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Ortiz Charneco G, McDonnell B, Kelleher P, Buivydas A, Dashko S, de Waal PP, van Rijswijck I, van Peij NNME, Mahony J, Van Sinderen D. Plasmid-mediated horizontal gene mobilisation: Insights from two lactococcal conjugative plasmids. Microb Biotechnol 2024; 17:e14421. [PMID: 38752994 PMCID: PMC11097999 DOI: 10.1111/1751-7915.14421] [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: 10/31/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 05/18/2024] Open
Abstract
The distinct conjugation machineries encoded by plasmids pNP40 and pUC11B represent the most prevalent plasmid transfer systems among lactococcal strains. In the current study, we identified genetic determinants that underpin pNP40- and pUC11B-mediated, high-frequency mobilisation of other, non-conjugative plasmids. The mobilisation frequencies of the smaller, non-conjugative plasmids and the minimal sequences required for their mobilisation were determined, owing to the determination of the oriT sequences of both pNP40 and pUC11B, which allowed the identification of similar sequences in some of the non-conjugative plasmids that were shown to promote their mobilisation. Furthermore, the auxiliary gene mobC, two distinct functional homologues of which are present in several plasmids harboured by the pNP40- and pUC11B-carrying host strains, was observed to confer a high-frequency mobilisation phenotype. These findings provide mechanistic insights into how lactococcal conjugative plasmids achieve conjugation and promote mobilisation of non-conjugative plasmids. Ultimately, these insights would be harnessed to optimise conjugation and mobilisation strategies for the rapid and predictable development of robust and technologically improved strains.
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Affiliation(s)
| | - Brian McDonnell
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Andrius Buivydas
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Sofia Dashko
- dsm‐firmenich, Taste, Texture & Health, Center for Food InnovationDelftThe Netherlands
| | - Paul P. de Waal
- dsm‐firmenich, Taste, Texture & Health, Center for Food InnovationDelftThe Netherlands
| | - Irma van Rijswijck
- dsm‐firmenich, Taste, Texture & Health, Center for Food InnovationDelftThe Netherlands
| | | | - Jennifer Mahony
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Douwe Van Sinderen
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
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Abdullahi IN, Latorre-Fernández J, Reuben RC, Trabelsi I, González-Azcona C, Arfaoui A, Usman Y, Lozano C, Zarazaga M, Torres C. Beyond the Wild MRSA: Genetic Features and Phylogenomic Review of mecC-Mediated Methicillin Resistance in Non- aureus Staphylococci and Mammaliicocci. Microorganisms 2023; 12:66. [PMID: 38257893 PMCID: PMC10818522 DOI: 10.3390/microorganisms12010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Methicillin resistance, mediated by the mecA gene in staphylococci and mammaliicocci, has caused tremendous setbacks in the use of antibiotics in human and veterinary medicine due to its high potential of presenting the multidrug resistance (MDR) phenotype. Three other mec analogs exist, of which the mecC has evolutionary been associated with methicillin-resistant Staphylococcus aureus (MRSA) in wild animals, thus loosely referred to as the wild MRSA. In this study, we present an epidemiological review and genomic analysis of non-aureus staphylococci and mammaliicocci that carry the mecC-mediated methicillin resistance trait and determine whether this trait has any relevant link with the One Health niches. All previous studies (2007 till 2023) that described the mecC gene in non-aureus staphylococci and mammaliicocci were obtained from bibliometric databases, reviewed, and systematically analyzed to obtain the antimicrobial resistance (AMR) and virulence determinants, mobilome, and other genetic contents. Moreover, core genome single-nucleotide polymorphism analysis was used to assess the relatedness of these strains. Of the 533 articles analyzed, only 16 studies (on livestock, environmental samples, milk bulk tanks, and wild animals) were eligible for inclusion, of which 17 genomes from 6 studies were used for various in silico genetic analyses. Findings from this systematic review show that all mecC-carrying non-aureus staphylococci were resistant to only beta-lactam antibiotics and associated with the classical SCCmec XI of S. aureusLGA251. Similarly, two studies on wild animals reported mecC-carrying Mammaliicoccus stepanovicii associated with SCCmec XI. Nevertheless, most of the mecC-carrying Mammaliicoccus species presented an MDR phenotype (including linezolid) and carried the SCCmec-mecC hybrid associated with mecA. The phylogenetic analysis of the 17 genomes revealed close relatedness (<20 SNPs) and potential transmission of M. sciuri and M. lentus strains in livestock farms in Algeria, Tunisia, and Brazil. Furthermore, closely related M. sciuri strains from Austria, Brazil, and Tunisia (<40 SNPs) were identified. This systematic review enhances our comprehension of the epidemiology and genetic organization of mecC within the non-aureus staphylococci and mammaliicocci. It could be hypothesized that the mecC-carrying non-aureus staphylococci are evolutionarily related to the wild MRSA-mecC. The potential implications of clonal development of a lineage of mecA/mecC carrying strains across multiple dairy farms in a vast geographical region with the dissemination of MDR phenotype is envisaged. It was observed that most mecC-carrying non-aureus staphylococci and mammaliicocci were reported in mastitis cases. Therefore, veterinarians and veterinary microbiology laboratories must remain vigilant regarding the potential existence of mecA/mecC strains originating from mastitis as a potential niche for this resistance trait.
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Affiliation(s)
- Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Javier Latorre-Fernández
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Rine Christopher Reuben
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Islem Trabelsi
- Bioresources, Environment and Biotechnology Laboratory, Higher Institute of Applied Biological Sciences of Tunis, University of Tunis El Manar, Tunis 1006, Tunisia;
| | - Carmen González-Azcona
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Ameni Arfaoui
- Laboratory of Microorganisms and Active Biomolecules, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis 1068, Tunisia;
| | - Yahaya Usman
- Department of Medical Laboratory Science, Ahmadu Bello University, Zaria 810107, Nigeria;
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, OneHealth-UR Research Group, University of La Rioja, 26006 Logroño, Spain; (I.N.A.); (J.L.-F.); (R.C.R.); (C.G.-A.); (C.L.); (M.Z.)
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3
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Ramsay JP, Parahitiyawa N, Mowlaboccus S, Mullally CA, Yee NW, Shoby P, Colombi E, Tan HL, Pearson JC, Coombs GW. Genomic characterization of a unique Panton-Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting on Australian indigenous communities. Microb Genom 2023; 9:001172. [PMID: 38117559 PMCID: PMC10763498 DOI: 10.1099/mgen.0.001172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/09/2023] [Indexed: 12/21/2023] Open
Abstract
In 2010 a single isolate of a trimethoprim-resistant multilocus sequence type 5, Panton-Valentine leucocidin-positive, community-associated methicillin-resistant Staphylococcus aureus (PVL-positive ST5 CA-MRSA), colloquially named WA121, was identified in northern Western Australia (WA). WA121 now accounts for ~14 % of all WA MRSA infections. To gain an understanding of the genetic composition and phylogenomic structure of WA121 isolates we sequenced the genomes of 155 WA121 isolates collected 2010-2021 and present a detailed genomic description. WA121 was revealed to be a single clonally expanding lineage clearly distinct from sequenced ST5 strains reported outside Australia. WA121 strains were typified by the presence of the distinct PVL phage φSa2wa-st5, the recently described methicillin resistance element SCCmecIVo carrying the trimethoprim resistance (dfrG) transposon Tn4791, the novel β-lactamase transposon Tn7702 and the epidermal cell differentiation inhibitor (EDIN-A) plasmid p2010-15611-2. We present evidence that SCCmecIVo together with Tn4791 has horizontally transferred to Staphylococcus argenteus and evidence of intragenomic movement of both Tn4791 and Tn7702. We experimentally demonstrate that p2010-15611-2 is capable of horizontal transfer by conjugative mobilization from one of several WA121 isolates also harbouring a pWBG749-like conjugative plasmid. In summary, WA121 is a distinct and clonally expanding Australian PVL-positive CA-MRSA lineage that is increasingly responsible for infections in indigenous communities in northern and western Australia. WA121 harbours a unique complement of mobile genetic elements and is capable of transferring antimicrobial resistance and virulence determinants to other staphylococci.
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Affiliation(s)
- Joshua P. Ramsay
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
| | - Nipuna Parahitiyawa
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
| | - Shakeel Mowlaboccus
- Microbiology Department, Fiona Stanley Hospital, PathWest Laboratory Medicine, Murdoch, WA, Australia
- Antimicrobial Resistance and Infectious Disease (AMRID) Research Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Christopher A. Mullally
- Antimicrobial Resistance and Infectious Disease (AMRID) Research Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Nicholas W.T. Yee
- Antimicrobial Resistance and Infectious Disease (AMRID) Research Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Princy Shoby
- Antimicrobial Resistance and Infectious Disease (AMRID) Research Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
| | - Elena Colombi
- Curtin Medical School, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
- Curtin Health Innovation Research Institute, Faculty of Health Sciences, Curtin University, Perth, WA, Australia
| | - Hui-Leen Tan
- Microbiology Department, Fiona Stanley Hospital, PathWest Laboratory Medicine, Murdoch, WA, Australia
| | - Julie C. Pearson
- Microbiology Department, Fiona Stanley Hospital, PathWest Laboratory Medicine, Murdoch, WA, Australia
| | - Geoffrey W. Coombs
- Microbiology Department, Fiona Stanley Hospital, PathWest Laboratory Medicine, Murdoch, WA, Australia
- Antimicrobial Resistance and Infectious Disease (AMRID) Research Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, Australia
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Houtak G, Bouras G, Nepal R, Shaghayegh G, Cooksley C, Psaltis AJ, Wormald PJ, Vreugde S. The intra-host evolutionary landscape and pathoadaptation of persistent Staphylococcus aureus in chronic rhinosinusitis. Microb Genom 2023; 9. [PMID: 38010322 DOI: 10.1099/mgen.0.001128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus paired isolates (34 pairs) were sourced from 34 CRS patients at least 6 months apart. Isolates were grown into 48 h biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41 % (14/34 pairs) of S. aureus isolates were persistent, while 59 % (20/34 pairs) were non-persistent. Persistent isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. Furthermore, a significant increase in the copy number of conserved plasmids of persistent strains was observed. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics, which was linked to a significant increase in biofilm biomass over time, indicating a potential biofilm pathoadaptive process in persistent isolates. In conclusion, our study provides important insights into the mutational changes during S. aureus persistence in CRS patients highlighting potential pathoadaptive mechanisms in S. aureus persistent isolates culminating in increased biofilm biomass.
