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Gil E, Hatcher J, Saram SD, Guy RL, Lamagni T, Brown JS. Streptococcus intermedius: an underestimated pathogen in brain infection? Future Microbiol 2025; 20:163-177. [PMID: 39552595 DOI: 10.1080/17460913.2024.2423524] [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: 09/18/2024] [Accepted: 10/28/2024] [Indexed: 11/19/2024] Open
Abstract
Streptococcus intermedius is an oral commensal organism belonging to the Streptococcus anginosus group (SAG). S. intermedius causes periodontitis as well as invasive, pyogenic infection of the central nervous system, pleural space or liver. Compared with other SAG organisms, S. intermedius has a higher mortality as well as a predilection for intracranial infection, suggesting it is likely to possess virulence factors that mediate specific interactions with the host resulting in bacteria reaching the brain. The mechanisms involved are not well described. Intracranial suppuration (ICS) due to S. intermedius infection can manifest as an abscess within the brain parenchyma, or a collection of pus (empyema) in the sub- or extra-dural space. These infections necessitate neurosurgery and prolonged antibiotic treatment and are associated with a considerable burden of morbidity and mortality. The incidence of ICS is increasing in several settings, with SAG species accounting for an increasing proportion of cases. There is a paucity of published literature regarding S. intermedius pathogenesis as well as few published genomes, hampering molecular epidemiological research. This perspective evaluates what is known about the clinical features and pathogenesis of ICS due to S. intermedius and explores hypothetical explanations why the incidence of these infections may be increasing.
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Affiliation(s)
- Eliza Gil
- UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF, UK
- Clinical Research Department, London School of Hygiene & Tropical Medicine, London, WC1E 7HT, UK
- Division of Infection, University College London Hospital, London, NW1 2BU, UK
- Department of Microbiology, Virology & Infection Control, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, WC1N 1EH, UK
| | - James Hatcher
- Department of Microbiology, Virology & Infection Control, Great Ormond Street Hospital for Children, NHS Foundation Trust, London, WC1N 1EH, UK
- Department of Infection, Immunity & Inflammation, UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Sophia de Saram
- Division of Infection, University College London Hospital, London, NW1 2BU, UK
| | - Rebecca L Guy
- Healthcare-Associated Infection & Antimicrobial Resistance Division, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Theresa Lamagni
- Healthcare-Associated Infection & Antimicrobial Resistance Division, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Jeremy S Brown
- UCL Respiratory, Division of Medicine, University College London, London, WC1E 6JF, UK
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Rodríguez-Ayala M, Vizcarra P, Díaz-Pollán B, Lázaro-Perona F, Cendejas-Bueno E. Invasive Streptococcus pseudopneumoniae infection in an adult patient with acute community-acquired meningitis: a case report. Eur J Clin Microbiol Infect Dis 2025; 44:187-192. [PMID: 39520620 DOI: 10.1007/s10096-024-04979-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Accepted: 10/29/2024] [Indexed: 11/16/2024]
Abstract
Rapid identification of pathogens in acute meningitis is critical for timely treatment. However, traditional methods often face limitations in differentiating closely related species such as Streptococcus pneumoniae and Streptococcus pseudopneumoniae. We report a case of community-acquired meningitis caused by S. pseudopneumoniae secondary to a cerebrospinal fluid fistula, highlighting the microbiological diagnostic challenges.
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Affiliation(s)
- Montserrat Rodríguez-Ayala
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz. P.º de la Castellana, 261, Fuencarral-El Pardo, Madrid, 28046, Spain
- Department of Preventive Medicine, Public Health and Microbiology, School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pilar Vizcarra
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz. P.º de la Castellana, 261, Fuencarral-El Pardo, Madrid, 28046, Spain
| | - Beatriz Díaz-Pollán
- Infectious Diseases Unit, Internal Medicine Department, Hospital La Paz. Institute for Health Research - IdiPAZ, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Fernando Lázaro-Perona
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz. P.º de la Castellana, 261, Fuencarral-El Pardo, Madrid, 28046, Spain
| | - Emilio Cendejas-Bueno
- Clinical Microbiology and Parasitology Department, Hospital Universitario La Paz. P.º de la Castellana, 261, Fuencarral-El Pardo, Madrid, 28046, Spain.
- CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
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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: 1] [Impact Index Per Article: 0.5] [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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Suleiman M, Elamin N, Nabor R, Roberts J, Tang P, Hasan MR, Pérez-López A. Evaluation of Immulex S. pneumoniae Omni test for the direct detection of S. pneumoniae from positive blood cultures. Heliyon 2023; 9:e22106. [PMID: 38027561 PMCID: PMC10658396 DOI: 10.1016/j.heliyon.2023.e22106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 09/06/2023] [Accepted: 11/04/2023] [Indexed: 12/01/2023] Open
Abstract
Rapid and early identification of Streptococcus pneumoniae from positive blood cultures is crucial for the management of patients with bloodstream infections (BSI). Many identification systems in microbiology laboratories have difficulty differentiating S. pneumoniae from other closely related species in the Streptococcus mitis group. To overcome this limitation, we developed a rapid workflow in our laboratory combining direct MALDI-TOF MS identification with the Immulex S. pneumoniae Omni test (SSI Diagnostica, Denmark) for rapid detection of S. pneumoniae directly from positive blood cultures. The workflow was evaluated using 51 Streptococcus isolates. Compared to conventional biochemical testing, our new workflow demonstrates 100 % specificity and sensitivity for the detection and differentiation of S. pneumoniae from other closely related species. Our new workflow is accurate, cost-effective, and can easily be implemented in microbiology laboratories that already perform direct MALDI-TOF identification from positive blood cultures to improve the management of patients with invasive pneumococcal disease. Importance Invasive pneumococcal disease remains a major public health problem worldwide. Reducing the time to identify Streptococcus pneumoniae in positive blood cultures allows patients to be treated sooner with more targeted and effective antibiotics. We evaluated a two-step protocol where positive blood cultures are first tested directly by MALDI-TOF MS and any samples containing Streptococcus species are tested by Immulex S. pneumoniae Omni test to both detect and differentiate S. pneumoniae from other closely related Streptococcus species. Our study results showed 100 % sensitivity and specificity, and a much faster turn-around time than conventional methods.
