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Comparative genome analysis of Streptococcus strains to identify virulent genes causing neonatal meningitis. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 107:105398. [PMID: 36572056 DOI: 10.1016/j.meegid.2022.105398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022]
Abstract
AIM To determine Streptococcus agalactiae genes responsible for causing neonatal meningitis. BACKGROUND Streptococcus agalactiae strain 2603 V/R is causative agent of neonatal meningitis, maternal infection and sepsis in young children. World health organisation reported high burden of new born death caused by this bacterium. Streptococcus agalactiae colonizing epithelial cells of vagina and endothelial cells have high resistance to available antibiotic drugs which makes it essential to determine new drug targets. OBJECTIVES To compare the genome of selected strain with the non-pathogenic strains of streptococcus and identify the virulent and antibiotic resistant genes for adaptation in host environment. METHOD The whole genome of human pathogen Streptococcus agalactiae strain 2603 V/R was analysed and compared with Streptococcus dysgalactiae strains using visualization and annotation tools. Genomic islands, mobile genetic elements, virulent and resistant genes were studied. RESULTS Genetically pathogenic strain is most similar to Streptococcus dysgalactiae subsp. equisimilis strain NCTC 7136. Comparative analysis revealed the importance of capsular polysaccharides and surface proteins responsible for avoiding immune system attachment to host epithelial cells and virulent behaviour. High number of genes coding for antibiotics resistance may provide a competitive advantage for survival of pathogenic Streptococcus agalactiae strain 2603 V/R in its niche. CONCLUSIONS The comparative analysis of pathogenic strain Streptococcus agalactiae with non-pathogenic strains of Streptococcus dysgalactiae provided new insights in pathogenicity that could aid in recognization for new regions and genes for development of new drug development strategies considering presence of high number of resistance genes.
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Feuerschuette OHM, Alves EV, Scheffer MC, Vilela APP, Barazzetti FH, Feuerschuette HM, Cancelier ACL, Bazzo ML. Genetic diversity and antimicrobial resistance of invasive, noninvasive and colonizing group B Streptococcus isolates in southern Brazil. Access Microbiol 2022; 4:acmi000370. [PMID: 36004365 PMCID: PMC9394672 DOI: 10.1099/acmi.0.000370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 05/12/2022] [Indexed: 11/18/2022] Open
Abstract
Introduction. Group B
Streptococcus
(GBS) is a human commensal bacterium that is also associated with infection in pregnant and non-pregnant adults, neonates and elderly people.
Gap Statement. The authors hypothesize that knowledge of regional GBS genetic patterns may allow the use of prevention and treatment measures to reduce the burden of streptococcal disease.
Aim. The aim was to report the genotypic diversity and antimicrobial sensitivity profiles of invasive, noninvasive urinary and colonizing GBS strains, and evaluate the relationships between these findings.
Methodology. The study included consecutive and non-duplicated GBS isolates recovered in southern Brazil from 2015 to 2017. We performed multiple-locus variable-number tandem repeat analysis (MLVA) and PCR analyses to determine capsular serotypes and identify the presence of the resistance genes mefA/E, ermB and ermA/TR, and also antibiotic susceptibility testing.
Results. The sample consisted of 348 GBS strains, 42 MLVA types were identified, and 4 of them represented 64 % of isolates. Serotype Ia was the most prevalent (42.2 %) and was found in a higher percentage associated with colonization, followed by serotypes V (24.4 %), II (17.8 %) and III (7.8 %). Serotype V was associated with invasive isolates and serotypes II and III with noninvasive isolates, without significant differences. All isolates were susceptible to penicillin. GBS 2018/ hvgA was observed in 17 isolates, with 11 belonging to serogroup III. The Hunter–Gaston diversity index was calculated as 0.879. The genes mefA/E, erm/B and erm/A/TR were found in 45, 19 and 46 isolates.
Conclusion. This report suggests that the circulating GBS belong to a limited number of genetic lineages. The most common genotypes were Ia/MT12 and V/MT18, which are associated with high resistance to macrolides and the presence of the genes mefA/E and ermA/TR. Penicillin remains the antibiotic of choice. Implementation of continuous surveillance of GBS infections will be essential to assess GBS epidemiology and develop accurate GBS prevention, especially strategies associated with vaccination.
