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Azarsa M, Mosadegh M, Habibi Ghahfarokhi S, Pourmand MR. Serotype Distribution and Multi Locus Sequence Type (MLST) of Erythromycin-Resistant Streptococcus Pneumoniae Isolates in Tehran, Iran. Rep Biochem Mol Biol 2023; 12:259-268. [PMID: 38317819 PMCID: PMC10838590 DOI: 10.61186/rbmb.12.2.259] [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: 04/29/2023] [Accepted: 07/04/2023] [Indexed: 02/07/2024]
Abstract
Background The number of erythromycin-resistant Streptococcus pneumoniae has significantly increased around the world. The present study aimed to determine the serotype distribution and molecular epidemiology of the erythromycin-resistant Streptococcus pneumoniae (ERSP) isolated from patients with invasive disease. Methods A total of 44 Streptococcus pneumoniae isolates were tested for susceptibility to several antimicrobial agents. Additionally, the polymerase chain reaction (PCR) was applied to evaluate ERSP isolates in terms of the presence of erythromycin resistance genes (e.g., ermB and mefA). The isolates were serotyped using the sequential multiplex-PCR method, and molecular epidemiology was assessed through the multilocus sequence typing (MLST) analysis. Results The results represented multidrug resistance (MDR) in approximately half of the pneumococcal isolates. Among 22 ERSP isolates, 20 (90.9%) and 12 (56%) ones contained ermB and mefA, respectively. Further, 14 (31.8%), 3 (22.7%), and 19A (18.1%) were the common serotypes among the isolates. No significant correlation was observed between serotypes and erythromycin resistance genes. Furthermore, the MLST results revealed 18 different sequence types (STs), the top ones of which were ST3130 (3 isolates) and ST166 (3 isolates). Population genetic analysis disclosed that CC63 (32%), CC156 (18%), and CC320 (18%) were identified as the predominant clonal complexes. Conclusions The ERSP isolates exhibited high genetic diversity. The large frequency of MDR isolates suggests the emergence of high resistant strains, as well as the need to implement vaccination in the immunization schedule of Iran. These accumulating evidences indicate that 13-valent pneumococcal conjugate vaccines provided higher serotype coverage in the ERSP isolates.
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Affiliation(s)
- Mohammad Azarsa
- Department of Microbiology, Khoy University of Medical Sciences, Khoy, Iran.
| | - Mehrdad Mosadegh
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Soheila Habibi Ghahfarokhi
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammad Reza Pourmand
- Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
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Manyahi J, Moyo SJ, Langeland N, Blomberg B. Genetic determinants of macrolide and tetracycline resistance in penicillin non-susceptible Streptococcus pneumoniae isolates from people living with HIV in Dar es Salaam, Tanzania. Ann Clin Microbiol Antimicrob 2023; 22:16. [PMID: 36803640 PMCID: PMC9942299 DOI: 10.1186/s12941-023-00565-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/09/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Over one million yearly deaths are attributable to Streptococcus pneumoniae and people living with HIV are particularly vulnerable. Emerging penicillin non-susceptible Streptococcus pneumoniae (PNSP) challenges therapy of pneumococcal disease. The aim of this study was to determine the mechanisms of antibiotic resistance among PNSP isolates by next generation sequencing. METHODS We assessed 26 PNSP isolates obtained from the nasopharynx from 537 healthy human immunodeficiency virus (HIV) infected adults in Dar es Salaam, Tanzania, participating in the randomized clinical trial CoTrimResist (ClinicalTrials.gov identifier: NCT03087890, registered on 23rd March, 2017). Next generation whole genome sequencing on the Illumina platform was used to identify mechanisms of resistance to antibiotics among PNSP. RESULTS Fifty percent (13/26) of PNSP were resistant to erythromycin, of these 54% (7/13) and 46% (6/13) had MLSB phenotype and M phenotype respectively. All erythromycin resistant PNSP carried macrolide resistance genes; six isolates had mef(A)-msr(D), five isolates had both erm(B) and mef(A)-msr(D) while two isolates carried erm(B) alone. Isolates harboring the erm(B) gene had increased MIC (> 256 µg/mL) towards macrolides, compared to isolates without erm(B) gene (MIC 4-12 µg/mL) p < 0.001. Using the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines, the prevalence of azithromycin resistance was overestimated compared to genetic correlates. Tetracycline resistance was detected in 13/26 (50%) of PNSP and all the 13 isolates harbored the tet(M) gene. All isolates carrying the tet(M) gene and 11/13 isolates with macrolide resistance genes were associated with the mobile genetic element Tn6009 transposon family. Of 26 PNSP isolates, serotype 3 was the most common (6/26), and sequence type ST271 accounted for 15% (4/26). Serotypes 3 and 19 displayed high-level macrolide resistance and frequently carried both macrolide and tetracycline resistance genes. CONCLUSION The erm(B) and mef(A)-msr(D) were common genes conferring resistance to MLSB in PNSP. Resistance to tetracycline was conferred by the tet(M) gene. Resistance genes were associated with the Tn6009 transposon.