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Affiliation(s)
| | | | | | | | - Patrick Tang
- Sidra Medicine, PO BOX 26999, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Mohammad Rubayet Hasan
- Medical Scientific Department, LifeLabs, Toronto, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Canada
| | - Andrés Pérez-López
- Sidra Medicine, PO BOX 26999, Doha, Qatar
- Weill Cornell Medical College in Qatar, Doha, Qatar
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Pan F, Zhao N, Zhao W, Wang C, Sun Y, Zhang H, Qin J, Liu Q, Zhang H. Performance of Two Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) Systems for Identification of the Viridans Group Streptococci. Infect Drug Resist 2023; 16:2901-2909. [PMID: 37193297 PMCID: PMC10183192 DOI: 10.2147/idr.s407667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/20/2023] [Indexed: 05/18/2023] Open
Abstract
Background Due to similar colony morphology among viridans group streptococci (VGS), the differentiation of VGS species remains difficult in routine clinical microbiology. Recently, matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) has been described as a fast method for identifying various bacteria at species level, and also for the VGS strains. Methods A total of 277 VGS isolates were identified with the two MALDI-TOF MS systems (VITEK MS and Bruker Biotyper). The tuf and rpoB gene sequencing was used as the reference identification method for comparison. Results Based on tuf and rpoB gene sequencing, 84 isolates were S. pneumoniae and 193 strains were other VGS isolates including S. anginosus group (n=91, 47.2%), S. mitis group (n=80, 41.5%), S. bovis group (n=11, 5.7%), S. salivarius group (n=10, 5.2%), and S. mutans group (n=1, 0.5%). VITEK MS and Bruker Biotyper accurately identified 94.6% and 89.9% of all VGS isolates, respectively. VITEK MS showed better identification results than Bruker Biotyper for S. mitis group including S. pneumoniae and S. bovis group, but for other VGS isolates, two MALDI-TOF MS systems showed comparable identification performance. However, VITEK MS was able to identify S. gallolyticus to the subspecies level with high-confidence (S. gallolyticus ssp. pasteurianus), while the Bruker Biotyper system could not. While Bruker Biotyper system could be able to correctly differentiate the subspecies of S. salivarius from S. vestibularis, VITEK MS poorly identify. Conclusion This study demonstrated that two MALDI-TOF MS systems allowed discrimination for most VGS isolates with different identification performance, but Bruker Biotyper could produce more misidentifications and VITEK MS system. It is crucial to be familiar with the performance of MALDI-TOF MS systems used in clinical microbiology.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, People’s Republic of China
| | - Na Zhao
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
| | - Wantong Zhao
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Chun Wang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yan Sun
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Haomin Zhang
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
| | - Juanxiu Qin
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
| | - Qian Liu
- Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China
- Qian Liu, Department of Laboratory Medicine, RenJi Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, People’s Republic of China, Email
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200062, People’s Republic of China
- Correspondence: Hong Zhang, Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China, Tel +86 189 1712 8200, Email
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Zhou ML, Wang ZR, Li YB, Kudinha T, Wang J, Wang Y, Xiao M, Xu YC, Liu ZY, Hsueh PR. Rapid identification of Streptococcus pneumoniae serotypes by cpsB gene-based sequetyping combined with multiplex PCR. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:870-879. [PMID: 34924338 DOI: 10.1016/j.jmii.2021.11.004] [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: 04/22/2021] [Revised: 11/07/2021] [Accepted: 11/20/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND/PURPOSE Streptococcus pneumoniae is an important human pathogen that causes invasive infections in adults and children. Accurate serotyping is important to study its epidemiological distribution and to assess vaccine efficacy. METHODS Invasive S. pneumoniae isolates (n = 300) from 27 teaching hospitals in China were studied. The Quellung reaction was used as the gold standard to identify the S. pneumoniae serotypes. Subsequently, multiplex PCR and cpsB gene-based sequetyping methods were used to identify the serotypes. RESULTS Based on the Quellung reaction, 299 S. pneumoniae isolates were accurately identified to the serotype level and 40 different serotypes were detected. Only one strain was non-typeable, and five most common serotypes were identified: 23F (43, 14.3%), 19A (41, 13.7%), 19F (41, 13.7%), 3 (31, 10.3%), and 14 (27, 9.0%). Overall, the multiplex PCR method identified 73.3 and 20.7% of the isolates to the serotype and cluster levels, respectively, with 1.7% of the isolates misidentified. In contrast, the cpsB sequetyping method identified 59.0 and 30.3% of the isolates to the serotype and cluster levels, respectively, and 7% were misidentified. CONCLUSIONS The cpsB gene sequetyping method combined with multiplex PCR, can greatly improve the accuracy and efficiency of serotyping, besides reducing the associated costs.