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Affiliation(s)
- Otto Henrique May Feuerschuette
- Universidade do Sul de Santa Catarina – UNISUL, Tubarão, Brazil
- Hospital Universitário Professor Polydoro Ernani de São Thiago, HU/UFSC, Florianópolis, Brazil
| | - Eduardo Venâncio Alves
- Laboratório de Biologia Molecular, Microbiologia e Sorologias, HU/UFSC, Florianópolis, Brazil
| | - Mara Cristina Scheffer
- Laboratório de Biologia Molecular, Microbiologia e Sorologias, HU/UFSC, Florianópolis, Brazil
- Hospital Universitário Professor Polydoro Ernani de São Thiago, HU/UFSC, Florianópolis, Brazil
| | - Ana Paula Pessoa Vilela
- Laboratório de Biologia Molecular, Microbiologia e Sorologias, HU/UFSC, Florianópolis, Brazil
| | | | | | | | - Maria Luiza Bazzo
- Laboratório de Biologia Molecular, Microbiologia e Sorologias, HU/UFSC, Florianópolis, Brazil
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Ghamari M, Jabalameli F, Emaneini M, Beigverdi R. Multiple-locus variable-number tandem repeat analysis for genotyping of erythromycin-resistant group B streptococci in Iran. New Microbes New Infect 2022; 45:100957. [PMID: 35198219 PMCID: PMC8851280 DOI: 10.1016/j.nmni.2022.100957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/26/2021] [Accepted: 01/10/2022] [Indexed: 12/02/2022] Open
Abstract
Background Group B Streptococcus (GBS or S. agalactiae) is an important pathogen causing severe invasive diseases in neonates, pregnant women, and adults with underlying medical conditions. Methods To investigate the incidence of resistance to macrolide, lincosamide and streptogramin type B (MLSB) antibiotics, macrolide and tetracycline resistance determinants and genetic relationships, a total of 146 clinical isolates of GBS were collected from Tehran, Iran. The genetic relationships between erythromycin-resistant strains were determined by multilocus variable tandem repeat analysis (MLVA). Results All isolates were susceptible to penicillin, vancomycin, linezolid, and quinupristin–dalfopristin, but were resistant to tetracycline (96.6%, 141/146), erythromycin (28.1%, 41/146) and clindamycin (16.4%, 24/146). Among the 41 erythromycin-resistant GBS (ERGBS), the most common antimicrobial resistance gene was tetM detected in 92.7% (38/41) of the isolates followed by ermTR and ermB found in 65.8% (27/41) and 29.3% (12/41) of isolates, respectively. Of the 41 ERGBS, 95% (39/41) exhibited the constitutive MLSB phenotype, 2.4% (1/41) displayed inducible MLSB and 2.4% (1/41) had M phenotype. The erm methylase genes were widely related to MLSB phenotype isolates, while the mefA gene was associated with M phenotype. MLVA analysis performed on the 41 ERGBS revealed that 34 MLVA types (MTs). MLVA analysis showed that infections due to ERGBS have been caused by a variety of genotypes, suggesting that ERGBS were clonally unrelated and dissemination of these isolates was not due to a clonal outbreak. Conclusion Careful usage of macrolide antibiotics in therapy, continued surveillance of resistance rate and appropriate infection control measures can help to reduce spreading of resistance isolates.
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Beauruelle C, Treluyer L, Pastuszka A, Cochard T, Lier C, Mereghetti L, Glaser P, Poyart C, Lanotte P. CRISPR Typing Increases the Discriminatory Power of Streptococcus agalactiae Typing Methods. Front Microbiol 2021; 12:675597. [PMID: 34349737 PMCID: PMC8328194 DOI: 10.3389/fmicb.2021.675597] [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: 03/04/2021] [Accepted: 06/15/2021] [Indexed: 11/25/2022] Open
Abstract
We explored the relevance of a Clustered regularly interspaced short palindromic repeats (CRISPR)-based genotyping tool for Streptococcus agalactiae typing and we compared this method to current molecular methods [multi locus sequence typing (MLST) and capsular typing]. To this effect, we developed two CRISPR marker schemes (using 94 or 25 markers, respectively). Among the 255 S. agalactiae isolates tested, 229 CRISPR profiles were obtained. The 94 and 25 markers made it possible to efficiently separate isolates with a high diversity index (0.9947 and 0.9267, respectively), highlighting a high discriminatory power, superior to that of both capsular typing and MLST (diversity index of 0.9017 for MLST). This method has the advantage of being correlated with MLST [through analysis of the terminal direct repeat (TDR) and ancestral spacers] and to possess a high discriminatory power (through analysis of the leader-end spacers recently acquired, which are the witnesses of genetic mobile elements encountered by the bacteria). Furthermore, this “one-shot” approach presents the benefit of much-reduced time and cost in comparison with MLST. On the basis of these data, we propose that this method could become a reference method for group B Streptococcus (GBS) typing.
