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Esmail GA, Al-Dhabi NA, AlDawood B, Somily AM. Shotgun whole genome sequencing of drug-resistance Streptococcus anginosus strain 47S1 isolated from a patient with pharyngitis in Saudi Arabia. J Infect Public Health 2021; 14:1740-1749. [PMID: 34836797 DOI: 10.1016/j.jiph.2021.11.010] [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: 10/03/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND Streptococcus anginosus is an emergence opportunistic pathogen that colonize the human upper respiratory tract (URT), S. anginosus alongside with S. intermedius and S. constellatus, members of S. anginosus group, are implicated in several human infections. However, our understanding this bacterium to the genotype level with determining the genes associated with pathogenicity and antimicrobial resistance (AMR) is scarce. S. anginosus 47S1 strain was isolated from sore throat infection, the whole genome was characterized and the virulence & AMR genes contributing in pathogenicity were investigated. METHODOLOGY The whole genome of 47S1 was sequenced by Illumina sequencing technology. Strain 47S1 genome was de novo assembled with different strategies and annotated via PGAP, PROKKA and RAST pipelines. Identifying the CRISPR-Cass system and prophages sequences was performed using CRISPRloci and PhiSpy tools respectively. Prediction the virulence genes were performed with the VFDB database. AMR genes were detected in silico using NCBI AMRFinderPlus pipeline and CARD database and compared with in vitro AST findings. RESULTS β-hemolytic strain 47S1 was identified with conventional microbiology techniques and confirmed by the sequences of 16S rRNA gene. Genome of 47S1 comprised of 1981512 bp. Type I-C CRISPR-Cas system and 4 prophages were detected among the genome of 47S1. Several virulence genes were predicted, most of these genes are found in other pathogenic streptococci, mainly lmb, pavA, htrA/degP, eno, sagA, psaA and cpsI which play a significant role in colonizing, invading host tissues and evade form immune system. In silico AMR findings showed that 47S1 gnome harbors (tetA, tetB &tet32), (aac(6')-I, aadK &aph(3')-IVa), fusC, and PmrA genes that mediated-resistance to tetracyclines, aminoglycosides, fusidic acid, and fluoroquinolone respectively which corresponds with in vitro AST obtained results. In conclusion, WGS is a key approach to predict the virulence and AMR genes, results obtained in this study may contribute for a better understanding of the opportunistic S. anginosus pathogenicity.
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Affiliation(s)
- Galal Ali Esmail
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia.
| | - Badr AlDawood
- Department of Emergency Medicine, College of Medicine, King Saud University, King Saud University Medical City, Riyadh 11461, Saudi Arabia
| | - Ali Mohammed Somily
- Department of Pathology and Laboratory Medicine/Microbiology, College of Medicine, King Saud University, King Saud University Medical City, Riyadh 11461, Saudi Arabia.
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Whole-genome sequencing reveals high genetic diversity of Streptococcus uberis isolated from cows with mastitis. BMC Vet Res 2021; 17:321. [PMID: 34620161 PMCID: PMC8496047 DOI: 10.1186/s12917-021-03031-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/17/2021] [Indexed: 11/18/2022] Open
Abstract
Background Bovine mastitis is an important cause of economic loss in dairy farms. Streptococcus uberis is among the most frequently isolated bacterial species isolated from cows with mastitis. The aim of this study was to perform an in-depth genetic assessment of S. uberis strains isolated from bovine clinical mastitis (CM) and to perform a phylogenetic analysis to represent the evolutionary relationship among S. uberis sequences. Results A total of 159 isolates was genetically characterized using whole genome sequencing. According to the virulence determinants, all strains harbored the hasC, leuS, perR, purH, and purN virulence genes. Thirty-four resistance genes were identified in at least one strain. In terms of acquired genes, we observed that 152 (95.6 %) strains had a resistance gene to lincosamine (lnuD), 48 (30.2 %) to tetracycline (tetM), 4 (2.51 %) to tobramicine (ant6), and 1 to lincosamide (lsa(E)). MLST detected the Sequence Type (ST)797 (n = 23), while 85.5 % of the strains did not match to known STs. Conclusions Then, eleven distinct ST were identified after we submitted the new alleles to assign new STs. The other prevalent STs observed were ST1215 (n = 58), ST1219 (n = 35), and ST1213 (n = 15). And it was not possible to identify the MLST of four strains. Phylogenetic lineages indicated a high genomic diversity of S. uberis in our collection, confirming that most strains isolated from bovine mastitis have different reservoirs, typical of environmental pathogens.
