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Viteri-Dávila C, Morales-Jadán D, Creel A, Jop Vidal AG, Boldo XM, Rivera-Olivero IA, Bautista-Muñoz C, Alibayov B, Garcia-Bereguiain MÁ, Vidal JE. The Crisis of Macrolide Resistance in Pneumococci in Latin America. Am J Trop Med Hyg 2024; 111:756-764. [PMID: 39084209 PMCID: PMC11448541 DOI: 10.4269/ajtmh.23-0913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/24/2024] [Indexed: 08/02/2024] Open
Abstract
Macrolide antibiotics are recommended for the treatment of pneumococcal pneumonia and invasive pneumococcal disease (IPD). Prior to 2000, ∼10% of Streptococcus pneumoniae strains isolated from IPD cases in Latin American countries were resistant to macrolides. The mechanism of resistance to macrolides was associated mainly with the efflux pump known as the macrolide efflux genetic assembly, since most pneumococcal strains carried the mef(A/E) gene, whereas <6% strains carried both the methylase gene ermB and mef(A/E). In the first decade of this century, a significant increase in the prevalence of macrolide resistance was observed in pneumococcal strains in both Mexico and Peru. Approximately 30% of S. pneumoniae strains in these countries were already resistant to erythromycin, while the prevalence in Colombia, Argentina, and Brazil remained below 10%. During the last decade, we have been experiencing a worrisome increase in pneumococcal strains carrying resistance to macrolides, with a prevalence of up to 80% for resistance to erythromycin. The mechanism for disseminating macrolide resistance has evolved. Currently, more than 55% of invasive S. pneumoniae macrolide-resistant strains carry both the ermB and the mef(A/E)/mel genes. Lessons learned from the current macrolide resistance crisis in Latin America can inform interventions in other regions.
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Affiliation(s)
| | | | - Aidan Creel
- Summer Undergraduate Research Experience Program, School of Graduate Studies in the Health Sciences, University of Mississippi Medical Center, Jackson, Mississippi
| | - Ana G. Jop Vidal
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi
| | - Xavier M. Boldo
- Research Center, Health Sciences Academic Division, Juarez Autonomous University of Tabasco, Villahermosa, Mexico
| | | | | | - Babek Alibayov
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi
| | | | - Jorge E. Vidal
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, Mississippi
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2
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Maladan Y, Retnaningrum E, Daryono BS, Salsabila K, Sarassari R, Khoeri MM, Sari RF, Balqis SA, Wahid GA, Safari D. Pneumococcal transposon profiling associated with macrolide, tetracycline, and chloramphenicol resistance from carriage isolates of serotype 19F in Indonesia. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 125:105672. [PMID: 39313084 DOI: 10.1016/j.meegid.2024.105672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/22/2024] [Accepted: 09/20/2024] [Indexed: 09/25/2024]
Abstract
Genetic evolution of resistance due to mutations and transposon insertions is the primary cause of antimicrobial resistance in Streptococcus pneumoniae. Resistance to macrolide, tetracycline, and chloramphenicol is caused by the insertion of specific genes that carried by transposon (Tn). This study aims to analyze transposon profiling associated with macrolide, tetracycline, and chloramphenicol resistance from carriage isolates of S. pneumoniae serotype 19F in Indonesia. S. pneumoniae serotype 19F isolates were collected from nasopharyngeal swab specimens from different regions in Indonesia. Genomic DNA was extracted from sixteen isolates and whole genome sequencing was performed on Illumina platform. Raw sequence data were analyzed using de novo assembly by ASA3P and Microscope server. The presence of transposons was identified with detection of int and xis genes and visualized by pyGenomeViz. The genome size of S. pneumoniae ranges from 2,040,117 bp to 2,437,939 bp, with a GC content of around 39 %. ST1464 (4/16) and ST271 (3/16) were found as the predominant sequence type among isolates. Tn2010 was the most common transposon among S. pneumoniae serotype 19F isolates (7/16) followed by Tn2009 (4/16), and Tn5253 (3/16). We identified two deletion sites within the tetM gene (2 bp and 58 bp) that confer tetracycline susceptibility from one isolate. This study suggests that genomic analysis can be employed for the detection and surveillance of antimicrobial resistance genes among S. pneumoniae strains isolated from various regions in Indonesia.
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Affiliation(s)
- Yustinus Maladan
- Biology Doctoral Students, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia; Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong Science Center, Bogor, Indonesia
| | - Endah Retnaningrum
- Microbiology Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia.
| | - Budi Setiadi Daryono
- Genetics Laboratory, Faculty of Biology, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Korrie Salsabila
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong Science Center, Bogor, Indonesia
| | - Rosantia Sarassari
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong Science Center, Bogor, Indonesia
| | - Miftahuddin Majid Khoeri
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong Science Center, Bogor, Indonesia; Doctoral program in Biomedical, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | - Ratna Fathma Sari
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong Science Center, Bogor, Indonesia
| | - Sarah Azhari Balqis
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong Science Center, Bogor, Indonesia
| | - Ghina Athyah Wahid
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong Science Center, Bogor, Indonesia
| | - Dodi Safari
- Eijkman Research Center for Molecular Biology, The National Research and Innovation Agency, Cibinong Science Center, Bogor, Indonesia.
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Wu X, Alibayov B, Xiang X, Lattar SM, Sakai F, Medders AA, Antezana BS, Keller LE, Vidal AGJ, Tzeng YL, Robinson DA, Stephens DS, Yu Y, Vidal JE. Ultrastructural, metabolic and genetic characteristics of determinants facilitating the acquisition of macrolide resistance by Streptococcus pneumoniae. Drug Resist Updat 2024; 77:101138. [PMID: 39167981 DOI: 10.1016/j.drup.2024.101138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 08/13/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024]
Abstract
AIMS To investigate the molecular events associated with acquiring macrolide resistance genes [mefE/mel (Mega) or ermB] in Streptococcus pneumoniae (Spn) during nasopharyngeal colonization. METHODS AND RESULTS Genomic analysis of 128 macrolide-resistant Spn isolates revealed recombination events in genes of the conjugation apparatus, or the competence system, in strains carrying Tn916-related elements. Studies using confocal and electron microscopy demonstrated that during the transfer of Tn916-related elements in nasopharyngeal cell biofilms, pneumococcal strains formed clusters facilitating their acquisition of resistance determinants at a high recombination frequency (rF). Remarkably, these aggregates comprise both encapsulated and nonencapsulated pneumococci that span extracellular and intracellular compartments. rF assessments showed similar rates regardless Mega was associated with large integrative and conjugative elements (ICEs) (>23 kb) or not (∼5.4 kb). The rF for Mega Class IV(c) insertion region (∼53 kb) was three orders of magnitude higher than the transformation of the capsule locus. Metabolomics studies of the microenvironment created by colonization of human nasopharyngeal cells revealed a link between the acquisition of ICEs and the pathways involving nicotinic acid and sucrose. CONCLUSIONS Pneumococcal clusters, both extracellular and intracellular, facilitate macrolide resistance acquisition, and ICEs were acquired at a higher frequency than the capsule locus. Metabolic changes could serve as intervention targets.
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Affiliation(s)
- Xueqing Wu
- Department of Infectious Diseases, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, China
| | - Babek Alibayov
- Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Xi Xiang
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Santiago M Lattar
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, United States
| | - Fuminori Sakai
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, United States
| | - Austin A Medders
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Brenda S Antezana
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, United States; Graduate Program in Microbiology and Molecular Genetics, Emory University, Atlanta, GA 30322, United States
| | - Lance E Keller
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States; Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Ana G J Vidal
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - Yih-Ling Tzeng
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, United States; Graduate Program in Microbiology and Molecular Genetics, Emory University, Atlanta, GA 30322, United States
| | - D Ashley Robinson
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States; Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS 39216, United States
| | - David S Stephens
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, United States; Graduate Program in Microbiology and Molecular Genetics, Emory University, Atlanta, GA 30322, United States
| | - Yunsong Yu
- Department of Infectious Diseases, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China; Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, China.
| | - Jorge E Vidal
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, MS 39216, United States; Center for Immunology and Microbial Research, University of Mississippi Medical Center, Jackson, MS 39216, United States.
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Wu X, Alibayov B, Xiang X, Lattar SM, Sakai F, Medders AA, Antezana B, Keller L, Vidal AGJ, Tzeng YL, Robinson DA, Stephens D, Yu Y, Vidal JE. Ultrastructural, metabolic and genetic determinants of the acquisition of macrolide resistance by Streptococcus pneumoniae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.27.573471. [PMID: 38234816 PMCID: PMC10793443 DOI: 10.1101/2023.12.27.573471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Aim Streptococcus pneumoniae (Spn) acquires genes for macrolide resistance, MEGA or ermB, in the human host. These genes are carried either in the chromosome, or on integrative conjugative elements (ICEs). Here, we investigated molecular determinants of the acquisition of macrolide resistance. Methods and Results Whole genome analysis was conducted for 128 macrolide-resistant pneumococcal isolates to identify the presence of MEGA (44.5%, 57/128) or ermB (100%), and recombination events in Tn916-related elements or in the locus comCDE encoding competence genes. Confocal and electron microscopy studies demonstrated that, during the acquisition of macrolide resistance, pneumococcal strains formed clusters of varying size, with the largest aggregates having a median size of ~1600 μm2. Remarkably, these pneumococcal aggregates comprise both encapsulated and nonencapsulated pneumococci, exhibited physical interaction, and spanned extracellular and intracellular compartments. We assessed the recombination frequency (rF) for the acquisition of macrolide resistance by a recipient D39 strain, from pneumococcal strains carrying MEGA (~5.4 kb) in the chromone, or in large ICEs (>23 kb). Notably, the rF for the acquisition of MEGA, whether in the chromosome or carried on an ICE was similar. However, the rF adjusted to the acquisition of the full-length ICE (~52 kb), compared to that of the capsule locus (~23 kb) that is acquired by transformation, was three orders of magnitude higher. Finally, metabolomics studies revealed a link between the acquisition of ICE and the metabolic pathways involving nicotinic acid and sucrose. Conclusions Extracellular and intracellular pneumococcal clusters facilitate the acquisition of full-length ICE at a rF higher than that of typical transformation events, involving distinct metabolic changes that present potential targets for interventions.