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Affiliation(s)
- Meng-Lan Zhou
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Zi-Ran Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Yan-Bing Li
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Timothy Kudinha
- Charles Sturt University, Leeds Parade, Orange, NSW, Australia; Regional and Rural, NSW Health Pathology, Orange Hospital, NSW 2800, Australia
| | - Jian Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Yao Wang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China.
| | - Zheng-Yin Liu
- Department of Infectious Disease, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Po-Ren Hsueh
- Departments of Laboratory Medicine and Internal Medicine, China Medical University Hospital, Taichung, Taiwan; School of Medicine, China Medical University, Taichung, Taiwan; Ph.D Programme for Aging, School of Medicine, China Medical University, Taichung, Taiwan; Departments of Laboratory Medicine and Internal Medicine, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan.
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Desiderato CK, Sachsenmaier S, Ovchinnikov KV, Stohr J, Jacksch S, Desef DN, Crauwels P, Egert M, Diep DB, Goldbeck O, Riedel CU. Identification of Potential Probiotics Producing Bacteriocins Active against Listeria monocytogenes by a Combination of Screening Tools. Int J Mol Sci 2021; 22:ijms22168615. [PMID: 34445321 PMCID: PMC8395247 DOI: 10.3390/ijms22168615] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/07/2021] [Accepted: 08/09/2021] [Indexed: 12/19/2022] Open
Abstract
Listeria monocytogenes is an important food-borne pathogen and a serious concern to food industries. Bacteriocins are antimicrobial peptides produced naturally by a wide range of bacteria mostly belonging to the group of lactic acid bacteria (LAB), which also comprises many strains used as starter cultures or probiotic supplements. Consequently, multifunctional strains that produce bacteriocins are an attractive approach to combine a green-label approach for food preservation with an important probiotic trait. Here, a collection of bacterial isolates from raw cow's milk was typed by 16S rRNA gene sequencing and MALDI-Biotyping and supernatants were screened for the production of antimicrobial compounds. Screening was performed with live Listeria monocytogenes biosensors using a growth-dependent assay and pHluorin, a pH-dependent protein reporting membrane damage. Purification by cation exchange chromatography and further investigation of the active compounds in supernatants of two isolates belonging to the species Pediococcus acidilactici and Lactococcus garvieae suggest that their antimicrobial activity is related to heat-stable proteins/peptides that presumably belong to the class IIa bacteriocins. In conclusion, we present a pipeline of methods for high-throughput screening of strain libraries for potential starter cultures and probiotics producing antimicrobial compounds and their identification and analysis.
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Affiliation(s)
- Christian K. Desiderato
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (C.K.D.); (S.S.); (J.S.); (D.N.D.); (P.C.); (O.G.)
| | - Steffen Sachsenmaier
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (C.K.D.); (S.S.); (J.S.); (D.N.D.); (P.C.); (O.G.)
| | - Kirill V. Ovchinnikov
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Universitetstunet 3, 1433 Ås, Norway; (K.V.O.); (D.B.D.)
| | - Jonas Stohr
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (C.K.D.); (S.S.); (J.S.); (D.N.D.); (P.C.); (O.G.)
| | - Susanne Jacksch
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Campus Schwenningen, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (S.J.); (M.E.)
| | - Dominique N. Desef
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (C.K.D.); (S.S.); (J.S.); (D.N.D.); (P.C.); (O.G.)
| | - Peter Crauwels
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (C.K.D.); (S.S.); (J.S.); (D.N.D.); (P.C.); (O.G.)
| | - Markus Egert
- Faculty of Medical and Life Sciences, Institute of Precision Medicine, Furtwangen University, Campus Schwenningen, Jakob-Kienzle-Straße 17, 78054 Villingen-Schwenningen, Germany; (S.J.); (M.E.)
| | - Dzung B. Diep
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Universitetstunet 3, 1433 Ås, Norway; (K.V.O.); (D.B.D.)
| | - Oliver Goldbeck
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (C.K.D.); (S.S.); (J.S.); (D.N.D.); (P.C.); (O.G.)
| | - Christian U. Riedel
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany; (C.K.D.); (S.S.); (J.S.); (D.N.D.); (P.C.); (O.G.)
- Correspondence: ; Tel.: +49-731-5024853
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Jensen CS, Dargis R, Shewmaker P, Nielsen XC, Christensen JJ. Identification of Streptococcus pseudopneumoniae and other mitis group streptococci using matrix assisted laser desorption/ionization - time of flight mass spectrometry. Diagn Microbiol Infect Dis 2021; 101:115487. [PMID: 34339919 DOI: 10.1016/j.diagmicrobio.2021.115487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 07/02/2021] [Accepted: 07/03/2021] [Indexed: 11/19/2022]
Abstract
This study evaluated the ability of the MALDI-ToF MS from Bruker Daltonics to identify clinical Mitis-Group-Streptococcus isolates with a focus on Streptococcus pseudopneumoniae. The results were analyzed using the standard log(score) and the previously published list(score). Importantly, using the log(score) no misidentifications occurred and 27 of 29 (93%) S. pneumoniae and 27 of 30 (90%) S. oralis strains were identified, but only 1 of 31 (3%) S. pseudopneumoniae and 1 of 13 (8%) S. mitis strains were identified. However, our results show that 30 of 31 S. pseudopneumoniae strains had a S. pseudopneumoniae Main Spectral Profiles within the 3 best matches. Using the list(score) all S. oralis and S. pneumoniae strains were identified correctly, but list(score) misidentified 10 S. pseudopneumoniae and 5 S. mitis. We propose to use the log(score) for identification of S. pneumoniae, S. pseudopneumoniae, S. mitis and S. oralis, but for some strains additional testing may be needed.