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Affiliation(s)
- Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Roshan Nepal
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Gohar Shaghayegh
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Clare Cooksley
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Alkis James Psaltis
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Peter-John Wormald
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
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Kovařovic V, Finstrlová A, Sedláček I, Petráš P, Švec P, Mašlaňová I, Neumann-Schaal M, Šedo O, Botka T, Staňková E, Doškař J, Pantůček R. Staphylococcus brunensis sp. nov. isolated from human clinical specimens with a staphylococcal cassette chromosome-related genomic island outside of the rlmH gene bearing the ccrDE recombinase gene complex. Microbiol Spectr 2023; 11:e0134223. [PMID: 37712674 PMCID: PMC10581047 DOI: 10.1128/spectrum.01342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/03/2023] [Indexed: 09/16/2023] Open
Abstract
Novel species of coagulase-negative staphylococci, which could serve as reservoirs of virulence and antimicrobial resistance factors for opportunistic pathogens from the genus Staphylococcus, are recognized in human and animal specimens due to advances in diagnostic techniques. Here, we used whole-genome sequencing, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize five coagulase-negative strains from the Staphylococcus haemolyticus phylogenetic clade obtained from human ear swabs, wounds, and bile. Based on the results of polyphasic taxonomy, we propose the species Staphylococcus brunensis sp. nov. (type strain NRL/St 16/872T = CCM 9024T = LMG 31872T = DSM 111349T). The genomic analysis revealed numerous variable genomic elements, including staphylococcal cassette chromosome (SCC), prophages, plasmids, and a unique 18.8 kb-long genomic island SbCIccrDE integrated into the ribosomal protein L7 serine acetyltransferase gene rimL. SbCIccrDE has a cassette chromosome recombinase (ccr) gene complex with a typical structure found in SCCs. Based on nucleotide and amino acid identity to other known ccr genes and the distinct integration site that differs from the canonical methyltransferase gene rlmH exploited by SCCs, we classified the ccr genes as novel variants, ccrDE. The comparative genomic analysis of SbCIccrDE with related islands shows that they can accumulate virulence and antimicrobial resistance factors creating novel resistance elements, which reflects the evolution of SCC. The spread of these resistance islands into established pathogens such as Staphylococcus aureus would pose a great threat to the healthcare system. IMPORTANCE The coagulase-negative staphylococci are important opportunistic human pathogens, which cause bloodstream and foreign body infections, mainly in immunocompromised patients. The mobile elements, primarily the staphylococcal cassette chromosome mec, which confers resistance to methicillin, are the key to the successful dissemination of staphylococci into healthcare and community settings. Here, we present a novel species of the Staphylococcus genus isolated from human clinical material. The detailed analysis of its genome revealed a previously undescribed genomic island, which is closely related to the staphylococcal cassette chromosome and has the potential to accumulate and spread virulence and resistance determinants. The island harbors a set of conserved genes required for its mobilization, which we recognized as novel cassette chromosome recombinase genes ccrDE. Similar islands were revealed not only in the genomes of coagulase-negative staphylococci but also in S. aureus. The comparative genomic study contributes substantially to the understanding of the evolution and pathogenesis of staphylococci.
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Affiliation(s)
- Vojtěch Kovařovic
- Department of Experimental Biology, Division of Genetics and Molecular Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Adéla Finstrlová
- Department of Experimental Biology, Division of Genetics and Molecular Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ivo Sedláček
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Petráš
- Reference Laboratory for Staphylococci, National Institute of Public Health, Praha, Czech Republic
| | - Pavel Švec
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Ivana Mašlaňová
- Department of Experimental Biology, Division of Genetics and Molecular Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Ondrej Šedo
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Tibor Botka
- Department of Experimental Biology, Division of Genetics and Molecular Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Eva Staňková
- Department of Experimental Biology, Czech Collection of Microorganisms, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Doškař
- Department of Experimental Biology, Division of Genetics and Molecular Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Division of Genetics and Molecular Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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Almuhayawi MS, Gattan HS, Alruhaili MH, Alharbi MT, Nagshabandi MK, Tarabulsi MK, Almuhayawi SM, Al Jaouni SK, Selim S, Alanazi A, Alruwaili Y, Faried OA, Amin I, Elnosary ME. Molecular Profile and the Effectiveness of Antimicrobials Drugs Against Staphylococcus aureus and Pseudomonas aeruginosa in the Diagnostic Approaches of Otitis Infection. Infect Drug Resist 2023; 16:4397-4408. [PMID: 37431447 PMCID: PMC10329836 DOI: 10.2147/idr.s418685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
Background Otitis externa and otitis media are two types of ear infections that affect people of all ages, although they are more common in newborns and young children. Antibiotic usage, healthcare, and advanced age all play a role in the development of this illness. Methods Fifty-eight patients with various kinds of infections of the ears were voluntary patients attending the outpatient clinics of the Prince Mutaib Bin Abdulaziz Hospital in Sakaka, Al Jouf, Saudi Arabia, examined to evaluate the role of bacteria and the likely significance of plasmids in their antibiotic resistance as ear infectious agents. Results Staphylococcus aureus and Pseudomonas aeruginosa are the most prevalent bacteria found in ear infections. The greatest number of major bacterial isolates were S. aureus (54%), followed by P. aeruginosa (13%), whereas a smaller number of isolates (3%) were from Streptococcus pyogenes, Bacillus subtilis, and Proteus vulgaris, respectively. Mixed growth was noted in 3.4% of instances. The isolation rate for Gram-positive organisms was 72%, while the rate for Gram-negative species was 28%. All the isolates had DNA greater than 14 kilobases. Hind III analysis of the plasmid DNA extracted from the resistant strains of ear infection demonstrated that antibiotic-resistance plasmids were extensively dispersed. Exotoxin A PCR amplification indicated 396 pb PCR-positive DNA for all identified samples, with the exception of three strains for which no band was observed. Patients in the epidemiological study ranged in number, but all were linked together for the purposes of the study because of their shared epidemiological characteristics. Conclusion Vancomycin, linezolid, tigecycline, rifampin, and daptomycin are all antibiotics that have been shown to be effective against S. aureus and P. aeruginosa. Microbiological pattern evaluation and antibiotic sensitivity patterns of the microorganisms providing empirical antibiotics are becoming increasingly crucial to minimize issues and the development of antibiotic-resistant strains.
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Affiliation(s)
- Mohammed S Almuhayawi
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King AbdulAziz University, Jeddah, 21589, Saudi Arabia
| | - Hattan S Gattan
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
- Special Infectious Agents Unit, King Fahad Medical Research Center, King AbdulAziz University, Jeddah, 21589, Saudi Arabia
| | - Mohammed H Alruhaili
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King AbdulAziz University, Jeddah, 21589, Saudi Arabia
- Special Infectious Agents Unit, King Fahad Medical Research Center, King AbdulAziz University, Jeddah, 21589, Saudi Arabia
| | - Mohanned Talal Alharbi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, University of Jeddah, Jeddah, 23218, Saudi Arabia
| | - Mohammed K Nagshabandi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, University of Jeddah, Jeddah, 23218, Saudi Arabia
| | - Muyassar K Tarabulsi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, University of Jeddah, Jeddah, 23218, Saudi Arabia
| | - Saad M Almuhayawi
- Department of Otolaryngology-Head and Neck Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Soad K Al Jaouni
- Department of Hematology/Oncology, Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, 72341, Saudi Arabia
| | - Awadh Alanazi
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, 72341, Saudi Arabia
| | - Yasir Alruwaili
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, 72341, Saudi Arabia
| | - Osama Ahmed Faried
- Medical Microbiology and Immunology Department, Faculty of Medicine, Beni-Suef University, Beni-Suef, 62513, Egypt
| | - Islam Amin
- Central Laboratory, Ismailia General Hospital, Ismailia, Egypt
| | - Mohamed E Elnosary
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Nasr City, Cairo, 11884, Egypt
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7
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Siguier P, Campos M, Cornet F, Bouet JY, Guynet C. Atypical low-copy number plasmid segregation systems, all in one? Plasmid 2023; 127:102694. [PMID: 37301314 DOI: 10.1016/j.plasmid.2023.102694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Plasmid families harbor different maintenances functions, depending on their size and copy number. Low copy number plasmids rely on active partition systems, organizing a partition complex at specific centromere sites that is actively positioned using NTPase proteins. Some low copy number plasmids lack an active partition system, but carry atypical intracellular positioning systems using a single protein that binds to the centromere site but without an associated NTPase. These systems have been studied in the case of the Escherichia coli R388 and of the Staphylococcus aureus pSK1 plasmids. Here we review these two systems, which appear to be unrelated but share common features, such as their distribution on plasmids of medium size and copy number, certain activities of their centromere-binding proteins, StbA and Par, respectively, as well as their mode of action, which may involve dynamic interactions with the nucleoid-packed chromosome of their hosts.
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Affiliation(s)
- Patricia Siguier
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Manuel Campos
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - François Cornet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France
| | - Catherine Guynet
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique, Université de Toulouse, UPS, Toulouse F-31000, France.
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Cavaiuolo M, Lefebvre D, Mutel I, Vingadassalon N, Merda D, Hennekinne JA, Nia Y. First report of enterotoxigenic Staphylococcus argenteus as a foodborne pathogen. Int J Food Microbiol 2023; 394:110182. [PMID: 36965358 DOI: 10.1016/j.ijfoodmicro.2023.110182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/07/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023]
Abstract
Staphylococcal enterotoxins preformed in food are the causative agents of staphylococcal food poisoning outbreaks (SFPO). In this study we characterised in depth two coagulase-positive non-pigmented staphylococci involved in two independent outbreaks that occurred in France. While indistinguishable from Staphylococcus aureus using PCR methods and growth phenotype comparisons, both isolates were identified as Staphylococcus argenteus by whole genome sequencing. The genomes were analysed for the presence of enterotoxin genes, whose expression was determined in laboratory medium and, for the first time, in artificially-contaminated milk samples by using liquid chromatography-mass spectrometry and ELISA methods. The concentration measured for the SEB toxin in milk (0.67 ng/ml) was comparable to concentrations reported for other types of enterotoxins behind SFPO. From a collection of publicly available genomes, we performed an unprecedented systematic investigation of the enterotoxin gene set of S. argenteus, including variants and pseudogenes. The most prevalent genes were sex, followed by sel26, sel27 and sey. The egc cluster was less frequent and most of the time carried a dysfunctional seg gene. Our results shed light on the enterotoxigenic properties of S. argenteus, and emphasize the importance in monitoring of S. argenteus as an emerging foodborne pathogen.