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Affiliation(s)
- Joel Manyahi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania.
| | - Sabrina J Moyo
- Department of Clinical Science, University of Bergen, Bergen, Norway.,National Advisory Unit for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway.,Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania
| | - Nina Langeland
- Department of Clinical Science, University of Bergen, Bergen, Norway.,National Advisory Unit for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Bjørn Blomberg
- Department of Clinical Science, University of Bergen, Bergen, Norway.,National Advisory Unit for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Li S, Wu Y, Zheng H, Li H, Zheng Y, Nan J, Ma J, Nagarajan D, Chang JS. Antibiotics degradation by advanced oxidation process (AOPs): Recent advances in ecotoxicity and antibiotic-resistance genes induction of degradation products. CHEMOSPHERE 2023; 311:136977. [PMID: 36309060 DOI: 10.1016/j.chemosphere.2022.136977] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/09/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Antibiotic contamination could cause serious risks of ecotoxicity and resistance gene induction. Advanced oxidation processes (AOPs) such as Fenton, photocatalysis, activated persulfate, electrochemistry and other AOPs technologies have been proven effective in the degradation of high-risk, refractory organic pollutants such as antibiotics. However, due to the limited mineralization ability, a large number of degradation intermediates will be produced in the oxidation process. The residual or undiscovered ecological risks of degradation products are potential safety hazards and problems necessitating comprehensive studies. In-depth investigations especially on the full assessments of ecotoxicity and resistance genes induction capability of antibiotic degradation products are important issues in reducing the environmental problems of antibiotics. Therefore, this review presents an overview of the current knowledge on the efficiency of different AOPs systems in reducing antibiotics toxicity and antibiotic resistance.
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Affiliation(s)
- Shuo Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China; Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Yanan Wu
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Heshan Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China.
| | - Hongbin Li
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Yongjie Zheng
- College of Chemistry and Chemical Engineering, Qiqihar University, Qiqihar, 161006, China
| | - Jun Nan
- Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Jun Ma
- Urban Water Resources Development and Northern National Engineering Research Center, Harbin, 150090, China; School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Dillirani Nagarajan
- Department of Chemical Engineering, National Cheng-Kung University, Tainan, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng-Kung University, Tainan, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung, 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung, 407, Taiwan; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-Li, Taiwan.
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Akdoğan Kittana FN, Mustak IB, Hascelik G, Saricam S, Gurler N, Diker KS. Erythromycin-resistant Streptococcus pneumoniae: phenotypes, genotypes, transposons and pneumococcal vaccine coverage rates. J Med Microbiol 2019; 68:874-881. [PMID: 31116101 DOI: 10.1099/jmm.0.000995] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
PURPOSE To assess the antibiotic resistance, transposon profiles, serotype distribution and vaccine coverage rates in 110 erythromycin-resistant S. pneumoniae clinical isolates. METHODOLOGY Erythromycin, clindamycin, tetracycline, chloramphenicol and kanamycin susceptibilities were assessed using the E-test/disc diffusion method. Inducible macrolide resistance was tested using the erythromycin-clindamycin double disc diffusion test. Serogrouping and serotyping were performed using latex particle agglutination and the Quellung reaction, respectively. Drug resistance genes and transposon-specific genes were investigated by PCR. RESULTS Of the isolates, 93 % were resistant to clindamycin; 81 % were resistant to tetracycline; 76 % were multi-drug-resistant, having resistance to both clindamycin and tetracycline; and 12 % had extended-drug resistance, being resistant to clindamycin, tetracycline, chloramphenicol and kanamycin. The majority of isolates (88.2 %) exhibited the cMLSB phenotype. The association between the cMLSB phenotype and tetracycline resistance was related to transposons Tn2010 (38.2 %), Tn6002 (21.8 %) and Tn3872 (18.2 %). M and iMLSB phenotypes were observed in 7 and 5 % of the isolates, respectively. The most frequent serotype was 19 F (40 %). Among the erythromycin-resistant pneumococci, vaccine coverage rates for the 13-valent pneumococcal conjugate vaccine (PCV-13) and the 23-valent pneumococcal polysaccharide vaccine (PPSV-23) were 76.4 and 79.1 %, respectively, compared to 82.2 and 85.1 % transposon-carrying isolates. CONCLUSIONS Multi-drug resistance among erythromycin-resistant S. pneumoniae isolates mainly occurs due to the horizontal spread of the Tn916 family of transposons. The majority of the transposon-carrying isolates are covered by 13- and 23-valent pneumococcal vaccines. Since serotype distribution and transposons in S. pneumoniae isolates may change over time, close monitoring is essential.
