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Emgård M, Andersson M, Gonzales-Siles L, Msuya SE, Nyombi BM, Nordén R, Muro F, Lindh M, Andersson R, Skovbjerg S. Co-occurrence of bacteria and viruses and serotype distribution of Streptococcus pneumoniae in the nasopharynx of Tanzanian children below 2 years of age following introduction of the PCV13. Front Public Health 2024; 12:1298222. [PMID: 38317802 PMCID: PMC10839969 DOI: 10.3389/fpubh.2024.1298222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
Introduction Pneumococcal conjugate vaccines have reduced severe disease attributed to vaccine-type pneumococci in children. However, the effect is dependent on serotype distribution in the population and disease development may be influenced by co-occurrence of viral and bacterial pathogens in the nasopharynx. Methods Following introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) in Tanzania we performed repeated cross-sectional surveys, including 775 children below 2 years of age attending primary healthcare centers. All children were sampled from nasopharynx and pneumococci were detected by single-target PCR. Pneumococcal serotypes/groups and presence of viruses and other bacteria were determined by two multiplex PCR assays. Results The prevalence of PCV13 vaccine-type pneumococci decreased by 50%, but residual vaccine-types were still detected in 21% of the children 2 years after PCV13 introduction. An increase in the non-vaccine-type 15 BC was observed. Pneumococci were often co-occurring with Haemophilus influenzae, and detection of rhino/enterovirus was associated with higher pneumococcal load. Discussion We conclude that presence of residual vaccine-type and emerging non-vaccine-type pneumococci in Tanzanian children demand continued pneumococcal surveillance. High co-occurrence of viral and bacterial pathogens may contribute to the disease burden and indicate the need of multiple public health interventions to improve child health in Tanzania.
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Affiliation(s)
- Matilda Emgård
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Pediatrics, Queen Silvia Children’s Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Maria Andersson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Lucia Gonzales-Siles
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Sia E. Msuya
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
| | - Balthazar M. Nyombi
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
| | - Rickard Nordén
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Florida Muro
- Institute of Public Health, Kilimanjaro Christian Medical University College (KCMUCo), Moshi, Tanzania
- Department of Community Medicine, Kilimanjaro Christian Medical Center (KCMC), Moshi, Tanzania
| | - Magnus Lindh
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Rune Andersson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Susann Skovbjerg
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Center for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Gothenburg, Sweden
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Bin Hafeez A, Pełka K, Worobo R, Szweda P. In Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates. Int J Mol Sci 2024; 25:666. [PMID: 38203838 PMCID: PMC10780176 DOI: 10.3390/ijms25010666] [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: 12/11/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.
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Affiliation(s)
- Ahmer Bin Hafeez
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Karolina Pełka
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
| | - Randy Worobo
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA;
| | - Piotr Szweda
- Department of Pharmaceutical Technology and Biochemistry, Faculty of Chemistry, Gdańsk University of Technology, Ul. G. Narutowicza 11/12, 80-233 Gdańsk, Poland; (A.B.H.); (K.P.)
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Jaén-Luchoro D, Kahnamouei A, Yazdanshenas S, Lindblom A, Samuelsson E, Åhrén C, Karami N. Comparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing E. coli Isolates from Patients with Recurrent and Sporadic Urinary Tract Infections. Microorganisms 2023; 11:1622. [PMID: 37512795 PMCID: PMC10384980 DOI: 10.3390/microorganisms11071622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/31/2023] [Accepted: 06/17/2023] [Indexed: 07/30/2023] Open
Abstract
The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is a major threat to human health. ESBL-E. coli sequence type (ST) 131 is the dominating clone worldwide, especially its subclade C2. Patients developing recurrent UTI (RUTI) due to ST131 subclade C2 appear to have an increased risk of recurrent infections. We have thus compared the whole genome of ST131 subclade C2 isolates from 14 patients with RUTI to those from 14 patients with sporadic UTI (SUTI). We aimed to elucidate if isolates causing RUTI can be associated with specific genomic features. Paired isolates from patients with RUTI were identical, presenting 2-18 single nucleotide polymorphism (SNP) differences for all six patients investigated. Comparative genomic analyses, including virulence factors, antibiotic resistance, pangenome and SNP analyses did not find any pattern associated with isolates causing RUTI. Despite extensive whole genome analyses, an increased risk of recurrences seen in patients with UTI due to ST131 subclade C2 isolates could not be explained by bacterial genetic differences in the two groups of isolates. Hence, additional factors that could aid in identifying bacterial properties contributing to the increased risk of RUTI due to ESBL-E. coli ST131 subclade C2 remains to be explored.