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Affiliation(s)
- Xueqing Wu
- Department of Infectious Diseases, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, China
| | - Babek Alibayov
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - Xi Xiang
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Santiago M. Lattar
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA 30322, United States
| | - Fuminori Sakai
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta GA 30322, United States
| | - Austin A. Medders
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - Brenda Antezana
- Department of Medicine, School of Medicine, Emory University, Atlanta GA 30322, United States
| | - Lance Keller
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - Ana G. J. Vidal
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - Yih-Ling Tzeng
- Department of Medicine, School of Medicine, Emory University, Atlanta GA 30322, United States
| | - D. Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
| | - David Stephens
- Department of Medicine, School of Medicine, Emory University, Atlanta GA 30322, United States
| | - Yunsong Yu
- Department of Infectious Diseases, Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310052, China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou 310052, China
| | - Jorge E. Vidal
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson MS 39056, United States
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Fox V, Santoro F, Apicella C, Diaz-Diaz S, Rodriguez-Martínez JM, Iannelli F, Pozzi G. The mef(A)/ msr(D)-carrying streptococcal prophage Φ1207.3 encodes an SOS-like system, induced by UV-C light, responsible for increased survival and increased mutation rate. J Bacteriol 2023; 205:e0019123. [PMID: 37695857 PMCID: PMC10521357 DOI: 10.1128/jb.00191-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/04/2023] [Indexed: 09/13/2023] Open
Abstract
Bacterial SOS response is an inducible system of DNA repair and mutagenesis. Streptococci lack a canonical SOS response, but an SOS-like response was reported in some species. The mef(A)-msr(D)-carrying prophage Ф1207.3 of Streptococcus pyogenes contains a region, spanning orf6 to orf11, showing homology to characterized streptococcal SOS-like cassettes. Genome-wide homology search showed the presence of the whole Φ1207.3 SOS-like cassette in three S. pyogenes prophages, while parts of it were found in other bacterial species. To investigate whether this cassette confers an SOS-mutagenesis phenotype, we constructed Streptococcus pneumoniae R6 isogenic derivative strains: (i) FR172, streptomycin resistant, (ii) FR173, carrying Φ1207.3, and (iii) FR174, carrying a recombinant Φ1207.3, where the SOS-like cassette was deleted. These strains were used in survival and mutation rate assays using a UV-C LED instrument, for which we designed and 3D-printed a customized equipment, constituted of an instrument support and swappable-autoclavable mini-plates and lids. Upon exposure to UV fluences ranging from 0 to 6,400 J/m2 at four different wavelengths, 255, 265, 275, and 285 nm, we found that the presence of Φ1207.3 SOS-like cassette increases bacterial survival up to 34-fold. Mutation rate was determined by measuring rifampicin resistance acquisition upon exposure to UV fluence of 50 J/m2 at the four wavelengths by fluctuation test. The presence of Φ1207.3 SOS-like cassette resulted in a significant increase in the mutation rate (up to 18-fold) at every wavelength. In conclusion, we demonstrated that Φ1207.3 carries a functional SOS-like cassette responsible for an increased survival and increased mutation rate in S. pneumoniae. IMPORTANCE Bacterial mutation rate is generally low, but stress conditions and DNA damage can induce stress response systems, which allow for improved survival and continuous replication. The SOS response is a DNA repair mechanism activated by some bacteria in response to stressful conditions, which leads to a temporary hypermutable phenotype and is usually absent in streptococcal genomes. Here, using a reproducible and controlled UV irradiation system, we demonstrated that the SOS-like gene cassette of prophage Φ1207.3 is functional, responsible for a temporary hypermutable phenotype, and enhances bacterial survival to UV irradiation. Prophage Φ1207.3 also carries erythromycin resistance genes and can lysogenize different pathogenic bacteria, constituting an example of a mobile genetic element which can confer multiple phenotypes to its host.
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Affiliation(s)
- Valeria Fox
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Carmen Apicella
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sara Diaz-Diaz
- Unidad Clínica de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospital Universitario Virgen Macarena, Sevilla, Spain
| | | | - Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gianni Pozzi
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena, Siena, Italy
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Fostier CR, Ousalem F, Leroy EC, Ngo S, Soufari H, Innis CA, Hashem Y, Boël G. Regulation of the macrolide resistance ABC-F translation factor MsrD. Nat Commun 2023; 14:3891. [PMID: 37393329 PMCID: PMC10314930 DOI: 10.1038/s41467-023-39553-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 06/19/2023] [Indexed: 07/03/2023] Open
Abstract
Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors that provide resistance against clinically important ribosome-targeting antibiotics which are proliferating among pathogens. Here, we combine genetic and structural approaches to determine the regulation of streptococcal ARE ABC-F gene msrD in response to macrolide exposure. We show that binding of cladinose-containing macrolides to the ribosome prompts insertion of the leader peptide MsrDL into a crevice of the ribosomal exit tunnel, which is conserved throughout bacteria and eukaryotes. This leads to a local rearrangement of the 23 S rRNA that prevents peptide bond formation and accommodation of release factors. The stalled ribosome obstructs the formation of a Rho-independent terminator structure that prevents msrD transcriptional attenuation. Erythromycin induction of msrD expression via MsrDL, is suppressed by ectopic expression of mrsD, but not by mutants which do not provide antibiotic resistance, showing correlation between MsrD function in antibiotic resistance and its action on this stalled complex.
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Affiliation(s)
- Corentin R Fostier
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Farès Ousalem
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Elodie C Leroy
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Saravuth Ngo
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France
| | - Heddy Soufari
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
- SPT Labtech Ltd., SG8 6HB, Melbourn, United Kingdom
| | - C Axel Innis
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France
| | - Yaser Hashem
- ARNA Laboratory, UMR 5320, U1212, Institut Européen de Chimie et Biologie, Univ. Bordeaux, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, 33607, Pessac, France.
| | - Grégory Boël
- Expression Génétique Microbienne, CNRS, Université Paris Cité, Institut de Biologie Physico-Chimique, 75005, Paris, France.
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Antezana BS, Lohsen S, Wu X, Vidal JE, Tzeng YL, Stephens DS. Dissemination of Tn 916-Related Integrative and Conjugative Elements in Streptococcus pneumoniae Occurs by Transformation and Homologous Recombination in Nasopharyngeal Biofilms. Microbiol Spectr 2023; 11:e0375922. [PMID: 36912669 PMCID: PMC10101023 DOI: 10.1128/spectrum.03759-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/02/2023] [Indexed: 03/14/2023] Open
Abstract
Multidrug resistance in Streptococcus pneumoniae (or pneumococcus) continues to be a global challenge. An important class of antibiotic resistance determinants disseminating in S. pneumoniae are >20-kb Tn916-related integrative and conjugative elements (ICEs), such as Tn2009, Tn6002, and Tn2010. Although conjugation has been implicated as the transfer mechanism for ICEs in several bacteria, including S. pneumoniae, the molecular basis for widespread dissemination of pneumococcal Tn916-related ICEs remains to be fully elucidated. We found that Tn2009 acquisition was not detectable via in vitro transformation nor conjugative mating with donor GA16833, yielding a transfer frequency of <10-7. GA16833 Tn2009 conjugative gene expression was not significantly induced, and ICE circular intermediate formation was not detected in biofilms. Consistently, Tn2009 transfer efficiency in biofilms was not affected by deletion of the ICE conjugative gene ftsK. However, GA16833 Tn2009 transfer occurred efficiently at a recombination frequency (rF) of 10-4 in dual-strain biofilms formed in a human nasopharyngeal cell bioreactor. DNase I addition and deletions of the early competence gene comE or transformation apparatus genes comEA and comEC in the D39 recipient strain prevented Tn2009 acquisition (rF of <10-7). Genome sequencing and single nucleotide polymorphism analyses of independent recombinants of recipient genotype identified ~33- to ~55-kb donor DNAs containing intact Tn2009, supporting homologous recombination. Additional pneumococcal donor and recipient combinations were demonstrated to efficiently transfer Tn916-related ICEs at a rF of 10-4 in the biofilms. Tn916-related ICEs horizontally disseminate at high frequency in human nasopharyngeal S. pneumoniae biofilms by transformation and homologous recombination of >30-kb DNA fragments into the pneumococcal genome. IMPORTANCE The World Health Organization has designated Streptococcus pneumoniae as a priority pathogen for research and development of new drug treatments due to extensive multidrug resistance. Multiple strains of S. pneumoniae colonize and form mixed biofilms in the human nasopharynx, which could enable exchange of antibiotic resistance determinants. Tn916-related integrative and conjugative elements (ICEs) are largely responsible for the widespread presence of macrolide and tetracycline resistance in S. pneumoniae. Utilizing a system that simulates colonization of donor and recipient S. pneumoniae strains in the human nasopharynx, efficient transfer of Tn916-related ICEs occurred in human nasopharyngeal biofilms, in contrast to in vitro conditions of planktonic cells with exogenous DNA. This high-frequency Tn916-related ICE transfer between S. pneumoniae strains in biofilms was due to transformation and homologous recombination, not conjugation. Understanding the molecular mechanism for dissemination of Tn916-related ICEs can facilitate the design of new strategies to combat antibiotic resistance.
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Affiliation(s)
- Brenda S. Antezana
- Microbiology and Molecular Genetics Program, Graduate Division of Biological and Biomedical Sciences, Emory University Laney Graduate School, Atlanta, Georgia, USA
| | - Sarah Lohsen
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Xueqing Wu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine, Hangzhou, China
| | - Jorge E. Vidal
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Yih-Ling Tzeng
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David S. Stephens
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, USA
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Min J, Kim P, Yun S, Hong M, Park W. Zoo animal manure as an overlooked reservoir of antibiotic resistance genes and multidrug-resistant bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:710-726. [PMID: 35906519 DOI: 10.1007/s11356-022-22279-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
Animal fecal samples collected in the summer and winter from 11 herbivorous animals, including sable antelope (SA), long-tailed goral (LTG), and common eland (CE), at a public zoo were examined for the presence of antibiotic resistance genes (ARGs). Seven antibiotics, including meropenem and azithromycin, were used to isolate culturable multidrug-resistant (MDR) strains. The manures from three animals (SA, LTG, and CE) contained 104-fold higher culturable MDR bacteria, including Chryseobacterium, Sphingobacterium, and Stenotrophomonas species, while fewer MDR bacteria were isolated from manure from water buffalo, rhinoceros, and elephant against all tested antibiotics. Three MDR bacteria-rich samples along with composite samples were further analyzed using nanopore-based technology. ARGs including lnu(C), tet(Q), and mef(A) were common and often associated with transposons in all tested samples, suggesting that transposons carrying ARGs may play an important role for the dissemination of ARGs in our tested animals. Although several copies of ARGs such as aph(3')-IIc, blaL1, blaIND-3, and tet(42) were found in the sequenced genomes of the nine MDR bacteria, the numbers and types of ARGs appeared to be less than expected in zoo animal manure, suggesting that MDR bacteria in the gut of the tested animals had intrinsic resistant phenotypes in the absence of ARGs.