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Affiliation(s)
| | - Inci Basak Mustak
- 2 Ankara University, Faculty of Veterinary Science, Department of Microbiology, Ankara Turkey
| | - Gulsen Hascelik
- 1 Hacettepe University, Faculty of Medicine, Department of Medical Microbiology, Ankara, Turkey
| | - Seyyide Saricam
- 2 Ankara University, Faculty of Veterinary Science, Department of Microbiology, Ankara Turkey
| | - Nezahat Gurler
- 3 Istanbul University, Faculty of Medicine, Department of Medical Microbiology, Istanbul, Turkey
| | - Kadir Serdar Diker
- 2 Ankara University, Faculty of Veterinary Science, Department of Microbiology, Ankara Turkey
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Pan F, Zhang H, Dong X, Ye W, He P, Zhang S, Zhu JX, Zhong N. Comparative genomic analysis of multidrug-resistant Streptococcus pneumoniae isolates. Infect Drug Resist 2018; 11:659-670. [PMID: 29765237 PMCID: PMC5939923 DOI: 10.2147/idr.s147858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Introduction Multidrug resistance in Streptococcus pneumoniae has emerged as a serious problem to public health. A further understanding of the genetic diversity in antibiotic-resistant S. pneumoniae isolates is needed. Methods We conducted whole-genome resequencing for 25 pneumococcal strains isolated from children with different antimicrobial resistance profiles. Comparative analysis focus on detection of single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) was conducted. Moreover, phylogenetic analysis was applied to investigate the genetic relationship among these strains. Results The genome size of the isolates was ~2.1 Mbp, covering >90% of the total estimated size of the reference genome. The overall G+C% content was ~39.5%, and there were 2,200–2,400 open reading frames. All isolates with different drug resistance profiles harbored many indels (range 131–171) and SNPs (range 16,103–28,128). Genetic diversity analysis showed that the variation of different genes were associated with specific antibiotic resistance. Known antibiotic resistance genes (pbps, murMN, ciaH, rplD, sulA, and dpr) were identified, and new genes (regR, argH, trkH, and PTS-EII) closely related with antibiotic resistance were found, although these genes were primarily annotated with functions in virulence as well as carbohydrate and amino acid transport and metabolism. Phylogenetic analysis unambiguously indicated that isolates with different antibiotic resistance profiles harbored similar genetic backgrounds. One isolate, 14-LC.ER1025, showed a much weaker phylogenetic relationship with the other isolates, possibly caused by genomic variation. Conclusion In this study, although pneumococcal isolates had similar genetic backgrounds, strains were diverse at the genomic level. These strains exhibited distinct variations in their indel and SNP compositions associated with drug resistance.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Xiaoyan Dong
- Department of Respiratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Weixing Ye
- Shanghai Personal Biotechnology Co., Ltd, Shanghai, China
| | - Ping He
- Department of Medical Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shulin Zhang
- Department of Medical Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Nanbert Zhong
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China.,Department of Respiratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China.,New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
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Fong IW, Shlaes D, Drlica K. Antimicrobial Resistance Among Streptococcus pneumoniae. ANTIMICROBIAL RESISTANCE IN THE 21ST CENTURY 2018:13-38. [PMCID: PMC7122384 DOI: 10.1007/978-3-319-78538-7_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Antibiotic resistance in Streptococcus pneumoniae (pneumococcus), the main pathogen responsible for community-acquired pneumonia (CAP), meningitis, bacteremia, and otitis media, is a major concern for clinicians. This pathogen is associated with high rates of morbidity and mortality, especially among children under 2 years old, immunocompromised persons, and the elderly population. The major anti-pneumococcus agents are β-lactams and macrolides, with fluoroquinolones ranking third. The emergence of antibiotic-resistant pneumococcus due to overuse of antibiotics is a global concern. While the discovery of novel classes of antibiotics for the pneumococcus is at a standstill, significant progress in reducing the problem of resistance is associated with antibacterial vaccines. Nevertheless, the World Health Organization recently considered drug-resistant S. pneumoniae as ranking among the 12 bacteria, for which there is an urgent need for new treatments. A challenge is to slow the evolution of new strains that are resistant to the vaccines.