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Affiliation(s)
- Marina Cavaiuolo
- University Paris Est, ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France.
| | - Donatien Lefebvre
- University Paris Est, ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - Isabelle Mutel
- University Paris Est, ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - Noémie Vingadassalon
- University Paris Est, ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - Déborah Merda
- University Paris Est, ANSES, SPAAD unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - Jacques-Antoine Hennekinne
- University Paris Est, ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France
| | - Yacine Nia
- University Paris Est, ANSES, Laboratory for Food Safety, SBCL Unit, Maisons-Alfort location, F-94701 Maisons-Alfort, France
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9
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First Genome-Based Characterisation and Staphylococcal Enterotoxin Production Ability of Methicillin-Susceptible and Methicillin-Resistant Staphylococcus aureus Strains Isolated from Ready-to-Eat Foods in Algiers (Algeria). Toxins (Basel) 2022; 14:toxins14110731. [PMID: 36355981 PMCID: PMC9694651 DOI: 10.3390/toxins14110731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/18/2022] [Accepted: 10/19/2022] [Indexed: 01/26/2023] Open
Abstract
Staphylococcus aureus is a pathogenic microorganism of humans and animals, able to cause foodborne intoxication due to the production of staphylococcal enterotoxins (SEs) and to resist antibiotic treatment as in the case of methicillin-resistant S. aureus (MRSA). In this study, we performed a genomic characterisation of 12 genetically diverse S. aureus strains isolated from ready-to-eat foods in Algiers (Algeria). Moreover, their ability to produce some classical and new staphylococcal enterotoxins (SEs) was investigated. The 12 S. aureus strains resulted to belong to nine known sequence types (STs) and to the novel ST7199 and ST7200. Furthermore, S. aureus SA46 was assigned to the European clone MRSA-ST80-SCCmec-IV. The 12 strains showed a wide endowment of se and sel (staphylococcal enterotoxin-like toxin) genes (sea, seb, sed, seg, seh, sei, selj, sek, sem, sen, seo, seq, ser, selu2, selw, selx, sey, sel30; ψent1-ψent2), including variants and pseudogenes, and harboured the enterotoxin gene cluster (egc) types 1 and 5. Additionally, they produced various amounts of SEA (64.54-345.02 ng/mL), SEB (2871.28-14739.17 ng/mL), SED (322.70-398.94 ng/mL), SEH (not detectable-239.48 ng/mL), and SER (36,720.10-63,176.06 ng/mL) depending on their genotypes. The genetic determinants related to their phenotypic resistance to β-lactams (blaZ, mecA), ofloxacin (gyrA-S84L), erythromycin (ermB), lincomycin (lmrS), kanamycin (aph(3')-III, ant(6)-I), and tetracyclin (tet(L), tet(38)) were also detected. A plethora of virulence-related genes, including major virulence genes such as the tst gene, determinant for the toxic shock syndrome toxin-1, and the lukF-PV and lukS-PV genes, encoding the panton-valentine leukocidin (PVL), were present in the S. aureus strains, highlighting their pathogenic potential. Furthermore, a phylogenomic reconstruction including worldwide foodborne S. aureus showed a clear clustering based on ST and geographical origin rather than the source of isolation.
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10
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Molecular Analysis of pSK1 par: A Novel Plasmid Partitioning System Encoded by Staphylococcal Multiresistance Plasmids. J Mol Biol 2022; 434:167770. [PMID: 35907571 DOI: 10.1016/j.jmb.2022.167770] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/23/2022]
Abstract
The segregation of prokaryotic plasmids typically requires a centromere-like site and two proteins, a centromere-binding protein (CBP) and an NTPase. By contrast, a single 245 residue Par protein mediates partition of the prototypical staphylococcal multiresistance plasmid pSK1 in the absence of an identifiable NTPase component. To gain insight into centromere binding by pSK1 Par and its segregation function we performed structural, biochemical and in vivo studies. Here we show that pSK1 Par binds a centromere consisting of seven repeat elements. We demonstrate this Par-centromere interaction also mediates Par autoregulation. To elucidate the Par centromere binding mechanism, we obtained a structure of the Par N-terminal DNA-binding domain bound to centromere DNA to 2.25 Å. The pSK1 Par structure, which harbors a winged-helix-turn-helix (wHTH), is distinct from other plasmid CBP structures but shows homology to the B. subtilis chromosome segregation protein, RacA. Biochemical studies suggest the region C-terminal to the Par wHTH forms coiled coils and mediates oligomerization. Fluorescence microscopy analyses show that pSK1 Par enhances the separation of plasmids from clusters, driving effective segregation upon cell division. Combined the data provide insight into the molecular properties of a single protein partition system.
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11
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12
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Forde BM, De Oliveira DMP, Falconer C, Graves B, Harris PNA. Strengths and caveats of identifying resistance genes from whole genome sequencing data. Expert Rev Anti Infect Ther 2021; 20:533-547. [PMID: 34852720 DOI: 10.1080/14787210.2022.2013806] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Antimicrobial resistance (AMR) continues to present major challenges to modern healthcare. Recent advances in whole-genome sequencing (WGS) have made the rapid molecular characterization of AMR a realistic possibility for diagnostic laboratories; yet major barriers to clinical implementation exist. AREAS COVERED We describe and compare short- and long-read sequencing platforms, typical components of bioinformatics pipelines, tools for AMR gene detection and the relative merits of read- or assembly-based approaches. The challenges of characterizing mobile genetic elements from genomic data are outlined, as well as the complexities inherent to the prediction of phenotypic resistance from WGS. Practical obstacles to implementation in diagnostic laboratories, the critical role of quality control and external quality assurance, as well as standardized reporting standards are also discussed. Future directions, such as the application of machine-learning and artificial intelligence algorithms, linked to clinically meaningful outcomes, may offer a new paradigm for the clinical application of AMR prediction. EXPERT OPINION AMR prediction from WGS data presents an exciting opportunity to advance our capacity to comprehensively characterize infectious pathogens in a rapid manner, ultimately aiming to improve patient outcomes. Collaborative efforts between clinicians, scientists, regulatory bodies and healthcare administrators will be critical to achieve the full promise of this approach.
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Affiliation(s)
- Brian M Forde
- University of Queensland, Faculty of Medicine, Uq Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Australia
| | - David M P De Oliveira
- University of Queensland, Faculty of Science, School of Chemistry and Molecular Biosciences, St Lucia, Australia
| | - Caitlin Falconer
- University of Queensland, Faculty of Medicine, Uq Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Australia
| | - Bianca Graves
- Herston Infectious Disease Institute, Royal Brisbane & Women's Hospital, Herston, Australia
| | - Patrick N A Harris
- University of Queensland, Faculty of Medicine, Uq Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Herston, Australia.,Herston Infectious Disease Institute, Royal Brisbane & Women's Hospital, Herston, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Herston, Australia
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13
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Goswami C, Fox S, Holden M, Leanord A, Evans TJ. Genomic Analysis of Global Staphylococcus argenteus Strains Reveals Distinct Lineages With Differing Virulence and Antibiotic Resistance Gene Content. Front Microbiol 2021; 12:795173. [PMID: 34925305 PMCID: PMC8677677 DOI: 10.3389/fmicb.2021.795173] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Infections due to Staphylococcus argenteus have been increasingly reported worldwide and the microbe cannot be distinguished from Staphylococcus aureus by standard methods. Its complement of virulence determinants and antibiotic resistance genes remain unclear, and how far these are distinct from those produced by S. aureus remains undetermined. In order to address these uncertainties, we have collected 132 publicly available sequences from fourteen different countries, including the United Kingdom, between 2005 and 2018 to study the global genetic structure of the population. We have compared the genomes for antibiotic resistance genes, virulence determinants and mobile genetic elements such as phages, pathogenicity islands and presence of plasmid groups between different clades. 20% (n = 26) isolates were methicillin resistant harboring a mecA gene and 88% were penicillin resistant, harboring the blaZ gene. ST2250 was identified as the most frequent strain, but ST1223, which was the second largest group, contained a marginally larger number of virulence genes compared to the other STs. Novel S. argenteus pathogenicity islands were identified in our isolates harboring tsst-1, seb, sec3, ear, selk, selq toxin genes, as well as chromosomal clusters of enterotoxin and superantigen-like genes. Strain-specific type I modification systems were widespread which would limit interstrain transfer of genetic material. In addition, ST2250 possessed a CRISPR/Cas system, lacking in most other STs. S. argenteus possesses important genetic differences from S. aureus, as well as between different STs, with the potential to produce distinct clinical manifestations.
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Affiliation(s)
- Cosmika Goswami
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Stephen Fox
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Matthew Holden
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Alistair Leanord
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | - Thomas J. Evans
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
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14
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Lianou DT, Petinaki E, Cripps PJ, Gougoulis DA, Michael CK, Tsilipounidaki K, Skoulakis A, Katsafadou AI, Vasileiou NGC, Giannoulis T, Katsarou EI, Voidarou C, Mavrogianni VS, Caroprese M, Fthenakis GC. Prevalence, Patterns, Association with Biofilm Formation, Effects on Milk Quality and Risk Factors for Antibiotic Resistance of Staphylococci from Bulk-Tank Milk of Goat Herds. Antibiotics (Basel) 2021; 10:1225. [PMID: 34680806 PMCID: PMC8532619 DOI: 10.3390/antibiotics10101225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/28/2022] Open
Abstract
The objectives of this work were to study the prevalence and the patterns of antibiotic resistance of staphylococcal isolates from bulk-tank milk of goat herds across Greece, to assess possible associations of the presence of antibiotic resistance with the quality of milk in these herds and to evaluate herd-related factors potentially associated with the presence of antibiotic resistance among these staphylococcal isolates. A cross-sectional study was performed on 119 goat herds in Greece. Bulk-tank milk samples were collected for bacteriological examination; staphylococcal isolates were evaluated for resistance to 20 antibiotics. Oxacillin-resistant, resistant to at least one antibiotic, and multi-resistant staphylococcal isolates were recovered from 5.0%, 30.3%, and 16.0% of herds, respectively. Of 80 isolates, 7.5% were resistant to oxacillin, 50.0% were resistant to at least one antibiotic and 27.5% were multi-resistant. Resistance was seen more frequently among coagulase-negative staphylococci (59.3%) than among Staphylococcus aureus (23.8%). Resistance was more frequent against penicillin and ampicillin (41.3% of isolates) and fosfomycin (27.5%). No association was found with biofilm formation by staphylococci. For recovery of oxacillin-resistant isolates, the presence of working staff in the herds emerged as a significant factor; respective factors for the isolation of staphylococci resistant to at least one antibiotic were part-time farming and high (>10) number of systemic disinfections in the farm annually. The same three factors concurrently were also identified to be significant for the recovery of multi-resistant isolates.
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Affiliation(s)
- Daphne T. Lianou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (P.J.C.); (D.A.G.); (C.K.M.); (E.I.K.); (V.S.M.)
| | - Efthymia Petinaki
- University Hospital of Larissa, 41110 Larissa, Greece; (E.P.); (K.T.); (A.S.)
| | - Peter J. Cripps
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (P.J.C.); (D.A.G.); (C.K.M.); (E.I.K.); (V.S.M.)
| | - Dimitris A. Gougoulis
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (P.J.C.); (D.A.G.); (C.K.M.); (E.I.K.); (V.S.M.)
| | - Charalambia K. Michael
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (P.J.C.); (D.A.G.); (C.K.M.); (E.I.K.); (V.S.M.)
| | | | - Anargyros Skoulakis
- University Hospital of Larissa, 41110 Larissa, Greece; (E.P.); (K.T.); (A.S.)
| | | | - Natalia G. C. Vasileiou
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece; (N.G.C.V.); (T.G.)
| | - Themis Giannoulis
- Faculty of Animal Science, University of Thessaly, 41110 Larissa, Greece; (N.G.C.V.); (T.G.)
| | - Eleni I. Katsarou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (P.J.C.); (D.A.G.); (C.K.M.); (E.I.K.); (V.S.M.)
| | | | - Vasia S. Mavrogianni
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (P.J.C.); (D.A.G.); (C.K.M.); (E.I.K.); (V.S.M.)
| | - Mariangela Caroprese
- Department of Agriculture, Food, Natural Resources and Engineering (DAFNE), University of Foggia, 71122 Foggia, Italy;
| | - George C. Fthenakis
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.T.L.); (P.J.C.); (D.A.G.); (C.K.M.); (E.I.K.); (V.S.M.)
