples from natural environments are also discussed.
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Affiliation(s)
- Masaki Shintani
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Shizuoka, Japan ; Department of Bioscience, Graduate School of Science and Technology, Shizuoka University Shizuoka, Japan
| | - Zoe K Sanchez
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Shizuoka, Japan
| | - Kazuhide Kimbara
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University Shizuoka, Japan
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22
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Roberts AP, Kreth J. The impact of horizontal gene transfer on the adaptive ability of the human oral microbiome. Front Cell Infect Microbiol 2014; 4:124. [PMID: 25250243 PMCID: PMC4157583 DOI: 10.3389/fcimb.2014.00124] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/19/2014] [Indexed: 02/06/2023] Open
Abstract
The oral microbiome is composed of a multitude of different species of bacteria, each capable of occupying one or more of the many different niches found within the human oral cavity. This community exhibits many types of complex interactions which enable it to colonize and rapidly respond to changes in the environment in which they live. One of these interactions is the transfer, or acquisition, of DNA within this environment, either from co-resident bacterial species or from exogenous sources. Horizontal gene transfer in the oral cavity gives some of the resident bacteria the opportunity to sample a truly enormous metagenome affording them considerable adaptive potential which may be key to survival in such a varying environment. In this review the underlying mechanisms of HGT are discussed in relation to the oral microbiome with numerous examples described where the direct acquisition of exogenous DNA has contributed to the fitness of the bacterial host within the human oral cavity.
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Affiliation(s)
- Adam P Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London London, UK
| | - Jens Kreth
- Department of Microbiology and Immunology, College of Medicine, University of Oklahoma Health Sciences Center Oklahoma City, OK, USA
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23
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Yamashita A, Sekizuka T, Kuroda M. Characterization of Antimicrobial Resistance Dissemination across Plasmid Communities Classified by Network Analysis. Pathogens 2014; 3:356-76. [PMID: 25437804 PMCID: PMC4243450 DOI: 10.3390/pathogens3020356] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 04/04/2014] [Accepted: 04/09/2014] [Indexed: 12/17/2022] Open
Abstract
The global clustering of gene families through network analysis has been demonstrated in whole genome, plasmid, and microbiome analyses. In this study, we carried out a plasmidome network analysis of all available complete bacterial plasmids to determine plasmid associations. A blastp clustering search at 100% aa identity cut-off and sharing at least one gene between plasmids, followed by a multilevel community network analysis revealed that a surprisingly large number of the plasmids were connected by one largest connected component (LCC), with dozens of community sub-groupings. The LCC consisted mainly of Bacilli and Gammaproteobacteria plasmids. Intriguingly, horizontal gene transfer (HGT) was noted between different phyla (i.e., Staphylococcus and Pasteurellaceae), suggesting that Pasteurellaceae can acquire antimicrobial resistance (AMR) genes from closely contacting Staphylococcus spp., which produce the external supplement of V-factor (NAD). Such community network analysis facilitate displaying possible recent HGTs like a class 1 integron, str and tet resistance markers between communities. Furthermore, the distribution of the Inc replicon type and AMR genes, such as the extended-spectrum ß-lactamase (ESBL) CTX-M or the carbapenemases KPC NDM-1, implies that such genes generally circulate within limited communities belonging to typical bacterial genera. Thus, plasmidome network analysis provides a remarkable discriminatory power for plasmid-related HGT and evolution.
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Affiliation(s)
- Akifumi Yamashita
- Pathogen Genomics Center, National institute of infectious diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National institute of infectious diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
| | - Makoto Kuroda
- Pathogen Genomics Center, National institute of infectious diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640, Japan.
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Wardal E, Gawryszewska I, Hryniewicz W, Sadowy E. Abundance and diversity of plasmid-associated genes among clinical isolates of Enterococcus faecalis. Plasmid 2013; 70:329-42. [PMID: 23906674 DOI: 10.1016/j.plasmid.2013.07.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Revised: 07/18/2013] [Accepted: 07/21/2013] [Indexed: 11/18/2022]
Abstract
Enterococcus faecalis, a normal compound of the human intestinal microbiome, plays an important role in hospital-acquired infections. Plasmids make a significant contribution to the acquisition of the novel traits such as antimicrobial resistance and virulence by this pathogen. The study investigated the plasmid content and the diversity of plasmid-associated genes in a group of 152 hospital isolates of E. faecalis. The majority of plasmids visualized by pulsed-field gel electrophoresis of S1 nuclease-digested DNA fell into the range of 50-100 kb. PCR-based screening allowed detection of genes of the rep1(pIP501), rep2(pRE25), rep4(pMBB1), rep6(pS86), rep7(pT181), rep8(pAM373), rep9(pAD1/pTEF2/pCF10), rep10(pIM13) and rep13(pC194) families in 29 different combinations. The par and ω-ε-ζ plasmid stabilization systems were ubiquitous (45 isolates, 29.6% and 88 isolates, 57.9%, respectively), while the axe-txe system was not found. The asa1 gene homologues encoding aggregation substance characteristic for the pAD1 and related group of pheromone-responsive plasmids were present in 106 isolates. A variety of sequence variants, including novel ones, of genes associated with pheromone-responsive plasmids, such as rep8(pAM373), rep9(pAD1/pTEF2/pCF10), par, and asa1 were observed. In conclusion, there is a big and only partially characterized pool of diverse plasmids in clinical E. faecalis.
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Affiliation(s)
- Ewa Wardal
- National Medicines Institute, ul. Chełmska 30/34, 00-725 Warsaw, Poland.
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