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Affiliation(s)
- I. W. Fong
- Department of Medicine, University of Toronto, Toronto, ON Canada
| | - David Shlaes
- Anti-infectives Consulting, LLC, Stonington, CT USA
| | - Karl Drlica
- Public Health Research Institute, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ USA
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Muurinen J, Stedtfeld R, Karkman A, Pärnänen K, Tiedje J, Virta M. Influence of Manure Application on the Environmental Resistome under Finnish Agricultural Practice with Restricted Antibiotic Use. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:5989-5999. [PMID: 28453251 DOI: 10.1021/acs.est.7b00551] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The co-occurrence of antibiotic-resistance genes (ARGs) and mobile genetic elements (MGEs) in farm environments can potentially foster the development of antibiotic-resistant pathogens. We studied the resistome of Finnish dairy and swine farms where use of antibiotics is limited to treating bacterial infections and manure is only applied from April to September. The resistome of manure, soil, and tile drainage water from the ditch was investigated from the beginning of the growing season until forage harvest. The relative ARG and MGE abundance was measured using a qPCR array with 363 primer pairs. Manure samples had the highest abundance of ARGs and MGEs, which increased during storage. Immediately following land application, the ARGs abundant in manure were detected in soil, but their abundance decreased over time with many becoming undetectable. This suggests that increases in ARG abundances after fertilizing are temporary and occur annually under agricultural practices that restrict antibiotic use. A few of the ARGs were detected in the ditch water, but most of them were undetected in the manure. Our results document the dissipation and dissemination off farm of ARGs under Finnish limited antibiotic use and suggest that such practices could help reduce the load of antibiotic-resistance genes in the environment.
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Affiliation(s)
- Johanna Muurinen
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki , Viikinkaari 9, Helsinki 00014, Finland
| | - Robert Stedtfeld
- Center for Microbial Ecology, Department of Civil and Environmental Engineering, Michigan State University , East Lansing, Michigan 48824-1325, United States
| | - Antti Karkman
- Department of Biosciences, University of Helsinki , Viikinkaari 1, Helsinki 00014, Finland
| | - Katariina Pärnänen
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki , Viikinkaari 9, Helsinki 00014, Finland
| | - James Tiedje
- Center for Microbial Ecology, Department of Civil and Environmental Engineering, Michigan State University , East Lansing, Michigan 48824-1325, United States
| | - Marko Virta
- Department of Food and Environmental Sciences, Division of Microbiology and Biotechnology, University of Helsinki , Viikinkaari 9, Helsinki 00014, Finland
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Yılmaz Ç, Özcengiz G. Antibiotics: Pharmacokinetics, toxicity, resistance and multidrug efflux pumps. Biochem Pharmacol 2017; 133:43-62. [DOI: 10.1016/j.bcp.2016.10.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 10/14/2016] [Indexed: 02/03/2023]
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Talebi M, Azadegan A, Sadeghi J, Ahmadi A, Ghanei M, Katouli M, Owlia P, Pourshafie MR. Determination of Characteristics of Erythromycin Resistant Streptococcus pneumoniae with Preferred PCV Usage in Iran. PLoS One 2016; 11:e0167803. [PMID: 28033345 PMCID: PMC5199012 DOI: 10.1371/journal.pone.0167803] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 11/21/2016] [Indexed: 11/19/2022] Open
Abstract
Amongst 100 Streptococcus pneumoniae isolated from clinical cases and nasopharynx of healthy individuals, 60 erythromycin resistant strains were isolated and characterized using MLST, PFGE, transposon analysis and Quellung reaction. Most of the S. pneumoniae erythromycin resistant (80%) were found to be attributable to the ermB-edncoded ribosome methylase activity which differs from the dominant mechanism of macrolide resistance seen in North America. The most predominant transposons were; Tn1545/6003 (27%), Tn6002 (22%), Tn2009 (20%), Tn2010 (17%). Number of the clinical isolates carrying Tn2010 was more significant than the normal flora. The serotypes found were; 14 (33%), 3 (22%), 23F (15%), 19F (15%), 19A (7%), 6A (3%), 9V (3%) and 6B (2%). The most prevalent serotypes among the clinical (n = 28) and normal flora (n = 32) isolates were serotypes 14 (46%) and 3 (31%), respectively. The most prevalent vaccine serotypes amongst the clinical isolates and