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Affiliation(s)
- Daniel Jaén-Luchoro
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
| | - Arezou Kahnamouei
- Department of Life Sciences and Systems Biology, University of Turin, 10124 Turin, Italy
| | - Shora Yazdanshenas
- Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, 41345 Gothenburg, Sweden
| | - Anna Lindblom
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
- Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, 41345 Gothenburg, Sweden
| | - Emma Samuelsson
- Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Region Västra Götaland, 41345 Gothenburg, Sweden
| | - Christina Åhrén
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
- Swedish Strategic Program against Antimicrobial Resistance (Strama), Region Västra Götaland, 40544 Gothenburg, Sweden
| | - Nahid Karami
- Institute of Biomedicine, Department of Infectious Diseases, University of Gothenburg, 40530 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, 40530 Gothenburg, Sweden
- Sahlgrenska University Hospital, Department of Clinical Microbiology, Region Västra Götaland, 41345 Gothenburg, Sweden
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Pauter-Iwicka K, Railean V, Złoch M, Pomastowski P, Szultka-Młyńska M, Błońska D, Kupczyk W, Buszewski B. Characterization of the salivary microbiome before and after antibiotic therapy via separation technique. Appl Microbiol Biotechnol 2023; 107:2515-2531. [PMID: 36843196 PMCID: PMC10033590 DOI: 10.1007/s00253-023-12371-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 02/28/2023]
Abstract
In the present research, the MALDI-TOF MS technique was applied as a tool to rapidly identify the salivary microbiome. In this fact, it has been monitored the changes occurred in molecular profiles under different antibiotic therapy. Significant changes in the composition of the salivary microbiota were noticed not only in relation to the non antibiotic (non-AT) and antibiotic treatment (AT) groups, but also to the used media, the antibiotic therapy and co-existed microbiota. Each antibiotic generates specific changes in molecular profiles. The highest number of bacterial species was isolated in the universal culture medium (72%) followed by the selective medium (48% and 38%). In the case of non-AT patients, the prevalence of Streptococcus salivarius (25%), Streptococcus vestibularis (19%), Streptococcus oralis (13%), and Staphylococcus aureus (6%) was identified while in the case of AT, Streptococcus salivarius (11%), Streptococcus parasanguinis (11%), Staphylococcus epidermidis (12%), Enterococcus faecalis (9%), Staphylococcus hominis (8%), and Candida albicans (6%) were identified. Notable to specified that the Candida albicans was noticed only in AT samples, indicating a negative impact on the antibiotic therapy. The accuracy of the MALDI-TOF MS technique was performed by the 16S rRNA gene sequencing analysis-as a reference method. Conclusively, such an approach highlighted in the present study can help in developing the methods enabling a faster diagnosis of disease changes at the cellular level before clinical changes occur. Once the MALDI tool allows for the distinguishing of the microbiota of non-AT and AT, it may enable to monitor the diseases treatment and develop a treatment regimen for individual patients in relation to each antibiotic. KEY POINTS: The salivary microbiota of antibiotic-treated patients was more bacteria variety MALDI-TOF MS is a promising tool for recording of reproducible molecular profiles Our data can allow to monitor the treatment of bacterial diseases for patients.
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Affiliation(s)
- Katarzyna Pauter-Iwicka
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Viorica Railean
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
- Department of Infectious, Invasive Diseases and Veterinary Administration, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Gagarina 7, 87-100, Toruń, Poland
| | - Michał Złoch
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Paweł Pomastowski
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Małgorzata Szultka-Młyńska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
| | - Dominika Błońska
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland
| | - Wojciech Kupczyk
- Department of General, Gastroenterological&Oncological Surgery Collegium Medicum, Nicolaus Copernicus University, Torun, Poland
| | - Bogusław Buszewski
- Department of Environmental Chemistry and Bioanalytics, Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100, Torun, Poland.
- Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Wilenska 4, 87-100, Torun, Poland.
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Juscamayta-López E, Valdivia F, Soto MP, Nureña B, Horna H. A pangenome approach-based loop-mediated isothermal amplification assay for the specific and early detection of Bordetella pertussis. Sci Rep 2023; 13:4356. [PMID: 36928221 PMCID: PMC10018623 DOI: 10.1038/s41598-023-29773-9] [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: 10/07/2022] [Accepted: 02/10/2023] [Indexed: 03/18/2023] Open
Abstract
Despite widespread vaccination, Bordetella pertussis continues to cause pertussis infections worldwide, leaving infants at the highest risk of severe illness and death, while people around them are likely the main sources of infection and rapidly spread the disease. Rapid and less complex molecular testing for the specific and timely diagnosis of pertussis remains a challenge that could help to prevent the disease from worsening and prevent its transmission. We aimed to develop and validate a colorimetric loop-mediated isothermal amplification (LAMP) assay using a new target uvrD_2 informed by the pangenome for the specific and early detection of B. pertussis. Compared to that of multitarget quantitative polymerase chain reaction (multitarget qPCR) using a large clinical DNA specimen (n = 600), the diagnostic sensitivity and specificity of the uvrD_2 LAMP assay were 100.0% and 98.6%, respectively, with a 99.7% degree of agreement between the two assays. The novel colorimetric uvrD_2 LAMP assay is highly sensitive and specific for detecting B. pertussis DNA in nasopharyngeal swabs and showed similar diagnostic accuracy to complex and high-cost multitarget qPCR, but it is faster, simpler, and inexpensive, which makes it very helpful for the reliable and timely diagnosis of pertussis in primary health care and resource-limited settings.
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Affiliation(s)
- Eduardo Juscamayta-López
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú.
- Facultad de Salud Pública y Administración (GA, AGL), Universidad Peruana Cayetano Heredia, Lima, Perú.
| | - Faviola Valdivia
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - María Pía Soto
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Brenda Nureña
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Helen Horna
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
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Pan-Genomics of Escherichia albertii for Antibiotic Resistance Profiling in Different Genome Fractions and Natural Product Mediated Intervention: In Silico Approach. Life (Basel) 2023; 13:life13020541. [PMID: 36836896 PMCID: PMC9962377 DOI: 10.3390/life13020541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Escherichia albertii is an emerging, enteric pathogen of significance. It was first isolated in 2003 from a pediatric diarrheal sample from Bangladesh. In this study, a comprehensive in silico strategy was followed to first list out antibiotic-resistant genes from core, accessory and unique genome fractions of 95 available genomes of E. albertii. Then, 56 drug targets were identified from the core essential genome. Finally, ZipA, an essential cell division protein that stabilizes the FtsZ protofilaments by cross-linking them and serves as a cytoplasmic membrane anchor for the Z ring, was selected for further downstream processing. It was computationally modeled using a threading approach, followed by virtual screening of two phytochemical libraries, Ayurvedic (n = 2103 compounds) and Traditional Chinese Medicine (n = 36,043 compounds). ADMET profiling, followed by PBPK modeling in the central body compartment, in a population of 250 non-diseased, 250 cirrhotic and 250 renally impaired people was attempted. ZINC85624912 from Chinese medicinal library showed the highest bioavailability and plasma retention. This is the first attempt to simulate the fate of natural products in the body through PBPK. Dynamics simulation of 20 ns for the top three compounds from both libraries was also performed to validate the stability of the compounds. The obtained information from the current study could aid wet-lab scientists to work on the scaffold of screened drug-like compounds from natural resources and could be useful in our quest for therapy against antibiotic-resistant E. albertii.