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Affiliation(s)
- Jihyeon Min
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Pureun Kim
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Sohyeon Yun
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Minyoung Hong
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Woojun Park
- Laboratory of Molecular Environmental Microbiology, Department of Environmental Science and Ecological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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Johannessen H, Anthonisen IL, Zecic N, Hegstad K, Ranheim TE, Skaare D. Characterization and Fitness Cost of Tn7100, a Novel Integrative and Conjugative Element Conferring Multidrug Resistance in Haemophilus influenzae. Front Microbiol 2022; 13:945411. [PMID: 35935209 PMCID: PMC9355037 DOI: 10.3389/fmicb.2022.945411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 06/16/2022] [Indexed: 12/15/2022] Open
Abstract
A multidrug-resistant (MDR) strain of Haemophilus influenzae, Hi-228, with phenotypic resistance toward ampicillin, cefotaxime, chloramphenicol, gentamicin, and azithromycin, was isolated in Oslo, Norway. The strain was part of a clonal outbreak (2016–2017) comprising five ST143 strains with identical resistotypes. Hi-228 carries a novel integrative and conjugative element (ICE), Tn7100, contributing to this remarkable and previously unreported MDR profile. Tn7100 contains the following resistance genes: blaTEM−1B, catA2, aac(6′)-Im, aph(2″)-Ib, mef (E), and mel. The latter four are previously unreported or rarely reported in H. influenzae. In this study, we investigated the genetic environment, mechanisms of transfer, impact on phenotypic susceptibility, and fitness cost of this ICE. We found that Tn7100 has an overall structure similar to the previously described ICE Tn6686, with blaTEM−1B and catA2 carried by Tn3 and Tn10, respectively. The major difference between Tn7100 and Tn6686 is that Tn7100 lacks tet(B) but carries the resistance gene pairs aac(6′)-Im and aph(2″)-Ib and mef (E) and mel. The gene pairs are located on the novel transposable elements Tn7470 and Tn7471, which have high sequence identities to a plasmid in Enterobacterales and an ICE in streptococcal species, respectively. Tn7100 does circularize and is transferable, however, at a low frequency. Head-to-head competition experiments showed that uptake of Tn7100 reduces bacterial fitness. Our study shows that MDR strains are capable of clonal spread and that the H. influenzae supragenome comprises an increasingly wide range of transferable resistance genes, with evidence of transfer from unrelated genera. The findings offer a glimpse into the genome dynamics of H. influenzae, highlighting the importance of rational antibiotic usage to contain antimicrobial resistance and the emergence of MDR strains in this important pathogen.
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Affiliation(s)
- Helene Johannessen
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
- *Correspondence: Helene Johannessen
| | | | - Nermin Zecic
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
| | - Kristin Hegstad
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
- Research Group for Host-Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | | | - Dagfinn Skaare
- Department of Microbiology, Vestfold Hospital Trust, Tønsberg, Norway
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Induction of the macrolide-resistance efflux pump Mega inhibits intoxication of Staphylococcus aureus strains by Streptococcus pneumoniae. Microbiol Res 2022; 263:127134. [PMID: 35905580 DOI: 10.1016/j.micres.2022.127134] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 07/06/2022] [Accepted: 07/13/2022] [Indexed: 11/21/2022]
Abstract
Streptococcus pneumoniae (Spn) kills Staphylococcus aureus (Sau) through a contact-dependent mechanism that is catalyzed by cations, including iron, to convert hydrogen peroxide (H2O2) to highly toxic hydroxyl radicals (•OH). There are two well-characterized ABC transporters that contribute to the pool of iron in Spn, named Pia and Piu. Some Spn strains have acquired genes mef(E)/mel encoding another ABC trasporter (Mega) that produces an inducible efflux pump for resistance to macrolides. In macrolide-resistant Spn clinical isolates the insertion of Mega class 1. IV and 2. IVc deleted the locus piaABCD and these strains were attenuated for intoxicating Sau. The goal of this study was to investigate if the disruption of iron acquisition, or the antimicrobial-resistance activity of Mega, contributed to inhibiting the killing mechanism. Neither depletion of iron with 2,2'-dipyridyl-d8 (DP) nor incubating with a double knockout mutant SpnΔpiaAΔpiuA, inhibited killing of Sau. Clinical Spn strains carrying Mega1. IV or Mega2. IVc showed a significant delay for killing Sau. An ex vivo recombination system was used to transfer Mega1. IV or Mega2. IVc to reference Spn strains, which was confirmed by whole genome sequencing, and recombinants TIGR4Mega2. IVc, D39Mega2. IVc, and D39Mega1. IV were delayed for killing Sau. We then compared Sau killing of selected Mega-carrying Spn strains when incubated with sub-inhibitory erythromycin (Mega-induced) or sub-inhibitory cefuroxime. Remarkably, killing of Sau was completely inhibited under the Mega-induced condition whereas incubation with cefuroxime did not interfere with killing. Both mef(E) and mel were upregulated > 400-fold, and spxB (encoding an enzyme responsible for production of most H2O2) was upregulated 14.2-fold, whereas transcription of the autolysin (lytA) gene was downregulated when incubated with erythromycin. We demonstrated that erythromycin induction of Mega inhibits the •OH-mediated intoxication of Sau and that the inhibition occurred at the post-translational level suggesting that an imbalance of ions in the membrane inhibits these reactions.
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Wang Y, Taylor SL, Choo JM, Papanicolas LE, Keating R, Hindmarsh K, Thomson RM, Morgan L, Rogers GB, Burr LD. Carriage and Transmission of Macrolide Resistance Genes in Patients With Chronic Respiratory Conditions and Their Close Contacts. Chest 2022; 162:56-65. [DOI: 10.1016/j.chest.2022.01.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 11/16/2022] Open
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Fox V, Santoro F, Pozzi G, Iannelli F. Predicted transmembrane proteins with homology to Mef(A) are not responsible for complementing mef(A) deletion in the mef(A)-msr(D) macrolide efflux system in Streptococcus pneumoniae. BMC Res Notes 2021; 14:432. [PMID: 34823574 PMCID: PMC8620141 DOI: 10.1186/s13104-021-05856-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
Objectives In streptococci, the type M resistance to macrolides is due to the mef(A)–msr(D) efflux transport system of the ATP-Binding cassette (ABC) superfamily, where it is proposed that mef(A) codes for the transmembrane channel and msr(D) for the two ATP-binding domains. Phage ϕ1207.3 of Streptococcus pyogenes, carrying the mef(A)–msr(D) gene pair, is able to transfer the macrolide efflux phenotype to Streptococcus pneumoniae. Deletion of mef(A) in pneumococcal ϕ1207.3-carrying strains did not affect erythromycin efflux. In order to identify candidate genes likely involved in complementation of mef(A) deletion, the Mef(A) amino acid sequence was used as probe for database searching. Results In silico analysis identified 3 putative candidates in the S. pneumoniae R6 genome, namely spr0971, spr1023 and spr1932. Isogenic deletion mutants of each candidate gene were constructed and used in erythromycin sensitivity assays to investigate their contribution to mef(A) complementation. Since no change in erythromycin sensitivity was observed compared to the parental strain, we produced double and triple mutants to assess the potential synergic activity of the selected genes. Also these mutants did not complement the mef(A) function. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05856-6.
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Affiliation(s)
- Valeria Fox
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Santoro
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gianni Pozzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Iannelli
- Department of Medical Biotechnologies, University of Siena, Siena, Italy.
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Lunde TM, Hjerde E, Al-Haroni M. Prevalence, diversity and transferability of the Tn 916-Tn 1545 family ICE in oral streptococci. J Oral Microbiol 2021; 13:1896874. [PMID: 33796228 PMCID: PMC7971310 DOI: 10.1080/20002297.2021.1896874] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Background: The Tn916-Tn1545 family of Integrative Conjugative Elements (ICE) are mobile genetic elements (MGEs) that play a role in the spread of antibiotic resistance genes. The Tn916 harbors the tetracycline resistance gene tet(M) and it has been reported in various bacterial species. The increase in the levels of tetracycline resistance among oral streptococci is of great concern primarily due to the abundance of these species in the oral cavity and their ability to act as reservoirs for antibiotic resistance genes.Methods: In the current study, we screened 100 Norwegian clinical oral streptococcal isolates for the presence and diversity of the Tn916-Tn1545 family. In addition, we investigated the transferability the elements, and the associated transfer frequencies.Results: We observed that 21 isolates harboured the Tn916-Tn1545 family and that two of these elements were the novel Tn6815 and Tn6816. The most prevalent member of the Tn916 -Tn1545 family observed in the Norwegian clinical oral streptococcal isolates was the wild type Tn916.Conclusion: The detection of other members of this family of ICE and varying transfer frequencies suggests high versatility of the Tn916 element in oral streptococci in Norway.
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Affiliation(s)
- Tracy Munthali Lunde
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø
| | - Erik Hjerde
- bCenter for Bioinformatics, Faculty of Science and Technology, UiT the Arctic University of Norway, Tromsø, Norway
| | - Mohammed Al-Haroni
- Department of Clinical Dentistry, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø
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14
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Penicillin-Binding Protein Typing, Antibiotic Resistance Gene Identification, and Molecular Phylogenetic Analysis of Meropenem-Resistant Streptococcus pneumoniae Serotype 19A-CC3111 Strains in Japan. Antimicrob Agents Chemother 2019; 63:AAC.00711-19. [PMID: 31235623 DOI: 10.1128/aac.00711-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 06/15/2019] [Indexed: 11/20/2022] Open
Abstract
Since the introduction of pneumococcal conjugate vaccines, the prevalence of non-meropenem-susceptible pneumococci has been increasing in Japan. In an earlier study, we demonstrated that multidrug-resistant serotype 15A-ST63 in Japan has a specific pbp1a sequence (pbp1a-13) that could promote meropenem resistance. To trace the origin of pbp1a, we analyzed isolates of serotype 19A-CC3111, which is the most prevalent non-meropenem-susceptible clone in Japan. We analyzed a total of 119 serotype 19A-CC3111 strains recovered in Japan using whole-genome sequencing. Of the 119 isolates, 53 (44.5%) harbored pbp1a-13, indicating that the clone may be the primary reservoir of the pbp1a type and that the pbp1a region may be horizontally transferred between different serotype strains. The single acquisition of pbp1a-13 seemed to cause only penicillin resistance and not multidrug resistance; a combination of penicillin-binding protein (PBP) recombination in the pbp2b and/or pbp2x region(s) with acquisition of pbp1a-13 caused multidrug resistance. Conserved amino acid motif analysis suggested that the pbp1a 370SXXK, pbp2b 448SXN, and pbp2x 337SXXN motifs were the candidates for amino acid substitutions increasing the MICs of meropenem, cefotaxime, and penicillin. We identified a specific clone that was correlated with multidrug resistance, although no correlation was observed between phylogenetic trees generated using core genomes and those generated with only the cps locus. All tested isolates were highly erythromycin resistant, and most harbored mefE within macrolide efflux genetic assembly (MEGA) elements and ermB within Tn917, which was inserted within Tn916 and exhibited a structure identical to that of Tn2017.
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15
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Schroeder MR, Lohsen S, Chancey ST, Stephens DS. High-Level Macrolide Resistance Due to the Mega Element [ mef(E)/ mel] in Streptococcus pneumoniae. Front Microbiol 2019; 10:868. [PMID: 31105666 PMCID: PMC6491947 DOI: 10.3389/fmicb.2019.00868] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/04/2019] [Indexed: 01/06/2023] Open
Abstract
Transferable genetic elements conferring macrolide resistance in Streptococcus pneumoniae can encode the efflux pump and ribosomal protection protein, mef(E)/mel, in an operon of the macrolide efflux genetic assembly (Mega) element- or induce ribosomal methylation through a methyltransferase encoded by erm(B). During the past 30 years, strains that contain Mega or erm(B) or both elements on Tn2010 and other Tn916-like composite mobile genetic elements have emerged and expanded globally. In this study, we identify and define pneumococcal isolates with unusually high-level macrolide resistance (MICs > 16 μg/ml) due to the presence of the Mega element [mef(E)/mel] alone. High-level resistance due to mef(E)/mel was associated with at least two specific genomic insertions of the Mega element, designated Mega-2.IVa and Mega-2.IVc. Genome analyses revealed that these strains do not possess erm(B) or known ribosomal mutations. Deletion of mef(E)/mel in these isolates eliminated macrolide resistance. We also found that Mef(E) and Mel of Tn2010-containing pneumococci were functional but the high-level of macrolide resistance was due to Erm(B). Using in vitro competition experiments in the presence of macrolides, high-level macrolide-resistant S. pneumoniae conferred by either Mega-2.IVa or erm(B), had a growth fitness advantage over the lower-level, mef(E)/mel-mediated macrolide-resistant S. pneumoniae phenotypes. These data indicate the ability of S. pneumoniae to generate high-level macrolide resistance by macrolide efflux/ribosomal protection [Mef(E)/Mel] and that high-level resistance regardless of mechanism provides a fitness advantage in the presence of macrolides.
