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Chanchaithong P, Chueahiran S, Pinpimai K, Sroithongkham P, Leelapsawas C, Indra R, Yindee J, Chuanchuen R. Chromosomal and plasmid localization of ileS2 in high-level mupirocin-resistant Staphylococcus pseudintermedius and Staphylococcus aureus isolated from canine and feline origins. J Antimicrob Chemother 2024; 79:1856-1864. [PMID: 38863334 DOI: 10.1093/jac/dkae172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 05/11/2024] [Indexed: 06/13/2024] Open
Abstract
OBJECTIVES To characterize the mobile genetic elements and genetic localization of ileS2 in high-level mupirocin-resistant (Hi-MupR) methicillin-resistant Staphylococcus pseudintermedius (MRSP) and MRSA isolates recovered from canine and feline clinical samples. METHODS The identification of bacterial species and presence of mecA and ileS2 genes in MRSP and MRSA isolates were performed using MALDI-TOF MS and PCR, respectively. Antimicrobial resistance (AMR) phenotypes were determined by broth microdilution assays. The genome characteristics, ileS2-containing elements and staphylococcal cassette chromosome mec (SCCmec) were illustrated using complete circular genomes obtained from hybrid assembly of Illumina short-reads and Oxford Nanopore Technologies long-reads. These were analysed through phylogenetic and bioinformatics approaches. RESULTS A total of 18 MRSP clinical isolates and four MRSA clinical isolates exhibited the Hi-MupR phenotype and carried multiple AMR genes, including mecA and ileS2 genes. MRSP ST182-SCCmec V (n = 6) and ST282-ΨSCCmec57395-t10 (n = 4) contained the ileS2 transposable unit associated with IS257 on the chromosome. Three MRSA ST398-SCCmec V-t034/t4652 isolates carried ∼42 kb pSK41-like ileS2 plasmids, whereas similar ileS2 plasmids lacking tra genes were found in MRSP ST282-ΨSCCmec57395-t72/t21 isolates. Furthermore, a new group of ileS2 plasmids, carried by MRSP ST45-ΨSCCmec57395, ST433-ΨSCCmecKW21-t05 and ST2165-SCCmec IV-t06, and by one MRSA ST398-SCCmec V-t034 strain, shared the plasmid backbone with the cfr/fexA-carrying plasmid pM084526_1 in MRSA ST398. CONCLUSIONS This study provides the first evidence of ileS2 integration into the S. pseudintermedius chromosome, which is a rare occurrence in staphylococcal species, and plasmids played a pivotal role in dissemination of ileS2 in both staphylococcal species.
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Affiliation(s)
- Pattrarat Chanchaithong
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Surawit Chueahiran
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Komkiew Pinpimai
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Parinya Sroithongkham
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Chavin Leelapsawas
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rusmin Indra
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Jitrapa Yindee
- Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Rungtip Chuanchuen
- Research Unit in Microbial Food Safety and Antimicrobial Resistance, Chulalongkorn University, Bangkok, 10330, Thailand
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, 10330, Thailand
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Robertson A, Sall J, Venzon M, Olivas JJ, Zheng X, Cammer M, Antao N, Zhou C, Devlin JC, Saes Thur R, Bethony J, Nejsum P, Shopsin B, Torres VJ, Liang FX, Cadwell K. Bacterial contact induces polar plug disintegration to mediate whipworm egg hatching. PLoS Pathog 2023; 19:e1011647. [PMID: 37738244 PMCID: PMC10550136 DOI: 10.1371/journal.ppat.1011647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 10/04/2023] [Accepted: 08/30/2023] [Indexed: 09/24/2023] Open
Abstract
The bacterial microbiota promotes the life cycle of the intestine-dwelling whipworm Trichuris by mediating hatching of parasite eggs ingested by the mammalian host. Despite the enormous disease burden associated with Trichuris colonization, the mechanisms underlying this transkingdom interaction have been obscure. Here, we used a multiscale microscopy approach to define the structural events associated with bacteria-mediated hatching of eggs for the murine model parasite Trichuris muris. Through the combination of scanning electron microscopy (SEM) and serial block face SEM (SBFSEM), we visualized the outer surface morphology of the shell and generated 3D structures of the egg and larva during the hatching process. These images revealed that exposure to hatching-inducing bacteria catalyzed asymmetric degradation of the polar plugs prior to exit by the larva. Unrelated bacteria induced similar loss of electron density and dissolution of the structural integrity of the plugs. Egg hatching was most efficient when high densities of bacteria were bound to the poles. Consistent with the ability of taxonomically distant bacteria to induce hatching, additional results suggest chitinase released from larva within the eggs degrade the plugs from the inside instead of enzymes produced by bacteria in the external environment. These findings define at ultrastructure resolution the evolutionary adaptation of a parasite for the microbe-rich environment of the mammalian gut.
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Affiliation(s)
- Amicha Robertson
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Joseph Sall
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America
- Department of Cell Biology, New York University Grossman School of Medicine, New York New York, United States of America
| | - Mericien Venzon
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Janet J. Olivas
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Xuhui Zheng
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Michael Cammer
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America
- Department of Cell Biology, New York University Grossman School of Medicine, New York New York, United States of America
| | - Noelle Antao
- Department of Cell Biology, New York University Grossman School of Medicine, New York New York, United States of America
| | - Chunyi Zhou
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
- Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Joseph C. Devlin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Rafaela Saes Thur
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC, United States of America
| | - Jeffrey Bethony
- Department of Microbiology, Immunology and Tropical Medicine, George Washington University, Washington DC, United States of America
| | - Peter Nejsum
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Bo Shopsin
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
- Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, United States of America
- Department of Medicine, Division of Infectious Diseases, New York University Grossman School of Medicine, New York, New York, United States of America
| | - Victor J. Torres
- Department of Microbiology, New York University Grossman School of Medicine, New York, New York, United States of America
- Antimicrobial-Resistant Pathogens Program, New York University Langone Health, New York, New York, United States of America
| | - Feng-Xia Liang
- Microscopy Laboratory, Division of Advanced Research Technologies, New York University Langone Health, New York, New York, United States of America
- Department of Cell Biology, New York University Grossman School of Medicine, New York New York, United States of America
| | - Ken Cadwell
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
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3
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Spreading of cfr-Carrying Plasmids among Staphylococci from Humans and Animals. Microbiol Spectr 2022; 10:e0246122. [PMID: 36413029 PMCID: PMC9769919 DOI: 10.1128/spectrum.02461-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The multidrug resistance gene cfr mediates resistance to multiple antimicrobial agents, including linezolid. Plasmids are the preferred vector for the dissemination of cfr. However, the presence and transmission of cfr-carrying plasmids among staphylococci from humans and animals have rarely been studied. Here, we investigated the presence of the cfr gene in 2,250 staphylococci of human clinical origin collected in Zhejiang, China, in 1998 to 2021 and in 3,329 porcine staphylococci preserved in our laboratories. The cfr gene was detected in 38 human isolates; its presence in Staphylococcus haemolyticus and Staphylococcus cohnii in 2003 was earlier than that identified in 2005, and Staphylococcus capitis (n = 30) was the predominant species. The cfr-carrying fragment in 38 isolates exhibited >99% nucleotide sequence similarity to plasmid pLRSA417 (39,504 bp), which was identified in 2015 and originated from a human clinical methicillin-resistant Staphylococcus aureus isolate from Zhejiang, China. The cfr-carrying plasmids in 18 MinION-sequenced staphylococci ranged in size from 32,697 bp to 43,457 bp. Fifteen plasmids were identical to pLRSA417, except for the inversion of an 8.4-kb segment comprising IS256-aacA/aphD-ISEnfa4_1-cfr-ISEnfa4_2, while the remaining 3 plasmids exhibited slightly different structures. Among the 114 cfr-positive staphylococci from pigs, pLRSA417-like plasmids were detected in 3 isolates. Intraspecies and interspecies conjugation occurred in human-derived pLRSA417-like plasmids. The presence of pLRSA417-like plasmids in staphylococci from multiple geographic regions and different hosts implied the possible transmission of the respective isolates between humans and animals. IMPORTANCE The therapeutic efficacy of the oxazolidinone antimicrobial linezolid is reduced by the emergence and dissemination of the multidrug resistance gene cfr. The cfr-carrying plasmid pLRSA417 was first identified in a clinical methicillin-resistant Staphylococcus aureus isolate, but its presence in staphylococci of human and animal origin has not been reported previously. This study showed that conjugative plasmids similar to pLRSA417 were detected mainly in Staphylococcus capitis and existed in different staphylococci in 2003 to 2021 in various clinical departments in the same hospital. pLRSA417-like plasmids were also present in staphylococci of food animal sources from different geographic regions, which suggested possible transmission among humans and animals.