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15
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Staphylococcal phages and pathogenicity islands drive plasmid evolution. Nat Commun 2021; 12:5845. [PMID: 34615859 PMCID: PMC8494744 DOI: 10.1038/s41467-021-26101-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
Conjugation has classically been considered the main mechanism driving plasmid transfer in nature. Yet bacteria frequently carry so-called non-transmissible plasmids, raising questions about how these plasmids spread. Interestingly, the size of many mobilisable and non-transmissible plasmids coincides with the average size of phages (~40 kb) or that of a family of pathogenicity islands, the phage-inducible chromosomal islands (PICIs, ~11 kb). Here, we show that phages and PICIs from Staphylococcus aureus can mediate intra- and inter-species plasmid transfer via generalised transduction, potentially contributing to non-transmissible plasmid spread in nature. Further, staphylococcal PICIs enhance plasmid packaging efficiency, and phages and PICIs exert selective pressures on plasmids via the physical capacity of their capsids, explaining the bimodal size distribution observed for non-conjugative plasmids. Our results highlight that transducing agents (phages, PICIs) have important roles in bacterial plasmid evolution and, potentially, in antimicrobial resistance transmission.
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16
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Yui Eto K, Kwong SM, LaBreck PT, Crow JE, Traore DAK, Parahitiyawa N, Fairhurst HM, Merrell DS, Firth N, Bond CS, Ramsay JP. Evolving origin-of-transfer sequences on staphylococcal conjugative and mobilizable plasmids-who's mimicking whom? Nucleic Acids Res 2021; 49:5177-5188. [PMID: 33939800 PMCID: PMC8136818 DOI: 10.1093/nar/gkab303] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 11/22/2022] Open
Abstract
In Staphylococcus aureus, most multiresistance plasmids lack conjugation or mobilization genes for horizontal transfer. However, most are mobilizable due to carriage of origin-of-transfer (oriT) sequences mimicking those of conjugative plasmids related to pWBG749. pWBG749-family plasmids have diverged to carry five distinct oriT subtypes and non-conjugative plasmids have been identified that contain mimics of each. The relaxasome accessory factor SmpO, encoded by each conjugative plasmid, determines specificity for its cognate oriT. Here we characterized the binding of SmpO proteins to each oriT. SmpO proteins predominantly formed tetramers in solution and bound 5′-GNNNNC-3′ sites within each oriT. Four of the five SmpO proteins specifically bound their cognate oriT. An F7K substitution in pWBG749 SmpO switched oriT-binding specificity in vitro. In vivo, the F7K substitution reduced but did not abolish self-transfer of pWBG749. Notably, the substitution broadened the oriT subtypes that were mobilized. Thus, this substitution represents a potential evolutionary intermediate with promiscuous DNA-binding specificity that could facilitate a switch between oriT specificities. Phylogenetic analysis suggests pWBG749-family plasmids have switched oriT specificity more than once during evolution. We hypothesize the convergent evolution of oriT specificity in distinct branches of the pWBG749-family phylogeny reflects indirect selection pressure to mobilize plasmids carrying non-cognate oriT-mimics.
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Affiliation(s)
- Karina Yui Eto
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia.,Curtin Medical School, Curtin University, Perth, WA 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Stephen M Kwong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Patrick T LaBreck
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, MD 20814, USA
| | - Jade E Crow
- Curtin Medical School, Curtin University, Perth, WA 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Daouda A K Traore
- Department of Biochemistry and Molecular Biology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia.,Faculty of Natural Sciences, School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK.,Life Sciences Group, Institut Laue Langevin, Grenoble 38000, France.,Faculté des Sciences et Techniques, Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako BP E423, Mali
| | | | | | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, MD 20814, USA
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | - Charles S Bond
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Joshua P Ramsay
- Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia.,Curtin Medical School, Curtin University, Perth, WA 6102, Australia.,School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
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17
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Mores CR, Montelongo C, Putonti C, Wolfe AJ, Abouelfetouh A. Investigation of Plasmids Among Clinical Staphylococcus aureus and Staphylococcus haemolyticus Isolates From Egypt. Front Microbiol 2021; 12:659116. [PMID: 34149648 PMCID: PMC8213342 DOI: 10.3389/fmicb.2021.659116] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 05/07/2021] [Indexed: 11/21/2022] Open
Abstract
Staphylococci can cause a wide array of infections that can be life threatening. These infections become more deadly when the isolates are antibiotic resistant and thus harder to treat. Many resistance determinants are plasmid-mediated; however, staphylococcal plasmids have not yet been fully characterized. In particular, plasmids and their contributions to antibiotic resistance have not been investigated within the Arab states, where antibiotic use is not universally regulated. Here, we characterized the putative plasmid content among 56 Staphylococcus aureus and 10 Staphylococcus haemolyticus clinical isolates from Alexandria, Egypt. Putative plasmid sequences were detected in over half of our collection. In total, we identified 72 putative plasmid sequences in 27 S. aureus and 1 S. haemolyticus isolates. While these isolates typically carried one or two plasmids, we identified one isolate-S. aureus AA53-with 11 putative plasmids. The plasmid sequences most frequently encoded a Rep_1, RepL, or PriCT_1 type replication protein. As expected, antibiotic resistance genes were widespread among the identified plasmid sequences. Related plasmids were identified amongst our clinical isolates; homologous plasmids present in multiple isolates clustered into 11 groups based upon sequence similarity. Plasmids from the same cluster often shared antibiotic resistance genes, including blaZ, which is associated with β-lactam resistance. Our analyses suggest that plasmids are a key factor in the pathology and epidemiology of S. aureus in Egypt. A better characterization of plasmids and the role they contribute to the success of Staphylococci as pathogens will guide the design of effective control strategies to limit their spread.
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Affiliation(s)
- Carine R. Mores
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL, United States
| | - Cesar Montelongo
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL, United States
| | - Catherine Putonti
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL, United States
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, United States
- Department of Biology, Loyola University Chicago, Chicago, IL, United States
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Chicago, IL, United States
| | - Alaa Abouelfetouh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alalamein University, Alalamein, Egypt
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18
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Wan TW, Liu YJ, Wang YT, Lin YT, Hsu JC, Tsai JC, Chiu HC, Hsueh PR, Hung WC, Teng LJ. Potentially conjugative plasmids harboring Tn6636, a multidrug-resistant and composite mobile element, in Staphylococcus aureus. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2021; 55:225-233. [PMID: 33840606 DOI: 10.1016/j.jmii.2021.03.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/18/2020] [Accepted: 03/11/2021] [Indexed: 10/21/2022]
Abstract
OBJECTIVES This study aimed to provide detailed genetic characterization of Tn6636, a multidrug-resistant and composite mobile element, in clinical isolates of Staphylococcus aureus. METHODS A total of 112 ermB-positive methicillin-susceptible S. aureus (MSSA) and 224 ermB-positive methicillin-resistant S. aureus (MRSA) isolates collected from 2000 to 2015 were tested for the presence of Tn6636. Detection of the plasmids harboring Tn6636 was performed by S1 nuclease digestion pulsed-field gel electrophoresis (PFGE) analysis, conjugation test, and whole genome sequencing (WGS). RESULTS Prevalence of Tn6636 in MSSA is higher than that in MRSA. Ten MSSA isolates and 10 MRSA isolates carried Tn6636. The 10 MSSA isolates belonged to three sequence types (ST), including ST7 (n = 6), ST5 (n = 3), and ST59 (n = 1). The 10 MRSA isolates belonged to ST188 (n = 8) and ST965 (n = 2). Analysis of plasmid sequences revealed that Tn6636 was harbored by six different mosaic plasmids. In addition to resistance genes, some plasmids also harbored toxin genes. CONCLUSION The presence of multi-resistant Tn6636 in plasmids of both MSSA and MRSA with various STs suggests its broad dissemination. Results indicate that Tn6636 has existed for at least 16 years in Taiwan. The mosaic plasmids harboring Tn6636 can be transferred by conjugation. Ongoing surveillance of Tn6636 is essential to avoid continued spreading of resistant plasmids.
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Affiliation(s)
- Tsai-Wen Wan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan
| | - Yu-Jung Liu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan
| | - Yu-Ting Wang
- Division of Research and Analysis, Food and Drug Administration, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Tzu Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
| | - Jia-Chuan Hsu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan
| | - Jui-Chang Tsai
- Division of Neurosurgery, Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Hao-Chieh Chiu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Chun Hung
- Department of Microbiology and Immunology, Kaohsiung Medical University, Kaohsiung, Taiwan.
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan UniversityCollege of Medicine, Taipei, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan.
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19
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Al Yousef SA. Degree of bacterial contamination in barbershops using hair dryers in Riyadh. Saudi J Biol Sci 2021; 28:2692-2694. [PMID: 34025154 PMCID: PMC8117043 DOI: 10.1016/j.sjbs.2021.02.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/16/2021] [Accepted: 02/28/2021] [Indexed: 11/26/2022] Open
Abstract
Barbershops provide areas for the growth and transfer of bacterial pathogens and thereby have an impact on public health. Barbershops are ideal places for the interactive spread of infections, including community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA). Here, the work determines the degree of bacterial contamination of hair dryers used in barbershops. The samples were collected in the city of Riyadh, the Kingdom of Saudi Arabia on March 2019. Significant bacterial contamination was seen, with total bacterial count increasing when the hair dryers were run for 20 instead of 10 s. The study shows a high level of bacterial contamination barbershops using hair dryers, with MRSA being isolated in some. The results suggest that high quality filters should be used inside hair dryers and filters, and theses should be cleaned frequently.
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Affiliation(s)
- Sulaiman A Al Yousef
- Department of Clinical Laboratory Sciences, College Applied Medical Science, University of Hafr Al Batin, P. O. Box 1803, Hafar Al-batin 31991, Saudi Arabia
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20
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Ene A, Miller-Ensminger T, Mores CR, Giannattasio-Ferraz S, Wolfe AJ, Abouelfetouh A, Putonti C. Examination of Staphylococcus aureus Prophages Circulating in Egypt. Viruses 2021; 13:337. [PMID: 33671574 PMCID: PMC7926752 DOI: 10.3390/v13020337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/10/2021] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
Abstract
Staphylococcus aureus infections are of growing concern given the increased incidence of antibiotic resistant strains. Egypt, like several other countries, has seen alarming increases in methicillin-resistant S. aureus (MRSA) infections. This species can rapidly acquire genes associated with resistance, as well as virulence factors, through mobile genetic elements, including phages. Recently, we sequenced 56 S. aureus genomes from Alexandria Main University Hospital in Alexandria, Egypt, complementing 17 S. aureus genomes publicly available from other sites in Egypt. In the current study, we found that the majority (73.6%) of these strains contain intact prophages, including Biseptimaviruses, Phietaviruses, and Triaviruses. Further investigation of these prophages revealed evidence of horizontal exchange of the integrase for two of the prophages. These Egyptian S. aureus prophages are predicted to encode numerous virulence factors, including genes associated with immune evasion and toxins, including the Panton-Valentine leukocidin (PVL)-associated genes lukF-PV/lukS-PV. Thus, prophages are likely to be a major contributor to the virulence of S. aureus strains in circulation in Egypt.