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Affiliation(s)
- Max R Schroeder
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States.,Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, GA, United States
| | - Sarah Lohsen
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States
| | - Scott T Chancey
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States.,Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, GA, United States
| | - David S Stephens
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, United States.,Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center, Atlanta, GA, United States
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16
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Iannelli F, Santoro F, Santagati M, Docquier JD, Lazzeri E, Pastore G, Cassone M, Oggioni MR, Rossolini GM, Stefani S, Pozzi G. Type M Resistance to Macrolides Is Due to a Two-Gene Efflux Transport System of the ATP-Binding Cassette (ABC) Superfamily. Front Microbiol 2018; 9:1670. [PMID: 30108557 PMCID: PMC6079230 DOI: 10.3389/fmicb.2018.01670] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 07/04/2018] [Indexed: 11/19/2022] Open
Abstract
The mef(A) gene was originally identified as the resistance determinant responsible for type M resistance to macrolides, a phenotype frequently found in clinical isolates of Streptococcus pneumoniae and Streptococcus pyogenes. MefA was defined as a secondary transporter of the major facilitator superfamily driven by proton-motive force. However, when characterizing the mef(A)-carrying elements Tn1207.1 and Φ1207.3, another macrolide resistance gene, msr(D), was found adjacent to mef(A). To define the respective contribution of mef(A) and msr(D) to macrolide resistance, three isogenic deletion mutants were constructed by transformation of a S. pneumoniae strain carrying Φ1207.3: (i) Δmef(A)–Δmsr(D); (ii) Δmef(A)–msr(D); and (iii) mef(A)–Δmsr(D). Susceptibility testing of mutants clearly showed that msr(D) is required for macrolide resistance, while deletion of mef(A) produced only a twofold reduction in the minimal inhibitory concentration (MIC) for erythromycin. The contribution of msr(D) to macrolide resistance was also studied in S. pyogenes, which is the original host of Φ1207.3. Two isogenic strains of S. pyogenes were constructed: (i) FR156, carrying Φ1207.3, and (ii) FR155, carrying Φ1207.3/Δmsr(D). FR155 was susceptible to erythromycin, whereas FR156 was resistant, with an MIC value of 8 μg/ml. Complementation experiments showed that reintroduction of the msr(D) gene could restore macrolide resistance in Δmsr(D) mutants. Radiolabeled erythromycin was retained by strains lacking msr(D), while msr(D)-carrying strains showed erythromycin efflux. Deletion of mef(A) did not affect erythromycin efflux. This data suggest that type M resistance to macrolides in streptococci is due to an efflux transport system of the ATP-binding cassette (ABC) superfamily, in which mef(A) encodes the transmembrane channel, and msr(D) the two ATP-binding domains.
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Affiliation(s)
- Francesco Iannelli
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Francesco Santoro
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Maria Santagati
- Section of Microbiology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | | | - Elisa Lazzeri
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gabiria Pastore
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco Cassone
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Marco R Oggioni
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Gian M Rossolini
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Stefania Stefani
- Section of Microbiology, Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Gianni Pozzi
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
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17
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El Moujaber G, Osman M, Rafei R, Dabboussi F, Hamze M. Molecular mechanisms and epidemiology of resistance in Streptococcus pneumoniae in the Middle East region. J Med Microbiol 2017. [DOI: 10.1099/jmm.0.000503] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Grace El Moujaber
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Marwan Osman
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Rayane Rafei
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Ecole Doctorale des Sciences et de Technologie, Faculté de Santé Publique, Université Libanaise, Tripoli, Lebanon
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18
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Deng X, Memari N, Teatero S, Athey T, Isabel M, Mazzulli T, Fittipaldi N, Gubbay JB. Whole-genome Sequencing for Surveillance of Invasive Pneumococcal Diseases in Ontario, Canada: Rapid Prediction of Genotype, Antibiotic Resistance and Characterization of Emerging Serotype 22F. Front Microbiol 2016; 7:2099. [PMID: 28082965 PMCID: PMC5187366 DOI: 10.3389/fmicb.2016.02099] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/12/2016] [Indexed: 11/13/2022] Open
Abstract
Background: Molecular typing is essential for inferring genetic relatedness between bacterial pathogens. In this study, we applied whole genome sequencing (WGS) for rapid prediction of sequence type and antibiotic resistance for invasive pneumococcal isolates. Methods: 240 isolates from adults (≥50 years old) in Ontario, Canada during 2009 to 2013 were subjected to WGS. Sequence type, antibiotic susceptibility and resistance were predicted directly from short reads. Emerging non-vaccine serotype 22F was further characterized by WGS. Results: Sequence type was successfully determined for 98.3% of isolates. The overall sensitivity and specificity for antibiotic resistance prediction were 95 and 100% respectively, compared to standard susceptibility testing methods. WGS-based phylogeny divided emerging 22F (ST433) strains into two distinct clades: clade A harboring a 23 kb-prophage and anti-phage PhD/Doc system and clade B with virulence-related proteases. Five isolates in clade A developed macrolide resistance via 5.1 kb mega element recombination (encoding mefE and msrD), while one isolate in clade B displayed quinolone resistance via a gyrA mutation. Conclusions: WGS is valuable for routine surveillance of pneumococcal clinical isolates and facilitates prediction of genotype and antibiotic resistance. The emergence of 22F in Ontario in the post-vaccine era and evidence of evolution and divergence of the 22F population warrants heightened pneumococcal molecular surveillance.
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Affiliation(s)
- Xianding Deng
- Public Health Ontario LaboratoryToronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
- Mount Sinai Hospital and University Health NetworkToronto, ON, Canada
| | - Nader Memari
- Public Health Ontario LaboratoryToronto, ON, Canada
| | | | - Taryn Athey
- Public Health Ontario LaboratoryToronto, ON, Canada
| | - Marc Isabel
- Department of Mathematics and Statistics, University of LavalQuebec, QC, Canada
| | - Tony Mazzulli
- Public Health Ontario LaboratoryToronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
- Mount Sinai Hospital and University Health NetworkToronto, ON, Canada
| | - Nahuel Fittipaldi
- Public Health Ontario LaboratoryToronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
| | - Jonathan B. Gubbay
- Public Health Ontario LaboratoryToronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, ON, Canada
- Mount Sinai Hospital and University Health NetworkToronto, ON, Canada
- The Hospital for Sick ChildrenToronto, ON, Canada
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19
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Fyfe C, Grossman TH, Kerstein K, Sutcliffe J. Resistance to Macrolide Antibiotics in Public Health Pathogens. Cold Spring Harb Perspect Med 2016; 6:a025395. [PMID: 27527699 PMCID: PMC5046686 DOI: 10.1101/cshperspect.a025395] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Macrolide resistance mechanisms can be target-based with a change in a 23S ribosomal RNA (rRNA) residue or a mutation in ribosomal protein L4 or L22 affecting the ribosome's interaction with the antibiotic. Alternatively, mono- or dimethylation of A2058 in domain V of the 23S rRNA by an acquired rRNA methyltransferase, the product of an erm (erythromycin ribosome methylation) gene, can interfere with antibiotic binding. Acquired genes encoding efflux pumps, most predominantly mef(A) + msr(D) in pneumococci/streptococci and msr(A/B) in staphylococci, also mediate resistance. Drug-inactivating mechanisms include phosphorylation of the 2'-hydroxyl of the amino sugar found at position C5 by phosphotransferases and hydrolysis of the macrocyclic lactone by esterases. These acquired genes are regulated by either translation or transcription attenuation, largely because cells are less fit when these genes, especially the rRNA methyltransferases, are highly induced or constitutively expressed. The induction of gene expression is cleverly tied to the mechanism of action of macrolides, relying on antibiotic-bound ribosomes stalled at specific sequences of nascent polypeptides to promote transcription or translation of downstream sequences.
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Affiliation(s)
- Corey Fyfe
- Tetraphase Pharmaceuticals, Watertown, Massachusetts 02472
| | | | - Kathy Kerstein
- Tetraphase Pharmaceuticals, Watertown, Massachusetts 02472
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20
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Schroeder MR, Stephens DS. Macrolide Resistance in Streptococcus pneumoniae. Front Cell Infect Microbiol 2016; 6:98. [PMID: 27709102 PMCID: PMC5030221 DOI: 10.3389/fcimb.2016.00098] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/26/2016] [Indexed: 01/21/2023] Open
Abstract
Streptococcus pneumoniae is a common commensal and an opportunistic pathogen. Suspected pneumococcal upper respiratory infections and pneumonia are often treated with macrolide antibiotics. Macrolides are bacteriostatic antibiotics and inhibit protein synthesis by binding to the 50S ribosomal subunit. The widespread use of macrolides is associated with increased macrolide resistance in S. pneumoniae, and the treatment of pneumococcal infections with macrolides may be associated with clinical failures. In S. pneumoniae, macrolide resistance is due to ribosomal dimethylation by an enzyme encoded by erm(B), efflux by a two-component efflux pump encoded by mef (E)/mel(msr(D)) and, less commonly, mutations of the ribosomal target site of macrolides. A wide array of genetic elements have emerged that facilitate macrolide resistance in S. pneumoniae; for example erm(B) is found on Tn917, while the mef (E)/mel operon is carried on the 5.4- or 5.5-kb Mega element. The macrolide resistance determinants, erm(B) and mef (E)/mel, are also found on large composite Tn916-like elements most notably Tn6002, Tn2009, and Tn2010. Introductions of 7-valent and 13-valent pneumococcal conjugate vaccines (PCV-7 and PCV-13) have decreased the incidence of macrolide-resistant invasive pneumococcal disease, but serotype replacement and emergence of macrolide resistance remain an important concern.