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Miellet WR, van Veldhuizen J, Litt D, Mariman R, Wijmenga-Monsuur AJ, Nieuwenhuijsen T, Christopher J, Thombre R, Eletu S, Bosch T, Rots NY, van Houten MA, Miller E, Fry NK, Sanders EAM, Trzciński K. A spitting image: molecular diagnostics applied to saliva enhance detection of Streptococcus pneumoniae and pneumococcal serotype carriage. Front Microbiol 2023; 14:1156695. [PMID: 37138599 PMCID: PMC10149683 DOI: 10.3389/fmicb.2023.1156695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/27/2023] [Indexed: 05/05/2023] Open
Abstract
Background Despite strong historical records on the accuracy of saliva testing, oral fluids are considered poorly suited for pneumococcal carriage detection. We evaluated an approach for carriage surveillance and vaccine studies that increases the sensitivity and specificity of pneumococcus and pneumococcal serotype detection in saliva samples. Methods Quantitative PCR (qPCR)-based methods were applied to detect pneumococcus and pneumococcal serotypes in 971 saliva samples collected from 653 toddlers and 318 adults. Results were compared with culture-based and qPCR-based detection in nasopharyngeal samples collected from children and in nasopharyngeal and oropharyngeal samples collected from adults. Optimal C q cut-offs for positivity in qPCRs were determined via receiver operating characteristic curve analysis and accuracy of different approaches was assessed using a composite reference for pneumococcal and for serotype carriage based on isolation of live pneumococcus from the person or positivity of saliva samples determined with qPCR. To evaluate the inter-laboratory reproducibility of the method, 229 culture-enriched samples were tested independently in the second center. Results In total, 51.5% of saliva samples from children and 31.8% of saliva samples from adults were positive for pneumococcus. Detection of pneumococcus by qPCR in culture-enriched saliva exhibited enhanced sensitivity and higher agreement with a composite reference compared to diagnostic culture of nasopharyngeal samples in children (Cohen's κ: 0.69-0.79 vs. 0.61-0.73) and in adults (κ: 0.84-0.95 vs. 0.04-0.33) and culture of oropharyngeal samples in adults (κ: 0.84-0.95 vs. -0.12-0.19). Similarly, detection of serotypes with qPCR in culture-enriched saliva exhibited enhanced sensitivity and higher agreement with a composite reference compared to nasopharyngeal culture in children (κ: 0.73-0.82 vs. 0.61-0.73) and adults (κ: 0.90-0.96 vs. 0.00-0.30) and oropharyngeal culture in adults (κ: 0.90-0.96 vs. -0.13 to 0.30). However, results of qPCRs targeting serotype 4, 5, and 17F and serogroups 9, 12, and 35 were excluded due to assays' lack of specificity. We observed excellent quantitative agreement for qPCR-based detection of pneumococcus between laboratories. After exclusion of serotype/serogroup-specific assays with insufficient specificity, moderate agreement (κ 0.68, 95% CI 0.58-0.77) was observed. Conclusion Molecular testing of culture-enriched saliva samples improves the sensitivity of overall surveillance of pneumococcal carriage in children and adults, but limitations of qPCR-based approaches for pneumococcal serotypes carriage detection should be considered.
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Affiliation(s)
- Willem R. Miellet
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
- Willem R. Miellet,
| | - Janieke van Veldhuizen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - David Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
| | - Rob Mariman
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Alienke J. Wijmenga-Monsuur
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Tessa Nieuwenhuijsen
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands
| | - Jennifer Christopher
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
| | - Rebecca Thombre
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
| | - Seyi Eletu
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Nynke Y. Rots
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | | | - Elizabeth Miller
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Norman K. Fry
- Respiratory and Vaccine Preventable Bacteria Reference Unit (RVPBRU), UK Health Security Agency, London, United Kingdom
- Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, United Kingdom
| | - Elisabeth A. M. Sanders
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, Netherlands
- *Correspondence: Krzysztof Trzciński,
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Tabata A, Matsumoto A, Fujimoto A, Ohkura K, Ikeda T, Oda H, Yokohata S, Kobayashi M, Tomoyasu T, Takao A, Ohkuni H, Nagamune H. Dual functions of discoidinolysin, a cholesterol-dependent cytolysin with N-terminal discoidin domain produced from Streptococcus mitis strain Nm-76. J Oral Microbiol 2022; 14:2105013. [PMID: 35937899 PMCID: PMC9351568 DOI: 10.1080/20002297.2022.2105013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Some strains of Streptococcus mitis exhibit β-hemolysis due to the β-hemolytic activity of cholesterol-dependent cytolysin (CDC). Recently, a gene encoding an atypical lectinolysin-related CDC was found in S. mitis strain Nm-76. However, the product of this gene remains uncharacterized. We aimed to characterize this atypical CDC and its molecular functions and contribution to the pathogenicity of S. mitis strain Nm-76. Methods Phylogenetic analysis of the CDC gene was conducted based on the web-deposited information. The molecular characteristics of CDC were investigated using a gene-deletion mutant strain and recombinant proteins expressed in Escherichia coli. Results The gene encoding CDC found in Nm-76 and its homolog are distributed among many S. mitis strains. This CDC is phylogenetically different from other previously characterized CDCs, such as S. mitis-derived human platelet aggregation factor (Sm-hPAF)/lectinolysin and mitilysin. Because this CDC possesses an additional N-terminal domain, including a discoidin motif, it was termed discoidinolysin (DLY). In addition to the preferential lysis of human cells, DLY displayed N-terminal domain-dependent facilitation of human erythrocyte aggregation and intercellular associations between human cells. Conclusion DLY functions as a hemolysin/cytolysin and erythrocyte aggregation/intercellular association molecule. This dual-function DLY could be an additional virulence factor in S. mitis.