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Affiliation(s)
- Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA; (A.E.); (T.M.-E.)
| | - Taylor Miller-Ensminger
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA; (A.E.); (T.M.-E.)
| | - Carine R. Mores
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA; (C.R.M.); (A.J.W.)
| | - Silvia Giannattasio-Ferraz
- Departmento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA; (C.R.M.); (A.J.W.)
| | - Alaa Abouelfetouh
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alexandria University, Alexandria 25435, Egypt;
- Department of Microbiology and Immunology, Faculty of Pharmacy, Alalamein International University, Alalamein 51718, Egypt
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA; (A.E.); (T.M.-E.)
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA; (C.R.M.); (A.J.W.)
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
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21
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França A, Gaio V, Lopes N, Melo LDR. Virulence Factors in Coagulase-Negative Staphylococci. Pathogens 2021; 10:170. [PMID: 33557202 PMCID: PMC7913919 DOI: 10.3390/pathogens10020170] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 01/29/2021] [Indexed: 12/13/2022] Open
Abstract
Coagulase-negative staphylococci (CoNS) have emerged as major pathogens in healthcare-associated facilities, being S. epidermidis, S. haemolyticus and, more recently, S. lugdunensis, the most clinically relevant species. Despite being less virulent than the well-studied pathogen S. aureus, the number of CoNS strains sequenced is constantly increasing and, with that, the number of virulence factors identified in those strains. In this regard, biofilm formation is considered the most important. Besides virulence factors, the presence of several antibiotic-resistance genes identified in CoNS is worrisome and makes treatment very challenging. In this review, we analyzed the different aspects involved in CoNS virulence and their impact on health and food.
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Affiliation(s)
- Angela França
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (V.G.); (N.L.)
| | | | | | - Luís D. R. Melo
- Laboratory of Research in Biofilms Rosário Oliveira, Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (V.G.); (N.L.)
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22
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Isolation and Visualization of Plasmids from Gram-Positive Bacteria of Interest in Public Health. Methods Mol Biol 2021. [PMID: 31584152 DOI: 10.1007/978-1-4939-9877-7_2] [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: 09/29/2023]
Abstract
This chapter describes the methods to extract and characterize plasmids of Gram-positive bacterial species of interest in public health (biomedicine, veterinary, and food safety) as Staphylococcus, Streptococcus, Enterococcus, Listeria, and Clostridium and lactic acid bacteria. References for detailed plasmid classification are given in order to provide a comprehensive landscape in the interpretation of their plasmidomes.
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23
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Leite EL, Oliveira AFDE, Carmo FLRDO, Berkova N, Barh D, Ghosh P, Azevedo V. Bacteriocins as an alternative in the treatment of infections by Staphylococcus aureus. AN ACAD BRAS CIENC 2020; 92:e20201216. [PMID: 33084762 DOI: 10.1590/0001-3765202020201216] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 08/18/2020] [Indexed: 01/19/2023] Open
Abstract
Staphylococcus aureus (S. aureus) is a highly versatile Gram-positive bacterium that is carried asymptomatically by up to 30% of healthy people, while being a major cause of healthcare-associated infections, making it a worldwide problem in clinical medicine. The adaptive evolution of S. aureus strains is demonstrated by its remarkable capacity to promptly develop high resistance to multiple antibiotics, thus limiting treatment choice. Nowadays, there is a continuous demand for an alternative to the use of antibiotics for S. aureus infections and a strategy to control the spread or to kill phylogenetically related strains. In this scenario, bacteriocins fit as with a promising and interesting alternative. These molecules are produced by a range of bacteria, defined as ribosomally synthesized peptides with bacteriostatic or bactericidal activity against a wide range of pathogens. This work reviews ascertained the main antibiotic-resistance mechanisms of S. aureus strains and the current, informative content concerning the applicability of the use of bacteriocins overlapping the use of conventional antibiotics in the context of S. aureus infections. Besides, we highlight the possible application of these biomolecules on an industrial scale in future work.
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Affiliation(s)
- Elma L Leite
- Institut National de la Recherche Agronomique (INRA), 65 Rue de Saint-Brieuc, 35000 Rennes, France.,Departamento de Genética, Ecologia e Evolução, ICB/UFMG, Av. Antonio Carlos, 6627, Pampulha, Caixa Postal 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Alberto F DE Oliveira
- Institut National de la Recherche Agronomique (INRA), 65 Rue de Saint-Brieuc, 35000 Rennes, France
| | - Fillipe L R DO Carmo
- Departamento de Genética, Ecologia e Evolução, ICB/UFMG, Av. Antonio Carlos, 6627, Pampulha, Caixa Postal 486, 31270-901 Belo Horizonte, MG, Brazil
| | - Nadia Berkova
- Institut National de la Recherche Agronomique (INRA), 65 Rue de Saint-Brieuc, 35000 Rennes, France
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, 721172 West Bengal, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA-23284, USA
| | - Vasco Azevedo
- Departamento de Genética, Ecologia e Evolução, ICB/UFMG, Av. Antonio Carlos, 6627, Pampulha, Caixa Postal 486, 31270-901 Belo Horizonte, MG, Brazil
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24
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De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, Paterson DL, Walker MJ. Antimicrobial Resistance in ESKAPE Pathogens. Clin Microbiol Rev 2020; 23:788-99. [PMID: 32404435 DOI: 10.1111/imb.12124] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.
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Affiliation(s)
- David M P De Oliveira
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Patrick N A Harris
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - David L Paterson
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
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Abstract
Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.
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26
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Neyaz L, Rajagopal N, Wells H, Fakhr MK. Molecular Characterization of Staphylococcus aureus Plasmids Associated With Strains Isolated From Various Retail Meats. Front Microbiol 2020; 11:223. [PMID: 32140145 PMCID: PMC7042431 DOI: 10.3389/fmicb.2020.00223] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 01/30/2020] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus aureus is considered one of the most important foodborne bacterial pathogens causing food poisoning and related illnesses. S. aureus strains harbor plasmids encoding genes for virulence and antimicrobial resistance, but few studies have investigated S. aureus plasmids, especially megaplasmids, in isolates from retail meats. Furthermore, knowledge about the distribution of genes encoding replication (rep) initiation proteins in food isolates is lacking. In this study, the prevalence of plasmids in S. aureus strains isolated from retail meats purchased in Oklahoma was investigated; furthermore, we evaluated associations between rep families, selected virulence and antimicrobial resistance genes, and food source origin. Two hundred and twenty-two S. aureus isolates from chicken (n = 55), beef liver (n = 43), pork (n = 42), chicken liver (n = 29), beef (n = 24), turkey (n = 22), and chicken gizzards (n = 7) were subjected to plasmid screening with alkaline lysis and PFGE to detect small-to-medium sized and large plasmids, respectively. The S. aureus isolates contained variable sizes of plasmids, and PFGE was superior to alkaline lysis in detecting large megaplasmids. A total of 26 rep families were identified by PCR, and the most dominant rep families were rep10 and rep7 in 164 isolates (89%), rep21 in 124 isolates (56%), and rep12 in 99 isolates (45%). Relationships between selected rep genes, antimicrobial resistance and virulence genes, and meat sources were detected. In conclusion, S. aureus strains isolated from retail meats harbor plasmids with various sizes and there is an association between rep genes on these plasmids and the meat source or the antimicrobial resistance of the strains harboring them.
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Affiliation(s)
- Leena Neyaz
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Nisha Rajagopal
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Harrington Wells
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
| | - Mohamed K Fakhr
- Department of Biological Science, The University of Tulsa, Tulsa, OK, United States
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27
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Mc Carlie S, Boucher CE, Bragg RR. Molecular basis of bacterial disinfectant resistance. Drug Resist Updat 2019; 48:100672. [PMID: 31830738 DOI: 10.1016/j.drup.2019.100672] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 11/19/2019] [Accepted: 11/22/2019] [Indexed: 01/08/2023]
Abstract
Antibiotic resistance could accelerate humanity towards an already fast-approaching post-antibiotic era, where disinfectants and effective biosecurity measures will be critically important to control microbial diseases. Disinfectant resistance has the potential to change our way of life from compromising food security to threatening our medical health systems. Resistance to antimicrobial agents occurs through either intrinsic or acquired resistance mechanisms. Acquired resistance occurs through the efficient transfer of mobile genetic elements, which can carry single, or multiple resistance determinants. Drug resistance genes may form part of integrons, transposons and insertions sequences which are capable of intracellular transfer onto plasmids or gene cassettes. Thereafter, resistance plasmids and gene cassettes mobilize by self-transmission between bacteria, increasing the prevalence of drug resistance determinants in a bacterial population. An accumulation of drug resistance genes through these mechanisms gives rise to multidrug resistant (MDR) bacteria. The study of this mobility is integral to safeguard current antibiotics, disinfectants and other antimicrobials. Literature evidence, however, indicates that knowledge regarding disinfectant resistance is severly limited. Genome engineering such as the CRISPR-Cas system, has identified disinfectant resistance genes, and reversed resistance altogether in certain prokaryotes. Demonstrating that these techniques could prove invaluable in the combat against disinfectant resistance by uncovering the secrets of MDR bacteria.
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28
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Evolution of a 72-Kilobase Cointegrant, Conjugative Multiresistance Plasmid in Community-Associated Methicillin-Resistant Staphylococcus aureus Isolates from the Early 1990s. Antimicrob Agents Chemother 2019; 63:AAC.01560-19. [PMID: 31501140 DOI: 10.1128/aac.01560-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 09/03/2019] [Indexed: 12/13/2022] Open
Abstract
Horizontal transfer of plasmids encoding antimicrobial resistance and virulence determinants has been instrumental in Staphylococcus aureus evolution, including the emergence of community-associated methicillin-resistant S. aureus (CA-MRSA). In the early 1990s, the first CA-MRSA strain isolated in Western Australia (WA), WA-5, encoded cadmium, tetracycline, and penicillin resistance genes on plasmid pWBG753 (∼30 kb). WA-5 and pWBG753 appeared only briefly in WA; however, fusidic acid resistance plasmids related to pWBG753 were also present in the first European CA-MRSA isolates at the time. Here, we characterize a 72-kb conjugative plasmid, pWBG731, present in multiresistant WA-5-like clones from the same period. pWBG731 was a cointegrant formed from pWBG753 and a pWBG749 family conjugative plasmid. pWBG731 carried mupirocin, trimethoprim, cadmium, and penicillin resistance genes. The stepwise evolution of pWBG731 likely occurred through the combined actions of IS257, IS257-dependent miniature inverted-repeat transposable elements (MITEs), and the BinL resolution system of the β-lactamase transposon Tn552 An evolutionarily intermediate ∼42-kb nonconjugative plasmid, pWBG715, possessed the same resistance genes as pWBG731 but retained an integrated copy of the small tetracycline resistance plasmid pT181. IS257 likely facilitated the replacement of pT181 with conjugation genes on pWBG731, thus enabling autonomous transfer. Like conjugative plasmid pWBG749, pWBG731 also mobilized nonconjugative plasmids carrying oriT mimics. It seems likely that pWBG731 represents the product of multiple recombination events between the WA-5 pWBG753 plasmid and other mobile genetic elements present in indigenous community-associated methicillin-sensitive S. aureus (CA-MSSA) isolates. The molecular evolution of pWBG731 saliently illustrates how diverse mobile genetic elements can together facilitate rapid accrual and horizontal dissemination of multiresistance in S. aureus CA-MRSA.
