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Wan TW, Lee TF, Chen XJ, Hunag YT, Teng LJ, Hsueh PR, Chiu HC. Performance assessment of the Bruker Biotyper MALDI-TOF MS for the identification of difficult-to-identify viridans group streptococci. J Clin Microbiol 2023; 61:e0114323. [PMID: 38038480 PMCID: PMC10729738 DOI: 10.1128/jcm.01143-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 10/22/2023] [Indexed: 12/02/2023] Open
Abstract
Differentiating Streptococcus pneumoniae among nonpneumococcal viridans group streptococci (VGS) is challenging in conventional laboratories. Therefore, we aimed to evaluate the performance of the latest Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) system in identifying VGS by comparing the results to those of the specific gene sequencing approach. Clinical isolates were initially identified using the BD Phoenix system to identify Streptococcus species. The optochin test was used to distinguish nonpneumococcal VGS from S. pneumoniae. The species of individual reference strains and clinical isolates were determined by comparing the sequences of the 16S rDNA, gyrB, sodA, groESL, or coaE genes with those in the GenBank sequence databases. We evaluated the performance of the Bruker Biotyper MALDI-TOF MS in VGS identification using two different machines with three databases. We collected a total of 103 nonpneumococcal VGS and 29 S. pneumoniae blood isolates at a medical center in northern Taiwan. Among these isolates, only seven could not be identified at the species level by the specific gene sequencing approach. We found that none of the nonpneumococcal VGS isolates were misidentified as pneumococci by the latest Biotyper system, and vice versa. However, certain strains, especially those in the mitis and bovis groups, could still not be correctly identified. The latest Bruker Biotyper 4.1 (DB_10833) showed significant improvement in identifying VGS strains. However, a specific gene sequencing test is still needed to precisely differentiate the species of strains in the mitis and bovis groups.
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Affiliation(s)
- Tsai-Wen Wan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Tai-Fen Lee
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Xiang-Jun Chen
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yun-Tsung Hunag
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Lee-Jene Teng
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Po-Ren Hsueh
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
- Department of Internal Medicine, Division of Infectious Diseases, China Medical University Hospital, School of Medicine, China Medical University, Taichung, Taiwan
| | - Hao-Chieh Chiu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
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Trabelsi I, Soltane R, Nejma MB, Albogami BM, Nour M. Genetic variability of the helix 54 of the 23S rDNA and its use as a molecular target for identification of species within the viridans group streptococci (VGS). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105321. [PMID: 35753621 DOI: 10.1016/j.meegid.2022.105321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The aim of the present study is to establish a method, based on sequence analysis of the helix 54 of 23S rRNA gene, to identify clinical relevant strains belonging to viridans group streptococci (VGS). A set of 25 randomly selected clinical isolates of alpha-hemolytic streptococci from upper respiratory tract were characterized by the routine phenotypic methods (API 20 Strep test). Molecular characterization was assessed by genotypic analysis of the nucleotide sequence of the helix 54 of 23S rRNA and Intergenic spacer region 16S23S. Partial sequencing of the gdh gene was used on 10 strains of mitis group. Sequence variations of the helix 54 allowed the identification of strains to group level and even to species level for certain strains within sanguinis and anginosus groups. Infact, species identification was ambiguous for some strains belonged to the salivarius group (of VGS16 to VGS20) and the mitis group (of VGS1 to VGS14). These results are almost similar to those obtained by sequencing the 16S23S intergenic region. Thus, we use the gdh gene sequencing for the identification of strains, not recognized, within the mitis group. The results generated herein indicate that no single methodology can be used to provide an accurate identification to the species level of all VGS, although nucleotide sequence analysis of the helix 54 of 23S rRNA gene proved to be a reliable method for the identification of VGS to the group level and even to the species level within sanguinis and anginosus groups.