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Affiliation(s)
| | - David S Stephens
- Departments of Medicine, Emory UniversityAtlanta, GA, USA; Departments of Microbiology and Immunology, Emory UniversityAtlanta, GA, USA; Departments of Epidemiology, Emory UniversityAtlanta, GA, USA
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Tantivitayakul P, Lapirattanakul J, Vichayanrat T, Muadchiengka T. Antibiotic Resistance Patterns and Related Mobile Genetic Elements of Pneumococci and β-Hemolytic Streptococci in Thai Healthy Children. Indian J Microbiol 2016; 56:417-425. [PMID: 27784937 DOI: 10.1007/s12088-016-0607-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/23/2016] [Indexed: 11/29/2022] Open
Abstract
Transmission of antibiotic resistance genes among Streptococcus pneumoniae and beta-hemolytic streptococcus (BHS) was generally associated with transmissible genetic elements. The objectives of this study were to investigate carriage rate, antibiotic resistance and related mobile genetic elements of pneumococci and BHS from school-children. The pneumococci and BHS were recovered from 220 Thai school-children, and then tested for antibiotic susceptibility pattern by disc diffusion. Antibiotic resistance genes and related genetic elements were detected by PCR with specific primers. A total of 77 pneumococcal isolates were resistant to erythromycin (42 %), tetracycline (44 %), clindamycin (8 %), or penicillin (3 %). Fifty-four BHS isolates were resistant to erythromycin (28 %), tetracycline (52 %), or clindamycin (13 %). All isolates tested were 100 % sensitive to penicillin and levofloxacin. Among erythromycin-resistant streptococcal isolates showed different phenotypes of clindamycin resistance. It was found that isolated pneumococci showed constitutive clindamycin resistance (19 %), and inducible clindamycin resistance (12 %). The BHS isolates exhibited constitutive clindamycin resistance (40 %), and inducible resistance (20 %) phenotypes. The predominant erythromycin resistance genes in pneumococci and BHS were mefE and ermB, while the most common tetracycline resistance gene in this population was tetM. Furthermore, almost all erythromycin- and tetracycline-resistant streptococci (97 %) mainly contained various genetic elements, including mega elements and six different transposon types (Tn2009, Tn2017, Tn917, Tn3872, Tn6002 and Tn916). Therefore, carriages of pneumococci and BHS with multidrug resistance in children might be important reservoirs of antibiotic-resistance genes carried by transposons. Tn916-like elements could lead to dissemination of the antibiotic resistance genes among genus streptococcus in human oral cavity and nasopharynx.
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Affiliation(s)
- P Tantivitayakul
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, 6 Yothi Street, Rajthevi, Bangkok, 10400 Thailand
| | - J Lapirattanakul
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, 6 Yothi Street, Rajthevi, Bangkok, 10400 Thailand
| | - T Vichayanrat
- Department of Community Dentistry, Faculty of Dentistry, Mahidol University, Bangkok, 10400 Thailand
| | - T Muadchiengka
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, 6 Yothi Street, Rajthevi, Bangkok, 10400 Thailand
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ICESpy009, a Conjugative Genetic Element Carrying mef(E) in Streptococcus pyogenes. Antimicrob Agents Chemother 2016; 60:3906-12. [PMID: 27067338 DOI: 10.1128/aac.03082-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 04/01/2016] [Indexed: 01/19/2023] Open
Abstract
Efflux-mediated macrolide resistance due to mef(E) and mel, carried by the mega element, is common in Streptococcus pneumoniae, for which it was originally characterized, but it is rare in Streptococcus pyogenes In S. pyogenes, mega was previously found to be enclosed in Tn2009, a composite genetic element of the Tn916 family containing tet(M) and conferring erythromycin and tetracycline resistance. In this study, S. pyogenes isolates containing mef(E), apparently not associated with other resistance determinants, were examined to characterize the genetic context of mega. By whole-genome sequencing of one isolate, MB56Spyo009, we identified a novel composite integrative and conjugative element (ICE) carrying mega, designated ICESpy009, belonging to the ICESa2603 family. ICESpy009 was 55 kb long, contained 61 putative open reading frames (ORFs), and was found to be integrated into hylA, a novel integration site for the ICESa2603 family. The modular organization of the ICE was similar to that of members of the ICESa2603 family carried by different streptococcal species. In addition, a novel cluster of accessory resistance genes was found inside a region that encloses mega. PCR mapping targeting ICESpy009 revealed the presence of a similar ICE in five other isolates under study. While in three isolates the integration site was the same as that of ICESpy009, in two isolates the ICE was integrated into rplL, the typical integration site of the ICESa2603 family. ICESpy009 was able to transfer macrolide resistance by conjugation to both S. pyogenes and S. pneumoniae, showing the first evidence of the transferability of mega from S. pyogenes.
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Deng X, Peirano G, Schillberg E, Mazzulli T, Gray-Owen SD, Wylie JL, Robinson DA, Mahmud SM, Pillai DR. Whole-Genome Sequencing Reveals the Origin and Rapid Evolution of an Emerging Outbreak Strain ofStreptococcus pneumoniae12F. Clin Infect Dis 2016; 62:1126-1132. [DOI: 10.1093/cid/ciw050] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 01/26/2016] [Indexed: 11/13/2022] Open
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Chancey ST, Agrawal S, Schroeder MR, Farley MM, Tettelin H, Stephens DS. Composite mobile genetic elements disseminating macrolide resistance in Streptococcus pneumoniae. Front Microbiol 2015; 6:26. [PMID: 25709602 PMCID: PMC4321634 DOI: 10.3389/fmicb.2015.00026] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/08/2015] [Indexed: 01/17/2023] Open
Abstract
Macrolide resistance in Streptococcus pneumoniae emerged in the U.S. and globally during the early 1990's. The RNA methylase encoded by erm(B) and the macrolide efflux genes mef(E) and mel were identified as the resistance determining factors. These genes are disseminated in the pneumococcus on mobile, often chimeric elements consisting of multiple smaller elements. To better understand the variety of elements encoding macrolide resistance and how they have evolved in the pre- and post-conjugate vaccine eras, the genomes of 121 invasive and ten carriage isolates from Atlanta from 1994 to 2011 were analyzed for mobile elements involved in the dissemination of macrolide resistance. The isolates were selected to provide broad coverage of the genetic variability of antibiotic resistant pneumococci and included 100 invasive isolates resistant to macrolides. Tn916-like elements carrying mef(E) and mel on the Macrolide Genetic Assembly (Mega) and erm(B) on the erm(B) element and Tn917 were integrated into the pneumococcal chromosome backbone and into larger Tn5253-like composite elements. The results reported here include identification of novel insertion sites for Mega and characterization of the insertion sites of Tn916-like elements in the pneumococcal chromosome and in larger composite elements. The data indicate that integration of elements by conjugation was infrequent compared to recombination. Thus, it appears that conjugative mobile elements allow the pneumococcus to acquire DNA from distantly related bacteria, but once integrated into a pneumococcal genome, transformation and recombination is the primary mechanism for transmission of novel DNA throughout the pneumococcal population.
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Affiliation(s)
- Scott T Chancey
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine Atlanta, GA, USA ; Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center Atlanta, GA, USA
| | - Sonia Agrawal
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA
| | - Max R Schroeder
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine Atlanta, GA, USA ; Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center Atlanta, GA, USA
| | - Monica M Farley
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine Atlanta, GA, USA ; Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center Atlanta, GA, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine Baltimore, MD, USA ; Department of Microbiology and Immunology, University of Maryland School of Medicine Baltimore, MD, USA
| | - David S Stephens
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine Atlanta, GA, USA ; Laboratories of Microbial Pathogenesis, Department of Veterans Affairs Medical Center Atlanta, GA, USA
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Santoro F, Vianna ME, Roberts AP. Variation on a theme; an overview of the Tn916/Tn1545 family of mobile genetic elements in the oral and nasopharyngeal streptococci. Front Microbiol 2014; 5:535. [PMID: 25368607 PMCID: PMC4202715 DOI: 10.3389/fmicb.2014.00535] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 09/25/2014] [Indexed: 11/17/2022] Open
Abstract
The oral and nasopharyngeal streptococci are a major part of the normal microbiota in humans. Most human associated streptococci are considered commensals, however, a small number of them are pathogenic, causing a wide range of diseases including oral infections such as dental caries and periodontitis and diseases at other body sites including sinusitis and endocarditis, and in the case of Streptococcus pneumoniae, meningitis. Both phenotypic and sequence based studies have shown that the human associated streptococci from the mouth and nasopharynx harbor a large number of antibiotic resistance genes and these are often located on mobile genetic elements (MGEs) known as conjugative transposons or integrative and conjugative elements of the Tn916/Tn1545 family. These MGEs are responsible for the spread of the resistance genes between streptococci and also between streptococci and other bacteria. In this review we describe the resistances conferred by, and the genetic variations between the many different Tn916-like elements found in recent studies of oral and nasopharyngeal streptococci and show that Tn916-like elements are important mediators of antibiotic resistance genes within this genus. We will also discuss the role of the oral environment and how this is conducive to the transfer of these elements and discuss the contribution of both transformation and conjugation on the transfer and evolution of these elements in different streptococci.
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Affiliation(s)
- Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of SienaSiena, Italy
| | - Morgana E. Vianna
- Unit of Endodontology, UCL Eastman Dental Institute, University College LondonLondon, UK
| | - Adam P. Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College LondonLondon, UK
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Zhou W, Yao K, Zhang G, Yang Y, Li Y, Lv Y, Feng J. Mechanism for transfer of transposon Tn2010 carrying macrolide resistance genes in Streptococcus pneumoniae and its effects on genome evolution. J Antimicrob Chemother 2014; 69:1470-3. [DOI: 10.1093/jac/dku019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Brenciani A, Tiberi E, Tili E, Mingoia M, Palmieri C, Varaldo PE, Giovanetti E. Genetic determinants and elements associated with antibiotic resistance in viridans group streptococci. J Antimicrob Chemother 2013; 69:1197-204. [PMID: 24343896 DOI: 10.1093/jac/dkt495] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
OBJECTIVES To investigate the distribution of erythromycin, tetracycline and chloramphenicol resistance mechanisms and determinants and the relevant genetic environments and elements in viridans group streptococci (VGS). METHODS A total of 263 VGS collected from routine throat swabs in 2010-12 and identified to the species level were studied. Antibiotic resistance determinants and the relevant genetic contexts and elements were determined using amplification and sequencing assays and restriction analysis. RESULTS The investigation provided original information on the distribution of resistance mechanisms, determinants and genetic elements in VGS. Erythromycin-resistant isolates totalled 148 (56.3%; 37 belonging to the cMLS phenotype and 111 belonging to the M phenotype); there were 72 (27.4%) and 7 (2.7%) tetracycline- and chloramphenicol-resistant isolates, respectively. A number of variants of known genetic contexts and elements carrying determinants of resistance to these antibiotics were detected, including the mega element, Φ10394.4, Tn2009, Tn2010, the IQ element, Tn917, Tn3872, Tn6002, Tn916, Tn5801, a tet(O) fragment from ICE2096-RD.2 and ICESp23FST81. CONCLUSIONS These findings shed new light on the distribution of antibiotic resistance mechanisms and determinants and their genetic environments in VGS, for which very few such data are currently available. The high frequency and broad variety of such elements supports the notion that VGS may be important reservoirs of resistance genes for the more pathogenic streptococci. The high rates of macrolide resistance confirm the persistence of a marked prevalence of resistant VGS in Europe, where macrolide resistance is, conversely, declining among the major streptococcal pathogens.