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Affiliation(s)
| | - Rimtas Dargis
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark
| | | | | | - Jens Jørgen Christensen
- The Regional Department of Clinical Microbiology, Region Zealand, Denmark; Institute of Clinical Medicine, University of Copenhagen, Copenhagen N, Denmark
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Streptococcus pseudopneumoniae: Use of Whole-Genome Sequences To Validate Species Identification Methods. J Clin Microbiol 2021; 59:JCM.02503-20. [PMID: 33208473 DOI: 10.1128/jcm.02503-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 11/20/2022] Open
Abstract
A correct identification of Streptococcus pseudopneumoniae is a prerequisite for investigating the clinical impact of the bacterium. The identification has traditionally relied on phenotypic methods. However, these phenotypic traits have been shown to be unreliable, with some S. pseudopneumoniae strains giving conflicting results. Therefore, sequence-based identification methods have increasingly been used for identification of S. pseudopneumoniae In this study, we used 64 S. pseudopneumoniae strains, 59 S. pneumoniae strains, 22 S. mitis strains, 24 S. oralis strains, 6 S. infantis strains, and 1 S. peroris strain to test the capability of three single genes (rpoB, gyrB, and recA), two multilocus sequence analysis (MLSA) schemes, the single nucleotide polymorphism (SNP)-based phylogeny tool CSI phylogeny, a k-mer-based identification method (KmerFinder), average nucleotide identity (ANI) using fastANI, and core genome analysis to identify S. pseudopneumoniae Core genome analysis and CSI phylogeny were able to cluster all strains into distinct clusters related to their respective species. It was not possible to identify all S. pseudopneumoniae strains correctly using only one of the single genes. The MLSA schemes were unable to identify some of the S. pseudopneumoniae strains, which could be misidentified. KmerFinder identified all S. pseudopneumoniae strains but misidentified one S. mitis strain as S. pseudopneumoniae, and fastANI differentiated between S. pseudopneumoniae and S. pneumoniae using an ANI cutoff of 96%.
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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: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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11
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Performance and Application of 16S rRNA Gene Cycle Sequencing for Routine Identification of Bacteria in the Clinical Microbiology Laboratory. Clin Microbiol Rev 2020; 33:33/4/e00053-19. [PMID: 32907806 DOI: 10.1128/cmr.00053-19] [Citation(s) in RCA: 138] [Impact Index Per Article: 27.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
This review provides a state-of-the-art description of the performance of Sanger cycle sequencing of the 16S rRNA gene for routine identification of bacteria in the clinical microbiology laboratory. A detailed description of the technology and current methodology is outlined with a major focus on proper data analyses and interpretation of sequences. The remainder of the article is focused on a comprehensive evaluation of the application of this method for identification of bacterial pathogens based on analyses of 16S multialignment sequences. In particular, the existing limitations of similarity within 16S for genus- and species-level differentiation of clinically relevant pathogens and the lack of sequence data currently available in public databases is highlighted. A multiyear experience is described of a large regional clinical microbiology service with direct 16S broad-range PCR followed by cycle sequencing for direct detection of pathogens in appropriate clinical samples. The ability of proteomics (matrix-assisted desorption ionization-time of flight) versus 16S sequencing for bacterial identification and genotyping is compared. Finally, the potential for whole-genome analysis by next-generation sequencing (NGS) to replace 16S sequencing for routine diagnostic use is presented for several applications, including the barriers that must be overcome to fully implement newer genomic methods in clinical microbiology. A future challenge for large clinical, reference, and research laboratories, as well as for industry, will be the translation of vast amounts of accrued NGS microbial data into convenient algorithm testing schemes for various applications (i.e., microbial identification, genotyping, and metagenomics and microbiome analyses) so that clinically relevant information can be reported to physicians in a format that is understood and actionable. These challenges will not be faced by clinical microbiologists alone but by every scientist involved in a domain where natural diversity of genes and gene sequences plays a critical role in disease, health, pathogenicity, epidemiology, and other aspects of life-forms. Overcoming these challenges will require global multidisciplinary efforts across fields that do not normally interact with the clinical arena to make vast amounts of sequencing data clinically interpretable and actionable at the bedside.