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Affiliation(s)
- Clémence Beauruelle
- Département de Bactériologie-Virologie, Hygiène Hospitalière et Parasitologie-Mycologie, Centre Hospitalier Régional Universitaire (CHRU) de Brest, Brest, France.,Inserm, EFS, UMR 1078, GGB, Universitè de Bretagne Occidentale, Brest, France
| | - Ludovic Treluyer
- Institut Cochin, Team Bacteria and Perinatality, INSERM U1016, Paris, France
| | - Adeline Pastuszka
- INRAE, ISP, Université de Tours, Tours, France.,Service de Bactériologie-Virologie, CHRU de Tours, Tours, France
| | | | - Clément Lier
- INRAE, ISP, Université de Tours, Tours, France.,Service de Bactériologie-Virologie, CHRU de Tours, Tours, France
| | - Laurent Mereghetti
- INRAE, ISP, Université de Tours, Tours, France.,Service de Bactériologie-Virologie, CHRU de Tours, Tours, France
| | - Philippe Glaser
- Evolution and Ecology of Resistance to Antibiotics (EERA) Unit, Institut Pasteur, Paris, France.,UMR CNRS 3525, Paris, France
| | - Claire Poyart
- Institut Cochin, Team Bacteria and Perinatality, INSERM U1016, Paris, France.,CNRS UMR 8104, Paris Descartes University, Paris, France.,Department of Bacteriology, University Hospitals Paris Centre-Cochin, Assistance Publique-Hôpitaux de Paris, Paris, France
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Perinatal Streptococcus agalactiae Epidemiology and Surveillance Targets. Clin Microbiol Rev 2018; 31:31/4/e00049-18. [PMID: 30111577 DOI: 10.1128/cmr.00049-18] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Streptococcus agalactiae, or group B streptococcus (GBS), is a major neonatal pathogen. Recent data have elucidated the global prevalence of maternal and neonatal colonization, but gaps still remain in the epidemiology of this species. A number of phenotypic and genotypic classifications can be used to identify the diversity of GBS strains, and some are more discriminatory than others. This review explores the main schemes used for GBS epidemiology and further details the targets for epidemiological surveillance. Current screening practices across the world provide a unique opportunity to gain detailed information on maternal colonizing strains and neonatal disease-causing strains, which is vital for monitoring and therapeutics, if sufficient detail can be extracted. Deciphering which isolates are circulating within specific populations and recording targets within invasive strains are crucial steps in monitoring the implementation of therapeutics, such as vaccines, as well as developing novel therapies against prevalent GBS strains. Having a detailed understanding of global GBS epidemiology will prove invaluable for understanding the pathogenesis of this organism and equipping future prevention strategies for success.
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6
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Beauruelle C, Pastuszka A, Mereghetti L, Lanotte P. Group B Streptococcus Vaginal Carriage in Pregnant Women as Deciphered by Clustered Regularly Interspaced Short Palindromic Repeat Analysis. J Clin Microbiol 2018; 56:e01949-17. [PMID: 29618502 PMCID: PMC5971545 DOI: 10.1128/jcm.01949-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/28/2018] [Indexed: 11/20/2022] Open
Abstract
We evaluated the diversity of group B Streptococcus (GBS) vaginal carriage populations in pregnant women. For this purpose, we studied each isolate present in a primary culture of a vaginal swab using a new approach based on clustered regularly interspaced short palindromic repeats (CRISPR) locus analysis. To evaluate the CRISPR array composition rapidly, a restriction fragment length polymorphism (RFLP) analysis was performed. For each different pattern observed, the CRISPR array was sequenced and capsular typing and multilocus sequence typing (MLST) were performed. A total of 970 isolates from 10 women were analyzed by CRISPR-RFLP. Each woman carrying GBS isolates presented one to five specific "personal" patterns. Five women showed similar isolates with specific and unique restriction patterns, suggesting the carriage of a single GBS clone. Different patterns were observed among isolates from the other five women. For three of these, CRISPR locus sequencing highlighted low levels of internal modifications in the locus backbone, whereas there were high levels of modifications for the last two women, suggesting the carriage of two different clones. These two clones were closely related, having the same ancestral spacer(s), the same capsular type and, in one case, the same ST, but showed different antibiotic resistance patterns in pairs. Eight of 10 women were colonized by a single GBS clone, while two of them were colonized by two strains, leading to a risk of selection of more-virulent and/or more-resistant clones during antibiotic prophylaxis. This CRISPR analysis made it possible to separate isolates belonging to a single capsular type and sequence type, highlighting the greater discriminating power of this approach.