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Affiliation(s)
- Andrea Brenciani
- Unit of Microbiology, Department of Biomedical Sciences and Public Health, Polytechnic University of Marche Medical School, 60126 Ancona, Italy
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Wyres KL, van Tonder A, Lambertsen LM, Hakenbeck R, Parkhill J, Bentley SD, Brueggemann AB. Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974. BMC Genomics 2013; 14:500. [PMID: 23879707 PMCID: PMC3726389 DOI: 10.1186/1471-2164-14-500] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Accepted: 07/23/2013] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Antimicrobial resistance among pneumococci has greatly increased over the past two to three decades. Resistance to tetracycline (tet(M)), chloramphenicol (cat) and macrolides (erm(B) and/or mef(A/E)) is generally conferred by acquisition of specific genes that are associated with mobile genetic elements, including those of the Tn916 and Tn5252 families. The first tetracycline-, chloramphenicol- and macrolide-resistant pneumococci were detected between 1962 and 1970; however, until now the oldest pneumococcus shown to harbour Tn916 and/or Tn5252 was isolated in 1974. In this study the genomes of 38 pneumococci isolated prior to 1974 were probed for the presence of tet(M), cat, erm(B), mef(A/E) and int (integrase) to indicate the presence of Tn916/Tn5252-like elements. RESULTS Two Tn916-like, tet(M)-containing, elements were identified among pneumococci dated 1967 and 1968. The former element was highly similar to that of the PMEN1 multidrug-resistant, globally-distributed pneumococcal reference strain, which was isolated in 1984. The latter element was associated with a streptococcal phage. A third, novel genetic element, designated ICESpPN1, was identified in the genome of an isolate dated 1972. ICESpPN1 contained a region of similarity to Tn5252, a region of similarity to a pneumococcal pathogenicity island and novel lantibiotic synthesis/export-associated genes. CONCLUSIONS These data confirm the existence of pneumococcal Tn916 elements in the first decade within which pneumococcal tetracycline resistance was described. Furthermore, the discovery of ICESpPN1 demonstrates the dynamic variability of pneumococcal genetic elements and is contrasted with the evidence for Tn916 stability.
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Affiliation(s)
- Kelly L Wyres
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Andries van Tonder
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
| | - Lotte M Lambertsen
- Department of Microbiology Surveillance and Research, Statens Serum Institut, 5 Artillerivej, Copenhagen 2300, Denmark
| | - Regine Hakenbeck
- Department of Microbiology, University Kaiserslautern, Kaiserslautern, Germany
| | - Julian Parkhill
- Pathogen Genomics Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Stephen D Bentley
- Pathogen Genomics Team, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Angela B Brueggemann
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
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Cascone C, Mezzatesta ML, Santagati M, Cafiso V, Nicoletti G, Stefani S. Activity of Telithromycin Against Multi-Drug ResistantStreptococcus pneumoniaeand Molecular Characterization of Macrolide and Tetracycline Resistance Determinants. J Chemother 2013; 17:502-8. [PMID: 16323438 DOI: 10.1179/joc.2005.17.5.502] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The antistreptococcal activity of telithromycin and 11 different comparators was evaluated in 26 multi-drug resistant (MDR) Streptococcus pneumoniae strains collected during 2002-2003 as part of the ongoing PROTEKT (Prospective Resistant Organism Tracking and Epidemiology for the Ketolide Telithromycin) Italian Surveillance Program. The strains were characterized for their susceptibility to antibiotics both at the phenotypic and genotypic levels; furthermore, the association of erm(B), mef(A) class and tet(M) genes, as well as the mobile elements carrying them were determined. The strains in this study were resistant to penicillin (MIC > or = 2 mg/l) in 23.1% of cases, resistant to tetracycline in 88.4%, to cotrimoxazole in 34.6% and cefuroxime in 26.9% while only telithromycin and levofloxacin retained 100% activity against all microorganisms. Co-existence of different resistance determinants was found in 19.2% of all isolates collected in our laboratory, coming from southern Italy. Twenty-three isolates showing the MLSB phenotype of resistance possessing the erm(B) gene (88.5%), associated with tet(M), were carried on the same Tn1545-like element, while two isolates showing the M phenotype possessing the mef(A) gene alone, were carried on Tn1207.1. In only one strain were mef(E) and tet(M) together carried on Tn2009.
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Affiliation(s)
- C Cascone
- Department of Microbiological Science, University of Catania, Italy
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30
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Bryant J, Chewapreecha C, Bentley SD. Developing insights into the mechanisms of evolution of bacterial pathogens from whole-genome sequences. Future Microbiol 2012; 7:1283-1296. [PMID: 23075447 PMCID: PMC3996552 DOI: 10.2217/fmb.12.108] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Evolution of bacterial pathogen populations has been detected in a variety of ways including phenotypic tests, such as metabolic activity, reaction to antisera and drug resistance and genotypic tests that measure variation in chromosome structure, repetitive loci and individual gene sequences. While informative, these methods only capture a small subset of the total variation and, therefore, have limited resolution. Advances in sequencing technologies have made it feasible to capture whole-genome sequence variation for each sample under study, providing the potential to detect all changes at all positions in the genome from single nucleotide changes to large-scale insertions and deletions. In this review, we focus on recent work that has applied this powerful new approach and summarize some of the advances that this has brought in our understanding of the details of how bacterial pathogens evolve.
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Affiliation(s)
- Josephine Bryant
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Claire Chewapreecha
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
| | - Stephen D Bentley
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
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Bhargava K, Zhang Y. Multidrug-resistant coagulase-negative Staphylococci in food animals. J Appl Microbiol 2012; 113:1027-36. [PMID: 22816491 DOI: 10.1111/j.1365-2672.2012.05410.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Revised: 07/13/2012] [Accepted: 07/16/2012] [Indexed: 01/22/2023]
Abstract
AIMS To study the antimicrobial resistance of coagulase-negative staphylococci (CoNS) in animals. METHODS AND RESULTS In the present study, a total of 87 CoNS recovered from food animals were characterized by antimicrobial susceptibility testing, resistance gene identification and conjugation. Of the seven species studied, Staphylococcus lentus, Staphylococcus sciuri, Staphylococcus xylosus and Staphylococcus haemolyticus accounted for over 96% of the isolates. In addition to β-lactam resistance (100%), high percentages of CoNS were resistant to tetracycline (67·8%), erythromycin (36·7%), clindamycin (27·5%) and quinopristin/dalfopristin (14·9%). Importantly, 47 (54%) isolates were resistant to at least three antimicrobial classes, including six CoNS resistant to six antimicrobial classes. The common genes for the above-mentioned resistance phenotypes were mec(A), tet(M), erm(A) and vga(A)(LC) , which were identified from 68·7%, 61%, 56·2% and 69·2% of the isolates, respectively. tet(M) was conjugatively transferable from 10 tetracycline-resistant CoNS to a Enterococcus strain, underlining the potential of antimicrobial resistance transfer from Staphylococcus to the commensal bacteria in human. CONCLUSIONS Multidrug resistance and resistance to non-β-lactam antimicrobials are common in CoNS in animals. SIGNIFICANCE AND IMPACT OF THE STUDY The data improve our understanding on the extent to which CoNS contribute to the dissemination of antimicrobial resistance in the food production environment.
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Affiliation(s)
- K Bhargava
- Department of Nutrition and Food Science, Wayne State University, Detroit, MI, USA
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Molecular basis for different levels of tet(M) expression in Streptococcus pneumoniae clinical isolates. Antimicrob Agents Chemother 2012; 56:5040-5. [PMID: 22802249 DOI: 10.1128/aac.00939-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Seventy-four unrelated clinical isolates of Streptococcus pneumoniae harboring the tet(M) gene were studied. Seven strains with low tetracycline (Tc) MICs (0.25 to 0.5 μg/ml) were found to harbor truncated tet(M) alleles that were inactivated by different frameshift mutations. In contrast, five strains bore deletions in the tet(M) promoter region, among which four displayed increased Tc MICs (16 to 64 μg/ml). The same promoter mutations were detected in Tc-resistant mutants selected in vitro from various susceptible strains. Sequence analysis revealed that these deletions might impede the formation of the transcriptional attenuator located immediately upstream of tet(M). Expression in Enterococcus faecalis of a tet(M) reporter gene transcribed from these promoter mutants conferred a level of Tc resistance similar to that observed in the parental S. pneumoniae strains. These results show that different levels of Tc susceptibility found in clinical isolates of S. pneumoniae can be explained by frameshift mutations within tet(M) and by alterations of the upstream transcriptional attenuator.
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The antibiotic resistance arrow of time: efflux pump induction is a general first step in the evolution of mycobacterial drug resistance. Antimicrob Agents Chemother 2012; 56:4806-15. [PMID: 22751536 DOI: 10.1128/aac.05546-11] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We hypothesize that low-level efflux pump expression is the first step in the development of high-level drug resistance in mycobacteria. We performed 28-day azithromycin dose-effect and dose-scheduling studies in our hollow-fiber model of disseminated Mycobacterium avium-M. intracellulare complex. Both microbial kill and resistance emergence were most closely linked to the within-macrophage area under the concentration-time curve (AUC)/MIC ratio. Quantitative PCR revealed that subtherapeutic azithromycin exposures over 3 days led to a 56-fold increase in expression of MAV_3306, which encodes a putative ABC transporter, and MAV_1406, which encodes a putative major facilitator superfamily pump, in M. avium. By day 7, a subpopulation of M. avium with low-level resistance was encountered and exhibited the classic inverted U curve versus AUC/MIC ratios. The resistance was abolished by an efflux pump inhibitor. While the maximal microbial kill started to decrease after day 7, a population with high-level azithromycin resistance appeared at day 28. This resistance could not be reversed by efflux pump inhibitors. Orthologs of pumps encoded by MAV_3306 and MAV_1406 were identified in Mycobacterium tuberculosis, Mycobacterium leprae, Mycobacterium marinum, Mycobacterium abscessus, and Mycobacterium ulcerans. All had highly conserved protein secondary structures. We propose that induction of several efflux pumps is the first step in a general pathway to drug resistance that eventually leads to high-level chromosomal-mutation-related resistance in mycobacteria as ordered events in an "antibiotic resistance arrow of time."
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Cornick J, Bentley S. Streptococcus pneumoniae: the evolution of antimicrobial resistance to beta-lactams, fluoroquinolones and macrolides. Microbes Infect 2012; 14:573-83. [DOI: 10.1016/j.micinf.2012.01.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/24/2012] [Accepted: 01/24/2012] [Indexed: 11/29/2022]
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Bowers JR, Driebe EM, Nibecker JL, Wojack BR, Sarovich DS, Wong AH, Brzoska PM, Hubert N, Knadler A, Watson LM, Wagner DM, Furtado MR, Saubolle M, Engelthaler DM, Keim PS. Dominance of multidrug resistant CC271 clones in macrolide-resistant streptococcus pneumoniae in Arizona. BMC Microbiol 2012; 12:12. [PMID: 22251616 PMCID: PMC3285076 DOI: 10.1186/1471-2180-12-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2011] [Accepted: 01/18/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rates of resistance to macrolide antibiotics in Streptococcus pneumoniae are rising around the world due to the spread of mobile genetic elements harboring mef(E) and erm(B) genes and post-vaccine clonal expansion of strains that carry them. RESULTS Characterization of 592 clinical isolates collected in Arizona over a 10 year period shows 23.6% are macrolide resistant. The largest portion of the macrolide-resistant population, 52%, is dual mef(E)/erm(B)-positive. All dual-positive isolates are multidrug-resistant clonal lineages of Taiwan19F-14, mostly multilocus sequence type 320, carrying the recently described transposon Tn2010. The remainder of the macrolide resistant S. pneumoniae collection includes 31% mef(E)-positive, and 9% erm(B)-positive strains. CONCLUSIONS The dual-positive, multidrug-resistant S. pneumoniae clones have likely expanded by switching to non-vaccine serotypes after the heptavalent pneumococcal conjugate vaccine release, and their success limits therapy options. This upsurge could have a considerable clinical impact in Arizona.