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12
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Yu SY, Guo LN, Xiao M, Zhou ML, Yuan Y, Wang Y, Zhang L, Sun TS, Ning YT, Jia PY, Kang W, Kong F, Chen SCA, Zhao Y, Xu YC. Clinical and Microbiological Characterization of Invasive Pulmonary Aspergillosis Caused by Aspergillus lentulus in China. Front Microbiol 2020; 11:1672. [PMID: 32849346 PMCID: PMC7399017 DOI: 10.3389/fmicb.2020.01672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 06/25/2020] [Indexed: 12/24/2022] Open
Abstract
Invasive aspergillosis (IA) due to Aspergillus lentulus is associated with high mortality. In this study, we investigated the clinical and microbiological characteristics of 6 fatal cases of proven or probable IA caused by A. lentulus in China. Underlying immunosuppression, prior antifungal exposure, and intensive care unit (ICU) hospitalization were important risk factors for invasive A. lentulus infection. Phenotypic differences were observed for A. lentulus isolates including slower growth, reduced sporulation, and inability to grow at 48°C, compared with Aspergillus fumigatus complex. ITS sequencing was unable to distinguish A. lentulus from A. fumigatus, but sequencing of the benA, CaM, and rod A loci enabled reliable distinction of these closely related species. Phylogenetic analysis further confirmed that the ITS region had little variation within the Aspergillus section Fumigati while the benA gene offered the highest intraspecific discrimination. Microsatellite typing results revealed that only loci on chromosomes 1, 3, 5, and 6b generated detectable amplicons for identification. All A. lentulus isolates showed in vitro resistance to multiple antifungal drugs including amphotericin B (MIC range 4 to 8 μg/ml), itraconazole (MIC 2 μg/ml), voriconazole (MIC of 4–16 μg/ml), and posaconazole (MIC of 0.5–1 μg/ml). However, MECs for the echinocandin drugs ranged from 0.03–0.25, ≤0.008–0.015, and ≤0.015–0.03 μg/ml for caspofungin, micafungin, and anidulafungin, respectively. A. lentulus is an emerging fungal pathogen in China, causing fatal disease, and clinicians as well as laboratories should be alert to their increasing presence.
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Affiliation(s)
- Shu-Ying Yu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Li-Na Guo
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Meng-Lan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Ying Yuan
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Yao Wang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Li Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Tian-Shu Sun
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.,Department of Central Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ya-Ting Ning
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Pei-Yao Jia
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Wei Kang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR -New South Wales Health Pathology, The University of Sydney, Westmead, NSW, Australia
| | - Sharon C-A Chen
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR -New South Wales Health Pathology, The University of Sydney, Westmead, NSW, Australia
| | - Yanan Zhao
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, United States.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, United States
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
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Li Y, Chen X, Zhang Z, Wang L, Wang J, Zeng J, Yang J, Lu B. Microbiological and clinical characteristics of Streptococcus gallolyticus subsp. pasteurianus infection in China. BMC Infect Dis 2019; 19:791. [PMID: 31500570 PMCID: PMC6734276 DOI: 10.1186/s12879-019-4413-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/27/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Infections by Streptococcus gallolyticus subsp. pasteurianus (SGSP) is often underestimated. Herein, the epidemiological features and resistant characteristics of SGSP in mainland China are characterized to enable a better understanding of its role in clinical infections. METHODS In the present work, 45 SGSP isolates were collected from the samples of bloodstream, urine, aseptic body fluid, and fetal membrane/placenta from patients in 8 tertiary general hospitals of 6 cities/provinces in China from 2011 to 2017. The identification of all isolates was performed using traditional biochemical methods, 16S rRNA and gyrB sequencing, followed by the characterization of their antibiotic resistance profiling and involved genes. RESULTS Among 34 non-pregnancy-related patients, 4 (4/34,11.8%) patients had gastrointestinal cancer, 10 (10/34, 29.4%) patients had diabetes, and one patient had infective endocarditis. Moreover, 11 cases of pregnant women were associated with intrauterine infection (9/11, 81.2%) and urinary tract infection (1/11, 9.1%), respectively. Except one, all other SGSP isolates were correctly identified by the BD Phoenix automated system. We found that all SGSP isolates were phenotypically susceptible to penicillin, ampicillin, cefotaxime, meropenem, and vancomycin. Forty strains (40/45, 88.9%) were both erythromycin and clindamycin-resistant, belonging to the cMLSB phenotype, and the majority of them carried erm(B) gene (39/40, 97.5%). Although the cMLSB/erm(B) constituted the most frequently identified phenotype/genotype combination (25/40, 62.5%) among all erythromycin-resistant cMLSB isolates, erm(B)/erm(A), erm(B)/mef(A/E), and erm(B)/erm(T) was detected in 7, 4, and 3 isolates, respectively. Furthermore, 43 strains (43/45, 95.6%) were tetracycline-resistant, and out of these, 39 strains (39/45, 86.7%) carried tet(L), 27(27/45, 60.0%) strains carried tet(O), and 7 (7/45, 15.6%) strains carried tet(M), alone or combined, respectively. All erythromycin-resistant isolates were also resistant to tetracycline. CONCLUSIONS It is important to study and draw attention on SGSP, an underreported opportunistic pathogen targeting immunodeficient populations, notably elderly subjects, pregnant women and neonates.