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Affiliation(s)
- Ines Trabelsi
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia.
| | - Raya Soltane
- Departement of Basic Sciences, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia; Departement of Biology, Faculty of sciences, Tunis El Manar University, Tunis 1068, Tunisia.
| | - Mouna Ben Nejma
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia
| | - Bander M Albogami
- Taif University, College of Science, Laboratory of Applied and Molecular Microbiology, Saudi Arabia
| | - Mohamed Nour
- University of Monastir, Higher Institute of Biotechnology of Monastir, Bioresources: Integrative Biology & Valuation "BIOLIVAL", Avenue Taher Hadded, (BP 74), 5000 Monastir, Tunisia
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Sadowy E, Hryniewicz W. Identification of Streptococcus pneumoniae and other Mitis streptococci: importance of molecular methods. Eur J Clin Microbiol Infect Dis 2020; 39:2247-2256. [PMID: 32710352 PMCID: PMC7669753 DOI: 10.1007/s10096-020-03991-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/15/2020] [Indexed: 02/06/2023]
Abstract
The Mitis group of streptococci includes an important human pathogen, Streptococcus pneumoniae (pneumococcus) and about 20 other related species with much lower pathogenicity. In clinical practice, some representatives of these species, especially Streptococcus pseudopneumoniae and Streptococcus mitis, are sometimes mistaken for S. pneumoniae based on the results of classical microbiological methods, such as optochin susceptibility and bile solubility. Several various molecular approaches that address the issue of correct identification of pneumococci and other Mitis streptococci have been proposed and are discussed in this review, including PCR- and gene sequencing-based tests as well as new developments in the genomic field that represents an important advance in our understanding of relationships within the Mitis group.
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Affiliation(s)
- Ewa Sadowy
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
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Species-Specific Identification of Streptococcus based on DNA Marker in 16S-23S rDNA Internal Transcribed Spacer. Curr Microbiol 2020; 77:1569-1579. [PMID: 32253469 DOI: 10.1007/s00284-020-01975-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/27/2020] [Indexed: 02/04/2023]
Abstract
Streptococcus is closely correspondent to human. The accurate species-specific identification method of Streptococcus is important for the bacteria clinical diagnosis, molecular epidemiological analysis, and microecological study. In the last decades, DNA markers are widely utilized for identification of prokaryotic species. However, 16S rDNA, the most popular bacterial DNA marker, cannot properly distinguish closely related Streptococcus species. In present study, we employed 16S-23S rRNA gene internal transcribed spacer (ITS) sequence to explore the species-specific DNA marker. We predicted the secondary structure of Streptococcus ITS sequence transcribed products. Then we identified that the specific and consensus sequences in the primary structure can be found occupying an individual subunit in the secondary structure, which explained the foundation of the mosaic-like structure of ITS. We evaluated the specificity of ITS in Streptococcus, and found that the specificity can be detected by a further analysis of a BLAST result. Then, we developed an identification procedure based on the ITS sequence. We verified the procedure by 500 ITS sequence. The accuracy rate of this procedure was 100% for Streptococcus at genus level, and 99.3% at species level. It suggested that ITS can be utilized to accurately identify Streptococcus at the species level. This work suggests that further exploration of ITS could be applied in other bacterial genera for identification and classification, which may be a useful topic for future microbiology studies.
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Moore JE, Hirayama J, Hayashi K, Mason C, Coulter W, Matsuda M, Goldsmith CE. Examination of 16S-23S rRNA intergenic spacer region (ISR) heterogeneity in a population of clinical Streptococcus pneumoniae- a new laboratory epidemiological genotyping tool to aid outbreak analysis. Br J Biomed Sci 2018; 75:95-97. [DOI: 10.1080/09674845.2017.1382025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- JE Moore
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland, UK
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University of Belfast, Royal Group of Hospitals, Belfast, Northern Ireland, UK
- School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland, UK
| | - J Hirayama
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland, UK
- Laboratory for Molecular Biology, School of Environmental Health Sciences, Azabu University, Sagamihara, Japan
| | - K Hayashi
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland, UK
- Laboratory for Molecular Biology, School of Environmental Health Sciences, Azabu University, Sagamihara, Japan
| | - C Mason
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University of Belfast, Royal Group of Hospitals, Belfast, Northern Ireland, UK
| | - W Coulter
- School of Medicine, Dentistry and Biomedical Sciences, Queen’s University of Belfast, Royal Group of Hospitals, Belfast, Northern Ireland, UK
| | - M Matsuda
- Laboratory for Molecular Biology, School of Environmental Health Sciences, Azabu University, Sagamihara, Japan
| | - CE Goldsmith
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, Northern Ireland, UK
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Abstract
The viridans group streptococci are a heterogeneous group of organisms which exist as commensals in the oropharynx and the gut. They cause serious infections when they gain entry into sterile sites particularly in patients with predisposing conditions. Classification and species differentiation of these organisms has always been a challenge because of phenotypic differences between strains of the same species. Facklam's typing scheme based on six metabolic properties has been the most widely used and many commercial identification systems are based on it. Due to the ambiguity in species differentiation based on phenotypic tests, nucleic acid-based methods have been developed to improve the identification of these organisms. Results using genotypic methods such as 16S rRNA and sodA gene sequencing have been promising. Multilocus sequence analysis of seven house-keeping genes map, pfl, pyk, ppaC, rpoB, soda and tuf amplified by polymerase chain reaction was found to be an accurate alternative to other methods and could be useful in the characterisation of larger collections of isolates.