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Catabolic Ornithine Carbamoyltransferase Activity Facilitates Growth of Staphylococcus aureus in Defined Medium Lacking Glucose and Arginine. mBio 2022; 13:e0039522. [PMID: 35475645 PMCID: PMC9239276 DOI: 10.1128/mbio.00395-22] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Previous studies have found that arginine biosynthesis in Staphylococcus aureus is repressed via carbon catabolite repression (CcpA), and proline is used as a precursor. Unexpectedly, however, robust growth of S. aureus is not observed in complete defined medium lacking both glucose and arginine (CDM-R). Mutants able to grow on agar-containing defined medium lacking arginine (CDM-R) were selected and found to contain mutations within ahrC, encoding the canonical arginine biosynthesis pathway repressor (AhrC), or single nucleotide polymorphisms (SNPs) upstream of the native arginine deiminase (ADI) operon arcA1B1D1C1. Reverse transcription-PCR (RT-PCR) studies found that mutations within ccpA or ahrC or SNPs identified upstream of arcA1B1D1C1 increased the transcription of both arcB1 and argGH, encoding ornithine carbamoyltransferase and argininosuccinate synthase/lyase, respectively, facilitating arginine biosynthesis. Furthermore, mutations within the AhrC homologue argR2 facilitated robust growth within CDM-R. Complementation with arcB1 or arcA1B1D1C1, but not argGH, rescued growth in CDM-R. Finally, supplementation of CDM-R with ornithine stimulated growth, as did mutations in genes (proC and rocA) that presumably increased the pyrroline-5-carboxylate and ornithine pools. Collectively, these data suggest that the transcriptional regulation of ornithine carbamoyltransferase and, in addition, the availability of intracellular ornithine pools regulate arginine biosynthesis in S. aureus in the absence of glucose. Surprisingly, ~50% of clinical S. aureus isolates were able to grow in CDM-R. These data suggest that S. aureus is selected to repress arginine biosynthesis in environments with or without glucose; however, mutants may be readily selected that facilitate arginine biosynthesis and growth in specific environments lacking arginine.
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5
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Abstract
Strains of Staphylococcus aureus, and to a lesser extent other staphylococcal species, are a significant cause of morbidity and mortality. An important factor in the notoriety of these organisms stems from their frequent resistance to many antimicrobial agents used for chemotherapy. This review catalogues the variety of mobile genetic elements that have been identified in staphylococci, with a primary focus on those associated with the recruitment and spread of antimicrobial resistance genes. These include plasmids, transposable elements such as insertion sequences and transposons, and integrative elements including ICE and SCC elements. In concert, these diverse entities facilitate the intra- and inter-cellular gene mobility that enables horizontal genetic exchange, and have also been found to play additional roles in modulating gene expression and genome rearrangement.
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6
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Partridge SR, Kwong SM, Firth N, Jensen SO. Mobile Genetic Elements Associated with Antimicrobial Resistance. Clin Microbiol Rev 2018; 31:e00088-17. [PMID: 30068738 PMCID: PMC6148190 DOI: 10.1128/cmr.00088-17] [Citation(s) in RCA: 1189] [Impact Index Per Article: 198.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Strains of bacteria resistant to antibiotics, particularly those that are multiresistant, are an increasing major health care problem around the world. It is now abundantly clear that both Gram-negative and Gram-positive bacteria are able to meet the evolutionary challenge of combating antimicrobial chemotherapy, often by acquiring preexisting resistance determinants from the bacterial gene pool. This is achieved through the concerted activities of mobile genetic elements able to move within or between DNA molecules, which include insertion sequences, transposons, and gene cassettes/integrons, and those that are able to transfer between bacterial cells, such as plasmids and integrative conjugative elements. Together these elements play a central role in facilitating horizontal genetic exchange and therefore promote the acquisition and spread of resistance genes. This review aims to outline the characteristics of the major types of mobile genetic elements involved in acquisition and spread of antibiotic resistance in both Gram-negative and Gram-positive bacteria, focusing on the so-called ESKAPEE group of organisms (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., and Escherichia coli), which have become the most problematic hospital pathogens.
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Affiliation(s)
- Sally R Partridge
- Centre for Infectious Diseases and Microbiology, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Slade O Jensen
- Microbiology and Infectious Diseases, School of Medicine, Western Sydney University, Sydney, New South Wales, Australia
- Antibiotic Resistance & Mobile Elements Group, Ingham Institute for Applied Medical Research, Sydney, New South Wales, Australia
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7
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Abstract
Staphylococcus aureus is a serious human pathogen with remarkable adaptive powers. Antibiotic-resistant clones rapidly emerge mainly by acquisition of antibiotic-resistance genes from other S. aureus strains or even from other genera. Transfer is mediated by a diverse complement of mobile genetic elements and occurs primarily by conjugation or bacteriophage transduction, with the latter traditionally being perceived as the primary route. Recent work on conjugation and transduction suggests that transfer by these mechanisms may be more extensive than previously thought, in terms of the range of plasmids that can be transferred by conjugation and the efficiency with which transduction occurs. Here, we review the main routes of antibiotic resistance gene transfer in S. aureus in the context of its biology as a human commensal and a life-threatening pathogen.
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Affiliation(s)
- Jakob Haaber
- Department of Veterinary and Animal Sciences, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Hanne Ingmer
- Department of Veterinary and Animal Sciences, Faculty of Health & Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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8
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Conjugative Transfer in Staphylococcus aureus. Methods Mol Biol 2016; 1373:83-7. [PMID: 26194708 DOI: 10.1007/7651_2015_276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The acquisition of plasmids has led to a significant increase in antimicrobial resistance within the staphylococci. In order to study these plasmids effectively, one must be able move the plasmid DNA into genetically clean backgrounds. While the smaller staphylococcal class I (1-5 kb) and class II (10-30 kb) plasmids are readily transferred using bacteriophage transduction or electroporation, these methods are inefficient at moving the larger class III (30-60 kb) plasmids. This review describes methods to transfer class III plasmids via conjugative mobilization.
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9
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Ramsay JP, Kwong SM, Murphy RJT, Yui Eto K, Price KJ, Nguyen QT, O'Brien FG, Grubb WB, Coombs GW, Firth N. An updated view of plasmid conjugation and mobilization in Staphylococcus. Mob Genet Elements 2016; 6:e1208317. [PMID: 27583185 PMCID: PMC4993578 DOI: 10.1080/2159256x.2016.1208317] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 06/15/2016] [Accepted: 06/23/2016] [Indexed: 11/13/2022] Open
Abstract
The horizontal gene transfer facilitated by mobile genetic elements impacts almost all areas of bacterial evolution, including the accretion and dissemination of antimicrobial-resistance genes in the human and animal pathogen Staphylococcus aureus. Genome surveys of staphylococcal plasmids have revealed an unexpected paucity of conjugation and mobilization loci, perhaps suggesting that conjugation plays only a minor role in the evolution of this genus. In this letter we present the DNA sequences of historically documented staphylococcal conjugative plasmids and highlight that at least 3 distinct and widely distributed families of conjugative plasmids currently contribute to the dissemination of antimicrobial resistance in Staphylococcus. We also review the recently documented "relaxase-in trans" mechanism of conjugative mobilization facilitated by conjugative plasmids pWBG749 and pSK41, and discuss how this may facilitate the horizontal transmission of around 90% of plasmids that were previously considered non-mobilizable. Finally, we enumerate unique sequenced S. aureus plasmids with a potential mechanism of mobilization and predict that at least 80% of all non-conjugative S. aureus plasmids are mobilizable by at least one mechanism. We suggest that a greater research focus on the molecular biology of conjugation is essential if we are to recognize gene-transfer mechanisms from our increasingly in silico analyses.
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Affiliation(s)
- Joshua P. Ramsay
- School of Biomedical Sciences and Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
- ACCESS Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Stephen M. Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Riley J. T. Murphy
- School of Biomedical Sciences and Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
- ACCESS Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Karina Yui Eto
- School of Biomedical Sciences and Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
- ACCESS Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, WA, Australia
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA, Australia
| | - Karina J. Price
- School of Biomedical Sciences and Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Quang T. Nguyen
- School of Biomedical Sciences and Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Frances G. O'Brien
- ACCESS Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Warren B. Grubb
- ACCESS Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Geoffrey W. Coombs
- ACCESS Typing and Research, School of Veterinary Sciences and Life Sciences, Murdoch University and School of Biomedical Sciences, Curtin University, Perth, WA, Australia
- PathWest Laboratory Medicine–WA, Fiona Stanley Hospital, Perth, WA, Australia
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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Processing of Nonconjugative Resistance Plasmids by Conjugation Nicking Enzyme of Staphylococci. J Bacteriol 2016; 198:888-97. [PMID: 26728193 DOI: 10.1128/jb.00832-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 12/19/2015] [Indexed: 01/17/2023] Open
Abstract
UNLABELLED Antimicrobial resistance in Staphylococcus aureus presents an increasing threat to human health. This resistance is often encoded on mobile plasmids, such as pSK41; however, the mechanism of transfer of these plasmids is not well understood. In this study, we first examine key protein-DNA interactions formed by the relaxase enzyme, NES, which initiates and terminates the transfer of the multidrug resistance plasmid pSK41. Two loops on the NES protein, hairpin loops 1 and 2, form extensive contacts with the DNA hairpin formed at the oriT region of pSK41, and here we establish that these contacts are essential for proper DNA cleavage and religation by the full 665-residue NES protein in vitro. Second, pSK156 and pCA347 are nonconjugative Staphylococcus aureus plasmids that contain sequences similar to the oriT region of pSK41 but differ in the sequence predicted to form a DNA hairpin. We show that pSK41-encoded NES is able to bind, cleave, and religate the oriT sequences of these nonconjugative plasmids in vitro. Although pSK41 could mobilize a coresident plasmid harboring its cognate oriT, it was unable to mobilize plasmids containing the pSK156 and pCA347 variant oriT mimics, suggesting that an accessory protein like that previously shown to confer specificity in the pWBG749 system may also be involved in transmission of plasmids containing a pSK41-like oriT. These data indicate that the conjugative relaxase in trans mechanism recently described for the pWBG749 family of plasmids also applies to the pSK41 family of plasmids, further heightening the potential significance of this mechanism in the horizontal transfer of staphylococcal plasmids. IMPORTANCE Understanding the mechanism of antimicrobial resistance transfer in bacteria such as Staphylococcus aureus is an important step toward potentially slowing the spread of antimicrobial-resistant infections. This work establishes protein-DNA interactions essential for the transfer of the Staphylococcus aureus multiresistance plasmid pSK41 by its relaxase, NES. This enzyme also processed variant oriT-like sequences found on numerous plasmids previously considered nontransmissible, suggesting that in conjunction with an uncharacterized accessory protein, these plasmids may be transferred horizontally via a relaxase in trans mechanism. These findings have important implications for our understanding of staphylococcal resistance plasmid evolution.