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Affiliation(s)
- Jolene R Bowers
- Translational Genomics Research Institute, Flagstaff, AZ, USA.
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Ciric L, Mullany P, Roberts AP. Antibiotic and antiseptic resistance genes are linked on a novel mobile genetic element: Tn6087. J Antimicrob Chemother 2011; 66:2235-9. [PMID: 21816764 PMCID: PMC3172042 DOI: 10.1093/jac/dkr311] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Objectives Tn916-like elements are one of the most common types of integrative and conjugative element (ICE). In this study we aimed to determine whether novel accessory genes, i.e. genes whose products are not involved in mobility or regulation, were present on a Tn916-like element (Tn6087) isolated from Streptococcus oralis from the human oral cavity. Methods A minocycline-resistant isolate was analysed using restriction fragment length polymorphism (RFLP) analysis on amplicons derived from Tn916 and DNA sequencing to determine whether there were genetic differences in Tn6087 compared with Tn916. Mutational analysis was used to determine whether the novel accessory gene found was responsible for an observed extra phenotype. Results A novel Tn916-like element, Tn6087, is described that encodes both antibiotic and antiseptic resistance. The antiseptic resistance protein is encoded by a novel small multidrug resistance gene, designated qrg, that was shown to encode resistance to cetyltrimethylammonium bromide (CTAB), also known as cetrimide bromide. Conclusions This is the first Tn916-like element described that confers both antibiotic and antiseptic resistance, suggesting that selection of either antibiotic or antiseptic resistance will also select for the other and further highlights the need for prudent use of both types of compound.
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Affiliation(s)
- Lena Ciric
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, 256 Gray's Inn Road, London WC1X 8LD, UK
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Roberts AP, Mullany P. Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance. FEMS Microbiol Rev 2011; 35:856-71. [PMID: 21658082 DOI: 10.1111/j.1574-6976.2011.00283.x] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Antibiotic-resistant Gram-positive bacteria are responsible for morbidity and mortality in healthcare environments. Enterococcus faecium, Enterococcus faecalis, Staphylococcus aureus and Streptococcus pneumoniae can all exhibit clinically relevant multidrug resistance phenotypes due to acquired resistance genes on mobile genetic elements. It is possible that clinically relevant multidrug-resistant Clostridium difficile strains will appear in the future, as the organism is adept at acquiring mobile genetic elements (plasmids and transposons). Conjugative transposons of the Tn916/Tn1545 family, which carry major antibiotic resistance determinants, are transmissible between these different bacteria by a conjugative mechanism during which the elements are excised by a staggered cut from donor cells, converted to a circular form, transferred by cell-cell contact and inserted into recipient cells by a site-specific recombinase. The ability of these conjugative transposons to acquire additional, clinically relevant antibiotic resistance genes importantly contributes to the emergence of multidrug resistance.
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Affiliation(s)
- Adam P Roberts
- Department of Microbial Diseases, UCL Eastman Dental Institute, University College London, London, UK
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Genetic resistance elements carrying mef subclasses other than mef(A) in Streptococcus pyogenes. Antimicrob Agents Chemother 2011; 55:3226-30. [PMID: 21502613 DOI: 10.1128/aac.01713-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In Streptococcus pyogenes, efflux-mediated erythromycin resistance is associated with the mef gene, represented mostly by mef(A), although a small portion of strains carry different mef subclasses. We characterized the composite genetic elements, including mef subclasses other than mef(A), associated with other resistance genes in S. pyogenes isolates. Determination of the genetic elements was performed by PCR mapping. The strains carrying mosaic mef(A/E), in which the 5' region was identical to mef(A) and the 3' region was identical to mef(E), also carried tet(O). The two genes were found enclosed in an element similar to S. pyogenes prophage Φm46.1, designated the Φm46.1-like element. In S. pyogenes strains carrying mef(E) and tet(M), mef(E) was included in a typical mega element, and in some strains, it was physically associated with tet(M) in the composite element Tn2009. S. pyogenes strains carrying mef(I) also carried catQ; the two genes were linked in a fragment representing a portion of the 5216IQ complex of Streptococcus pneumoniae, designated the defective IQ element. In the only isolate carrying a novel mef gene, this was associated with catQ and tet(M) in a genetic element similar to the 5216IQ complex of S. pneumoniae (5216IQ-like complex), suggesting that the novel mef is in fact a variant of mef(I). This study demonstrates that the composite elements containing mef are shared between S. pyogenes and S. pneumoniae and suggests that it is important to distinguish the mef subclass on the basis of the genetic element containing it.
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Heterogeneity of Tn5253-like composite elements in clinical Streptococcus pneumoniae isolates. Antimicrob Agents Chemother 2011; 55:1453-9. [PMID: 21263055 DOI: 10.1128/aac.01087-10] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several drug resistances in Streptococcus pneumoniae are associated with mobile genetic elements, which are loosely subdivided into a group of smaller (18- to 27-kb) and a group of larger (>50-kb) elements. While the elements of the former group, which typically carry the tetracycline resistance determinant tet(M) and whose prototype is Tn916 (18 kb), have been studied extensively, the larger elements, whose prototype is Tn5253 (∼65.5 kb), are not as well explored. Tn5253 is a composite structure consisting of two independent conjugative transposons, Tn5251 (which is virtually identical to Tn916) and Tn5252 (∼47.5 kb), with the former inserted into the latter. Tn5252, which so far has only partially been sequenced, carries an integrase gene, driving its site-specific insertion into the host cell genome, and the chloramphenicol resistance cat(pC194) determinant. This study investigated 20 clinical isolates of S. pneumoniae, which were selected on the basis of cat(pC194)-mediated chloramphenicol resistance. All 20 isolates harbored a Tn5253-like element. The composite elements (some of which have been completely sequenced) demonstrated considerable heterogeneity that stemmed from a dual variability: in the Tn5252-like element, due primarily to differences in the integrase gene but also to differences in cargo genes and in the overall genetic organization, and in the Tn916-like element, with the possible involvement, besides Tn916, of a number of Tn916 family pneumococcal elements carrying different erythromycin resistance genes. In mating experiments, only one composite element, containing a less typical Tn916 family element, appeared to be nonmobile. Being part of a Tn5253-like composite element may confer on some Tn916-like transposons, which are apparently nontransferable as independent genetic elements, the ability to be mobilized.
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Li Y, Tomita H, Lv Y, Liu J, Xue F, Zheng B, Ike Y. Molecular characterization of erm(B)- and mef(E)-mediated erythromycin-resistant Streptococcus pneumoniae in China and complete DNA sequence of Tn2010. J Appl Microbiol 2010; 110:254-65. [PMID: 20961364 DOI: 10.1111/j.1365-2672.2010.04875.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS To characterize the erm(B)- and mef(E)-mediated erythromycin-resistant Streptococcus pneumoniae clinical isolates obtained from ten hospitals located different cities in China. METHODS AND RESULTS Totally 83 S. pneumoniae were collected, and eighteen representative strains of 66 strains that exhibited erythromycin resistance were used for further characterization by antibiograms, serotyping, PFGE, MLST, DNA sequencing of the macrolide-resistance elements and mapping of the elements on the chromosome. Twelve isolates showed a high-level resistance to erythromycin, and six other isolates showed a low-level resistance to erythromycin. Thirteen isolates harboured a Tn2010 transposon (26·4 kbp) encoding the erm(B), tet(M) and mef(E) genes and were classified into three types by Tn2010 structures. The remaining five isolates harboured a Tn6002 transposon (20·9 kbp) encoding the erm(B) and tet(M) genes and were classified into three types by Tn6002 locations on the chromosome. Three of the Tn6002 elements were located within the Tn5252-like element, implying that these composed a large mobile element. The MLST analyses showed that several clones had been disseminated and that the CC271 strains carrying the Tn2010 element expressing the high-level resistance to erythromycin were predominant in China. Four new MLST strains, which were designated as ST3262, ST3263, ST3397 and ST3398 were also identified. CONCLUSIONS The erythromycin resistance determinant of S.pneumoniae that had been isolated in China was located in Tn2010 or the Tn6002 element and several clones had been disseminated, and the CC271 strains carrying the Tn2010 element expressing the high-level resistance to erythromycin were predominant in China. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first molecular analysis of erythromycin-resistant Streptococcus pneumoniae clinical isolates in China, and the first report of the complete nucleotide sequence of Tn2010 (26,390 bp).
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Affiliation(s)
- Y Li
- Department of Bacteriology, Gunma University Graduate School of Medicine, Maebashi, Gunma, Japan
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Nielsen KL, Hammerum AM, Lambertsen LM, Lester CH, Arpi M, Knudsen JD, Stegger M, Tolker-Nielsen T, Frimodt-Møller N. Characterization and transfer studies of macrolide resistance genes in Streptococcus pneumoniae from Denmark. ACTA ACUST UNITED AC 2010; 42:586-93. [PMID: 20429715 DOI: 10.3109/00365541003754451] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Over the last decade, erythromycin resistance has been increasing in frequency in Streptococcus pneumoniae in Denmark. In the present study, 49 non-related erythromycin-resistant S. pneumoniae isolates from invasive sites and 20 isolates from non-invasive sites were collected; antimicrobial susceptibility was tested, and they were genotyped and serotyped. Gene transfer was studied for selected isolates. The frequency of erm(B) was significantly higher in non-invasive isolates compared to invasive isolates (p = 0.001). For the first time, mef(I) was detected in 1 isolate in Denmark. All tested mef(E) isolates had an identical mef(E) sequence, apart from 1 gene with a point mutation, and mef(E) was correlated to 7 different sero-types. The tested erm(B) sequences were 99.3% similar with 5 point mutations at different positions distributed among different serotypes, which did not cause a detectable influence on the protein. Transformation was detectable in 5 out of 13 isolates and transfer of erm(B), mef(I) and mef(E) was detected. To our knowledge, this is the first time mef(I) has been proved transformable. Gene transfer by conjugation was not detectable. Erythromycin resistance in pneumococcal isolates is likely to be caused primarily by horizontal spread of mef(E) and erm(B), as well as clonal spread of a serotype 14 strain carrying mef(A) primarily detected in invasive isolates.
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Affiliation(s)
- Karen L Nielsen
- National Centre for Antimicrobials and Infection Control, Statens Serum Institut, Copenhagen, Denmark.