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Trejo CS, Rock RS, Stark WM, Boocock MR, Rice PA. Snapshots of a molecular swivel in action. Nucleic Acids Res 2019; 46:5286-5296. [PMID: 29315406 PMCID: PMC6007550 DOI: 10.1093/nar/gkx1309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 12/20/2017] [Indexed: 12/22/2022] Open
Abstract
Members of the serine family of site-specific recombinases exchange DNA strands via 180° rotation about a central protein-protein interface. Modeling of this process has been hampered by the lack of structures in more than one rotational state for any individual serine recombinase. Here we report crystal structures of the catalytic domains of four constitutively active mutants of the serine recombinase Sin, providing snapshots of rotational states not previously visualized for Sin, including two seen in the same crystal. Normal mode analysis predicted that each tetramer's lowest frequency mode (i.e. most accessible large-scale motion) mimics rotation: two protomers rotate as a pair with respect to the other two. Our analyses also suggest that rotation is not a rigid body movement around a single symmetry axis but instead uses multiple pivot points and entails internal motions within each subunit.
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Affiliation(s)
- Caitlin S Trejo
- Department of Biochemistry and Molecular Biology, the University of Chicago, Chicago, IL 60637, USA
| | - Ronald S Rock
- Department of Biochemistry and Molecular Biology, the University of Chicago, Chicago, IL 60637, USA
| | - W Marshall Stark
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G128QQ, UK
| | - Martin R Boocock
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G128QQ, UK
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, the University of Chicago, Chicago, IL 60637, USA
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30
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Bukowski M, Piwowarczyk R, Madry A, Zagorski-Przybylo R, Hydzik M, Wladyka B. Prevalence of Antibiotic and Heavy Metal Resistance Determinants and Virulence-Related Genetic Elements in Plasmids of Staphylococcus aureus. Front Microbiol 2019; 10:805. [PMID: 31068910 PMCID: PMC6491766 DOI: 10.3389/fmicb.2019.00805] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/29/2019] [Indexed: 12/16/2022] Open
Abstract
The use of antibiotics on a mass scale, particularly in farming, and their release into the environment has led to a rapid emergence of resistant bacteria. Once emerged, resistance determinants are spread by horizontal gene transfer among strains of the same as well as disparate bacterial species. Their accumulation in free-living as well as livestock and community-associated strains results in the widespread multiple-drug resistance among clinically relevant species posing an increasingly pressing problem in healthcare. One of these clinically relevant species is Staphylococcus aureus, a common cause of hospital and community outbreaks. Among the rich diversity of mobile genetic elements regularly occurring in S. aureus such as phages, pathogenicity islands, and staphylococcal cassette chromosomes, plasmids are the major mean for dissemination of resistance determinants and virulence factors. Unfortunately, a vast number of whole-genome sequencing projects does not aim for complete sequence determination, which results in a disproportionately low number of known complete plasmid sequences. To address this problem we determined complete plasmid sequences derived from 18 poultry S. aureus strains and analyzed the prevalence of antibiotic and heavy metal resistance determinants, genes of virulence factors, as well as genetic elements relevant for their maintenance. Some of the plasmids have been reported before and are being found in clinical isolates of strains typical for humans or human ones of livestock origin. This shows that livestock-associated staphylococci are a significant reservoir of resistance determinants and virulence factors. Nevertheless, nearly half of the plasmids were unknown to date. In this group we found a potentially mobilizable plasmid pPA3 being a unique example of accumulation of resistance determinants and virulence factors likely stabilized by a presence of a toxin–antitoxin system.
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Affiliation(s)
- Michal Bukowski
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Rafal Piwowarczyk
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Madry
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Rafal Zagorski-Przybylo
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Marcin Hydzik
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Benedykt Wladyka
- Department of Analytical Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
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31
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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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32
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Iwalokun BA, Akinloye O, Udoh BE, Akinyemi KO. Efficacy of silver nanoparticles against multidrug resistant clinical Staphylococcus aureus isolates from Nigeria. J Immunoassay Immunochem 2019; 40:214-236. [PMID: 30696349 DOI: 10.1080/15321819.2018.1555765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Multidrug resistant (MDR) S. aureus infections continue to account for excess mortality in hospital and community settings and constitute a rising global health problem. However, data on the efficacy and mechanism of actions of alternative solutions like silver nanoparticles in developing countries are lacking. This study investigated anti-staphylococcal activity of silver nanoparticles (AgNP) against local strains from Nigeria. A total 119 clinical isolates of S. aureus from five Nigerian laboratories categorized as MRSA (n = 52) and MSSA (n = 67) by PCR were studied. The MIC of AgNP produced by chemical reduction method and characterized by surface plasmon resonance absorbance and size equivalence by scanning electron microscopy was determined by microbroth dilution method. Its effect on protease activity and plasmids were also investigated. Baseline characteristics of the isolates revealed MDR phenotype of the isolates, carriage of diverse plasmids (15-32 kb) among the MDR MSSA, and mean extracellular protease activity of 24.8-55.7 U/mL. The chemically synthesized AgNP had a peak absorbance at 400 nm with a size equivalence of 4.58 nm. The MICs of AgNP against the isolates were 4.7 μg/mL and 4.9 μg/mL, respectively, for MRSA and MSSA (P > 0.05). The bactericidal effect of AgNP at 2.5-5 μg/mL on the MSSA and MRSA isolates was observed at 2.7-5.5 h post exposure in vitro. Further analysis revealed plasmid eviction in the MDR MSSA isolates exposed to 5 μg/mL AgNP and dose-dependent reduction in extracellular protease activity by 84.6-93.1%. Hemolysis of human erythrocytes by AgNP was not observed at the MIC range. Conclusion: This study revealed safety and efficacy of AgNP against clinical MDR S. aureus isolates from Nigeria, using plasmid eviction and protease inhibition as mechanisms of action.
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Affiliation(s)
- B A Iwalokun
- a Molecular Biology & Biotechnology Department , Nigerian Institute of Medical Research , Lagos , Nigeria
| | - O Akinloye
- a Molecular Biology & Biotechnology Department , Nigerian Institute of Medical Research , Lagos , Nigeria.,b Clinical Chemistry and Molecular Diagnostic Research Laboratory, Department of Medical Laboratory Science, College of Medicine , University of Lagos , Lagos , Nigeria
| | - B E Udoh
- c Department of Medical Microbiology and Parasitology , Olabisi Onabanjo University , Sagamu , Nigeria
| | - K O Akinyemi
- d Department of Microbiology , Lagos State University , Lagos , Nigeria
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Becker K, van Alen S, Idelevich EA, Schleimer N, Seggewiß J, Mellmann A, Kaspar U, Peters G. Plasmid-Encoded Transferable mecB-Mediated Methicillin Resistance in Staphylococcus aureus. Emerg Infect Dis 2019; 24:242-248. [PMID: 29350135 PMCID: PMC5782906 DOI: 10.3201/eid2402.171074] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During cefoxitin-based nasal screening, phenotypically categorized methicillin-resistant Staphylococcus aureus (MRSA) was isolated and tested negative for the presence of the mecA and mecC genes as well as for the SCCmec-orfX junction region. The isolate was found to carry a mecB gene previously described for Macrococcus caseolyticus but not for staphylococcal species. The gene is flanked by β-lactam regulatory genes similar to mecR, mecI, and blaZ and is part of an 84.6-kb multidrug-resistance plasmid that harbors genes encoding additional resistances to aminoglycosides (aacA-aphD, aphA, and aadK) as well as macrolides (ermB) and tetracyclines (tetS). This further plasmidborne β-lactam resistance mechanism harbors the putative risk of acceleration or reacceleration of MRSA spread, resulting in broad ineffectiveness of β-lactams as a main therapeutic application against staphylococcal infections.
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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: 1130] [Impact Index Per Article: 188.3] [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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Rasigade JP, Leclère A, Alla F, Tessier A, Bes M, Lechiche C, Vernet-Garnier V, Laouénan C, Vandenesch F, Leport C. Staphylococcus aureus CC30 Lineage and Absence of sed, j, r-Harboring Plasmid Predict Embolism in Infective Endocarditis. Front Cell Infect Microbiol 2018; 8:187. [PMID: 29938201 PMCID: PMC6003251 DOI: 10.3389/fcimb.2018.00187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/14/2018] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus aureus induces severe infective endocarditis (IE) where embolic complications are a major cause of death. Risk factors for embolism have been reported such as a younger age or larger IE vegetations, while methicillin resistance conferred by the mecA gene appeared as a protective factor. It is unclear, however, whether embolism is influenced by other S. aureus characteristics such as clonal complex (CC) or virulence pattern. We examined clinical and microbiological predictors of embolism in a prospective multicentric cohort of 98 French patients with monomicrobial S. aureus IE. The genomic contents of causative isolates were characterized using DNA array. To preserve statistical power, genotypic predictors were restricted to CC, secreted virulence factors and virulence regulators. Multivariate regularized logistic regression identified three independent predictors of embolism. Patients at higher risk were younger than the cohort median age of 62.5 y (adjusted odds ratio [OR] 0.14; 95% confidence interval [CI] 0.05-0.36). S. aureus characteristics predicting embolism were a CC30 genetic background (adjusted OR 9.734; 95% CI 1.53-192.8) and the absence of pIB485-like plasmid-borne enterotoxin-encoding genes sed, sej, and ser (sedjr; adjusted OR 0.07; 95% CI 0.004-0.457). CC30 S. aureus has been repeatedly reported to exhibit enhanced fitness in bloodstream infections, which might impact its ability to cause embolism. sedjr-encoded enterotoxins, whose superantigenic activity is unlikely to protect against embolism, possibly acted as a proxy to others genes of the pIB485-like plasmid found in genetically unrelated isolates from mostly embolism-free patients. mecA did not independently predict embolism but was strongly associated with sedjr. This mecA-sedjr association might have driven previous reports of a negative association of mecA and embolism. Collectively, our results suggest that the influence of S. aureus genotypic features on the risk of embolism may be stronger than previously suspected and independent of clinical risk factors.