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11
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Abstract
Whole genome sequencing and microarrays have revealed the population structure of Staphylococcus aureus, and identified epidemiological shifts, transmission routes, and adaptation of major clones. S. aureus genomes are highly diverse. This is partly due to a population structure of conserved lineages, each with unique combinations of genes encoding surface proteins, regulators, immune evasion and virulence pathways. Even more variable are the mobile genetic elements (MGE), which encode key proteins for antibiotic resistance, virulence and host-adaptation. MGEs can transfer at high frequency between isolates of the same lineage by horizontal gene transfer (HGT). There is increasing evidence that HGT is key to bacterial adaptation and success. Recent studies have shed light on new mechanisms of DNA transfer such as transformation, the identification of receptors for transduction, on integration of DNA pathways, mechanisms blocking transfer including CRISPR and new restriction systems, strategies for evasion of restriction barriers, as well as factors influencing MGE selection and stability. These studies have also lead to new tools enabling construction of genetically modified clinical S. aureus isolates. This review will focus on HGT mechanisms and their importance in shaping the evolution of new clones adapted to antibiotic resistance, healthcare, communities and livestock.
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Takahata M, Toh H, Nakano A, Takagi M, Murakami M, Ishii Y, Takizawa T, Tanabe S, Morita H. Complete sequence analysis of two cryptic plasmids from Bifidobacterium kashiwanohense JCM 15439 (type strain) isolated from healthy infant feces. Anim Sci J 2013; 85:158-63. [PMID: 23865717 DOI: 10.1111/asj.12095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 04/18/2013] [Indexed: 11/26/2022]
Abstract
Bifidobacterial plasmids reported so far are derived from a limited number of strains and plasmids of bifidobacterial type strains isolated from humans are unknown. We found that Bifidobacterium kashiwanohense JCM 15439 (type strain) isolated from a healthy infant contained two cryptic plasmids, designated pBBKW-1 and pBBKW-2. We determined and analyzed the complete sequences of both plasmids. pBBKW-1 (7716 bp) was predicted to replicate by a rolling-circle mechanism and encode six protein-coding genes, two of which are putative replication proteins. pBBKW-1 seems to be a cointegrate plasmid containing two copies of the plasmid pMG1 from Bifidobacterium longum. pBBKW-2 (2920 bp) was predicted to encode six protein-coding genes and be a theta-type replicating plasmid, which has been reported to be more stable than a rolling circle-type replicating plasmid frequently found in bifidobacteria. Our finding will provide new insights into safe recombinant plasmid constructions for humans.
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Affiliation(s)
- Muneaki Takahata
- School of Veterinary Medicine, Azabu University, Sagamihara; BioBank Co., Ltd, Okayama
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13
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Liu MA, Kwong SM, Jensen SO, Brzoska AJ, Firth N. Biology of the staphylococcal conjugative multiresistance plasmid pSK41. Plasmid 2013; 70:42-51. [PMID: 23415796 DOI: 10.1016/j.plasmid.2013.02.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/01/2013] [Accepted: 02/03/2013] [Indexed: 11/27/2022]
Abstract
Plasmid pSK41 is a large, low-copy-number, conjugative plasmid from Staphylococcus aureus that is representative of a family of staphylococcal plasmids that confer multiple resistances to a wide range of antimicrobial agents. The plasmid consists of a conserved plasmid backbone containing the genes for plasmid housekeeping functions, which is punctuated by copies of IS257 that flank a Tn4001-hybrid structure and cointegrated plasmids that harbour resistance genes. This review summarises the current understanding of the biology of pSK41, focussing on the systems responsible for its replication, maintenance and transmission, and their regulation.
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Affiliation(s)
- Michael A Liu
- School of Biological Sciences, University of Sydney, NSW 2006, Australia
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14
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Molecular basis of antibiotic multiresistance transfer in Staphylococcus aureus. Proc Natl Acad Sci U S A 2013; 110:2804-9. [PMID: 23359708 DOI: 10.1073/pnas.1219701110] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Multidrug-resistant Staphylococcus aureus infections pose a significant threat to human health. Antibiotic resistance is most commonly propagated by conjugative plasmids like pLW1043, the first vancomycin-resistant S. aureus vector identified in humans. We present the molecular basis for resistance transmission by the nicking enzyme in S. aureus (NES), which is essential for conjugative transfer. NES initiates and terminates the transfer of plasmids that variously confer resistance to a range of drugs, including vancomycin, gentamicin, and mupirocin. The NES N-terminal relaxase-DNA complex crystal structure reveals unique protein-DNA contacts essential in vitro and for conjugation in S. aureus. Using this structural information, we designed a DNA minor groove-targeted polyamide that inhibits NES with low micromolar efficacy. The crystal structure of the 341-residue C-terminal region outlines a unique architecture; in vitro and cell-based studies further establish that it is essential for conjugation and regulates the activity of the N-terminal relaxase. This conclusion is supported by a small-angle X-ray scattering structure of a full-length, 665-residue NES-DNA complex. Together, these data reveal the structural basis for antibiotic multiresistance acquisition by S. aureus and suggest novel strategies for therapeutic intervention.
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Onyibe J, Oluwole O, Ogunbanwo S, Sanni A. Antibiotic Susceptibility Profile and Survival of Bifidobacterium adolescentis and Bifidobacterium catenulatum of Human and Avian Origin in Stored Yoghurt. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/s0189-7241(15)30079-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Nuxoll AS, Halouska SM, Sadykov MR, Hanke ML, Bayles KW, Kielian T, Powers R, Fey PD. CcpA regulates arginine biosynthesis in Staphylococcus aureus through repression of proline catabolism. PLoS Pathog 2012; 8:e1003033. [PMID: 23209408 PMCID: PMC3510247 DOI: 10.1371/journal.ppat.1003033] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 10/01/2012] [Indexed: 12/19/2022] Open
Abstract
Staphylococcus aureus is a leading cause of community-associated and nosocomial infections. Imperative to the success of S. aureus is the ability to adapt and utilize nutrients that are readily available. Genomic sequencing suggests that S. aureus has the genes required for synthesis of all twenty amino acids. However, in vitro experimentation demonstrates that staphylococci have multiple amino acid auxotrophies, including arginine. Although S. aureus possesses the highly conserved anabolic pathway that synthesizes arginine via glutamate, we demonstrate here that inactivation of ccpA facilitates the synthesis of arginine via the urea cycle utilizing proline as a substrate. Mutations within putA, rocD, arcB1, argG and argH abolished the ability of S. aureus JE2 ccpA::tetL to grow in the absence of arginine, whereas an interruption in argJBCF, arcB2, or proC had no effect. Furthermore, nuclear magnetic resonance demonstrated that JE2 ccpA::ermB produced 13C5 labeled arginine when grown with 13C5 proline. Taken together, these data support the conclusion that S. aureus synthesizes arginine from proline during growth on secondary carbon sources. Furthermore, although highly conserved in all sequenced S. aureus genomes, the arginine anabolic pathway (ArgJBCDFGH) is not functional under in vitro growth conditions. Finally, a mutation in argH attenuated virulence in a mouse kidney abscess model in comparison to wild type JE2 demonstrating the importance of arginine biosynthesis in vivo via the urea cycle. However, mutations in argB, argF, and putA did not attenuate virulence suggesting both the glutamate and proline pathways are active and they, or their pathway intermediates, can complement each other in vivo. Although Staphylococcus aureus encodes the highly conserved arginine biosynthesis pathway via glutamate, arginine is an essential amino acid. We found that a mutation in ccpA, a gene encoding a protein facilitating carbon catabolite repression, mediates arginine biosynthesis under in vitro growth conditions. However, both genetic and biochemical evidence suggested that a S. aureus ccpA mutant synthesizes arginine via proline and the urea cycle, a pathway not demonstrated in bacteria before. Furthermore, an animal model of S. aureus infection demonstrated the importance of arginine biosynthesis in vivo. This new pathway sheds light on important host-pathogen interactions and suggests S. aureus has evolved to address arginine depletion in the host by synthesizing arginine from a readily available substrate such as proline.
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Affiliation(s)
- Austin S. Nuxoll
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Steven M. Halouska
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Marat R. Sadykov
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Mark L. Hanke
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Kenneth W. Bayles
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Tammy Kielian
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Robert Powers
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America
| | - Paul D. Fey
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
- * E-mail:
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Abstract
Sequence-directed genetic interference pathways control gene expression and preserve genome integrity in all kingdoms of life. The importance of such pathways is highlighted by the extensive study of RNA interference (RNAi) and related processes in eukaryotes. In many bacteria and most archaea, clustered, regularly interspaced short palindromic repeats (CRISPRs) are involved in a more recently discovered interference pathway that protects cells from bacteriophages and conjugative plasmids. CRISPR sequences provide an adaptive, heritable record of past infections and express CRISPR RNAs - small RNAs that target invasive nucleic acids. Here, we review the mechanisms of CRISPR interference and its roles in microbial physiology and evolution. We also discuss potential applications of this novel interference pathway.