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Affiliation(s)
- Clemence Beauruelle
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France
| | - Adeline Pastuszka
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France
| | - Laurent Mereghetti
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France
| | - Philippe Lanotte
- Université François Rabelais de Tours, UMR1282 Infectiologie et Santé Publique, Tours, France
- INRA, UMR1282 Infectiologie et Santé Publique, Nouzilly, France
- CHRU de Tours, Service de Bactériologie-Virologie, Tours, France
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7
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Lian DS, Zhao SJ. Capillary electrophoresis based on nucleic acid detection for diagnosing human infectious disease. Clin Chem Lab Med 2017; 54:707-38. [PMID: 26352354 DOI: 10.1515/cclm-2015-0096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/17/2015] [Indexed: 01/22/2023]
Abstract
Rapid transmission, high morbidity, and mortality are the features of human infectious diseases caused by microorganisms, such as bacteria, fungi, and viruses. These diseases may lead within a short period of time to great personal and property losses, especially in regions where sanitation is poor. Thus, rapid diagnoses are vital for the prevention and therapeutic intervention of human infectious diseases. Several conventional methods are often used to diagnose infectious diseases, e.g. methods based on cultures or morphology, or biochemical tests based on metabonomics. Although traditional methods are considered gold standards and are used most frequently, they are laborious, time consuming, and tedious and cannot meet the demand for rapid diagnoses. Disease diagnosis using capillary electrophoresis methods has the advantages of high efficiency, high throughput, and high speed, and coupled with the different nucleic acid detection strategies overcomes the drawbacks of traditional identification methods, precluding many types of false positive and negative results. Therefore, this review focuses on the application of capillary electrophoresis based on nucleic detection to the diagnosis of human infectious diseases, and offers an introduction to the limitations, advantages, and future developments of this approach.
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Gabrielsen C, Mæland JA, Lyng RV, Radtke A, Afset JE. Molecular characteristics of Streptococcus agalactiae strains deficient in alpha-like protein encoding genes. J Med Microbiol 2017; 66:26-33. [PMID: 28032541 DOI: 10.1099/jmm.0.000412] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptococcus agalactiae (group B streptococci, GBS) are important human and animal pathogens, which can be subdivided based on different capsular polysaccharides and surface-anchored alpha-like proteins (Alps), as well as other proteins. Nearly all GBS strains possess an Alp (Alp GBS), although Alp-negative GBS (non-Alp GBS) do occur. In this study, 10 (1.1 %) of 932 clinical human GBS tested lacked an Alp encoding gene. All 10 strains were from patients with bloodstream infection, confirming that non-Alp GBS can be highly virulent. All non-Alp GBS expressed one or more of the surface-anchored proteins R3, Z1 and Z2, while less than 10 % of unselected clinical strains express any of these proteins. In contrast to Alp GBS, all non-Alp strains tested were PCR negative for the upstream sequence of the insertion site of the Alp encoding gene of Alp GBS. Genome sequencing showed that all but one of the 10 clinical non-Alp strains and the non-Alp reference strain CNCTC 10/84 lacked a region surrounding the Alp gene commonly present in Alp GBS strains. These strains instead harboured an 849 bp region not present in the Cα prototype strain A909. We have shown that non-Alp GBS differ from Alp GBS in the region surrounding the insertion site of Alp genes of Alp GBS as well as in their content of other surface proteins and that PCR for the upstream flanking region of the Alp gene may be useful for differentiation between Alp and non-Alp GBS.
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Affiliation(s)
- Christina Gabrielsen
- Department of Medical Microbiology, St Olavs University Hospital, Trondheim, Norway
| | - Johan A Mæland
- Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Randi Valsø Lyng
- Department of Medical Microbiology, St Olavs University Hospital, Trondheim, Norway
| | - Andreas Radtke
- Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Medical Microbiology, St Olavs University Hospital, Trondheim, Norway
| | - Jan Egil Afset
- Department of Medical Microbiology, St Olavs University Hospital, Trondheim, Norway.,Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
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Obszańska K, Kern-Zdanowicz I, Sitkiewicz I. MLVF analysis of anginosus (milleri) group streptococci. Diagn Microbiol Infect Dis 2015; 83:124-9. [PMID: 26234478 DOI: 10.1016/j.diagmicrobio.2015.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 06/30/2015] [Accepted: 07/06/2015] [Indexed: 11/17/2022]
Abstract
We developed a new method of typing for anginosus group streptococci (SAG). It is the first SAG-dedicated, PCR-based method, which allows to determine the relationship between strains. The method is based on the detection of tandem repeats among 9 genomic loci and is classified as multilocus variable number tandem repeats fingerprint (MLVF) type of analysis. Using the described method, it is possible to detect over half million MLVF patterns, which correlate with pulsed-field gel electrophoresis profiles. The other advantage of the method is relatively short time from "cell to data", low costs, and easy application for epidemiological and evolutionary studies.
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Affiliation(s)
- Katarzyna Obszańska
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Izabella Kern-Zdanowicz
- Department of Microbial Biochemistry, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warszawa, Poland
| | - Izabela Sitkiewicz
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warszawa, Poland.
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Durney BC, Crihfield CL, Holland LA. Capillary electrophoresis applied to DNA: determining and harnessing sequence and structure to advance bioanalyses (2009-2014). Anal Bioanal Chem 2015; 407:6923-38. [PMID: 25935677 PMCID: PMC4551542 DOI: 10.1007/s00216-015-8703-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/09/2015] [Accepted: 04/13/2015] [Indexed: 12/17/2022]
Abstract
This review of capillary electrophoresis methods for DNA analyses covers critical advances from 2009 to 2014, referencing 184 citations. Separation mechanisms based on free-zone capillary electrophoresis, Ogston sieving, and reptation are described. Two prevalent gel matrices for gel-facilitated sieving, which are linear polyacrylamide and polydimethylacrylamide, are compared in terms of performance, cost, viscosity, and passivation of electroosmotic flow. The role of capillary electrophoresis in the discovery, design, and characterization of DNA aptamers for molecular recognition is discussed. Expanding and emerging techniques in the field are also highlighted.
