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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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Ribeiro M, Sousa M, Borges V, Gomes JP, Duarte S, Isidro J, Vieira L, Torres C, Santos H, Capelo JL, Poeta P, Igrejas G. Bioinformatics study of expression from genomes of epidemiologically related MRSA CC398 isolates from human and wild animal samples. J Proteomics 2022; 268:104714. [PMID: 36058542 DOI: 10.1016/j.jprot.2022.104714] [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: 07/16/2022] [Accepted: 08/28/2022] [Indexed: 10/14/2022]
Abstract
One of the most important livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) genetic lineages is the clonal complex (CC) 398, which can cause typical S. aureus-associated infections in people. In this work, whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics were applied to study the genetic characteristics of three MRSA CC398 isolates recovered from humans (strains C5621 and C9017), and from an animal (strain OR418). Of the three strains, C9017 presented the broadest resistance genotype, including resistance to fluroquinolone, clindamycin, tiamulin, macrolide and aminoglycoside antimicrobial classes. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains. For example, the immunoglobulin-binding protein Sbi was more abundant in OR418. Considering that Sbi is a multifunctional immune evasion factor in S. aureus, the results point to OR418 strain having high zoonotic potential. Overall, multiomics biomarker signatures can assume an important role to advance precision medicine in the years to come. SIGNIFICANCE: MRSA is one of the most representative drug-resistant pathogens and its dissemination is increasing due to MRSA capability of establishing new reservoirs. LA-MRSA is considered an emerging problem worldwide and CC398 is one of the most important genetic lineages. In this study, three MRSA CC398 isolates recovered from humans and from a wild animal were analyzed through whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics in order to gather systems-wide omics data and better understand the genetic characteristics of this lineage to identify distinctive markers and genomic features of relevance to public health. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains.
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Affiliation(s)
- Miguel Ribeiro
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal
| | - Margarida Sousa
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal
| | - Vítor Borges
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal
| | - Sílvia Duarte
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Joana Isidro
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1600-609 Lisbon, Portugal; Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Luís Vieira
- Technology and Innovation Unit, Department of Human Genetics, National Institute of Health, Lisbon, Portugal
| | - Carmen Torres
- Biochemistry and Molecular Biology Unit, Faculty of Science and Technology, University of La Rioja, 26006 Logroño, Spain
| | - Hugo Santos
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal; Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
| | - José Luís Capelo
- BIOSCOPE Research Group, LAQV-REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal; PROTEOMASS Scientific Society, Madan Parque, Rua dos Inventores, 2825-182 Caparica, Portugal
| | - Patrícia Poeta
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal; Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real 5000-801, Portugal; CECAV-Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), Faculty of Science and Technology, University Nova of Lisbon, 2829-546 Caparica, Portugal.
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Comparative Genomic Analysis of a Panton–Valentine Leukocidin-Positive ST22 Community-Acquired Methicillin-Resistant Staphylococcus aureus from Pakistan. Antibiotics (Basel) 2022; 11:antibiotics11040496. [PMID: 35453247 PMCID: PMC9033113 DOI: 10.3390/antibiotics11040496] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/27/2022] [Accepted: 04/06/2022] [Indexed: 02/01/2023] Open
Abstract
Staphylococcus aureus (S. aureus) ST22 is considered a clinically important clone because an epidemic strain EMRSA-15 belongs to ST22, and several outbreaks of this clone have been documented worldwide. We performed genomic analysis of an S. aureus strain Lr2 ST22 from Pakistan and determined comparative analysis with other ST22 strains. The genomic data show that Lr2 belongs to spa-type t2986 and harbors staphylococcal cassette chromosome mec (SCCmec) type IVa(2B), one complete plasmid, and seven prophages or prophage-like elements. The strain harbors several prophage-associated virulence factors, including Panton–Valentine leukocidin (PVL) and toxic shock syndrome toxin (TSST). The single nucleotide polymorphism (SNPs)-based phylogenetic relationship inferred from whole genome and core genome revealed that strain Lr2 exhibits the nearest identities to a South African community-acquired methicillin-resistant S. aureus (CA-MRSA) ST22 strain and makes a separate clade with an Indian CA-MRSA ST22 strain. Although most ST22 strains carry blaZ, mecA, and mutations in gyrA, the Lr2 strain does not have the blaZ gene but, unlike other ST22 strains, carries the antibiotic resistance genes erm(C) and aac(6′)-Ie-aph(2″)-Ia. Among ST22 strains analyzed, only the strain Lr2 possesses both PVL and TSST genes. The functional annotation of genes unique to Lr2 revealed that mobilome is the third-largest Cluster of Orthologous Genes (COGs) category, which encodes genes associated with prophages and transposons. This possibly makes methicillin-resistant S. aureus (MRSA) Lr2 ST22 strain highly virulent, and this study would improve the knowledge of MRSA ST22 strains in Pakistan. However, further studies are needed on a large collection of MRSA to comprehend the genomic epidemiology and evolution of this clone in Pakistan.