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Abstract
Since the discovery in 1899 of bifidobacteria as numerically dominant microbes in the feces of breast-fed infants, there have been numerous studies addressing their role in modulating gut microflora as well as their other potential health benefits. Because of this, they are frequently incorporated into foods as probiotic cultures. An understanding of their full interactions with intestinal microbes and the host is needed to scientifically validate any health benefits they may afford. Recently, the genome sequences of nine strains representing four species of Bifidobacterium became available. A comparative genome analysis of these genomes reveals a likely efficient capacity to adapt to their habitats, with B. longum subsp. infantis exhibiting more genomic potential to utilize human milk oligosaccharides, consistent with its habitat in the infant gut. Conversely, B. longum subsp. longum exhibits a higher genomic potential for utilization of plant-derived complex carbohydrates and polyols, consistent with its habitat in an adult gut. An intriguing observation is the loss of much of this genome potential when strains are adapted to pure culture environments, as highlighted by the genomes of B. animalis subsp. lactis strains, which exhibit the least potential for a gut habitat and are believed to have evolved from the B. animalis species during adaptation to dairy fermentation environments.
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Affiliation(s)
- Ju-Hoon Lee
- Department of Food Science and Nutrition, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Ave., St. Paul, Minnesota 55108
| | - Daniel J. O'Sullivan
- Department of Food Science and Nutrition, Microbial and Plant Genomics Institute, University of Minnesota, 1500 Gortner Ave., St. Paul, Minnesota 55108
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Complete nucleotide sequence and comparative analysis of pPR9, a 41.7-kilobase conjugative staphylococcal multiresistance plasmid conferring high-level mupirocin resistance. Antimicrob Agents Chemother 2010; 54:2252-7. [PMID: 20211895 DOI: 10.1128/aac.01074-09] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have sequenced the conjugative plasmid pPR9, which carries the ileS2 gene, which had contributed to the dissemination of high-level mupirocin resistance at our institution. The plasmid backbone shows extensive genetic conservation with plasmids belonging to the pSK41/pGO1 family, but comparative analyses have revealed key differences that provide important insights into the evolution of these medically important plasmids and high-level mupirocin resistance in staphylococci and highlight the role of insertion sequence IS257 in these processes.
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20
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Self versus non-self discrimination during CRISPR RNA-directed immunity. Nature 2010; 463:568-71. [PMID: 20072129 PMCID: PMC2813891 DOI: 10.1038/nature08703] [Citation(s) in RCA: 449] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2009] [Accepted: 11/25/2009] [Indexed: 12/30/2022]
Abstract
All immune systems must distinguish self from non-self to repel invaders without inducing autoimmunity. Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci protect bacteria and archaea from invasion by phage and plasmid DNA through a genetic interference pathway1–9. CRISPR loci are present in ~ 40% and ~90% of sequenced bacterial and archaeal genomes respectively10 and evolve rapidly, acquiring new spacer sequences to adapt to highly dynamic viral populations1, 11–13. Immunity requires a sequence match between the invasive DNA and the spacers that lie between CRISPR repeats1–9. Each cluster is genetically linked to a subset of the cas (CRISPR-associated) genes14–16 that collectively encode >40 families of proteins involved in adaptation and interference. CRISPR loci encode small CRISPR RNAs (crRNAs) that contain a full spacer flanked by partial repeat sequences2, 17–19. CrRNA spacers are thought to identify targets by direct Watson-Crick pairing with invasive “protospacer” DNA2, 3, but how they avoid targeting the spacer DNA within the encoding CRISPR locus itself is unknown. Here we have defined the mechanism of CRISPR self/non-self discrimination. In Staphylococcus epidermidis, target/crRNA mismatches at specific positions outside of the spacer sequence license foreign DNA for interference, whereas extended pairing between crRNA and CRISPR DNA repeats prevents autoimmunity. Hence, this CRISPR system uses the base-pairing potential of crRNAs not only to specify a target but also to spare the bacterial chromosome from interference. Differential complementarity outside of the spacer sequence is a built-in feature of all CRISPR systems, suggesting that this mechanism is a broadly applicable solution to the self/non-self dilemma that confronts all immune pathways.
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The effect of daily bathing with chlorhexidine on the acquisition of methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus, and healthcare-associated bloodstream infections: Results of a quasi-experimental multicenter trial*. Crit Care Med 2009; 37:1858-65. [DOI: 10.1097/ccm.0b013e31819ffe6d] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Caryl JA, O'Neill AJ. Complete nucleotide sequence of pGO1, the prototype conjugative plasmid from the Staphylococci. Plasmid 2009; 62:35-8. [PMID: 19298835 DOI: 10.1016/j.plasmid.2009.03.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Revised: 03/06/2009] [Accepted: 03/10/2009] [Indexed: 11/25/2022]
Abstract
In view of its historical significance as the prototype class III plasmid from the staphylococci, and its ongoing importance as a laboratory tool, we have determined the complete nucleotide sequence of pGO1. At exactly 54kb, pGO1 is 2-4kb larger than previously reported, and shares extensive ( approximately 31-46kb) regions of near identical DNA sequence with other class III plasmids. In particular, we confirm that pGO1 is almost identical to plasmid pSK41 along the entire length of the latter, but additionally contains a co-integrated copy of plasmid pSK639, which accounts for the difference in size ( approximately 8kb), and the fact that pGO1, but not pSK41, confers resistance to trimethoprim. The pSK639 co-integrant appeared to have undergone mutational inactivation of its mobilization functions, a finding which was confirmed experimentally. Although originally identified through an association with aminoglycoside resistance, the pGO1/pSK41 backbone replicon continues to play a key role in the dissemination of antibiotic resistance determinants in the staphylococci.
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Affiliation(s)
- J A Caryl
- Antimicrobial Research Centre and Institute of Molecular and Cellular Biology, University of Leeds, Garstang Building, Leeds LS2 9JT, United Kingdom
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23
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Marraffini LA, Sontheimer EJ. CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA. Science 2009; 322:1843-5. [PMID: 19095942 DOI: 10.1126/science.1165771] [Citation(s) in RCA: 1197] [Impact Index Per Article: 79.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Horizontal gene transfer (HGT) in bacteria and archaea occurs through phage transduction, transformation, or conjugation, and the latter is particularly important for the spread of antibiotic resistance. Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci confer sequence-directed immunity against phages. A clinical isolate of Staphylococcus epidermidis harbors a CRISPR spacer that matches the nickase gene present in nearly all staphylococcal conjugative plasmids. Here we show that CRISPR interference prevents conjugation and plasmid transformation in S. epidermidis. Insertion of a self-splicing intron into nickase blocks interference despite the reconstitution of the target sequence in the spliced mRNA, which indicates that the interference machinery targets DNA directly. We conclude that CRISPR loci counteract multiple routes of HGT and can limit the spread of antibiotic resistance in pathogenic bacteria.
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Affiliation(s)
- Luciano A Marraffini
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
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24
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LeBard RJ, Jensen SO, Arnaiz IA, Skurray RA, Firth N. A multimer resolution system contributes to segregational stability of the prototypical staphylococcal conjugative multiresistance plasmid pSK41. FEMS Microbiol Lett 2008; 284:58-67. [DOI: 10.1111/j.1574-6968.2008.01190.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Spontaneous deletion of the methicillin resistance determinant, mecA, partially compensates for the fitness cost associated with high-level vancomycin resistance in Staphylococcus aureus. Antimicrob Agents Chemother 2008; 52:1221-9. [PMID: 18212094 DOI: 10.1128/aac.01164-07] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Treatment of infections caused by Staphylococcus aureus is often confounded by the bacterium's ability to develop resistance to chemotherapeutic agents. Methicillin-resistant S. aureus (MRSA) arises through the acquisition of staphylococcal chromosomal cassette mec (SCCmec), a genomic island containing the methicillin resistance determinant, mecA. In contrast, resistance to vancomycin can result from exposure to the drug, a mechanism that is not dependent upon a gene acquisition event. Here we describe three MRSA strains that became resistant to vancomycin during passage in the presence of increasing concentrations of the drug. In each case two derivative strains were isolated, one that had lost mecA and one that retained mecA during passage. Strain 5836VR lost mecA by the site-specific chromosomal excision of SCCmec, while the other two strains (strains 3130VR and VP32) deleted portions of their SCCmec elements in a manner that appeared to involve IS431. Conversion to vancomycin resistance caused a decrease in the growth rate that was partially compensated for by the deletion of mecA. In mixed-culture competition experiments, vancomycin-resistant strains that lacked mecA readily outcompeted their mecA-containing counterparts, suggesting that the loss of mecA during conversion to vancomycin resistance was advantageous to the organism.
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26
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Noto MJ, Archer GL. A subset of Staphylococcus aureus strains harboring staphylococcal cassette chromosome mec (SCCmec) type IV is deficient in CcrAB-mediated SCCmec excision. Antimicrob Agents Chemother 2006; 50:2782-8. [PMID: 16870772 PMCID: PMC1538682 DOI: 10.1128/aac.00032-06] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The gene encoding resistance to beta-lactam antibiotics in the staphylococci is found on the chromosome in a genomic island designated staphylococcal cassette chromosome mec, or SCCmec. In addition to the resistance gene mecA, SCCmec also contains site-specific recombinase genes that are capable of catalyzing the chromosomal excision and reintegration of SCCmec. SCCmec is found in five major isotypes partially defined by the recombinase genes present, either ccrAB or ccrC. Of these, SCCmec type IV is presumed to be mobile in the environment, and this mobility may be partially responsible for the rise in community-associated methicillin-resistant staphylococcal infections. In this study, we investigate the presumptive first step in type IV SCCmec mobility: chromosomal excision of the element. CcrAB from a panel of six Staphylococcus aureus and four Staphylococcus epidermidis strains were able to catalyze chromosomal excision of SCCmec types I and II, indicating that these proteins maintain recombinase activity despite varying by up to 3.7% at the amino acid level. Excision of type IV SCCmec was not universally seen, as a subset of S. aureus strains with type IV SCCmec did not excise their element. These strains are all highly related and represent a lineage of successful community-associated pathogens. In addition, the inability to excise SCCmec in these strains is associated with the insertion of a presumptive mobile element containing the gene for staphylococcal enterotoxin H (seh) immediately downstream of SCCmec on the chromosome. Acquisition of this mobile element, containing a known virulence gene, appears to have stabilized the chromosomal integration of the methicillin resistance gene in these strains.