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Alves-Barroco C, Rivas-García L, Fernandes AR, Baptista PV. Tackling Multidrug Resistance in Streptococci - From Novel Biotherapeutic Strategies to Nanomedicines. Front Microbiol 2020; 11:579916. [PMID: 33123110 PMCID: PMC7573253 DOI: 10.3389/fmicb.2020.579916] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023] Open
Abstract
The pyogenic streptococci group includes pathogenic species for humans and other animals and has been associated with enduring morbidity and high mortality. The main reason for the treatment failure of streptococcal infections is the increased resistance to antibiotics. In recent years, infectious diseases caused by pyogenic streptococci resistant to multiple antibiotics have been raising with a significant impact to public health and veterinary industry. The rise of antibiotic-resistant streptococci has been associated to diverse mechanisms, such as efflux pumps and modifications of the antimicrobial target. Among streptococci, antibiotic resistance emerges from previously sensitive populations as result of horizontal gene transfer or chromosomal point mutations due to excessive use of antimicrobials. Streptococci strains are also recognized as biofilm producers. The increased resistance of biofilms to antibiotics among streptococci promote persistent infection, which comprise circa 80% of microbial infections in humans. Therefore, to overcome drug resistance, new strategies, including new antibacterial and antibiofilm agents, have been studied. Interestingly, the use of systems based on nanoparticles have been applied to tackle infection and reduce the emergence of drug resistance. Herein, we present a synopsis of mechanisms associated to drug resistance in (pyogenic) streptococci and discuss some innovative strategies as alternative to conventional antibiotics, such as bacteriocins, bacteriophage, and phage lysins, and metal nanoparticles. We shall provide focused discussion on the advantages and limitations of agents considering application, efficacy and safety in the context of impact to the host and evolution of bacterial resistance.
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Affiliation(s)
- Cinthia Alves-Barroco
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Lorenzo Rivas-García
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal.,Biomedical Research Centre, University of Granada, Granada, Spain
| | - Alexandra R Fernandes
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Pedro Viana Baptista
- UCIBIO, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, Caparica, Portugal
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Pillai A, Thomas S, Williams C. Clindamycin in the treatment of group G beta-haemolytic streptococcal infections. J Infect 2006; 51:e207-11. [PMID: 16291271 DOI: 10.1016/j.jinf.2005.02.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2005] [Indexed: 11/23/2022]
Abstract
We report a case of severe streptococcal cellulitis in a healthy 47 year old male, where the sole microbial isolate was a beta-haemolytic group G Streptococcus. Treatment failure with high dose penicillin was observed despite in vitro sensitivity. The addition of clindamycin resulted in dramatic clinical improvement. This may indicate an Eagle-type effect (whereby antibiotics exhibit paradoxically reduced bactericidal activities at high drug concentrations), in group G beta-haemolytic infections. Although well documented with group A streptococcal infections, this phenomenon has not been fully recognised with group G beta-haemolytic streptococcal infections. This may have important implications for clinical management.
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Affiliation(s)
- A Pillai
- Dumfries and Galloway Royal Infirmary, Dumfries, DG1 4AP, UK
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Lopardo HA, Vidal P, Sparo M, Jeric P, Centron D, Facklam RR, Paganini H, Pagniez NG, Lovgren M, Beall B. Six-month multicenter study on invasive infections due to Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis in Argentina. J Clin Microbiol 2005; 43:802-7. [PMID: 15695683 PMCID: PMC548053 DOI: 10.1128/jcm.43.2.802-807.2005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
During a 6-month period, 95 invasive infections due to Streptococcus pyogenes and group C or group G Streptococcus dysgalactiae subsp. equisimilis were recorded from 40 centers of 16 cities in Argentina. We describe here epidemiologic data available for 55 and 19 patients, respectively, associated with invasive infections due to S. pyogenes and S. dysgalactiae subsp. equisimilis. The associated isolates and 58 additional pharyngeal isolates were genotyped and subjected to serologic and/or antibiotic susceptibility testing. Group A streptococcal emm type distribution and strain association with toxic shock appeared to differ somewhat from results found within the United States; however, serologic characterization and sof sequence typing suggested that emm types found in both countries are reflective of shared clonal types.