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Affiliation(s)
- Atsushi Tabata
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Japan
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Airi Matsumoto
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
| | - Ai Fujimoto
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
| | - Kazuto Ohkura
- Division of Clinical Pharmacy and Pharmaceutical Sciences, Graduate School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka, Japan
| | - Takuya Ikeda
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Hiroki Oda
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Shuto Yokohata
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Miho Kobayashi
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
| | - Toshifumi Tomoyasu
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Japan
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
| | - Ayuko Takao
- Department of Oral Microbiology, School of Dental Medicine, Tsurumi University, Kanagawa, Japan
| | - Hisashi Ohkuni
- Research Institute, Health Science Research Institute East Japan Co., Ltd., Saitama, Japan
| | - Hideaki Nagamune
- Department of Bioengineering, Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University Graduate School, Tokushima, Japan
- Department of Biological Science and Technology, Life System, Institute of Technology and Science, Tokushima University Graduate School, Tokushima, Japan
- Department of Bioengineering, Faculty of Bioscience and Bioindustry, Tokushima University, Tokushima, Japan
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Karthik K, Anbazhagan S, Chitra MA, Sridhar R. First report of the whole genome of Moraxella bovoculi genotype 1 from India and comparative genomics of Moraxella bovoculi to identify genotype-specific markers. Arch Microbiol 2022; 204:663. [PMID: 36201053 DOI: 10.1007/s00203-022-03276-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/02/2022]
Abstract
Moraxella bovoculi has been isolated frequently from cattle with Infectious bovine keratoconjunctivitis (IBK). Two diverse genotypes of M. bovoculi, 1 and 2 were identified based on whole genome sequence analysis. It is essential to discriminate between the two genotypes to frame prevention and control measures. The whole genome of M. bovoculi TN7 was sequenced and compared to other M. bovoculi strains available in the NCBI database. M. bovoculi TN7 was found to be genotype 1, had an RTX toxin operon and pilA gene that are the known virulence factors in related Moraxella sp., but lacked antimicrobial resistance genes. M. bovoculi was found to have an open pangenome with 4051 (75.31%) accessory genes, and the addition of each new genome adds 18 genes to the pangenome. Comparison of pilin protein amino acid sequences revealed three new sequence types. Furthermore, the presence of linx, nagL, swrC and mdtA genes was found to be genotype 1 specific, whereas hyaD, garR, gbsA, yhdG, gabT, iclR, higB2, hmuU, hmuT and hemS were found only in genotype 2. Polymerase Chain Reaction (PCR) primers were designed and evaluated on strain TN7 plus seven additional strains accessible to us that had not been whole genome sequenced. This initial evaluation of the designed primers for the linX and hyaD genes produced the expected banding patterns on PCR gels for genotypes 1 and 2, respectively, among the 8 strains. The genotype-specific genes identified in this study can be used as markers for accurate diagnosis of genotype 1 isolates and this can aid in the development of autogenous or other molecular vaccines for treatment of infectious bovine keratoconjunctivitis (IBK) in resource-limited research settings.