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Affiliation(s)
- T Menon
- Department of Microbiology, Dr AL Mudaliar, Post Graduate Institute of Basic Medical Sciences, University of Madras, Chennai, Tamil Nadu, India
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Prevalence and impact of Streptococcus pneumoniae in adult cystic fibrosis patients: a retrospective chart review and capsular serotyping study. BMC Pulm Med 2015; 15:49. [PMID: 25930152 PMCID: PMC4434824 DOI: 10.1186/s12890-015-0041-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 04/16/2015] [Indexed: 11/20/2022] Open
Abstract
Background Cystic fibrosis (CF) is a genetic disease characterized by complex polymicrobial communities within the lower respiratory tract. S. pneumoniae, while a well-defined pathogen in the general population, has rarely been identified in CF. Furthermore, prevalence studies on Pneumococcus in CF have predominantly focused on the infant and pediatric populations, and outcome data is lacking. Methods Through a review of our comprehensive clinical and microbiologic database from a single adult CF center in Canada from 1978–2013 we sought to determine the incidence, prevalence, serotype and clinical impact of Pneumococcus in adults with CF. Results Only fifteen of 318 adult CF patients (5%) were ever found to have transient Pneumococcus colonization, and none developed persistent infection although length of carriage varied. As all isolates were stored, capsular serotyping could be performed using a multiplex PCR panel. Capsular serotyping revealed a varied distribution of several serotypes within these isolates. Lung function testing at time of incident Pneumococcus isolation was compared with values before and after isolation and showed no significant reduction in spirometry values, nor was there an increased need for rescue antibacterial therapy. Conclusion Within our center, incident Pneumococcus infection is neither common, associated with a disproportionate clinical deterioration nor results in chronic infection.
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Goldsmith CE, Hara Y, Sato T, Nakajima T, Nakanishi S, Mason C, Moore JE, Matsuda M, Coulter WA. Comparison of antibiotic susceptibility in viridans group streptococci in low and high antibiotic-prescribing General Practices. J Clin Pharm Ther 2015; 40:204-7. [PMID: 25604860 DOI: 10.1111/jcpt.12245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 12/30/2014] [Indexed: 11/28/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE Antibiotic resistance has become a global public health issue. Most antibiotics are prescribed in the community, although there is less stewardship of such agents in the community compared to secondary and tertiary care. Few studies have attempted to examine the prescribing practices in General Practice and its impact on antibiotic resistance and, therefore, a study was performed in order to compare antibiotic susceptibilities of commensal viridans group streptococci (VGS) obtained from patient cohorts in General Practices (GP), who were high and low prescribers of oral antibiotics. METHOD Sixty-five patients (<1 month-81 years; 77% female: 23% male) were enrolled onto the study, and viridans group streptococci (n = 5/patient) were collected from each patient's nasal passages and oropharynx region and tested for antibiotic susceptibility against (i) tetracyclines (doxycycline); (ii) macrolides (erythromycin); (iii) β-lactams (penicillin G); and (iv) fluoroquinolones (ofloxacin & levofloxacin). RESULTS AND DISCUSSION There were no significant differences in MICs between high and low GP prescribers with doxycycline (P = 0·094), erythromycin (P = 0·122), ofloxacin (P = 0·193) and levofloxacin (P = 0·058). However, there was a significant difference between high and low GP practices with regard to penicillin G (P = 0·031). This finding is important as the β-lactams are the most commonly prescribed oral antibiotic in the community. WHAT IS NEW AND CONCLUSION This study demonstrates that high prescribing practices may lead to an altered (higher) level of resistance to these agents in the commensal VGS population, which may be important as reservoirs of antibiotic resistance determinants in subsequent horizontal gene transfer events, particularly with newly colonizing pathogens, including pneumococci. Primary care physicians should be aware that increased prescribing of antibiotics may led to increased level of penicillin resistance.