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Affiliation(s)
- Brandon C Durney
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, 26506, USA
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Puymège A, Bertin S, Guédon G, Payot S. Analysis of Streptococcus agalactiae pan-genome for prevalence, diversity and functionality of integrative and conjugative or mobilizable elements integrated in the tRNA(Lys CTT) gene. Mol Genet Genomics 2015; 290:1727-40. [PMID: 25832353 DOI: 10.1007/s00438-015-1031-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/17/2015] [Indexed: 11/27/2022]
Abstract
Streptococcus agalactiae is the first cause of invasive infections in human neonates and is also a major bovine and fish pathogen. High genomic diversity was observed in this species that hosts numerous mobile genetic elements, in particular elements transferable by conjugation. This works aims to evaluate the contribution of these elements to GBS genome diversity. Focusing on genomic islands integrated in the tRNA(Lys) (CTT) gene, a known hotspot of recombination, an extensive in silico search was performed on the sequenced genome of 303 strains of S. agalactiae isolated from different hosts. In all the isolates (except 9), whatever their origin (human, bovine, camel, dog, gray seal, dolphin, fish species or bullfrog), this locus carries highly diverse genomic islands transferable by conjugation such as integrative and conjugative elements (ICEs), integrative and mobilizable elements (IMEs), CIs-mobilizable elements (CIMEs) or composite elements. Transfer of an ICE from an ST67 bovine strain to a phylogenetically distant ST23 human isolate was obtained experimentally indicating that there was no barrier to ICE transfer between strains from different hosts. Interestingly, a novel family of putative IMEs that site-specifically integrate in the nic site of oriT of ICEs belonging to Tn916/ICESt3 superfamily was detected in silico. These elements carry an antibiotic resistance gene (lsa(C)) already described to confer cross-resistance to lincosamides, streptogramins A and pleuromutilins. Further work is needed to evaluate the impact of these IMEs on the transfer of targeted ICEs and the mobility and the dissemination of these IMEs.
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Affiliation(s)
- Aurore Puymège
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France
| | - Stéphane Bertin
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France
| | - Gérard Guédon
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France
| | - Sophie Payot
- Faculté des Sciences et Technologies, INRA, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France. .,Faculté des Sciences et Technologies, Université de Lorraine, UMR1128 DynAMic, Bd des Aiguillettes, BP70239, 54506, Vandœuvre-lès-Nancy, France.
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Beigverdi R, Jabalameli F, Mirsalehian A, Hantoushzadeh S, Boroumandi S, Taherikalani M, Emaneini M. Virulence factors, antimicrobial susceptibility and molecular characterization of Streptococcus agalactiae isolated from pregnant women. Acta Microbiol Immunol Hung 2014; 61:425-34. [PMID: 25496971 DOI: 10.1556/amicr.61.2014.4.4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Forty-one Streptococcus agalactiae isolates collected from pregnant women at 35-37 weeks of gestation were analysed for their capsular types, antimicrobial resistance determinants, distribution of virulence factors and genetic relatedness using PCR and multiplex PCR. Capsular type III was predominant (65.8%), followed by capsular type II (14.6%), Ib (7.3%), and V(4.9%). All isolates were susceptible to penicillin, vancomycin, linezolid and quinupristin-dalfopristin. Resistance to tetracycline, erythromycin and clindamycin were found in 97.6%, 24.4%, and 14.6% of isolates, respectively. The most common antimicrobial resistance gene was tetM found in 97.6% of the isolates followed by ermTR and ermB found in 12% and 7.3% of isolates, respectively. The most common virulence gene was hly (100%), followed by scpB (97.6%), bca (97.6%), rib (53.65%) and bac (4.9%). The insertion sequence IS1548 was found in 63.4% of isolates. By multi locus variable number of tandem repeat analysis (MLVA) typing, 30 different allelic profiles or MLVA types (MTs) were identified. The most frequent was the MT1 (5/41, 12.2%) and followed by MT2 (4/41, 9.75%). Our data revealed that population structure of these isolates is highly diverse and indicates different MLVA types.