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Affiliation(s)
- Horacio A Lopardo
- Servicio de Microbiología. Hospital de Pediatría Prof. Dr. Juan P. Garrahan, Combate de los Pozos 1881. (1245) Buenos Aires, Argentina.
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Woodford N. Biological counterstrike: antibiotic resistance mechanisms of Gram-positive cocci. Clin Microbiol Infect 2005; 11 Suppl 3:2-21. [PMID: 15811020 DOI: 10.1111/j.1469-0691.2005.01140.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The development of antibiotic resistance by bacteria is an evolutionary inevitability, a convincing demonstration of their ability to adapt to adverse environmental conditions. Since the emergence of penicillinase-producing Staphylococcus aureus in the 1940s, staphylococci, enterococci and streptococci have proved themselves adept at developing or acquiring mechanisms that confer resistance to all clinically available antibacterial classes. The increasing problems of methicillin-resistant S. aureus and coagulase-negative staphylococci (MRSA and MRCoNS), glycopeptide-resistant enterococci and penicillin-resistant pneumococci in the 1980s, and recognition of glycopeptide-intermediate S. aureus in the 1990s and, most recently, of fully vancomycin-resistant isolates of S. aureus have emphasised our need for new anti-Gram-positive agents. Antibiotic resistance is one of the major public health concerns for the beginning of the 21st century. The pharmaceutical industry has responded with the development of oxazolidinones, lipopeptides, injectable streptogramins, ketolides, glycylcyclines, second-generation glycopeptides and novel fluoroquinolones. However, clinical use of these novel agents will cause new selective pressures and will continue to drive the development of resistance. This review describes the various antibiotic resistance mechanisms identified in isolates of staphylococci, enterococci and streptococci, including mechanisms of resistance to recently introduced anti-Gram-positive agents.
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Affiliation(s)
- N Woodford
- Antibiotic Resistance Monitoring and Reference Laboratory, Centre for Infections, Health Protection Agency, London NW9 5HT, UK.
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Werner G, Hildebrandt B, Witte W. Linkage of erm(B) and aadE-sat4-aphA-3 in multiple-resistant Enterococcus faecium isolates of different ecological origins. Microb Drug Resist 2004; 9 Suppl 1:S9-16. [PMID: 14633362 DOI: 10.1089/107662903322541847] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Enterococcus faecium shares its antibiotic resistance gene pool with various Gram-positive bacteria. A gene cluster aadE-sat4-aphA-3, which was first described in staphylococci, has been recently identified also in E. faecium. In staphylococci, this gene cluster was mostly integrated into the transposable element, Tn5405. We identified five different cluster types of Tn5405-like elements that were linked to erm(B) in 47 of 67 aadE-sat4-aphA-3 and erm(B) positive isolates (70.1%). Clusters differed by insertion of additional DNA between the IS1182 transposase gene and the left inverted repeat of IS1182, an integration of IS1216 between erm(B) and ORF X deleting IS1182 and the 5' end of ORF X, or a loss of the left end of Tn5405 including IS1182, ORF X, and the 5' end of ORF Y. Twenty isolates (29.8%) possessed neither a link between erm(B) and aadE-sat4-aphA-3 nor an arrangement of aadE-sat4-aphA-3 in a Tn5405-like element. A 17-kb composite cluster was identified in a single hospital isolate linking determinants for glycopeptide (vanA), macrolide-lincosamide-streptogramin B [erm(B)], and aminoglycoside-streptothricin (aadE-sat4-aphA-3) resistances.
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Affiliation(s)
- Guido Werner
- Robert Koch Institute, Wernigerode Branch, D-38855 Wernigerode, Germany.
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Affiliation(s)
- Glenn Isaacson
- Department of Otolaryngology-Head & Neck Surgery, Temple University School of Medicine, First Floor Kresge, 3400 North Broad Street, Philadelphia, PA 19140, USA.