the healthy individuals were pneumococcal conjugate vaccines (PCV) 13 and PCV10, respectively. PFGE revealed 34 pulsotypes with 9 common and 25 single types. Significant number of the normal isolates belonged to CT5 and CT6. On the other hand, significant number of clinical isolates belonged to CT8 as compared to the normal flora isolates. MLST showed 2 dominant sequence types. ST3130 (23%) and ST180 (22%) were the most predominant sequence types in the clinical and normal isolates, respectively. There was no significant difference in other sequence types between clinical and normal flora isolates. Three polyclonal complexes including Sweden15A -25, Spain23F-1 and Spain9V-3 constituted 58% of the isolates. Our results suggest that the genetic diversity and transposon distribution were high among S. pneumoniae, particularly in the isolates containing erm(B) and double antibiotic resistant genes (erm/mef). The results presented here could influence the change in the current vaccination practices in Iran which currently calls for vaccination with PCV7 or PCV10.
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Affiliation(s)
- Malihe Talebi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Azadeh Azadegan
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Javad Sadeghi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Ahmadi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mostafa Ghanei
- Tuberculosis Department, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Katouli
- Genecology Research Centre, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore, Queensland, Australia
| | - Parviz Owlia
- Molecular Microbiology Research Center (MMRC), Shahed University, Tehran, Iran
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Ambroset C, Coluzzi C, Guédon G, Devignes MD, Loux V, Lacroix T, Payot S, Leblond-Bourget N. New Insights into the Classification and Integration Specificity of Streptococcus Integrative Conjugative Elements through Extensive Genome Exploration. Front Microbiol 2016; 6:1483. [PMID: 26779141 PMCID: PMC4701971 DOI: 10.3389/fmicb.2015.01483] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 12/08/2015] [Indexed: 12/30/2022] Open
Abstract
Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the presence of ICEs in some species of Streptococci, the global prevalence and diversity of ICEs was not analyzed in this genus. In this study, we searched for ICEs in the completely sequenced genomes of 124 strains belonging to 27 streptococcal species. These exhaustive analyses revealed 105 putative ICEs and 26 slightly decayed elements whose limits were assessed and whose insertion site was identified. These ICEs were grouped in seven distinct unrelated or distantly related families, according to their conjugation modules. Integration of these streptococcal ICEs is catalyzed either by a site-specific tyrosine integrase, a low-specificity tyrosine integrase, a site-specific single serine integrase, a triplet of site-specific serine integrases or a DDE transposase. Analysis of their integration site led to the detection of 18 target-genes for streptococcal ICE insertion including eight that had not been identified previously (ftsK, guaA, lysS, mutT, rpmG, rpsI, traG, and ebfC). It also suggests that all specificities have evolved to minimize the impact of the insertion on the host. This overall analysis of streptococcal ICEs emphasizes their prevalence and diversity and demonstrates that exchanges or acquisitions of conjugation and recombination modules are frequent.
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Affiliation(s)
- Chloé Ambroset
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Charles Coluzzi
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Gérard Guédon
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Marie-Dominique Devignes
- Laboratoire Lorrain de Recherche en Informatique et ses Applications, Faculté des Sciences et Technologies, Université de Lorraine, UMR 7503Vandœuvre-lès-Nancy, France; CNRS, Laboratoire Lorrain de Recherche en Informatique et ses Applications, UMR 7503Vandśuvre-lès-Nancy, France
| | - Valentin Loux
- UR 1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique Jouy-en-Josas, France
| | - Thomas Lacroix
- UR 1404 Mathématiques et Informatique Appliquées du Génome à l'Environnement, Institut National de la Recherche Agronomique Jouy-en-Josas, France
| | - Sophie Payot
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
| | - Nathalie Leblond-Bourget
- DynAMic, Faculté des Sciences et Technologies, Université de Lorraine, UMR 1128Vandœuvre-lès-Nancy, France; DynAMic, Institut National de la Recherche Agronomique, UMR 1128Vandœuvre-lès-Nancy, France
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