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Affiliation(s)
- Reza Beigverdi
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Fereshteh Jabalameli
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Akbar Mirsalehian
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
| | - Sedigheh Hantoushzadeh
- 2 Tehran University of Medical Sciences Maternal, Fetal and Neonatal Research Center, Vali-asr Hospital Tehran Iran
| | | | - Morovat Taherikalani
- 4 Ilam University of Medical Sciences Clinical Microbiology Research Center Ilam Iran
| | - Mohammad Emaneini
- 1 Tehran University of Medical Sciences Department of Microbiology, School of Medicine Tehran Iran
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Otaguiri ES, Morguette AEB, Tavares ER, dos Santos PMC, Morey AT, Cardoso JD, Perugini MRE, Yamauchi LM, Yamada-Ogatta SF. Commensal Streptococcus agalactiae isolated from patients seen at University Hospital of Londrina, Paraná, Brazil: capsular types, genotyping, antimicrobial susceptibility and virulence determinants. BMC Microbiol 2013; 13:297. [PMID: 24359590 PMCID: PMC3878097 DOI: 10.1186/1471-2180-13-297] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 12/16/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Streptococcus agalactiae or Group B Streptococci (GBS) have the ability to access various host sites, which reflects its adaptability to different environments during the course of infection. This adaptation is due to the expression of virulence factors that are involved with survival, invasion and bacterial persistence in the host. This study aimed to characterize GBS isolates from women of reproductive age seen at University Hospital of Londrina, according to capsular typing, genetic relatedness, antimicrobial susceptibility profile and occurrence of virulence determinants. RESULTS A total of 83 GBS isolates were enrolled in this study. Capsular types Ia (42.2%), II (10.8%), III (14.5%) and V (30.1%) were identified in most GBS. One isolate each was classified as type IX and non-typeable.A total of 15 multiple locus variable number of tandem repeat analysis (MLVA) types were identified among the isolates, seven were singletons and eight were represented by more than four isolates. All isolates were susceptible to penicillin, ampicillin, cefepime, cefotaxime, chloramphenicol, levofloxacin and vancomycin. Resistance to erythromycin and clindamycin was observed in 19.3 and 13.3% of isolates, respectively. All isolates resistant to clindamycin were simultaneously resistant to erythromycin and were distributed in the capsular types III and V. One isolate showed the constitutive macrolide-lincosamide-streptogramin B (cMLS(B)) phenotype and ten showed the inducible MLS(B) (iMLS(B)) phenotype. The mechanism of resistance to erythromycin and clindamycin more prevalent among these isolates was mediated by the gene ermA, alone or in combination with the gene ermB. The isolates displaying resistance only to erythromycin belonged to capsular type Ia, and showed the M phenotype, which was mediated by the mefA/E gene. All isolates harbored the gene hylB and at least one pilus variant, PI-1, PI-2a or PI-2b. Although cylE was observed in all GBS, four isolates were classified as gamma-hemolytic and carotenoid pigment non-producers. CONCLUSIONS Our results indicate the potential virulence of commensal GBS isolates, reinforcing the need for continued screening for this bacterium to prevent infections. The distribution of capsular and pili antigens, and MLVA profiles was also identified, which may contribute to the development of new strategies for the prevention and treatment of GBS infection.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sueli Fumie Yamada-Ogatta
- Laboratório de Biologia Molecular de Microrganismos, Departamento de Microbiologia, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Rodovia Celso Garcia Cid, PR 445, km 380, Londrina, Paraná, CEP 86057-970, Brazil.
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Comparison of Z and R3 antigen expression and of genes encoding other antigenic markers in invasive human and bovine Streptococcus agalactiae strains from Norway. Vet Microbiol 2013; 167:729-33. [PMID: 24120184 DOI: 10.1016/j.vetmic.2013.09.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Revised: 09/06/2013] [Accepted: 09/09/2013] [Indexed: 11/20/2022]
Abstract
Streptococcus agalactiae (GBS) may cause a variety of infectious diseases in humans caused by human GBS and mastitis in cattle caused by bovine GBS. Over the last few years molecular testing has provided evidence that human and bovine GBS have evolved along diverse phylogenetic lines. In the present study 173 invasive human GBS strains and 52 invasive bovine strains were tested for altogether 18 strain-variable and surface-localized antigenic markers including all 10 capsular polysaccharides (CPS) and proteins including Cβ, the alpha-like proteins, R3 and the recently described Z1 and Z2 antigens. PCR was used to detect encoding genes and antibody-based methods to detect expression of antigens. Thirteen of the 18 markers were detected in isolates of both strain categories. Seven of the ten CPS antigens were detected in both groups with types III and V predominating in the human GBS strains, types IV and V in the bovine isolates. Z1, Z2 and/or R3 expression and the genes encoding Cβ, Cα, Alp1, Alp2/3 or R4 (Rib) were detected in both groups. Protein antigen-CPS associations well known for human strains were essentially the same in the bovine isolates. The results show that in spite of evolution along different lines, human and bovine GBS share a variety of surface-exposed antigenic markers, substantiating close relationship between the two GBS subpopulations.