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Sri Prabakusuma A, Zhu J, Shi Y, Ma Q, Zhao Q, Yang Z, Xu Y, Huang A. Prevalence and antimicrobial resistance profiling of Staphylococcus aureus isolated from traditional cheese in Yunnan, China. 3 Biotech 2022; 12:1. [PMID: 34926114 PMCID: PMC8639989 DOI: 10.1007/s13205-021-03072-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/22/2021] [Indexed: 01/03/2023] Open
Abstract
The prevalence of staphylococcal infection and the emergence of multidrug resistance of Staphylococcus aureus (S. aureus) are major concerns in food safety and public health. This study aimed to investigate the prevalence of S. aureus isolated from traditional Chinese Rubing and Rushan cheese, antimicrobial resistance profiles, genomic characteristics, and predict antimicrobial resistance genes (ARGs). From 124 samples, 18 of 62 (29.03%) of Rubing and 5 of 62 (8.06%) of Rushan cheese were confirmed to be S. aureus positive by standard culture-based methods. Twenty-three coagulase-positive staphylococci isolates were grouped into 16 clusters by pulsed-field gel electrophoresis and subjected to routine susceptibility testing to 12 antibiotics. Those isolates exhibited high resistance to penicillin (100%), erythromycin, trimethoprim-sulphamethoxazole (34.78%), oxacillin, clindamycin, and cefoxitin (21.74%). Multidrug-resistant (MDR) S. aureus was found in 34.78% (8 of 23) of isolates. Further, S. aureus strain DC.RB_015 isolated from Rubing cheese, recognized as the most resistant to six antibiotics, was selected for whole-genome sequencing (WGS), continued with in silico approaches. S. aureus DC.RB_015 had a single chromosome size of 2,794,578 bp and a plasmid size of 22,961 bp. The strain harbored 18 predicted ARGs, including eight efflux pump genes (mepA, tet(K), arlR, arlS, norA, mgrA, tet(38), LmrS), one peptidoglycan biosynthesis gene (bacA), two β-lactams resistance genes (mecA, blaZ), and seven genes conferring other antimicrobial resistance (APH(3')-IIIa, aad(6), ErmB, SAT-4, mecR1, GlpT, murA). The results of this study expand the knowledge of S. aureus strain DC.RB_015, increase food safety awareness, and will be helpful in establishing therapeutic therapy. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03072-4.