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Affiliation(s)
- Jean-Philippe Rasigade
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France.,Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Amélie Leclère
- UMR-1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Institut National de la Santé et de la Recherche Médicale, UMR-1137, Paris, France
| | - François Alla
- CIC-1433 Epidémiologie Clinique, Institut National de la Santé et de la Recherche Médicale, Centre Hospitalier Universitaire de Nancy, Nancy, France.,EA4360, Apemac, Université de Lorraine, Nancy, France
| | - Adrien Tessier
- UMR-1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Institut National de la Santé et de la Recherche Médicale, UMR-1137, Paris, France
| | - Michèle Bes
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France.,Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Catherine Lechiche
- Service de Maladies Infectieuses et Tropicales Centre Hospitalier Universitaire de Nîmes Caremeau, Nîmes, France
| | - Véronique Vernet-Garnier
- Faculté de Médecine EA 4687 Université de Reims Champagne Ardenne, Reims, France.,Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Reims Robert Debré, Reims, France
| | - Cédric Laouénan
- UMR-1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Institut National de la Santé et de la Recherche Médicale, UMR-1137, Paris, France.,Service de Biostatistiques, Hôpital Bichat, AP-HP, Paris, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Université Claude Bernard Lyon 1, CNRS UMR5308, ENS de Lyon, Lyon, France.,Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Catherine Leport
- UMR-1137, Université Paris Diderot, Sorbonne Paris Cité, Paris, France.,Institut National de la Santé et de la Recherche Médicale, UMR-1137, Paris, France.,Unité de Coordination du Risque Épidémique et Biologique, AP-HP, Paris, France
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36
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Bayliss SC, Hunt VL, Yokoyama M, Thorpe HA, Feil EJ. The use of Oxford Nanopore native barcoding for complete genome assembly. Gigascience 2018; 6:1-6. [PMID: 28327913 PMCID: PMC5467021 DOI: 10.1093/gigascience/gix001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/10/2017] [Indexed: 11/29/2022] Open
Abstract
Background The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short read data. The strain we used, MHO_001, represents the important community-acquired methicillin-resistant Staphylococcus aureus lineage USA300. Findings Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The long read data represented only ∼5% to 10% of an average MinION(TM) run (∼7x genomic coverage), but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss, and gain of mobile genetic elements. Conclusion Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short read data to fully complete a bacterial genome. The ability to complete multiple genomes, for which short read data is already available, from a single MinION(TM) run is set to impact our understanding of accessory genome content, plasmid diversity, and genome rearrangements.
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Affiliation(s)
- Sion C Bayliss
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
- Correspondence: The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK. Tel: +44 (0)1225 340959; E-mail:
| | - Vicky L Hunt
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Maho Yokoyama
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Harry A Thorpe
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Edward J Feil
- The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
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Faden A. Methicillin-resistant Staphylococcus aureus (MRSA) screening of hospital dental clinic surfaces. Saudi J Biol Sci 2018; 26:1795-1798. [PMID: 31762660 PMCID: PMC6864161 DOI: 10.1016/j.sjbs.2018.03.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/31/2018] [Accepted: 03/08/2018] [Indexed: 11/16/2022] Open
Abstract
We assessed the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) strains on surfaces of hospital dental clinics. Specimens were obtained from 5 clinically symptoms-free patients of five different specialties clinics (Implantology, Pediatric Dentistry, Prosthetics, Restorative Dentistry, and Oral Medicine) of the Dental Clinic Hospital of King Saud University before and after each patient. A Q-tip swabs were used from 10 surfaces in each clinic (Arm rest of dental chair, floor beneath dental chair, sink/faucet, towel dispenser, instrument table handle, light handle, X-ray viewer, paper dental records, head rest, and bench). Specimens were cultured in CHROMagar MRSA medium. Prevalence of MRSA colonization was compared between periods before and after patients visited each clinic for treatment. The results showed that the prevalence of MRSA was remarkably increased after patients visited the area. The results indicate that dental clinics should be considered as possible reservoirs of MRSA in the hospital setting.
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Affiliation(s)
- Asmaa Faden
- Department of Oral Medicine and Diagnostics Sciences, College of Dentistry, King Saud University, Riyadh, Saudi Arabia
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Topical Antibiotic Use Coselects for the Carriage of Mobile Genetic Elements Conferring Resistance to Unrelated Antimicrobials in Staphylococcus aureus. Antimicrob Agents Chemother 2018; 62:AAC.02000-17. [PMID: 29229636 PMCID: PMC5786761 DOI: 10.1128/aac.02000-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/27/2017] [Indexed: 12/25/2022] Open
Abstract
Topical antibiotics, such as mupirocin and fusidic acid, are commonly used in the prevention and treatment of skin infections, particularly those caused by staphylococci. However, the widespread use of these agents is associated with increased resistance to these agents, potentially limiting their efficacy. Of particular concern is the observation that resistance to topical antibiotics is often associated with multidrug resistance, suggesting that topical antibiotics may play a role in the emergence of multidrug-resistant (MDR) strains. New Zealand (NZ) has some of the highest globally recorded rates of topical antibiotic usage and resistance. Using a combination of Pacific Biosciences single-molecule real-time (SMRT) whole-genome sequencing, Illumina short-read sequencing, and Bayesian phylogenomic modeling on 118 new multilocus sequence type 1 (ST1) community Staphylococcus aureus isolates from New Zealand and 61 publically available international ST1 genome sequences, we demonstrate a strong correlation between the clinical introduction of topical antibiotics and the emergence of MDR ST1 S. aureus We also provide in vitro experimental evidence showing that exposure to topical antibiotics can lead to the rapid selection of MDR S. aureus isolates carrying plasmids that confer resistance to multiple unrelated antibiotics, from within a mixed population of competitor strains. These findings have important implications regarding the impact of the indiscriminate use of topical antibiotics.
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Águila-Arcos S, Álvarez-Rodríguez I, Garaiyurrebaso O, Garbisu C, Grohmann E, Alkorta I. Biofilm-Forming Clinical Staphylococcus Isolates Harbor Horizontal Transfer and Antibiotic Resistance Genes. Front Microbiol 2017; 8:2018. [PMID: 29085354 PMCID: PMC5650641 DOI: 10.3389/fmicb.2017.02018] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 10/02/2017] [Indexed: 12/11/2022] Open
Abstract
Infections caused by staphylococci represent a medical concern, especially when related to biofilms located in implanted medical devices, such as prostheses and catheters. Unfortunately, their frequent resistance to high doses of antibiotics makes the treatment of these infections a difficult task. Moreover, biofilms represent a hot spot for horizontal gene transfer (HGT) by bacterial conjugation. In this work, 25 biofilm-forming clinical staphylococcal isolates were studied. We found that Staphylococcus epidermidis isolates showed a higher biofilm-forming capacity than Staphylococcus aureus isolates. Additionally, horizontal transfer and relaxase genes of two common staphylococcal plasmids, pSK41 and pT181, were detected in all isolates. In terms of antibiotic resistance genes, aac6-aph2a, ermC, and tetK genes, which confer resistance to gentamicin, erythromycin, and tetracycline, respectively, were the most prevalent. The horizontal transfer and antibiotic resistance genes harbored on these staphylococcal clinical strains isolated from biofilms located in implanted medical devices points to the potential risk of the development and dissemination of multiresistant bacteria.
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Affiliation(s)
- Sandra Águila-Arcos
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Itxaso Álvarez-Rodríguez
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Olatz Garaiyurrebaso
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
| | - Carlos Garbisu
- Department of Conservation of Natural Resources, Soil Microbial Ecology Group, NEIKER-Tecnalia, Derio, Spain
| | - Elisabeth Grohmann
- Life Sciences and Technology, Beuth University of Applied Sciences, Berlin, Germany
| | - Itziar Alkorta
- Instituto Biofisika (UPV/EHU, CSIC), Department of Biochemistry and Molecular Biology, University of the Basque Country, Bilbao, Spain
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40
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Sansevere EA, Robinson DA. Staphylococci on ICE: Overlooked agents of horizontal gene transfer. Mob Genet Elements 2017; 7:1-10. [PMID: 28932624 DOI: 10.1080/2159256x.2017.1368433] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 08/08/2017] [Accepted: 08/14/2017] [Indexed: 10/19/2022] Open
Abstract
Horizontal gene transfer plays a significant role in spreading antimicrobial resistance and virulence genes throughout the genus Staphylococcus, which includes species of clinical relevance to humans and animals. While phages and plasmids are the most well-studied agents of horizontal gene transfer in staphylococci, the contribution of integrative conjugative elements (ICEs) has been mostly overlooked. Experimental work demonstrating the activity of ICEs in staphylococci remained frozen for years after initial work in the 1980s that showed Tn916 was capable of transfer from Enterococcus to Staphylococcus. However, recent work has begun to thaw this field. To date, 2 families of ICEs have been identified among staphylococci - Tn916 that includes the Tn5801 subfamily, and ICE6013 that includes at least 7 subfamilies. Both Tn5801 and ICE6013 commonly occur in clinical strains of S. aureus. Tn5801 is the most studied of the Tn916 family elements in staphylococci and encodes tetracycline resistance and a protein that, when expressed in Escherichia coli, inhibits restriction barriers to incoming DNA. ICE6013 is among the shortest known ICEs, but it still includes many uncharacterized open reading frames. This element uses an IS30-like transposase as its recombinase, providing some versatility in integration sites. ICE6013 also conjugatively transfers among receptive S. aureus strains at relatively higher frequency than Tn5801. Continued study of these mobile genetic elements may reveal the full extent to which ICEs impact horizontal gene transfer and the evolution of staphylococci.
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Affiliation(s)
- Emily A Sansevere
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
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41
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New Macrolide-Lincosamide-Streptogramin B Resistance Gene erm(48) on the Novel Plasmid pJW2311 in Staphylococcus xylosus. Antimicrob Agents Chemother 2017; 61:AAC.00066-17. [PMID: 28438941 DOI: 10.1128/aac.00066-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 04/14/2017] [Indexed: 11/20/2022] Open
Abstract
Whole-genome sequencing of Staphylococcus xylosus strain JW2311 from bovine mastitis milk identified the novel 49.3-kb macrolide-lincosamide-streptogramin B (MLSB) resistance plasmid pJW2311. It contained the macrolide resistance gene mph(C), the macrolide-streptogramin B resistance gene msr(A), and the new MLSB resistance gene erm(48) and could be transformed into Staphylococcus aureus by electroporation. Functionality of erm(48) was demonstrated by cloning and expression in S. aureus.
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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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Abstract
Penicillins are an important group of antibiotics used to treat various types of infections caused by Gram-positive bacteria. So far, the blaZ gene was the only known β-lactamase gene in staphylococci. However, other putative β-lactamases were identified, and one of them was shown to be a novel functional β-lactamase encoded by blaARL in Staphylococcus arlettae, further limiting treatment options. Whole-genome sequencing of penicillin-resistant Staphylococcus arlettae strain SAN1670 from bovine mastitis milk revealed a novel β-lactamase operon consisting of the β-lactamase-encoding gene blaARL, the antirepressor-encoding gene blaR1ARL, and the repressor-encoding gene blaIARL. The functionality of blaARL was demonstrated by gene expression in Staphylococcus aureus. The blaARL operon was chromosomally located in SAN1670 and present in 10 additional unrelated strains, suggesting intrinsic penicillin resistance in S. arlettae. Furthermore, a GenBank search revealed more unique potential β-lactamases in Staphylococcus species. IMPORTANCE Penicillins are an important group of antibiotics used to treat various types of infections caused by Gram-positive bacteria. So far, the blaZ gene was the only known β-lactamase gene in staphylococci. However, other putative β-lactamases were identified, and one of them was shown to be a novel functional β-lactamase encoded by blaARL in Staphylococcus arlettae, further limiting treatment options.