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Affiliation(s)
- Michael J Noto
- Department of Microbiology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298-0565, USA
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27
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Yang JC, Lessard PA, Sengupta N, Windsor SD, O'brien XM, Bramucci M, Tomb JF, Nagarajan V, Sinskey AJ. TraA is required for megaplasmid conjugation in Rhodococcus erythropolis AN12. Plasmid 2006; 57:55-70. [PMID: 16997374 DOI: 10.1016/j.plasmid.2006.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Revised: 08/01/2006] [Accepted: 08/04/2006] [Indexed: 11/13/2022]
Abstract
Pulsed-field gel electrophoresis (PFGE) revealed three previously uncharacterized megaplasmids in the genome of Rhodococcus erythropolis AN12. These megaplasmids, pREA400, pREA250, and pREA100, are approximately 400, 250, and 100kb, respectively, based on their migration in pulsed-field gels. Genetic screening of an AN12 transposon insertion library showed that two megaplasmids, pREA400, and pREA250, are conjugative. Mobilization frequencies of these AN12 megaplasmids to recipient R. erythropolis SQ1 were determined to be approximately 7x10(-4) and 5x10(-4) events per recipient cell, respectively. It is known for other bacterial systems that a relaxase encoded by the traA gene is required to initiate DNA transfer during plasmid conjugation. Sequences adjacent to the transposon insertion in megaplasmid pREA400 revealed a putative traA-like open reading frame. A targeted gene disruption method was developed to generate a traA mutation in AN12, which allowed us to address the role of the traA gene product for Rhodococcus megaplasmid conjugation. We found that the AN12 traA mutant is no longer capable of transferring the pREA400 megaplasmid to SQ1. Furthermore, we confirmed that the conjugation defect was specifically due to the disruption of the traA gene, as pREA400 megaplasmid conjugation defect is restored with a complementing copy of the traA gene.
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Affiliation(s)
- Joyce C Yang
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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28
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Lee JH, O'Sullivan DJ. Sequence analysis of two cryptic plasmids from Bifidobacterium longum DJO10A and construction of a shuttle cloning vector. Appl Environ Microbiol 2006; 72:527-35. [PMID: 16391088 PMCID: PMC1352255 DOI: 10.1128/aem.72.1.527-535.2006] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bifidobacterium longum DJO10A is a recent human isolate with probiotic characteristics and contains two plasmids, designated pDOJH10L and pDOJH10S. The complete sequences of both these plasmids have now been determined and consist of two circular DNA molecules of 10,073 and 3,661 bp, with G+C contents of 62.2% and 66.2%, respectively. Plasmid pDOJH10L is a cointegrate plasmid consisting of DNA regions exhibiting very high sequence identity to two other B. longum plasmids, pNAC2 (98%) and pKJ50 (96%), together with another region. Interestingly, the rolling circular replication (RCR) regions of both the pNAC2- and pKJ50-like plasmids were disrupted during the recombination event leading to a further recombination event to acquire a functional replicon. This consists of a new fused rep gene and an RCR-type ori consisting of a conserved DnaA box in an AT-rich region followed by four contiguous repeated sequences consistent with an iteron structure and an inverted repeat. The smaller pDOJH10S had no sequence similarity to any other characterized plasmid from bifidobacteria. In addition, it did not contain any features consistent with RCR, which is the replication mechanism proposed for all the bifidobacteria plasmids characterized to date. It did exhibit sequence similarity with several theta replication-related replication proteins from other gram-positive, high-G+C bacteria, with the closest match from a Rhodococcus rhodochrous plasmid, suggesting a theta mechanism of replication. S1 nuclease analysis of both plasmids in B. longum DJO10A revealed single-strand DNA intermediates for pDOJH10L, which is consistent for RCR, but none were detected for pDOJH10S. As the G+C content of pDOJH10S is similar to that of Rhodococcus rhodochrous (67%) and significantly higher than that of B. longum (60.1%), it may have been acquired through horizontal gene transfer from a Rhodococcus species, as both genera are members of the Actinomycetes and are intestinal inhabitants. An Escherichia coli-B. longum shuttle cloning vector was constructed from pDOJH10S and the E. coli ori region of p15A, a lacZ gene with a multiple cloning site of pUC18, and a chloramphenicol resistance gene (CAT) of pCI372 and was transformed successfully into E. coli and B. longum. It could not be introduced into lactic acid bacteria (Lactococcus and Lactobacillus), showing it was not very promiscuous. It was stably maintained in B. longum in the absence of antibiotic pressure for 92 generations, which is consistent with the segregational stability of theta-replicating plasmids in gram-positive bacteria. This is the first cloning vector for bifidobacteria that does not utilize RCR and should be useful for the stable introduction of heterologous genes into these dominant inhabitants of the large intestine.
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Affiliation(s)
- Ju-Hoon Lee
- Cargill Building for Microbial and Plant Genomics, 1500 Gortner Ave., St. Paul, MN 55108.
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29
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Brnáková Z, Farkasovská J, Godány A. The use of bacteriophages in eliminating polyresistant strains of Staphylococcus aureus and Streptococcus agalactiae. Folia Microbiol (Praha) 2005; 50:187-94. [PMID: 16295655 DOI: 10.1007/bf02931564] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Temperate bacteriophages were induced in and released from isolates of Staphylococcus aureus and Streptococcus agalactiae using mitomycin C. Various specific indicator cultures were tested for providing clear plaques after phage infection. Specific lytic mixture of bacteriophages was prepared using the induced, modified and laboratory variants of phages. Under laboratory conditions, the mixture eliminated all isolates from the tested collection of microorganisms. The restriction barrier of some bacterial isolates to bacteriophage infection was overcome either by UV irradiation or in vitro modification of bacteriophage DNA with specific methyltransferases. Conjugative R plasmids, capable of replication in G+ and G- bacteria, were detected and isolated from S. aureus and S. agalactiae antibiotic-resistant strains.
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Affiliation(s)
- Z Brnáková
- Institute of Molecular Biology, Centre of Excellence for Molecular Medicine, Slovak Academy of Sciences, Bratislava, Slovakia
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30
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Rodriguez-Bonano NM, Torres-Bauza LJ. Molecular analysis of oriT and MobA protein in the 7.4 kb mobilizable beta-lactamase plasmid pSJ7.4 from Neisseria gonorrhoeae. Plasmid 2005; 52:89-101. [PMID: 15336487 DOI: 10.1016/j.plasmid.2004.05.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2003] [Revised: 04/13/2004] [Indexed: 11/21/2022]
Abstract
The mobilization region of the 7.4 kb beta-lactamase plasmid pSJ7.4 from Neisseria gonorrhoeae was characterized. The 3.2 kb HindIII-BamHI fragment of pSJ7.4 was mobilized between Escherichia coli strains by conjugative plasmid RK2. Selected restriction enzyme-generated deletions of this fragment were subcloned in pACYC177 to obtain constructs that were suitable for analysis of the mobilization region. Mating experiments showed that a highly conserved 1.9 kb DNA region within coordinates 4096-5997 is required for mobilization of pSJ7.4. This region contains two genes encoding the mobilization protein MobA, another protein, MobC, putatively involved in mobilization from some hosts, and an intergenic oriT. The 168 bp intergenic sequence also contains the promoters for mobA and mobC in an arrangement that suggests divergent transcription and autoregulation from oriT. The 56 kDa MobA was expressed in E. coli as a (6x)His-Tag fusion protein. Purified MobA specifically induced plasmid relaxation by nicking at the oriT. MobA is exceptional because the N-terminal region alone can mobilize pSJ7.4, albeit at a lower frequency than the full-length protein, even in the absence of MobC. The carboxyl terminal region of MobA did not share homology with other mobilization proteins, but may be involved in promoting efficient transfer of pSJ7.4.
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Affiliation(s)
- Nydia M Rodriguez-Bonano
- School of Sciences, Mathematics and Technology, Universidad del Este, Carolina, Puerto Rico 00984.
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31
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Smith MCA, Thomas CD. An accessory protein is required for relaxosome formation by small staphylococcal plasmids. J Bacteriol 2004; 186:3363-73. [PMID: 15150221 PMCID: PMC415746 DOI: 10.1128/jb.186.11.3363-3373.2004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mobilization of the staphylococcal plasmid pC221 requires at least one plasmid-encoded protein, MobA, in order to form a relaxosome. pC221 and closely related plasmids also possess an overlapping reading frame encoding a protein of 15 kDa, termed MobC. By completing the nucleotide sequence of plasmid pC223, we have found a further example of this small protein, and gene knockouts have shown that MobC is essential for relaxosome formation and plasmid mobilization in both pC221 and pC223. Primer extension analysis has been used to identify the nic site in both of these plasmids, located upstream of the mobC gene in the sense strand. Although the sequence surrounding the nic site is highly conserved between pC221 and pC223, exchange of the oriT sequence between plasmids significantly reduces the extent of relaxation complex formation, suggesting that the Mob proteins are selective for their cognate plasmids in vivo.