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Santoro F, Oggioni MR, Pozzi G, Iannelli F. Nucleotide sequence and functional analysis of the tet (M)-carrying conjugative transposon Tn5251 of Streptococcus pneumoniae. FEMS Microbiol Lett 2010; 308:150-8. [PMID: 20487027 DOI: 10.1111/j.1574-6968.2010.02002.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The Tn916-like genetic element Tn5251 is part of the composite conjugative transposon (CTn) Tn5253 of Streptococcus pneumoniae, a 64.5-kb chromosomal element originally called Omega(cat-tet) BM6001. DNA sequence analysis showed that Tn5251 is 18 033-bp long and contains 22 ORFs, 20 of which have the same direction of transcription. Annotation was possible for 11 out of 22 ORFs, including the tet(M) tetracycline resistance gene and int and xis involved in the integration/excision process. Autonomous copies of Tn5251 were generated during matings of Tn5253-containing donors with S. pneumoniae and Enterococcus faecalis. Tn5251 was shown to integrate at different sites in the bacterial chromosome. It behaves as a fully functional CTn capable of independent conjugal transfer to a variety of bacterial species including S. pneumoniae, Streptococcus gordonii, Streptococcus pyogenes, Streptococcus agalactiae, E. faecalis and Bacillus subtilis. The excision of Tn5251 produces a circular intermediate and a deletion in Tn5253 at a level of 1.2 copies per 10(5) chromosomes.
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Affiliation(s)
- Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology (LAMMB), Department of Molecular Biology, University of Siena, Siena, Italy
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Takaya A, Kitagawa N, Kuroe Y, Endo K, Okazaki M, Yokoyama E, Wada A, Yamamoto T. Mutational analysis of reduced telithromycin susceptibility of Streptococcus pneumoniae isolated clinically in Japan. FEMS Microbiol Lett 2010; 307:87-93. [PMID: 20402783 DOI: 10.1111/j.1574-6968.2010.01962.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
A total of 132 Streptococcus pneumoniae isolates collected between 2005 and 2006 in Japan were examined for susceptibility to telithromycin (TEL) and macrolide. The overall resistance to macrolide was 80%. Among the isolates, 128 strains had low-level TEL susceptibility (minimal inhibitory concentrations [MICs] 0.03-1 microg mL(-1)), suggesting that pneumococci with reduced susceptibility to TEL have appeared without prior exposure to the drug, although none of the isolates were assigned as TEL-resistant (breakpoint, > or = 4 microg mL(-1)). Eight of these isolates (MIC 0.5-1 microg mL(-1)) were analyzed for macrolide resistance determinants and genetic relatedness. They all carried mefE-mel, which encodes the macrolide efflux genetic assembly, and three also harbored ermB, which encodes rRNA methylase. Allele replacement mutagenesis of the corresponding genes in the clinical isolates revealed that reduced TEL susceptibility (MIC 1 microg mL(-1)) in S. pneumoniae may be caused by acquisition of the mefE-mel element only and additionally conferred by the ermB determinant.
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Affiliation(s)
- Akiko Takaya
- Department of Microbiology and Molecular Genetics, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Japan
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Abstract
Drug efflux pumps play a key role in drug resistance and also serve other functions in bacteria. There has been a growing list of multidrug and drug-specific efflux pumps characterized from bacteria of human, animal, plant and environmental origins. These pumps are mostly encoded on the chromosome, although they can also be plasmid-encoded. A previous article in this journal provided a comprehensive review regarding efflux-mediated drug resistance in bacteria. In the past 5 years, significant progress has been achieved in further understanding of drug resistance-related efflux transporters and this review focuses on the latest studies in this field since 2003. This has been demonstrated in multiple aspects that include but are not limited to: further molecular and biochemical characterization of the known drug efflux pumps and identification of novel drug efflux pumps; structural elucidation of the transport mechanisms of drug transporters; regulatory mechanisms of drug efflux pumps; determining the role of the drug efflux pumps in other functions such as stress responses, virulence and cell communication; and development of efflux pump inhibitors. Overall, the multifaceted implications of drug efflux transporters warrant novel strategies to combat multidrug resistance in bacteria.
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Affiliation(s)
- Xian-Zhi Li
- Human Safety Division, Veterinary Drugs Directorate, Health Products and Food Branch, Health Canada, Ottawa, Ontario K1A OK9, Canada
| | - Hiroshi Nikaido
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3202, USA
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Roberts AP, Mullany P. A modular master on the move: the Tn916 family of mobile genetic elements. Trends Microbiol 2009; 17:251-8. [PMID: 19464182 DOI: 10.1016/j.tim.2009.03.002] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2008] [Revised: 03/18/2009] [Accepted: 03/25/2009] [Indexed: 10/20/2022]
Abstract
The Tn916 family is a group of mobile genetic elements that are widespread among many commensal and pathogenic bacteria. These elements are found primarily, but not exclusively, in the Firmicutes. They are integrated into the bacterial genome and are capable of conjugative transfer to a new host and, often, intracellular transposition to a different genomic site - hence their name: 'conjugative transposons', or 'integrative conjugative elements'. An increasing variety of Tn916 relatives are being reported from different bacteria, harbouring genes coding for resistance to various antibiotics and the potential to encode other functions, such as lantibiotic immunity. This family of mobile genetic elements has an extraordinary ability to acquire accessory genes, making them important vectors in the dissemination of various traits among environmental, commensal and clinical bacteria. These elements are also responsible for genome rearrangements, providing considerable raw material on which natural selection can act. Therefore, the study of this family of mobile genetic elements is essential for a better understanding and control of the current rise of antibiotic resistance among pathogenic bacteria.
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Affiliation(s)
- Adam P Roberts
- Division of Microbial Diseases, UCL Eastman Dental Institute, 256 Gray's Inn Road, London, WC1X 8LD, UK.
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Characterization of macrolide efflux pump mef subclasses detected in clinical isolates of Streptococcus pyogenes isolated between 1999 and 2005. Antimicrob Agents Chemother 2009; 53:1921-5. [PMID: 19258262 DOI: 10.1128/aac.01065-08] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The macrolide efflux mechanism of resistance, mef, was characterized in community-acquired respiratory tract infections with Streptococcus pyogenes. Fifty-four (4.6%) M phenotype isolates were screen tested as negative for mef(A). Of these 54 isolates, 5 (0.4%), 27 (2.3%), and 1 (0.1%) were considered to be mef(I) positive, a novel mosaic variant of mef, or a novel subclass of mef, respectively. This study shows (i) the definitive presence of mef(E) in S. pyogenes and its global distribution, (ii) the presence of a mosaic variant of mef composed of mef(A) and mef(E), (iii) the previously undescribed presence of mef(I) in S. pyogenes, and (iv) the presence of a novel subclass of mef in S. pyogenes.
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Santagati M, Lupo A, Scillato M, Di Martino A, Stefani S. Conjugal mobilization of the mega element carryingmef(E) fromStreptococcus salivariustoStreptococcus pneumoniae. FEMS Microbiol Lett 2009; 290:79-84. [DOI: 10.1111/j.1574-6968.2008.01408.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Genetic elements responsible for erythromycin resistance in streptococci. Antimicrob Agents Chemother 2008; 53:343-53. [PMID: 19001115 DOI: 10.1128/aac.00781-08] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Soge OO, Beck NK, White TM, No DB, Roberts MC. A novel transposon, Tn6009, composed of a Tn916 element linked with a Staphylococcus aureus mer operon. J Antimicrob Chemother 2008; 62:674-80. [PMID: 18583328 DOI: 10.1093/jac/dkn255] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES The aim of this study was to characterize a novel conjugative transposon Tn6009 composed of a Tn916 linked to a Staphylococcus aureus mer operon in representative Gram-positive and Gram-negative bacteria isolated in Nigeria and Portugal. METHODS Eighty-three Gram-positive and 34 Gram-negative bacteria were screened for the presence of the Tn6009 using DNA-DNA hybridization, PCR, hybridization of PCR products, sequencing and mating experiments by established procedures. RESULTS Forty-three oral and 23 urine Gram-negative and Gram-positive isolates carried the Tn6009. Sequencing was performed to verify the direct linkage between the mer resistance genes and the tet(M) gene. A Nigerian Klebsiella pneumoniae, isolated from a urinary tract infection patient, and one commensal isolate from each of the other Tn6009-positive genera, Serratia liquefaciens, Pseudomonas sp., Enterococcus sp. and Streptococcus sp. isolated from the oral and urine samples of healthy Portuguese children, were able to act as donors and conjugally transfer the Tn6009 to the Enterococcus faecalis JH2-2 recipient, resulting in tetracycline- and mercury-resistant E. faecalis transconjugants. CONCLUSIONS This study reports a novel non-composite conjugative transposon Tn6009 containing a Tn916 element linked to an S. aureus mer operon carrying genes coding for inorganic mercury resistance (merA), an organic mercury resistance (merB), a regulatory protein (merR) and a mercury transporter (merT). This transposon was identified in 66 isolates from two Gram-positive and three Gram-negative genera and is the first transposon in the Tn916 family to carry the Gram-positive mer genes directly linked to the tet(M) gene.
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Affiliation(s)
- Olusegun O Soge
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
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Simjee S, McDermott PF, White DG, Hofacre C, Berghaus RD, Carter PJ, Stewart L, Liu T, Maier M, Maurer JJ. Antimicrobial susceptibility and distribution of antimicrobial-resistance genes among Enterococcus and coagulase-negative Staphylococcus isolates recovered from poultry litter. Avian Dis 2008; 51:884-92. [PMID: 18251398 DOI: 10.1637/7973-032607-regr.1] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Data on the prevalence of antimicrobial resistant enterococci and staphylococci from the poultry production environment are sparse in the United States. This information is needed for science-based risk assessments of antimicrobial use in animal husbandry and potential public-health consequences. In this study, we assessed the susceptibility of staphylococci and enterococci isolated from poultry litter, recovered from 24 farms across Georgia, to several antimicrobials of veterinary and human health importance. Among the 90 Enterococcus isolates recovered, E. hirae (46%) was the most frequently encountered species, followed by E. faecium (27%), E. gallinarum (12%), and E. faecalis (10%). Antimicrobial resistance was most often observed to tetracycline (96%), followed by clindamycin (90%), quinupristin-dalfopristin (62%), penicillin (53%), erythromycin (50%), nitrofurantoin (49%), and clarithromycin (48%). Among the 110 staphylococci isolates recovered, only coagulase-negative staphylococci (CNS) were identified with the predominant Staphylococcus species being S. sciuri (38%), S. lentus (21%), S. xylosus (14%) and S. simulans (12%). Resistance was less-frequently observed among the Staphylococcus isolates for the majority of antimicrobials tested, as compared with Enterococcus isolates, and was primarily limited to clarithromycin (71%), erythromycin (71%), clindamycin (48%), and tetracycline (38%). Multidrug resistance (MDR) phenotypes were prevalent in both Enterococcus and Staphylococcus; however, Enterococcus exhibited a statistically significant difference in the median number of antimicrobials to which resistance was observed (median = 5.0) compared with Staphylococcus species (median = 3.0). Because resistance to several of these antimicrobials in gram-positive bacteria may be attributed to the shuttling of common drug-resistance genes, we also determined which common antimicrobial-resistance genes were present in both enterococci and staphylococci. The antimicrobial resistance genes vat(D) and erm(B) were present in enterococci, vgaB in staphylococci, and mobile genetic elements Tn916 and pheromone-inducible plasmids were only identified in enterococci. These data suggest that the disparity in antimicrobial-resistance phenotypes and genotypes between enterococci and staphylococci isolated from the same environment is, in part, because of barriers preventing exchange of mobile DNA elements.
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Affiliation(s)
- Shabbir Simjee
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, MD 20708, USA
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