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Godoy D, Carvalho-Castro G, Leal C, Pereira U, Leite R, Figueiredo H. Genetic diversity and new genotyping scheme for fish pathogenic Streptococcus agalactiae. Lett Appl Microbiol 2013; 57:476-83. [DOI: 10.1111/lam.12138] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 07/05/2013] [Accepted: 07/17/2013] [Indexed: 12/01/2022]
Affiliation(s)
- D.T. Godoy
- AQUAVET - Laboratory of Aquatic Animal Diseases, Veterinary School; Federal University of Minas Gerais; Belo Horizonte Brazil
| | - G.A. Carvalho-Castro
- AQUAVET - Laboratory of Aquatic Animal Diseases, Veterinary School; Federal University of Minas Gerais; Belo Horizonte Brazil
| | - C.A.G. Leal
- AQUAVET - Laboratory of Aquatic Animal Diseases, Veterinary School; Federal University of Minas Gerais; Belo Horizonte Brazil
| | - U.P. Pereira
- AQUAVET - Laboratory of Aquatic Animal Diseases, Veterinary School; Federal University of Minas Gerais; Belo Horizonte Brazil
| | - R.C. Leite
- AQUAVET - Laboratory of Aquatic Animal Diseases, Veterinary School; Federal University of Minas Gerais; Belo Horizonte Brazil
| | - H.C.P. Figueiredo
- AQUAVET - Laboratory of Aquatic Animal Diseases, Veterinary School; Federal University of Minas Gerais; Belo Horizonte Brazil
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A PCR-based intergenic spacer region-capillary gel electrophoresis typing method for identification and subtyping of Nocardia species. J Clin Microbiol 2012; 50:3478-84. [PMID: 22875897 DOI: 10.1128/jcm.01311-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
While 16S rRNA sequence-based identification of Nocardia species has become the gold standard, it is not without its limitations. We evaluated a novel approach encompassing the amplification of the Nocardia 16S-23S rRNA intergenic spacer (IGS) region followed by fragment analysis by capillary gel electrophoresis (CGE) of the amplified product for species identification of Nocardia. One hundred forty-five Nocardia isolates (19 species) and four non-Nocardia aerobic actinomycetes were studied. Reproducibility testing was performed in a subset (21%) of isolates. Ninety-five different electropherograms were identified, with heterogeneity within species being a general observation. Among common Nocardia species (e.g., Nocardia cyriacigeorgica, N. nova, N. farcinica), 2 or 3 dominant electropherogram subgroups were typical. While only a minority (8/19; 42%) of the different Nocardia species contained isolates displaying unique fragment sizes that were predictive of a particular species, virtually all isolates (142/145; 98%) could be assigned to the correct species using IGS-CGE typing based on the number and size of amplified fragments. The median number of fragments for each isolate was 2 (range, 1 to 5) with only a minority (17%) having a single fragment detected. The majority (93%) of amplified fragments were between 408 and 461 bp. The technique was also non-operator dependent, highly reproducible, and quicker and less expensive than 16S sequencing. In summary, PCR-based IGS-CGE typing is relatively simple, accurate, reproducible, and cost-effective and offers a potential alternative to 16S rRNA sequencing for identifying and subtyping Nocardia isolates.
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Radtke A, Bruheim T, Afset JE, Bergh K. Multiple-locus variant-repeat assay (MLVA) is a useful tool for molecular epidemiologic analysis of Streptococcus agalactiae strains causing bovine mastitis. Vet Microbiol 2012; 157:398-404. [PMID: 22266162 DOI: 10.1016/j.vetmic.2011.12.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2011] [Revised: 12/21/2011] [Accepted: 12/29/2011] [Indexed: 11/27/2022]
Abstract
Group B streptococci (GBS) were considered a major cause of mastitis in cattle until preventive measures succeeded in controlling the disease in the 1970s and 1980s. During the last 5-6 years an increasing number of cases have been observed in some Scandinavian countries. A total of 187 GBS isolates from mastitis cases were collected from 119 animals in 34 Norwegian farms in the period from April 2007 to November 2010. 133 (71%) of the isolates were from farms with automated milking systems. The strains underwent typing of capsular polysaccharides (CPS) and surface proteins, and were analyzed by multi-locus variable repeat assay (MLVA) to investigate the epidemiological relationship of strains within and between farms. The GBS strains were differentiated into 12 types by CPS and surface protein analysis, with CPS types V (54%) and IV (34%) predominating. MLVA was superior to CPS and protein typing for strain differentiation, resolving the 187 strains into 37 types. In 29 of 34 farms all GBS strains had identical MLVA profiles specific for each farm. However, in one farm represented with 48 isolates, four MLVA variants with differences in one repeat locus were observed during the almost 3-year long collection period. Similar variations were observed at four other farms. This might reflect the stability of repeat loci under in vivo conditions. Farms with automated milking systems were overrepresented in this material. In conclusion, the five-loci MLVA allowed rapid high-resolution genotyping of the bovine GBS strains within and between farms.