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Affiliation(s)
- Yi Li
- Department of Laboratory Medicine, Henan Provincial People's Hospital, Zhengzhou, 450003, China
| | - Xingchun Chen
- Department of Laboratory Medicine, People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Zhijun Zhang
- Department of Laboratory Medicine, Tai'an City Central Hospital (Tai'an), Shandong, 271016, China
| | - Lijun Wang
- Department of Laboratory Medicine, Beijing Tsinghua Chang Gung Hospital, Tsinghua University, Beijing, 102218, China
| | - Junrui Wang
- Department of clinical laboratory, Affiliated hospital of Inner Mongolia medical university, Hohhot, 010050, China
| | - Ji Zeng
- Department of Laboratory Medicine, Wuhan Pu Ai Hospital of Huazhong University of Science and Technology, Wuhan, 430034, China
| | - Junwen Yang
- Department of Laboratory Medicine, Zhengzhou children's hospital, Zhengzhou, 450018, China
| | - Binghuai Lu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, No 2, East Yinghua Road, Chaoyang District, Beijing, 100029, China. .,Center for Respiratory Diseases, China-Japan Friendship Hospital, No 2, East Yinghua Road, Chaoyang District, Beijing, 100029, China. .,National Clinical Research Center of Respiratory Diseases, No 2, East Yinghua Road, Chaoyang District, Beijing, 100029, China.
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14
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Abstract
S. pseudopneumoniae is an overlooked pathogen emerging as the causative agent of lower-respiratory-tract infections and associated with chronic obstructive pulmonary disease (COPD) and exacerbation of COPD. However, much remains unknown on its clinical importance and epidemiology, mainly due to the lack of specific markers to distinguish it from S. pneumoniae. Here, we provide a new molecular marker entirely specific for S. pseudopneumoniae and offer a comprehensive view of the virulence and colonization genes found in this species. Finally, our results pave the way for further studies aiming at understanding the pathogenesis and epidemiology of S. pseudopneumoniae. Streptococcus pseudopneumoniae is a close relative of the major human pathogen S. pneumoniae. It is increasingly associated with lower-respiratory-tract infections (LRTI) and a high prevalence of antimicrobial resistance (AMR). S. pseudopneumoniae is difficult to identify using traditional typing methods due to similarities with S. pneumoniae and other members of the mitis group (SMG). Using whole-genome sequencing of LRTI isolates and a comparative genomic approach, we found that a large number of pneumococcal virulence and colonization genes are present in the core S. pseudopneumoniae genome. We also reveal an impressive number of novel surface-exposed proteins encoded by the genome of this species. In addition, we propose a new and entirely specific molecular marker useful for the identification of S. pseudopneumoniae. Phylogenetic analyses of S. pseudopneumoniae show that specific clades are associated with allelic variants of core proteins. Resistance to tetracycline and macrolides, the two most common types of resistance, were found to be encoded by Tn916-like integrating conjugative elements and Mega-2. Overall, we found a tight association of genotypic determinants of AMR and phenotypic AMR with a specific lineage of S. pseudopneumoniae. Taken together, our results shed light on the distribution in S. pseudopneumoniae of genes known to be important during invasive disease and colonization and provide insight into features that could contribute to virulence, colonization, and adaptation.
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15
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Heine AC, García S, Barberis C, Vay C, E. Mollerach M, Bonofiglio L, Famiglietti Á. Identificación y sensibilidad a los antimicrobianos de aislados de estreptococos del grupo viridans provenientes de pacientes internados en un hospital universitario de la ciudad de Buenos Aires. Rev Argent Microbiol 2019; 51:26-31. [DOI: 10.1016/j.ram.2018.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 01/25/2018] [Accepted: 03/20/2018] [Indexed: 11/27/2022] Open
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16
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Su TY, Lee MH, Huang CT, Liu TP, Lu JJ. The clinical impact of patients with bloodstream infection with different groups of Viridans group streptococci by using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Medicine (Baltimore) 2018; 97:e13607. [PMID: 30558035 PMCID: PMC6320099 DOI: 10.1097/md.0000000000013607] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The accuracy of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) for identifying viridans group streptococcus (VGS) was improving. However, the clinical impact of identifying VGS had not been well recognized. Our study had comprehensively studied the clinical manifestations and outcome of VGS blood stream infection by using MALDI-TOF MS for identification.This retrospective study enrolled 312 adult patients with a monomicrobial blood culture positive for VGS. Blood culture was examined through MALDI-TOF MS.The most common VGS species were the Streptococcus anginosus group (38.8%) and Streptococcus mitis group (22.8%). Most species showed resistance to erythromycin (35.6%), followed by clindamycin (25.3%) and penicillin (12.5%). Skin and soft tissue infection and biliary tract infection were significantly related to S. anginosus group bacteremia (P = .001 and P = .005, respectively). S. mitis group bacteremia was related to infective endocarditis and bacteremia with febrile neutropenia (P = .005 and P < .001, respectively). Infective endocarditis was also more likely associated with S. sanguinis group bacteremia (P = .009). S. anginosus group had less resistance rate to ampicillin, erythromycin, clindamycin, and ceftriaxone (P = .019, <.001, .001, and .046, respectively). A more staying in intensive care unit, underlying solid organ malignancy, and a shorter treatment duration were independent risk factors for 30-day mortality. This study comprehensively evaluated different VGS group and their clinical manifestations, infection sources, concomitant diseases, treatments, and outcomes. Categorizing VGS into different groups by MALDI-TOF MS could help clinical physicians well understand their clinical presentations.