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Ramsay JP, Firth N. Diverse mobilization strategies facilitate transfer of non-conjugative mobile genetic elements. Curr Opin Microbiol 2017; 38:1-9. [PMID: 28391142 DOI: 10.1016/j.mib.2017.03.003] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/14/2017] [Indexed: 10/19/2022]
Abstract
Conjugation is a dominant mechanism of horizontal gene transfer and substantially contributes to the plasticity and evolvability of prokaryotic genomes. The impact of conjugation on genetic flux extends well beyond self-transmissible conjugative elements, because non-conjugative 'mobilizable elements' utilize other elements' conjugative apparatus for transfer. Bacterial genome comparisons highlight plasmids as vehicles for dissemination of pathogenesis and antimicrobial-resistance determinants, but for most non-conjugative plasmids, a mobilization mechanism is not apparent. Recently we discovered many Staphylococcus aureus plasmids lacking mobilization genes carry oriT sequences that mimic those on conjugative plasmids, suggesting that significantly more elements may be mobilizable than previously recognized. Here we summarize our findings, review the diverse mobilization strategies employed by mobile genetic elements and discuss implications for future gene-transfer research.
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Affiliation(s)
- Joshua P Ramsay
- School of Biomedical Sciences and Curtin Health Innovation Research Institute, Curtin University, Perth, Western Australia, Australia.
| | - Neville Firth
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
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45
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Transposase-Mediated Excision, Conjugative Transfer, and Diversity of ICE 6013 Elements in Staphylococcus aureus. J Bacteriol 2017; 199:JB.00629-16. [PMID: 28138100 DOI: 10.1128/jb.00629-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/25/2017] [Indexed: 01/04/2023] Open
Abstract
ICE6013 represents one of two families of integrative conjugative elements (ICEs) identified in the pan-genome of the human and animal pathogen Staphylococcus aureus Here we investigated the excision and conjugation functions of ICE6013 and further characterized the diversity of this element. ICE6013 excision was not significantly affected by growth, temperature, pH, or UV exposure and did not depend on recA The IS30-like DDE transposase (Tpase; encoded by orf1 and orf2) of ICE6013 must be uninterrupted for excision to occur, whereas disrupting three of the other open reading frames (ORFs) on the element significantly affects the level of excision. We demonstrate that ICE6013 conjugatively transfers to different S. aureus backgrounds at frequencies approaching that of the conjugative plasmid pGO1. We found that excision is required for conjugation, that not all S. aureus backgrounds are successful recipients, and that transconjugants acquire the ability to transfer ICE6013 Sequencing of chromosomal integration sites in serially passaged transconjugants revealed a significant integration site preference for a 15-bp AT-rich palindromic consensus sequence, which surrounds the 3-bp target site that is duplicated upon integration. A sequence analysis of ICE6013 from different host strains of S. aureus and from eight other species of staphylococci identified seven divergent subfamilies of ICE6013 that include sequences previously classified as a transposon, a plasmid, and various ICEs. In summary, these results indicate that the IS30-like Tpase functions as the ICE6013 recombinase and that ICE6013 represents a diverse family of mobile genetic elements that mediate conjugation in staphylococci.IMPORTANCE Integrative conjugative elements (ICEs) encode the abilities to integrate into and excise from bacterial chromosomes and plasmids and mediate conjugation between bacteria. As agents of horizontal gene transfer, ICEs may affect bacterial evolution. ICE6013 represents one of two known families of ICEs in the pathogen Staphylococcus aureus, but its core functions of excision and conjugation are not well studied. Here, we show that ICE6013 depends on its IS30-like DDE transposase for excision, which is unique among ICEs, and we demonstrate the conjugative transfer and integration site preference of ICE6013 A sequence analysis revealed that ICE6013 has diverged into seven subfamilies that are dispersed among staphylococci.
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46
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Orlek A, Stoesser N, Anjum MF, Doumith M, Ellington MJ, Peto T, Crook D, Woodford N, Walker AS, Phan H, Sheppard AE. Plasmid Classification in an Era of Whole-Genome Sequencing: Application in Studies of Antibiotic Resistance Epidemiology. Front Microbiol 2017; 8:182. [PMID: 28232822 PMCID: PMC5299020 DOI: 10.3389/fmicb.2017.00182] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 01/25/2017] [Indexed: 11/20/2022] Open
Abstract
Plasmids are extra-chromosomal genetic elements ubiquitous in bacteria, and commonly transmissible between host cells. Their genomes include variable repertoires of 'accessory genes,' such as antibiotic resistance genes, as well as 'backbone' loci which are largely conserved within plasmid families, and often involved in key plasmid-specific functions (e.g., replication, stable inheritance, mobility). Classifying plasmids into different types according to their phylogenetic relatedness provides insight into the epidemiology of plasmid-mediated antibiotic resistance. Current typing schemes exploit backbone loci associated with replication (replicon typing), or plasmid mobility (MOB typing). Conventional PCR-based methods for plasmid typing remain widely used. With the emergence of whole-genome sequencing (WGS), large datasets can be analyzed using in silico plasmid typing methods. However, short reads from popular high-throughput sequencers can be challenging to assemble, so complete plasmid sequences may not be accurately reconstructed. Therefore, localizing resistance genes to specific plasmids may be difficult, limiting epidemiological insight. Long-read sequencing will become increasingly popular as costs decline, especially when resolving accurate plasmid structures is the primary goal. This review discusses the application of plasmid classification in WGS-based studies of antibiotic resistance epidemiology; novel in silico plasmid analysis tools are highlighted. Due to the diverse and plastic nature of plasmid genomes, current typing schemes do not classify all plasmids, and identifying conserved, phylogenetically concordant genes for subtyping and phylogenetics is challenging. Analyzing plasmids as nodes in a network that represents gene-sharing relationships between plasmids provides a complementary way to assess plasmid diversity, and allows inferences about horizontal gene transfer to be made.
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Affiliation(s)
- Alex Orlek
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
| | - Muna F. Anjum
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
- Department of Bacteriology, Animal and Plant Health AgencyAddlestone, UK
| | - Michel Doumith
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK
| | - Matthew J. Ellington
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK
| | - Tim Peto
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Derrick Crook
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Neil Woodford
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
- Antimicrobial Resistance and Healthcare Associated Infections Reference Unit, Public Health EnglandLondon, UK
| | - A. Sarah Walker
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Hang Phan
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
| | - Anna E. Sheppard
- Nuffield Department of Medicine, John Radcliffe Hospital, University of OxfordOxford, UK
- National Institute for Health Research Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance, University of OxfordOxford, UK
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Zovčáková M, Španová A, Pantůček R, Doškař J, Rittich B. Efficient non-enzymatic cleavage of Staphylococcus aureus plasmid DNAs mediated by neodymium ions. Anal Biochem 2016; 507:66-70. [PMID: 27237372 DOI: 10.1016/j.ab.2016.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/10/2016] [Accepted: 05/15/2016] [Indexed: 11/25/2022]
Abstract
Staphylococcus aureus plasmids are the main factor in the spreading of antibacterial resistance among bacterial strains that has emerged on a worldwide scale. Plasmids recovered from 12 clinical and food isolates of S. aureus were treated with 10 mM free lanthanide Nd(3+) ions (non-enzymatic cleavage agent) in Hepes buffer (pH 7.5) at 70 °C. Topological forms of plasmids-closed circular (ccc), open circular (oc), and linear (lin)-produced by cleavage at different times were separated using pulsed-field agarose gel electrophoresis. The method is proposed to detect and differentiate several plasmids in the same bacterial strain according to their size.
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Affiliation(s)
- Monika Zovčáková
- Faculty of Chemistry, Brno University of Technology, CZ-612 00 Brno, Czech Republic
| | - Alena Španová
- Faculty of Chemistry, Brno University of Technology, CZ-612 00 Brno, Czech Republic
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-611 37 Brno, Czech Republic
| | - Jiří Doškař
- Department of Experimental Biology, Faculty of Science, Masaryk University, CZ-611 37 Brno, Czech Republic
| | - Bohuslav Rittich
- Faculty of Chemistry, Brno University of Technology, CZ-612 00 Brno, Czech Republic.
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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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Abstract
Serine resolvases are an interesting group of site-specific recombinases that, in their native contexts, resolve large fused replicons into smaller separated ones. Some resolvases are encoded by replicative transposons and resolve the transposition product, in which the donor and recipient molecules are fused, into separate replicons. Other resolvases are encoded by plasmids and function to resolve plasmid dimers into monomers. Both types are therefore involved in the spread and maintenance of antibiotic-resistance genes. Resolvases and the closely related invertases were the first serine recombinases to be studied in detail, and much of our understanding of the unusual strand exchange mechanism of serine recombinases is owed to those early studies. Resolvases and invertases have also served as paradigms for understanding how DNA topology can be harnessed to regulate enzyme activity. Finally, their relatively modular structure, combined with a wealth of structural and biochemical data, has made them good choices for engineering chimeric recombinases with designer specificity. This chapter focuses on the current understanding of serine resolvases, with a focus on the contributions of structural studies.
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The Plasmidome of Firmicutes: Impact on the Emergence and the Spread of Resistance to Antimicrobials. Microbiol Spectr 2016; 3:PLAS-0039-2014. [PMID: 26104702 DOI: 10.1128/microbiolspec.plas-0039-2014] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The phylum Firmicutes is one of the most abundant groups of prokaryotes in the microbiota of humans and animals and includes genera of outstanding relevance in biomedicine, health care, and industry. Antimicrobial drug resistance is now considered a global health security challenge of the 21st century, and this heterogeneous group of microorganisms represents a significant part of this public health issue.The presence of the same resistant genes in unrelated bacterial genera indicates a complex history of genetic interactions. Plasmids have largely contributed to the spread of resistance genes among Staphylococcus, Enterococcus, and Streptococcus species, also influencing the selection and ecological variation of specific populations. However, this information is fragmented and often omits species outside these genera. To date, the antimicrobial resistance problem has been analyzed under a "single centric" perspective ("gene tracking" or "vehicle centric" in "single host-single pathogen" systems) that has greatly delayed the understanding of gene and plasmid dynamics and their role in the evolution of bacterial communities.This work analyzes the dynamics of antimicrobial resistance genes using gene exchange networks; the role of plasmids in the emergence, dissemination, and maintenance of genes encoding resistance to antimicrobials (antibiotics, heavy metals, and biocides); and their influence on the genomic diversity of the main Gram-positive opportunistic pathogens under the light of evolutionary ecology. A revision of the approaches to categorize plasmids in this group of microorganisms is given using the 1,326 fully sequenced plasmids of Gram-positive bacteria available in the GenBank database at the time the article was written.
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