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Affiliation(s)
- C E Goldsmith
- Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Belfast, UK
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Identification of rare pathogenic bacteria in a clinical microbiology laboratory: impact of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2013; 51:2182-94. [PMID: 23637301 DOI: 10.1128/jcm.00492-13] [Citation(s) in RCA: 325] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
During the past 5 years, matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) has become a powerful tool for routine identification in many clinical laboratories. We analyzed our 11-year experience in routine identification of clinical isolates (40 months using MALDI-TOF MS and 91 months using conventional phenotypic identification [CPI]). Among the 286,842 clonal isolates, 284,899 isolates of 459 species were identified. The remaining 1,951 isolates were misidentified and required confirmation using a second phenotypic identification for 670 isolates and using a molecular technique for 1,273 isolates of 339 species. MALDI-TOF MS annually identified 112 species, i.e., 36 species/10,000 isolates, compared to 44 species, i.e., 19 species/10,000 isolates, for CPI. Only 50 isolates required second phenotypic identifications during the MALDI-TOF MS period (i.e., 4.5 reidentifications/10,000 isolates) compared with 620 isolates during the CPI period (i.e., 35.2/10,000 isolates). We identified 128 bacterial species rarely reported as human pathogens, including 48 using phenotypic techniques (22 using CPI and 37 using MALDI-TOF MS). Another 75 rare species were identified using molecular methods. MALDI-TOF MS reduced the time required for identification by 55-fold and 169-fold and the cost by 5-fold and 96-fold compared with CPI and gene sequencing, respectively. MALDI-TOF MS was a powerful tool not only for routine bacterial identification but also for identification of rare bacterial species implicated in human infectious diseases. The ability to rapidly identify bacterial species rarely described as pathogens in specific clinical specimens will help us to study the clinical burden resulting from the emergence of these species as human pathogens, and MALDI-TOF MS may be considered an alternative to molecular methods in clinical laboratories.
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Identification of clinical Streptococcus pneumoniae isolates among other alpha and nonhemolytic streptococci by use of the Vitek MS matrix-assisted laser desorption ionization-time of flight mass spectrometry system. J Clin Microbiol 2013; 51:1861-7. [PMID: 23576536 DOI: 10.1128/jcm.03069-12] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Discrimination between Streptococcus pneumoniae and its close relatives of the viridans group is a common difficulty in matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry-based identification. In the present study, the performances of the Vitek MS MALDI-TOF mass spectrometry system were assessed using 334 pneumococci, 166 other S. mitis group streptococci, 184 non-S. mitis group streptococci, and 19 related alpha- and nonhemolytic aerobic Gram-positive catalase-negative coccal isolates. Pneumococci had been identified by means of optochin susceptibility and bile solubility or serotyping, and other isolates mainly by use of RapidID32 Strep strips. In case of discordant or low-discrimination results, genotypic methods were used. The sensitivity of the Vitek MS for the identification of S. pneumoniae was 99.1%, since only three bile-insoluble isolates were misidentified as Streptococcus mitis/Streptococcus oralis. Conversely, two optochin-resistant pneumococci were correctly identified (specificity, 100%). Three Streptococcus pseudopneumoniae isolates were also correctly identified. Among nonpneumococcal isolates, 90.8% (n = 335) were correctly identified to the species or subspecies level and 2.4% (n = 9) at the group level. For the remaining 25 isolates, the Vitek MS proposed a bacterial species included in the list of possible species suggested by genotypic methods, except for 4 isolates which were not identified due to the absence of the species in the database. According to our study, the Vitek MS displays performance similar to that of the optochin susceptibility test for routine identification of pneumococcal isolates. Moreover, the Vitek MS is efficient for the identification of other viridans group streptococci and related isolates, provided that the species are included in the database.
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Yap J, Goldsmith C, Moore J. Integrity of bacterial genomic DNA after autoclaving: possible implications for horizontal gene transfer and clinical waste management. J Hosp Infect 2013; 83:247-9. [DOI: 10.1016/j.jhin.2012.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2012] [Accepted: 11/30/2012] [Indexed: 10/27/2022]
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