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Affiliation(s)
- Ting-Yi Su
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine
| | - Ming-Hsun Lee
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine
| | - Ching-Tai Huang
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine
| | - Tsui-Ping Liu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
| | - Jang-Jih Lu
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Linkou
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan
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17
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Huang YL, Sun QL, Li JP, Hu YY, Zhou HW, Zhang R. Evaluation of an in-house MALDI-TOF MS rapid diagnostic method for direct identification of micro-organisms from blood cultures. J Med Microbiol 2018; 68:41-47. [PMID: 30418107 DOI: 10.1099/jmm.0.000866] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Bloodstream infections are major causes of morbidity and mortality among hospitalized patients worldwide. Early identification of micro-organisms from blood culture can facilitate earlier optimization of treatment. The objective of this study was to assess an in-house method based on a new matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) platform (Clin-TOF MS) for direct organism identification. METHODOLOGY We studied the performance of the in-house method for direct identification and the conventional sub-culture method in parallel. Identification from subcultures was analysed with Bruker MS as the reference method. RESULTS A total of 666 blood cultures with a single micro-organism that flagged positive after no more than a 3-day incubation period were collected. The identification accuracy of the in-house Clin-TOF MS method for direct identification and the sub-culture method was 88.6 and 100 %, respectively. The in-house method exhibited better performance for Gram-negative bacteria than for Gram-positive bacteria (93.3 vs 81.6 %). The accuracy rate for anaerobes was 100 % (3/3). The lowest accurate identification rate was for yeast; this was only 20 %. Lytic Anaerobic/F (LAF) and Plus Aerobic/F (PAF) provided the highest accurate identification rates, and it was noteworthy that the accuracy rate for FAN Aerobic (FA) was 82 %, which is higher than previously reported and showed that the method was effective. CONCLUSION Our study provides an effective sample preparation method for the direct identification of pathogens from positive blood culture vials via Clin-TOF MS at a very low cost of about $0.5 per sample and with a short turnaround time of about 20 min. This will help clinicians make precise diagnoses and provide targeted prescriptions, reducing the risk of the potential development of resistance.
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Affiliation(s)
- Yong-Lu Huang
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Qiao-Ling Sun
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Jia-Ping Li
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Yan-Yan Hu
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Hong-Wei Zhou
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
| | - Rong Zhang
- Department of Clinical Laboratory, School of Medicine, Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, PR China
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18
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Kocurek KI, Stones L, Bunch J, May RC, Cooper HJ. Top-Down LESA Mass Spectrometry Protein Analysis of Gram-Positive and Gram-Negative Bacteria. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2066-2077. [PMID: 28681361 PMCID: PMC5594050 DOI: 10.1007/s13361-017-1718-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 05/15/2017] [Accepted: 05/16/2017] [Indexed: 05/21/2023]
Abstract
We have previously shown that liquid extraction surface analysis (LESA) mass spectrometry (MS) is a technique suitable for the top-down analysis of proteins directly from intact colonies of the Gram-negative bacterium Escherichia coli K-12. Here we extend the application of LESA MS to Gram-negative Pseudomonas aeruginosa PS1054 and Gram-positive Staphylococcus aureus MSSA476, as well as two strains of E. coli (K-12 and BL21 mCherry) and an unknown species of Staphylococcus. Moreover, we demonstrate the discrimination between three species of Gram-positive Streptococcus (Streptococcus pneumoniae D39, and the viridans group Streptococcus oralis ATCC 35037 and Streptococcus gordonii ATCC35105), a recognized challenge for matrix-assisted laser desorption ionization time-of-flight MS. A range of the proteins detected were selected for top-down LESA MS/MS. Thirty-nine proteins were identified by top-down LESA MS/MS, including 16 proteins that have not previously been observed by any other technique. The potential of LESA MS for classification and characterization of novel species is illustrated by the de novo sequencing of a new protein from the unknown species of Staphylococcus. Graphical Abstract ᅟ.
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Affiliation(s)
- Klaudia I Kocurek
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Leanne Stones
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Josephine Bunch
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK
- School of Pharmacy, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Robin C May
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Helen J Cooper
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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19
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Zhou M, Yang Q, Kudinha T, Sun L, Zhang R, Liu C, Yu S, Xiao M, Kong F, Zhao Y, Xu YC. An Improved In-house MALDI-TOF MS Protocol for Direct Cost-Effective Identification of Pathogens from Blood Cultures. Front Microbiol 2017; 8:1824. [PMID: 29033904 PMCID: PMC5625089 DOI: 10.3389/fmicb.2017.01824] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/06/2017] [Indexed: 11/23/2022] Open
Abstract
Background: Bloodstream infection is a major cause of morbidity and mortality in hospitalized patients worldwide. Delays in the identification of microorganisms often leads to a poor prognosis. The application of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) directly to blood culture (BC) broth can potentially identify bloodstream infections earlier, and facilitate timely management. Methods: We developed an “in-house” (IH) protocol for direct MALDI-TOF MS based identification of organisms in positive BCs. The IH protocol was initially evaluated and improved with spiked BC samples, and its performance was compared with the commercial Sepsityper™ kit using both traditional and modified cut-off values. We then studied in parallel the performance of the IH protocol and the colony MS identifications in positive clinical BC samples using only modified cut-off values. All discrepancies were investigated by “gold standard” of gene sequencing. Results: In 54 spiked BC samples, the IH method showed comparable results with Sepsityper™ after applying modified cut-off values. Specifically, accurate species and genus level identification was achieved in 88.7 and 3.9% of all the clinical monomicrobial BCs (284/301, 94.4%), respectively. The IH protocol exhibited superior performance for Gram negative bacteria than for Gram positive bacteria (92.8 vs. 82.4%). For anaerobes and yeasts, accurate species identification was achieved in 80.0 and 90.0% of the cases, respectively. For polymicrobial cultures (17/301, 5.6%), MALDI-TOF MS correctly identified a single species present in all the polymicrobial BCs under the Standard mode, while using the MIXED method, two species were correctly identified in 52.9% of the samples. Comparisons based on BC bottle type, showed that the BACTEC™ Lytic/10 Anaerobic/F culture vials performed the best. Conclusion: Our study provides a novel and effective sample preparation method for MALDI-TOF MS direct identification of pathogens from positive BC vials, with a lower cost ($1.5 vs. $ 7) albeit a slightly more laborious extracting process (an extra 15 min) compared with Sepsityper™ kit.