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Affiliation(s)
- Matthew C A Smith
- Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
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32
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Francia MV, Varsaki A, Garcillán-Barcia MP, Latorre A, Drainas C, de la Cruz F. A classification scheme for mobilization regions of bacterial plasmids. FEMS Microbiol Rev 2004; 28:79-100. [PMID: 14975531 DOI: 10.1016/j.femsre.2003.09.001] [Citation(s) in RCA: 268] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2003] [Revised: 08/28/2003] [Accepted: 09/01/2003] [Indexed: 10/27/2022] Open
Abstract
Transmissible plasmids can be classified according to their mobilization ability, as being conjugative (self-transmissible) or mobilizable (transmissible only in the presence of additional conjugative functions). Naturally occurring mobilizable plasmids carry the genetic information necessary for relaxosome formation and processing, but lack the functions required for mating pair formation. Mobilizable plasmids have a tremendous impact in horizontal gene transfer in nature, including the spread of antibiotic resistance. However, analysis of their promiscuity and diversity has attracted less attention than that of conjugative plasmids. This review will focus on the analysis of the diversity of mobilizable plasmids. For this purpose, we primarily compared the amino acid sequences of their relaxases and, when pertinent, we compared these enzymes with conjugative plasmid relaxases. In this way, we established phylogenetic relationships among the members of each superfamily. We conducted a database and literature analysis that led us to propose a classification system for small mobilizable plasmids in families and superfamilies according to their mobilization regions. This review outlines the genetic organization of each family of mobilization regions, as well as the most relevant properties and relationships among their constituent encoded proteins. In this respect, the present review constitutes a first approach to the characterization of the global gene pool of mobilization regions of small mobilizable plasmids.
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Affiliation(s)
- M Victoria Francia
- Laboratory of Biochemistry, Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Dourouti 45110, Ioannina, Greece
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Grohmann E, Muth G, Espinosa M. Conjugative plasmid transfer in gram-positive bacteria. Microbiol Mol Biol Rev 2003; 67:277-301, table of contents. [PMID: 12794193 PMCID: PMC156469 DOI: 10.1128/mmbr.67.2.277-301.2003] [Citation(s) in RCA: 388] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Conjugative transfer of bacterial plasmids is the most efficient way of horizontal gene spread, and it is therefore considered one of the major reasons for the increase in the number of bacteria exhibiting multiple-antibiotic resistance. Thus, conjugation and spread of antibiotic resistance represents a severe problem in antibiotic treatment, especially of immunosuppressed patients and in intensive care units. While conjugation in gram-negative bacteria has been studied in great detail over the last decades, the transfer mechanisms of antibiotic resistance plasmids in gram-positive bacteria remained obscure. In the last few years, the entire nucleotide sequences of several large conjugative plasmids from gram-positive bacteria have been determined. Sequence analyses and data bank comparisons of their putative transfer (tra) regions have revealed significant similarities to tra regions of plasmids from gram-negative bacteria with regard to the respective DNA relaxases and their targets, the origins of transfer (oriT), and putative nucleoside triphosphatases NTP-ases with homologies to type IV secretion systems. In contrast, a single gene encoding a septal DNA translocator protein is involved in plasmid transfer between micelle-forming streptomycetes. Based on these clues, we propose the existence of two fundamentally different plasmid-mediated conjugative mechanisms in gram-positive microorganisms, namely, the mechanism taking place in unicellular gram-positive bacteria, which is functionally similar to that in gram-negative bacteria, and a second type that occurs in multicellular gram-positive bacteria, which seems to be characterized by double-stranded DNA transfer.
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Affiliation(s)
- Elisabeth Grohmann
- Microbial Ecology Group, University of Technology Berlin, D-10587 Berlin, Germany.
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Inui M, Nakata K, Roh JH, Vertès AA, Yukawa H. Isolation and molecular characterization of pMG160, a mobilizable cryptic plasmid from Rhodobacter blasticus. Appl Environ Microbiol 2003; 69:725-33. [PMID: 12570988 PMCID: PMC143669 DOI: 10.1128/aem.69.2.725-733.2003] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A 3.4-kb cryptic plasmid was obtained from a new isolate of Rhodobacter blasticus. This plasmid, designated pMG160, was mobilizable by the conjugative strain Escherichia coli S17.1 into Rhodobacter sphaeroides, Rhodobacter capsulatus, and Rhodopseudomonas palustris. It replicated in the latter strains but not in Rhodospirillum rubrum, Rhodocyclus gelatinosus, or Bradyrhizobium species. Plasmid pMG160 was stably maintained in R. sphaeroides for more than 100 generations in the absence of selection but showed segregational instability in R. palustris. Instability in R. palustris correlated with a decrease in plasmid copy number compared to the copy number in R. sphaeroides. The complete nucleotide sequence of plasmid pMG160 contained three open reading frames (ORFs). The deduced amino acid sequences encoded by ORF1 and ORF2 showed high degrees of homology to the MobS and MobL proteins that are involved in plasmid mobilization of certain plasmids. Based on homology with the Rep protein of several other plasmids, ORF3 encodes a putative rep gene initiator of plasmid replication. The functions of these sequences were demonstrated by deletion mapping, frameshift analysis, and analysis of point mutations. Two 6.1-kb pMG160-based E. coli-R. sphaeroides shuttle cloning vectors were constructed and designated pMG170 and pMG171. These two novel shuttle vectors were segregationally stable in R. sphaeroides growing under nonselective conditions.
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Affiliation(s)
- Masayuki Inui
- Research Institute of Innovative Technology for the Earth, Kizu, Soraku, Kyoto 619-0292, Japan
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35
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Francia MV, Clewell DB. Transfer origins in the conjugative Enterococcus faecalis plasmids pAD1 and pAM373: identification of the pAD1 nic site, a specific relaxase and a possible TraG-like protein. Mol Microbiol 2002; 45:375-95. [PMID: 12123451 DOI: 10.1046/j.1365-2958.2002.03007.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The Enterococcus faecalis conjugative plasmids pAD1 and pAM373 encode a mating response to the peptide sex pheromones cAD1 and cAM373 respectively. Sequence determination of both plasmids has recently been completed with strong similarity evident over many of the structural genes related to conjugation. pAD1 has two origins of transfer, with oriT1 being located within the repA determinant, whereas the more efficiently utilized oriT2 is located between orf53 and orf57, two genes found in the present study to be essential for conjugation. We have found a similarly located oriT to be present in pAM373. oriT2 corresponds to about 285 bp based on its ability to facilitate mobilization by pAD1 when ligated to the shuttle vector pAM401; however, it was not mobilized by pAM373. In contrast, a similarly ligated fragment containing the oriT of pAM373 did not facilitate mobilization by pAD1 but was efficiently mobilized by pAM373. The oriT sites of the two plasmids each contained a homologous large inverted repeat (spanning about 140 bp) adjacent to a series of non-homologous short (6 bp) direct repeats. A hybrid construction containing the inverted repeat of pAM373 and direct repeats of pAD1 was mobilized efficiently by pAD1 but not by pAM373, indicating a significantly greater degree of specificity is associated with the direct repeats. Mutational (deletion) analyses of the pAD1 oriT2 inverted repeat structure suggested its importance in facilitating transfer or perhaps ligation of the ends of the newly transferred DNA strand. Analyses showed that Orf57 (to be called TraX) is the relaxase, which was found to induce a specific nick in the large inverted repeat inside oriT; the protein also facilitated site-specific recombination between two oriT2 sites. Orf53 (to be called TraW) exhibits certain structural similarities to TraG-like proteins, although there is little overall homology.
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Affiliation(s)
- M Victoria Francia
- Department of Biologic and Materials Sciences, School of Dentistry, The University of Michigan, Ann Arbor, 48109, USA
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Kurenbach B, Grothe D, Farías ME, Szewzyk U, Grohmann E. The tra region of the conjugative plasmid pIP501 is organized in an operon with the first gene encoding the relaxase. J Bacteriol 2002; 184:1801-5. [PMID: 11872736 PMCID: PMC134879 DOI: 10.1128/jb.184.6.1801-1805.2002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tra genes orf1 to orf11 of pIP501 were shown to be transcribed as a single operon of 11.3 kb in Enterococcus faecalis by reverse transcription-PCR. The transcriptional start site of the tra mRNA was mapped at 110 bp upstream from the predicted TTG start codon of the first gene of the operon, the traA relaxase. The TraA protein (660 amino acids) and a C-terminally truncated version of the TraA protein (293 amino acids) were purified as fusions with glutathione S-transferase. oriT cleavage activity of both TraA proteins was demonstrated in vitro on supercoiled plasmid pVA2241 DNA containing oriT(pIP501). The activity of the DNA relaxase TraA is strictly dependent on the presence of Mg(2+) or Mn(2+) and is highest at temperatures of between 42 and 45C.
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Affiliation(s)
- Brigitta Kurenbach
- Fachgebiet Okologie der Mikroorganismen, Institut für Technischen Umweltschutz, Technische Universität Berlin, D-10587 Berlin, Germany
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37
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Finan JE, Archer GL, Pucci MJ, Climo MW. Role of penicillin-binding protein 4 in expression of vancomycin resistance among clinical isolates of oxacillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2001; 45:3070-5. [PMID: 11600358 PMCID: PMC90784 DOI: 10.1128/aac.45.11.3070-3075.2001] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It has been reported that penicillin-binding protein 4 (PBP4) activity decreases when a vancomycin-susceptible Staphylococcus aureus isolate is passaged in vitro to vancomycin resistance. We analyzed the PBP profiles of four vancomycin intermediately susceptible S. aureus (VISA) clinical isolates and found that PBP4 was undetectable in three isolates (HIP 5827, HIP 5836, and HIP 6297) and markedly reduced in a fourth (Mu50). PBP4 was readily visible in five vancomycin-susceptible, oxacillin-resistant S. aureus (ORSA) isolates. The nucleotide sequences of the pbp4 structural gene and flanking sequences did not different between the VISA and vancomycin-susceptible isolates. Overproduction of PBP4 on a high-copy-number plasmid in the VISA isolates produced a two- to threefold decrease in vancomycin MICs. Inactivation of pbp4 by allelic replacement mutagenesis in three vancomycin-susceptible ORSA strains (COL, RN450M, and N315) led to a decrease in vancomycin susceptibility, an increase in highly vancomycin-resistant subpopulations, and decreased cell wall cross-linking by high-performance liquid chromatography analysis. Complementation of the COL mutant with plasmid-encoded pbp4 restored the vancomycin MIC and increased cell wall cross-linking. These data suggest that alterations in PBP4 expression are at least partially responsible for the VISA phenotype.