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Affiliation(s)
- Andreas Radtke
- Norwegian University of Science and Technology, Department of Laboratory Medicine, Children's and Women's Health, Trondheim, Norway.
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Haguenoer E, Baty G, Pourcel C, Lartigue MF, Domelier AS, Rosenau A, Quentin R, Mereghetti L, Lanotte P. A multi locus variable number of tandem repeat analysis (MLVA) scheme for Streptococcus agalactiae genotyping. BMC Microbiol 2011; 11:171. [PMID: 21794143 PMCID: PMC3163538 DOI: 10.1186/1471-2180-11-171] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Accepted: 07/27/2011] [Indexed: 11/10/2022] Open
Abstract
Background Multilocus sequence typing (MLST) is currently the reference method for genotyping Streptococcus agalactiae strains, the leading cause of infectious disease in newborns and a major cause of disease in immunocompromised children and adults. We describe here a genotyping method based on multiple locus variable number of tandem repeat (VNTR) analysis (MLVA) applied to a population of S. agalactiae strains of various origins characterized by MLST and serotyping. Results We studied a collection of 186 strains isolated from humans and cattle and three reference strains (A909, NEM316 and 2603 V/R). Among 34 VNTRs, 6 polymorphic VNTRs loci were selected for use in genotyping of the bacterial population. The MLVA profile consists of a series of allele numbers, corresponding to the number of repeats at each VNTR locus. 98 MLVA genotypes were obtained compared to 51 sequences types generated by MLST. The MLVA scheme generated clusters which corresponded well to the main clonal complexes obtained by MLST. However it provided a higher discriminatory power. The diversity index obtained with MLVA was 0.960 compared to 0.881 with MLST for this population of strains. Conclusions The MLVA scheme proposed here is a rapid, cheap and easy genotyping method generating results suitable for exchange and comparison between different laboratories and for the epidemiologic surveillance of S. agalactiae and analyses of outbreaks.
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Affiliation(s)
- Eve Haguenoer
- Université François-Rabelais de Tours, UFR de Médecine, EA 3854 Bactéries et risque materno-fœtal, Institut Fédératif de Recherche 136 Agents Transmissibles et Infectiologie, Tours, France
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Bacterial population genomics and infectious disease diagnostics. Trends Biotechnol 2010; 28:611-8. [PMID: 20961641 DOI: 10.1016/j.tibtech.2010.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 09/03/2010] [Accepted: 09/07/2010] [Indexed: 01/14/2023]
Abstract
New sequencing technologies have made the production of bacterial genome sequences increasingly easy, and it can be confidently forecasted that vast genomic databases will be generated in the next few years. Here, we detail how collections of bacterial genomes from a particular species (population genomics libraries) have already been used to improve the design of several diagnostic assays for bacterial pathogens. Genome sequencing itself is also becoming more commonly used for epidemiological, forensic and clinical investigations. There is an opportunity for the further development of bioinformatic tools to bring even further value to bacterial diagnostic genomics.
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Diversity and mobility of integrative and conjugative elements in bovine isolates of Streptococcus agalactiae, S. dysgalactiae subsp. dysgalactiae, and S. uberis. Appl Environ Microbiol 2010; 76:7957-65. [PMID: 20952646 DOI: 10.1128/aem.00805-10] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bovine isolates of Streptococcus agalactiae (n = 76), Streptococcus dysgalactiae subsp. dysgalactiae (n = 32), and Streptococcus uberis (n = 101) were analyzed for the presence of different integrative and conjugative elements (ICEs) and their association with macrolide, lincosamide, and tetracycline resistance. The diversity of the isolates included in this study was demonstrated by multilocus sequence typing for S. agalactiae and pulsed-field gel electrophoresis for S. dysgalactiae and S. uberis. Most of the erythromycin-resistant strains carry an ermB gene. Five strains of S. uberis that are resistant to lincomycin but susceptible to erythromycin carry the lin(B) gene, and one has both linB and lnuD genes. In contrast to S. uberis, most of the S. agalactiae and S. dysgalactiae tetracycline-resistant isolates carry a tet(M) gene. A tet(S) gene was also detected in the three species. A Tn916-related element was detected in 30 to 50% of the tetracycline-resistant strains in the three species. Tetracycline resistance was successfully transferred by conjugation to an S. agalactiae strain. Most of the isolates carry an ICE integrated in the rplL gene. In addition, half of the S. agalactiae isolates have an ICE integrated in a tRNA lysine (tRNA(Lys)) gene. Such an element is also present in 20% of the isolates of S. dysgalactiae and S. uberis. A circular form of these ICEs was detected in all of the isolates tested, indicating that these genetic elements are mobile. These ICEs could thus also be a vehicle for horizontal gene transfer between streptococci of animal and/or human origin.
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