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Affiliation(s)
- Menglan Zhou
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Timothy Kudinha
- Charles Sturt University, Leeds Parade, Orange, NSW, Australia
| | - Liying Sun
- Department of Clinical Laboratory, Peking University First Hospital, Beijing, China
| | - Rui Zhang
- Becton Dickinson Medical Devices Company, Shanghai, China
| | - Chang Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Shuying Yu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead Hospital, Westmead, NSW, Australia
| | - Yupei Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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Pathogenicity of Virulent Species of Group C Streptococci in Human. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2017; 2017:9509604. [PMID: 28694832 PMCID: PMC5485279 DOI: 10.1155/2017/9509604] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 04/24/2017] [Accepted: 05/21/2017] [Indexed: 11/18/2022]
Abstract
Group C streptococci (GCS) are livestock pathogens and they often cause zoonotic diseases in humans. They are Gram-positive, in mostly β-hemolytic and facultative anaerobes. Because of their close evolutionary kinship with group A streptococci (GAS), GCS share many common virulence factors with GAS and cause a similar range of diseases. Due to the exchange of genetic material with GAS, GCS belong to bacteria that are difficult to be distinguished from group A streptococci; GCS are often treated in microbiological diagnostics as contamination of the culture. This report focuses mainly on the pathogenicity of virulent species of GCS and their association with human diseases. The condition that is most frequently quoted is pharyngitis. In this paper, the virulence factors have also been mentioned and an interesting link has been made between GCS and the pathogenesis of rheumatic diseases among the native people of India and Aboriginal populations.
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Marín M, Cercenado E, Sánchez-Carrillo C, Ruiz A, Gómez González Á, Rodríguez-Sánchez B, Bouza E. Accurate Differentiation of Streptococcus pneumoniae from other Species within the Streptococcus mitis Group by Peak Analysis Using MALDI-TOF MS. Front Microbiol 2017; 8:698. [PMID: 28487677 PMCID: PMC5403922 DOI: 10.3389/fmicb.2017.00698] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 04/05/2017] [Indexed: 11/13/2022] Open
Abstract
Despite the benefits of MALDI-TOF MS technology (Matrix-Assisted Laser Desorption-Ionization Time-Of-Flight Mass Spectrometry) reported worldwide and the continuous improving of the available databases, discrimination between Streptococcus pneumoniae and closely related species within the Streptococcus mitis group (SMG) using this methodology has been suboptimal. However, the accurate identification at the species level of this group of microorganisms is important for the appropriate management of infected patients. In this study, 216 SMG isolates -101 S. pneumoniae and 115 corresponding to 7 non-pneumococcal species within this group- were analyzed. All the isolates had been previously identified by conventional methods (optochin and bile solubility tests) and non-pneumococcal isolates were confirmed by sequence analysis (sodA and plys genes) when required. The isolates were also identified with the MALDI Biotyper 3.1 (Bruker Daltonics, Bremen, Germany) using an updated library containing 6,903 Main Spectra Profiles (MSPs). All the analyzed S. pneumoniae were correctly identified with MALDI-TOF MS at species level using the most updated database and all the non-pneumococcal SMG isolates were also identified at the group level. Several peaks (4,964.32, 6,888.90, and 9,516.46 m/z) have been found to be specific of S. pneumoniae, whilst a different set of peaks have proved to be present only in S. mitis (6,839.07 m/z) and S. oralis (5,297.61, 5822.53, and 6,839.07 m/z). Peak analysis allowed correct species assignment of 101/101 S. pneumoniae isolates (100%) and 102/105 S. mitis/oralis isolates (97.1%). Thus, the implementation of MALDI-TOF MS plus peak analysis for the identification of this group of microorganisms may provide precise species-level information that will allow the early implementation of directed antibiotic therapy.
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Affiliation(s)
- Mercedes Marín
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)Madrid, Spain.,Medicine Department, Faculty of Medicine, Universidad Complutense de MadridMadrid, Spain
| | - Emilia Cercenado
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)Madrid, Spain.,Medicine Department, Faculty of Medicine, Universidad Complutense de MadridMadrid, Spain
| | - Carlos Sánchez-Carrillo
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain
| | - Adrián Ruiz
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain
| | | | - Belén Rodríguez-Sánchez
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)Madrid, Spain
| | - Emilio Bouza
- Clinical Microbiology and Infectious Diseases Department, Hospital General Universitario Gregorio MarañónMadrid, Spain.,Instituto de Investigación Sanitaria Gregorio MarañónMadrid, Spain.,CIBER de Enfermedades Respiratorias (CIBERES CB06/06/0058)Madrid, Spain.,Medicine Department, Faculty of Medicine, Universidad Complutense de MadridMadrid, Spain
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