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Affiliation(s)
- Kumaragurubaran Karthik
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India. .,Department of Veterinary Microbiology, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Udumalpet, Tamil Nadu, India.
| | - Subbaiyan Anbazhagan
- ICMR-National Animal Resource Facility for Biomedical Research, Hyderabad, Telangana, 500078, India
| | - Murugesan Ananda Chitra
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
| | - Ramaswamy Sridhar
- Central University Laboratory, Tamil Nadu Veterinary and Animal Sciences University, Chennai, Tamil Nadu, 600051, India
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10
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Tobuse AJ, Ang CW, Yeong KY. Modern vaccine development via reverse vaccinology to combat antimicrobial resistance. Life Sci 2022; 302:120660. [PMID: 35642852 DOI: 10.1016/j.lfs.2022.120660] [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: 03/25/2022] [Revised: 05/02/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
Abstract
With the continuous evolution of bacteria, the global antimicrobial resistance health threat is causing millions of deaths yearly. While depending on antibiotics as a primary treatment has its merits, there are no effective alternatives thus far in the pharmaceutical market against some drug-resistant bacteria. In recent years, vaccinology has become a key topic in scientific research. Combining with the growth of technology, vaccine research is seeing a new light where the process is made faster and more efficient. Although less discussed, bacterial vaccine is a feasible strategy to combat antimicrobial resistance. Some vaccines have shown promising results with good efficacy against numerous multidrug-resistant strains of bacteria. In this review, we aim to discuss the findings from studies utilizing reverse vaccinology for vaccine development against some multidrug-resistant bacteria, as well as provide a summary of multi-year bacterial vaccine studies in clinical trials. The advantages of reverse vaccinology in the generation of new bacterial vaccines are also highlighted. Meanwhile, the limitations and future prospects of bacterial vaccine concludes this review.
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Affiliation(s)
- Asuka Joy Tobuse
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia
| | - Chee Wei Ang
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia
| | - Keng Yoon Yeong
- School of Science, Monash University Malaysia Campus, Jalan Lagoon Selatan, Bandar Sunway 47500, Selangor, Malaysia.
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11
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Lee JI, Kim SS, Kang DH. Development of DNA probes to detect Cronobacter sakazakii based on comparative genomics and its application in food samples. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108853] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Edwards S, León-Zayas R, Ditter R, Laster H, Sheehan G, Anderson O, Beattie T, Mellies JL. Microbial Consortia and Mixed Plastic Waste: Pangenomic Analysis Reveals Potential for Degradation of Multiple Plastic Types via Previously Identified PET Degrading Bacteria. Int J Mol Sci 2022; 23:5612. [PMID: 35628419 PMCID: PMC9146961 DOI: 10.3390/ijms23105612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 02/01/2023] Open
Abstract
The global utilization of single-use, non-biodegradable plastics, such as bottles made of polyethylene terephthalate (PET), has contributed to catastrophic levels of plastic pollution. Fortunately, microbial communities are adapting to assimilate plastic waste. Previously, our work showed a full consortium of five bacteria capable of synergistically degrading PET. Using omics approaches, we identified the key genes implicated in PET degradation within the consortium's pangenome and transcriptome. This analysis led to the discovery of a novel PETase, EstB, which has been observed to hydrolyze the oligomer BHET and the polymer PET. Besides the genes implicated in PET degradation, many other biodegradation genes were discovered. Over 200 plastic and plasticizer degradation-related genes were discovered through the Plastic Microbial Biodegradation Database (PMBD). Diverse carbon source utilization was observed by a microbial community-based assay, which, paired with an abundant number of plastic- and plasticizer-degrading enzymes, indicates a promising possibility for mixed plastic degradation. Using RNAseq differential analysis, several genes were predicted to be involved in PET degradation, including aldehyde dehydrogenases and several classes of hydrolases. Active transcription of PET monomer metabolism was also observed, including the generation of polyhydroxyalkanoate (PHA)/polyhydroxybutyrate (PHB) biopolymers. These results present an exciting opportunity for the bio-recycling of mixed plastic waste with upcycling potential.