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Affiliation(s)
- Adhita Sri Prabakusuma
- Department of Food Technology, Faculty of Industrial Technology, Universitas Ahmad Dahlan, Yogyakarta, 55166 Indonesia
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Jingjing Zhu
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Yanan Shi
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Qingwen Ma
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Qiong Zhao
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
| | - Zushun Yang
- Yunnan Center for Disease Control and Prevention (CDC), Kunming, 650100 Yunnan China
| | - Yan Xu
- Yunnan Center for Disease Control and Prevention (CDC), Kunming, 650100 Yunnan China
| | - Aixiang Huang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201 China
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Naorem RS, Goswami G, Gyorgy S, Fekete C. Comparative analysis of prophages carried by human and animal-associated Staphylococcus aureus strains spreading across the European regions. Sci Rep 2021; 11:18994. [PMID: 34556764 PMCID: PMC8460829 DOI: 10.1038/s41598-021-98432-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023] Open
Abstract
Staphylococcus aureus is a major human and animal pathogen although the animal-associated S. aureus can be a potential risk of human zoonoses. Acquisition of phage-related genomic islands determines the S. aureus species diversity. This study characterized and compared the genome architecture, distribution nature, and evolutionary relationship of 65 complete prophages carried by human and animal-associated S. aureus strains spreading across the European regions. The analyzed prophage genomes showed mosaic architecture with extensive variation in genome size. The phylogenetic analyses generated seven clades in which prophages of the animal-associated S. aureus scattered in all the clades. The S. aureus strains with the same SCCmec type, and clonal complex favored the harboring of similar prophage sequences and suggested that the frequency of phage-mediated horizontal gene transfer is higher between them. The presence of various virulence factors in prophages of animal-associated S. aureus suggested that these prophages could have more pathogenic potential than prophages of human-associated S. aureus. This study showed that the S. aureus phages are dispersed among the several S. aureus serotypes and around the European regions. Further, understanding the phage functional genomics is necessary for the phage-host interactions and could be used for tracing the S. aureus strains transmission.
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Affiliation(s)
- Romen Singh Naorem
- grid.9679.10000 0001 0663 9479Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifjusag utja. 6, Pecs, 7624 Hungary
| | - Gunajit Goswami
- Multidisciplinary Research Unit, Jorhat Medical College and Hospital, Jorhat, Assam India
| | - Schneider Gyorgy
- grid.9679.10000 0001 0663 9479Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pecs, Hungary
| | - Csaba Fekete
- grid.9679.10000 0001 0663 9479Department of General and Environmental Microbiology, Institute of Biology and Sport Biology, University of Pécs, Ifjusag utja. 6, Pecs, 7624 Hungary
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Synergy between Phage Sb-1 and Oxacillin against Methicillin-Resistant Staphylococcus aureus. Antibiotics (Basel) 2021; 10:antibiotics10070849. [PMID: 34356770 PMCID: PMC8300854 DOI: 10.3390/antibiotics10070849] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) is a notorious pathogen responsible for not only a number of difficult-to-treat hospital-acquired infections, but also for infections that are community- or livestock-acquired. The increasing lack of efficient antibiotics has renewed the interest in lytic bacteriophages (briefly phages) as additional antimicrobials against multi-drug resistant bacteria, including MRSA. The aim of this study was to test the hypothesis that a combination of the well-known and strictly lytic S. aureus phage Sb-1 and oxacillin, which as sole agent is ineffective against MRSA, exerts a significantly stronger bacterial reduction than either antimicrobial alone. Eighteen different MRSA isolates and, for comparison, five MSSA and four reference strains were included in this study. The bacteria were challenged with a combination of varying dosages of the phage and the antibiotic in liquid medium using five different antibiotic levels and four different viral titers (i.e., multiplicity of infections (MOIs) ranging from 10-5 to 10). The dynamics of the cell density changes were determined via time-kill assays over 16 h. Positive interactions between both antimicrobials in the form of facilitation, additive effects, or synergism were observed for most S. aureus isolates. These enhanced antibacterial effects were robust with phage MOIs of 10-1 and 10 irrespective of the antibiotic concentrations, ranging from 5 to 100 µg/mL. Neutral effects between both antimicrobials were seen only with few isolates. Importantly, antagonism was a rare exception. As a conclusion, phage Sb-1 and oxacillin constitute a robust heterologous antimicrobial pair which extends the efficacy of a phage-only approach for controlling MRSA.
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