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Affiliation(s)
- J E Finan
- Department of Medicine, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia, USA
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38
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Hickey RM, Twomey DP, Ross RP, Hill C. Exploitation of plasmid pMRC01 to direct transfer of mobilizable plasmids into commercial lactococcal starter strains. Appl Environ Microbiol 2001; 67:2853-8. [PMID: 11375207 PMCID: PMC92951 DOI: 10.1128/aem.67.6.2853-2858.2001] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genetic analysis of the 60.2-kb lactococcal plasmid pMRC01 revealed a 19.6-kb region which includes putative genes for conjugal transfer of the plasmid and a sequence resembling an origin of transfer (oriT). This oriT-like sequence was amplified and cloned on a 312-bp segment into pCI372, allowing the resultant plasmid, pRH001, to be mobilized at a frequency of 3.4 x 10(-4) transconjugants/donor cell from an MG1363 (recA mutant) host containing pMRC01. All of the resultant chloramphenicol-resistant transconjugants contained both pRH001 and genetic determinants responsible for bacteriocin production and immunity of pMRC01. This result is expected, given that transconjugants lacking the lacticin 3147 immunity determinants (on pMRC01) would be killed by bacteriocin produced by the donor cells. Indeed, incorporation of proteinase K in the mating mixture resulted in the isolation of transformants, of which 47% were bacteriocin deficient. Using such an approach, the oriT-containing fragment was exploited to mobilize pRH001 alone to a number of lactococcal hosts. These results demonstrate that oriT of pMRC01 has the potential to be used in the development of mobilizable food-grade vectors for the genetic enhancement of lactococcal starter strains, some of which may be difficult to transform.
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Affiliation(s)
- R M Hickey
- Dairy Products Research Centre, Moorepark, Fermoy, Co. Cork
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39
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Climo MW, Ehlert K, Archer GL. Mechanism and suppression of lysostaphin resistance in oxacillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2001; 45:1431-7. [PMID: 11302806 PMCID: PMC90484 DOI: 10.1128/aac.45.5.1431-1437.2001] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The potential for the development of resistance in oxacillin-resistant Staphylococcus aureus (ORSA) to lysostaphin, a glycylglycine endopeptidase produced by Staphylococcus simulans biovar staphylolyticus, was examined in vitro and in an in vivo model of infection. Following in vitro exposure of ORSA to subinhibitory concentrations of lysostaphin, lysostaphin-resistant mutants were idenitifed among all isolates examined. Resistance to lysostaphin was associated with a loss of resistance to beta-lactams and a change in the muropeptide interpeptide cross bridge from pentaglycine to a single glycine. Mutations in femA, the gene required for incorporation of the second and third glycines into the cross bridge, were found following PCR amplification and nucleotide sequence analysis. Complementation of lysostaphin-resistant mutants with pBBB31, which encodes femA, restored the phenotype of oxacillin resistance and lysostaphin susceptibility. Addition of beta-lactam antibiotics to lysostaphin in vitro prevented the development of lysostaphin-resistant mutants. In the rabbit model of experimental endocarditis, administration of a low dose of lysostaphin for 3 days led predictably to the appearance of lysostaphin-resistant ORSA mutants in vegetations. Coadministration of nafcillin with lysostaphin prevented the emergence of lysostaphin-resistant mutants and led to a mean reduction in aortic valve vegetation counts of 7.5 log(10) CFU/g compared to those for untreated controls and eliminated the isolation of lysostaphin-resistant mutants from aortic valve vegetations. Treatment with nafcillin and lysostaphin given alone led to mean reductions of 1.35 and 1.65 log(10) CFU/g respectively. In ORSA, resistance to lysostaphin was associated with mutations in femA, but resistance could be suppressed by the coadministration of beta-lactam antibiotics.
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Affiliation(s)
- M W Climo
- Department of Medicine, Hunter Holmes McGuire Veterans Affairs Medical Center, Richmond, Virginia 23249, USA.
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40
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Ducote MJ, Prakash S, Pettis GS. Minimal and contributing sequence determinants of the cis-acting locus of transfer (clt) of streptomycete plasmid pIJ101 occur within an intrinsically curved plasmid region. J Bacteriol 2000; 182:6834-41. [PMID: 11073933 PMCID: PMC111431 DOI: 10.1128/jb.182.23.6834-6841.2000] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Efficient interbacterial transfer of streptomycete plasmid pIJ101 requires the pIJ101 tra gene, as well as a cis-acting plasmid function known as clt. Here we show that the minimal pIJ101 clt locus consists of a sequence no greater than 54 bp in size that includes essential inverted-repeat and direct-repeat sequences and is located in close proximity to the 3' end of the korB regulatory gene. Evidence that sequences extending beyond the minimal locus and into the korB open reading frame influence clt transfer function and demonstration that clt-korB sequences are intrinsically curved raise the possibility that higher-order structuring of DNA and protein within this plasmid region may be an inherent feature of efficient pIJ101 transfer.
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Affiliation(s)
- M J Ducote
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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41
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Meyer R. Identification of the mob genes of plasmid pSC101 and characterization of a hybrid pSC101-R1162 system for conjugal mobilization. J Bacteriol 2000; 182:4875-81. [PMID: 10940031 PMCID: PMC111367 DOI: 10.1128/jb.182.17.4875-4881.2000] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Similarities in DNA base sequence indicate that pSC101 and R1162 encode related systems for conjugal mobilization, although these plasmids are otherwise very different. The mob region of pSC101 was cloned, and two genes that are required for transfer were identified. One gene, mobA, encodes a protein similar in amino acid sequence to the DNA processing domain of the R1162 MobA protein. The other gene, mobX, is within the same transcriptional unit as the pSC101 mobA and is located just downstream, at the same position occupied by mobB in R1162. Despite this, the MobB and MobX proteins do not appear to be closely related based on a comparison of their amino acid sequences. Complementation analysis indicated that neither of the pSC101 Mob proteins could substitute for, or be replaced by, their R1162 counterparts, nor were they active together at the R1162 origin of transfer (oriT). However, the full set of R1162 Mob proteins did recognize the pSC101 oriT. A hybrid system for mobilization, active at the R1162 oriT site, was constructed. This system consists of MobX and a chimeric protein made up of the DNA cleaving-ligating domain of the R1162 MobA protein joined to a fragment of pSC101 MobA. Previous results suggested that MobB and a region of MobA distinct from the DNA processing domain together formed a functional unit in transfer. The present results support this model because the chimeric MobA, although active on R1162 oriT, requires the pSC101 protein MobX for efficient plasmid mobilization.
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Affiliation(s)
- R Meyer
- Section of Molecular Genetics and Microbiology, School of Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.
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42
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Becker EC, Meyer RJ. Recognition of oriT for DNA processing at termination of a round of conjugal transfer. J Mol Biol 2000; 300:1067-77. [PMID: 10903855 DOI: 10.1006/jmbi.2000.3902] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Conjugal transfer of plasmid DNA is terminated when the transferred strand, linearized at the 38 base-pair origin of transfer (oriT), is recircularized. For the plasmid R1162, it is the protein MobA, covalently linked to the linear strand, that rejoins the ends by a reversible transesterification reaction. We have identified from those oligonucleotides with a partially degenerate oriT base sequence, subpopulations bound by MobA that undergo transesterification, and support efficient termination of conjugal transfer. Two domains of oriT, a ten base-pair inverted repeat and an adjacent TAA, are required for tight binding by the protein, whereas the location of the dinucleotide YG determines the site of strand cleavage. The results indicate that capture of MobA by oriT, and subsequent processing of the DNA for termination, are determined by different sequence motifs within this locus.
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MESH Headings
- Bacterial Proteins/genetics
- Bacterial Proteins/metabolism
- Base Sequence
- Binding, Competitive
- Cloning, Molecular
- Conjugation, Genetic/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- DNA, Recombinant/genetics
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/metabolism
- DNA-Binding Proteins/genetics
- DNA-Binding Proteins/metabolism
- Escherichia coli/genetics
- Mutation
- Nucleic Acid Conformation
- Oligodeoxyribonucleotides/genetics
- Plasmids/chemistry
- Plasmids/genetics
- Plasmids/metabolism
- Protein Binding
- Regulatory Sequences, Nucleic Acid/genetics
- Sequence Analysis, DNA
- Trans-Activators/genetics
- Trans-Activators/metabolism
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Affiliation(s)
- E C Becker
- Section of Molecular Genetics and Microbiology School of Biology and Institute for Cellular and Molecular Biology, Austin, TX 78712, USA
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43
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Farías ME, Grohmann E, Espinosa M. Expression of the mobM gene of the streptococcal plasmid pMV158 in Lactococcus lactis subsp. lactis. FEMS Microbiol Lett 1999; 176:403-10. [PMID: 10427723 DOI: 10.1111/j.1574-6968.1999.tb13690.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The streptococcal plasmid pMV158 is not auto-transferable, but it can be mobilised between bacteria by the use of functions supplied by plasmids of the pIP501/pAM beta 1 family. Plasmid pMV158 encodes a protein, MobM, which is involved in its mobilisation. This process initiates when MobM specifically cleaves supercoiled pMV158 plasmid DNA at the origin of transfer, oriT. Plasmid pMV158 has been transferred to Lactococcus lactis by conjugation aided by plasmid pAM beta 1. In the lactococcal host, MobM-mediated specific pMV158-relaxed molecules were detected. The intracellular amount of MobM has been quantified by immunoblot analyses and shown to be about 3500 molecules per cell. In the same host, we have mapped the initiation point of transcription of mobM. Transcription of this gene is directed from a promoter with an extended--10 region which overlaps with the pMV158-oriT.