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Torres C. [Interpretative reading of the antibiogram in gram-positive cocci]. Enferm Infecc Microbiol Clin 2002; 20:354-63; quiz 363-4. [PMID: 12237003 DOI: 10.1016/s0213-005x(02)72815-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Resistance to methicillin in Staphylococcus is related to expression of the gene mecA, and implies resistance to all beta-lactams. Breakpoints for interpretation of this mechanism differ in S. aureus and in coagulase-negative species. In relation to macrolides-lincosamides-streptograminsB, the most frequent mechanism among resistant strains is expression of methylases (erm genes). Topoisomerase changes caused by point mutations and expression of the efflux pump NorA determine resistance to quinolones, but there are great differences on the activity of different compounds, which makes interpretative reading difficult. Strains of S. aureus with intermediate susceptibility to glycopeptides (GISA strains) have been recently described. In Spain, there is a high percentage of S. pneumoniae strains intermediate or resistant to penicillin, and a low percentage of strains intermediate or resistant to third generation cephalosporins, because of mutations in genes encoding penicillin-binding proteins. The most frequent phenotype of resistance to macrolides in this species is caused by methylase production. Resistance to quinolones is still uncommon, and is related to the mechanisms previously indicated for Staphylococcus, but clinical interpretation of the antibiograma for this organism is even more complex. No strains of S. pyogenes resistant to penicillin have yet been described. In Spain the most common phenotype of resistance to macrolides in S. pyogenes is determined by efflux pumps (mef genes), affecting 14- and 15-membered macrolides. E. faecalis is usually susceptible to ampicillin, in contrast to E. faecium. Enterococci show intrinsic resistance to aminoglycosides, but still remain susceptible to the combination of these antimicrobials and cell-wall active agents. Strains expressing different aminoglycoside-modifying enzymes became resistant to the combination. Glycopeptide-resistant strains of enterococci are uncommon in our country, but several genotypes, of which vanA is the most relevant from a clinical point of view, have been described in other regions.
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Affiliation(s)
- Carmen Torres
- Area de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, España.
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Jeric PE, Lopardo H, Vidal P, Arduino S, Fernandez A, Orman BE, Sordelli DO, Centrón D. Multicenter study on spreading of the tet(M) gene in tetracycline-resistant Streptococcus group G and C isolates in Argentina. Antimicrob Agents Chemother 2002; 46:239-41. [PMID: 11751143 PMCID: PMC127005 DOI: 10.1128/aac.46.2.239-241.2002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A prospective multicenter study on invasive infections caused by beta-hemolytic streptococci was performed over 6 months and involved 42 centers from 16 cities in Argentina. Among 33 isolates recovered, 9 group G Streptococcus isolates (39.1%) and 2 group C Streptococcus isolates (20%) exhibited resistance to tetracycline and harbored the tet(M) gene. Genealogical analysis revealed that tetracycline resistance has a polyclonal origin in Argentina.
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Affiliation(s)
- P E Jeric
- Departamento de Microbiología, Facultad de Medicina, Universidad de Buenos Aires, Argentina.
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Chow JW, Kak V, You I, Kao SJ, Petrin J, Clewell DB, Lerner SA, Miller GH, Shaw KJ. Aminoglycoside resistance genes aph(2")-Ib and aac(6')-Im detected together in strains of both Escherichia coli and Enterococcus faecium. Antimicrob Agents Chemother 2001; 45:2691-4. [PMID: 11557456 PMCID: PMC90718 DOI: 10.1128/aac.45.10.2691-2694.2001] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Escherichia coli SCH92111602 expresses an aminoglycoside resistance profile similar to that conferred by the aac(6')-Ie-aph(2")-Ia gene found in gram-positive cocci and was found to contain the aminoglycoside resistance genes aph(2")-Ib and aac(6')-Im (only 44 nucleotides apart). aph(2")-Ib had been reported previously in Enterococcus faecium SF11770. aac(6')-Im had not been detected previously in enterococci and was found to be present also 44 nucleotides downstream from aph(2")-Ib in E. faecium SF11770. aph(2")-Ib and aac(6')-Im are separate open reading frames, each with its own putative ribosome binding site, whereas aac(6')-Ie-aph(2")-Ia appears to be a fusion of two genes with just one start and one stop codon. The deduced AAC(6')-Im protein exhibits 56% identity and 80% similarity to the AAC(6')-Ie domain of the bifunctional enzyme AAC(6')-APH(2"). Our results document the existence of a member of the aph(2") family of genes in gram-negative bacteria and provide evidence suggesting the horizontal transfer of aph(2")-Ib and aac(6')-Im as a unit between gram-positive and gram-negative bacteria.
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Affiliation(s)
- J W Chow
- Research and Medical Service, John D. Dingell VA Medical Center, 4646 John R, Detroit, MI 48201-2097, USA.
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