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Affiliation(s)
- Sabrina Edwards
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
| | - Rosa León-Zayas
- Biology Department, Willamette University, Salem, OR 97301, USA; (R.L.-Z.); (G.S.); (O.A.)
| | - Riyaz Ditter
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
| | - Helen Laster
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
| | - Grace Sheehan
- Biology Department, Willamette University, Salem, OR 97301, USA; (R.L.-Z.); (G.S.); (O.A.)
| | - Oliver Anderson
- Biology Department, Willamette University, Salem, OR 97301, USA; (R.L.-Z.); (G.S.); (O.A.)
| | - Toby Beattie
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
| | - Jay L. Mellies
- Biology Department, Reed College, Portland, OR 97202, USA; (S.E.); (R.D.); (H.L.); (T.B.)
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13
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Kwon EA, Lee JI, Park JW, Kim SS. Application of comparative genomics in the development of DNA probes to detect Bacillus cereus and Bacillus subtilis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.110996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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14
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Choi HJ, Shin D, Shin M, Yun B, Kang M, Yang HJ, Jeong DY, Kim Y, Oh S. Comparative Genomic and Functional Evaluations of Bacillus subtilis Newly Isolated from Korean Traditional Fermented Foods. Foods 2020; 9:E1805. [PMID: 33291832 PMCID: PMC7762004 DOI: 10.3390/foods9121805] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/20/2020] [Accepted: 11/28/2020] [Indexed: 01/28/2023] Open
Abstract
Many fermented foods are known to have beneficial effects on human and animal health, offering anti-aging and immunomodulatory benefits to host. Microorganisms contained in the fermented foods are known to provide metabolic products possibly improving host health. However, despite of a number of studies on the functional effects of the fermented foods, isolation and identification of the effective bacterial strains in the products are still in progress. The objective of this study was to isolate candidate functional strains in various Korean traditional fermented foods, including ganjang, gochujang, doenjang, and jeotgal, and evaluate their beneficial effects on the host, using Caenorhabditis elegans as a surrogate animal model. Among the 30 strains isolated, five Bacillus spp. were selected that increased the expression level of pmk-1, an innate immune gene of C. elegans. These strains extended the nematode lifespan and showed intestinal adhesion to the host. Based on the bioinformatic analyses of whole genome sequences and pangenomes, the five strains of Bacillus subtilis were genetically different from the strains found in East Asian countries and previously reported strains isolated from Korean fermented foods. Our findings suggest that the newly isolated B. subtilis strains can be a good candidate for probiotic with further in-depth investigation on health benefits and safety.
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Affiliation(s)
- Hye Jin Choi
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea; (H.J.C.); (M.S.)
| | - Donghyun Shin
- Department of Agricultural Convergence Technology, Jeonbuk National University, Jeonju 54896, Korea;
| | - Minhye Shin
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea; (H.J.C.); (M.S.)
| | - Bohyun Yun
- Department of Animal Science and Institute of Milk Genomics, Jeonbuk National University, Jeonju 54896, Korea;
| | - Minkyoung Kang
- Department of Functional Food and Biotechnology, Jeonju University, Jeonju 55069, Korea;
| | - Hee-Jong Yang
- Microbial Institute for Fermentation Industry, Sunchang, Jeonbuk 56048, Korea; (H.-J.Y.); (D.-Y.J.)
| | - Do-Youn Jeong
- Microbial Institute for Fermentation Industry, Sunchang, Jeonbuk 56048, Korea; (H.-J.Y.); (D.-Y.J.)
| | - Younghoon Kim
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Science, Seoul National University, Seoul 08826, Korea; (H.J.C.); (M.S.)
| | - Sangnam Oh
- Department of Functional Food and Biotechnology, Jeonju University, Jeonju 55069, Korea;
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15
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Kim S, Kim S. Bacterial pathogen detection by conventional culture‐based and recent alternative (polymerase chain reaction, isothermal amplification, enzyme linked immunosorbent assay, bacteriophage amplification, and gold nanoparticle aggregation) methods in food samples: A review. J Food Saf 2020. [DOI: 10.1111/jfs.12870] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Sang‐Oh Kim
- Department of Plant and Food Sciences Sangmyung University Cheonan Republic of Korea
| | - Sang‐Soon Kim
- Department of Food Engineering Dankook University Cheonan Republic of Korea
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16
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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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