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Affiliation(s)
- M E Farías
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
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44
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Andrup L. Conjugation in gram-positive bacteria and kinetics of plasmid transfer. APMIS. SUPPLEMENTUM 1998; 84:47-55. [PMID: 9850682 DOI: 10.1111/j.1600-0463.1998.tb05648.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- L Andrup
- National Institute of Occupational Health, Copenhagen, Denmark
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45
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Maas RM, GUtz JU, Wohlleben W, Muth G. The conjugative plasmid pSG5 from Streptomyces ghanaensis DSM 2932 differs in its transfer functions from other Streptomyces rolling-circle-type plasmids. MICROBIOLOGY (READING, ENGLAND) 1998; 144 ( Pt 10):2809-2817. [PMID: 9802022 DOI: 10.1099/00221287-144-10-2809] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The Streptomyces ghanaensis plasmid pSG5 is self-transmissible but does not form the growth-retardation zones (pocks) normally characteristic of the Streptomyces plasmid-transfer process. The complete nucleotide sequence of pSG5 was determined on both strands. pSG5 is 12,208 bp in length and has a GC content of 68 mol%. Characterization of the open reading frames by insertion and deletion analysis revealed that only a single gene, traB, is involved in the transfer of pSG5. The deduced amino acid sequence of TraB is similar to the SpoIIIE protein that is responsible for chromosome translocation during prespore formation of Bacillus subtilis. In contrast to the tra genes of the other Streptomyces plasmids, the pSG5 traB does not represent a kill function. Although pSG5 transfer is not associated with pock formation, pSG5 was shown to possess putative spd genes that are responsible for the pock phenotype of other Streptomyces plasmids. However, promoter-probe experiments revealed that the spd genes of pSG5 are not transcribed, thus explaining the deficiency in pock formation.
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MESH Headings
- Amino Acid Sequence
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- Conjugation, Genetic/genetics
- Conjugation, Genetic/physiology
- Gene Deletion
- Gene Expression Regulation, Bacterial
- Genes, Bacterial/genetics
- Kanamycin/pharmacology
- Molecular Sequence Data
- Mutagenesis, Insertional
- Open Reading Frames/genetics
- Plasmids/genetics
- Plasmids/physiology
- Promoter Regions, Genetic/genetics
- Repressor Proteins/genetics
- Repressor Proteins/physiology
- Restriction Mapping
- Sequence Alignment
- Sequence Analysis, DNA
- Spores, Bacterial/genetics
- Spores, Bacterial/physiology
- Streptomyces/genetics
- Streptomyces/growth & development
- Streptomyces/physiology
- Time Factors
- Transcription, Genetic
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van Kranenburg R, de Vos WM. Characterization of multiple regions involved in replication and mobilization of plasmid pNZ4000 coding for exopolysaccharide production in Lactococcus lactis. J Bacteriol 1998; 180:5285-90. [PMID: 9765557 PMCID: PMC107574 DOI: 10.1128/jb.180.20.5285-5290.1998] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized the regions involved in replication and mobilization of the 40-kb plasmid pNZ4000, encoding exopolysaccharide (EPS) production in Lactococcus lactis NIZO B40. The plasmid contains four highly conserved replication regions with homologous rep genes (repB1, repB2, repB3, and repB4) that belong to the lactococcal theta replicon family. Subcloning of each replicon individually showed that all are functional and compatible in L. lactis. Plasmid pNZ4000 and genetically labeled derivatives could be transferred to different L. lactis strains by conjugation, and pNZ4000 was shown to be a mobilization plasmid. Two regions involved in mobilization were identified near two of the replicons; both included an oriT sequence rich in inverted repeats. Conjugative mobilization of the nonmobilizable plasmid pNZ124 was promoted by either one of these oriT sequences, demonstrating their functionality. One oriT sequence was followed by a mobA gene, coding for a trans-acting protein, which increased the frequency of conjugative transfer 100-fold. The predicted MobA protein and the oriT sequences show protein and nucleotide similarity, respectively, with the relaxase and with the inverted repeat and nic site of the oriT from the Escherichia coli plasmid R64. The presence on pNZ4000 of four functional replicons, two oriT sequences, and several insertion sequence-like elements strongly suggests that this EPS plasmid is a naturally occurring cointegrate.
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Affiliation(s)
- R van Kranenburg
- Microbial Ingredients Section, NIZO Food Research, Ede, The Netherlands
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47
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Berg T, Firth N, Apisiridej S, Hettiaratchi A, Leelaporn A, Skurray RA. Complete nucleotide sequence of pSK41: evolution of staphylococcal conjugative multiresistance plasmids. J Bacteriol 1998; 180:4350-9. [PMID: 9721269 PMCID: PMC107441 DOI: 10.1128/jb.180.17.4350-4359.1998] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/1998] [Accepted: 06/16/1998] [Indexed: 11/20/2022] Open
Abstract
The 46.4-kb nucleotide sequence of pSK41, a prototypical multiresistance plasmid from Staphylococcus aureus, has been determined, representing the first completely sequenced conjugative plasmid from a gram-positive organism. Analysis of the sequence has enabled the identification of the probable replication, maintenance, and transfer functions of the plasmid and has provided insights into the evolution of a clinically significant group of plasmids. The basis of deletions commonly associated with pSK41 family plasmids has been investigated, as has the observed insertion site specificity of Tn552-like beta-lactamase transposons within them. Several of the resistance determinants carried by pSK41-like plasmids were found to be located on up to four smaller cointegrated plasmids. pSK41 and related plasmids appear to represent a consolidation of antimicrobial resistance functions, collected by a preexisting conjugative plasmid via transposon insertion and IS257-mediated cointegrative capture of other plasmids.
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Affiliation(s)
- T Berg
- School of Biological Sciences, University of Sydney, New South Wales 2006, Australia
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Młynarczyk A, Młynarczyk G, Jeljaszewicz J. The genome of Staphylococcus aureus: a review. ZENTRALBLATT FUR BAKTERIOLOGIE : INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY 1998; 287:277-314. [PMID: 9638861 DOI: 10.1016/s0934-8840(98)80165-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The genome of Staphylococcus aureus consists of a single circular chromosome (2.7-2.8 mbp) plus an assortment of extrachromosomal accessory genetic elements: conjugative and nonconjugative plasmids, mobile elements (IS, Tn, Hi), prophages and other variable elements. Plasmids (1-60 kbp) are classified into 4 classes and there are 15 known incompatibility groups. Mobile elements of the genome (0.8-18 kbp) appear in the chromosome or in plasmids of classes II and III. Prophages (45-60 kbp) are integrated in the bacterial chromosome, and they are UV- or mitomycin-inducible. Temperate bacteriophages of S. aureus are members of the Siphoviridae and the serological groups A, B and F occur most frequently. In the paper presented, the characteristics of chromosome, plasmids, transposons and other genetic elements of S. aureus genome are given and an alphabetical list of known genes of this species is included.
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Mills DA, Phister TG, Dunny GM, McKay LL. An origin of transfer (oriT) on the conjugative element pRS01 from Lactococcus lactis subsp. lactis ML3. Appl Environ Microbiol 1998; 64:1541-4. [PMID: 9546191 PMCID: PMC106184 DOI: 10.1128/aem.64.4.1541-1544.1998] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Previous analysis of the Tra1 region of the conjugative element pRS01 from Lactococcus lactis subsp. lactis ML3 suggested that an origin of transfer (oriT) was present. Deletion derivatives of this cloned Tra1 region were assayed for mobilization in the presence of the wild-type pRS01 element in trans. The pRS01 oriT was localized to a 446-nucleotide segment in the intergenic region between open reading frames ltrD and ltrE. Sequence analysis of this region revealed a cluster of direct and inverted repeat structures characteristic of oriT regions associated with other conjugative systems.
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Affiliation(s)
- D A Mills
- Department of Microbiology, University of Minnesota, Minneapolis 55455-0312, USA
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Firth N, Skurray RA. Mobile elements in the evolution and spread of multiple-drug resistance in staphylococci. Drug Resist Updat 1998; 1:49-58. [PMID: 17092796 DOI: 10.1016/s1368-7646(98)80214-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Since the introduction of antimicrobial chemotherapy, staphylococci have shown a remarkable propensity to develop drug resistance. As a result, strains have evolved that are resistant to most classes of clinically useful antimicrobial agents. The emergence of these multiply-drug-resistant strains is primarily due to the capture of pre-existent resistance genes. In combination with plasmids and gene transfer mechanisms, mobile genetic elements have been central to the acquisition and dissemination of this resistance. In particular they have played a significant role in the assembly of drug-resistance gene clusters in these multiply-resistant staphylococci.
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Affiliation(s)
- N Firth
- School of Biological Sciences, University of Sydney, New South Wales, Australia
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