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Päll T, Abroi A, Avi R, Niglas H, Shablinskaja A, Pauskar M, Jõgeda EL, Soeorg H, Kallas E, Lahesaare A, Truusalu K, Hoidmets D, Sadikova O, Ratnik K, Sepp H, Dotsenko L, Epštein J, Suija H, Kaarna K, Smit S, Milani L, Metspalu M, Oopkaup OE, Koppel I, Jaaniso E, Kuzmin I, Inno H, Raudvere U, Härma MA, Naaber P, Reisberg T, Peterson H, Talas UG, Lutsar I, Huik K. SARS-CoV-2 clade dynamics and their associations with hospitalisations during the first two years of the COVID-19 pandemic. PLoS One 2024; 19:e0303176. [PMID: 38728305 PMCID: PMC11086870 DOI: 10.1371/journal.pone.0303176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 04/20/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic was characterised by rapid waves of disease, carried by the emergence of new and more infectious SARS-CoV-2 virus variants. How the pandemic unfolded in various locations during its first two years has yet to be sufficiently covered. To this end, here we are looking at the circulating SARS-CoV-2 variants, their diversity, and hospitalisation rates in Estonia in the period from March 2000 to March 2022. METHODS We sequenced a total of 27,550 SARS-CoV-2 samples in Estonia between March 2020 and March 2022. High-quality sequences were genotyped and assigned to Nextstrain clades and Pango lineages. We used regression analysis to determine the dynamics of lineage diversity and the probability of clade-specific hospitalisation stratified by age and sex. RESULTS We successfully sequenced a total of 25,375 SARS-CoV-2 genomes (or 92%), identifying 19 Nextstrain clades and 199 Pango lineages. In 2020 the most prevalent clades were 20B and 20A. The various subsequent waves of infection were driven by 20I (Alpha), 21J (Delta) and Omicron clades 21K and 21L. Lineage diversity via the Shannon index was at its highest during the Delta wave. About 3% of sequenced SARS-CoV-2 samples came from hospitalised individuals. Hospitalisation increased markedly with age in the over-forties, and was negligible in the under-forties. Vaccination decreased the odds of hospitalisation in over-forties. The effect of vaccination on hospitalisation rates was strongly dependent upon age but was clade-independent. People who were infected with Omicron clades had a lower hospitalisation likelihood in age groups of forty and over than was the case with pre-Omicron clades regardless of vaccination status. CONCLUSIONS COVID-19 disease waves in Estonia were driven by the Alpha, Delta, and Omicron clades. Omicron clades were associated with a substantially lower hospitalisation probability than pre-Omicron clades. The protective effect of vaccination in reducing hospitalisation likelihood was independent of the involved clade.
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Affiliation(s)
- Taavi Päll
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Aare Abroi
- Faculty of Science and Technology, Institute of Technology, University of Tartu, Tartu, Estonia
| | - Radko Avi
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Heiki Niglas
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Arina Shablinskaja
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Merit Pauskar
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Ene-Ly Jõgeda
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Hiie Soeorg
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Eveli Kallas
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | | | - Kai Truusalu
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Dagmar Hoidmets
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Olga Sadikova
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | | | - Hanna Sepp
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Liidia Dotsenko
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Jevgenia Epštein
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Heleene Suija
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Katrin Kaarna
- Clinical Research Centre, Faculty of Medicine, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Tartu University Hospital, Tartu, Estonia
| | - Steven Smit
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Lili Milani
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Mait Metspalu
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ott Eric Oopkaup
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Ivar Koppel
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Erik Jaaniso
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ivan Kuzmin
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Heleri Inno
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Uku Raudvere
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Mari-Anne Härma
- Department of Communicable Diseases, Health Board, Tallinn, Estonia
| | - Paul Naaber
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- SYNLAB Eesti OÜ, Tallinn, Estonia
| | - Tuuli Reisberg
- Institute of Genomics, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Hedi Peterson
- Institute of Computer Science, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ulvi Gerst Talas
- High Performance Computing Centre, Faculty of Science and Technology, Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Irja Lutsar
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristi Huik
- Department of Microbiology, Faculty of Medicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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Parm Ü, Tiit-Vesingi A, Soeorg H, Štšepetova J, Truusalu K, Vorobjov S, Lutsar I, Metsvaht T. Effect of early directed implementation of family-integrated care measures on colonisation with Enterobacteriaceae in preterm neonates in NICU. BMJ Paediatr Open 2023; 7:10.1136/bmjpo-2022-001712. [PMID: 37192777 DOI: 10.1136/bmjpo-2022-001712] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/22/2023] [Indexed: 05/18/2023] Open
Abstract
BACKGROUND Hospital-acquired strains (HASs) and multiresistant strains in neonatal intensive care unit often harbour virulence and resistance mechanisms, carrying the risk of invasive infections. We describe colonisation with Enterobacteriaceae in neonates receiving early directed versus routine family-integrated care (FIC) within the first month of life. METHODS A prospective cohort study included neonates with a gestational age below 34 weeks. During the first period, neonates were admitted to an open bay unit with transfer to the single-family room if available; feeding with the mother's own breast milk (MOBM) was introduced within 24 hours, and skin-to-skin contact (SSC) within 5 days of life (the routine care group). During the second period, following a wash-in of 2 months, care in a single-family room within 48 hours, the introduction of MOBM within two and SSC in 48 hours were applied (the intervention group). Enterobacteriaceae isolated from neonatal stool, breast milk and parental skin swabs were genotyped, Simpson's Index of Diversity (SID) calculated, and extended-spectrum beta-lactamases (ESBL) detected. RESULTS In 64 neonate-parents' groups, 176 Enterobacteriaceae, 87 in routine care and 89 in the intervention group were isolated; 26 vs 18 were HAS and one vs three ESBL positive, respectively. In the intervention group compared with the routine care group, SSC and MOBM feeding was started significantly earlier (p<0.001); during the first week of life, time spent in SSC was longer (median hours per day 4.8 (4-5.1) vs 1.9 (1.4-2.6), p<0.001) and the proportion of MOBM in enteral feeds was higher (median (IQR) 97.8% (95.1-100) vs 95.1% (87.2-97.4), p=0.011). Compared with the routine care group, the intervention group had higher SID and a reduction of HAS by 33.1% (95% CI 24.4% to 42.4%) in time series analysis. CONCLUSIONS Early implementation of FIC measures may hold the potential to increase diversity and reduce colonisation with HAS Enterobacteriaceae.
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Affiliation(s)
- Ülle Parm
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Annika Tiit-Vesingi
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Neonatal Intensive Care Unit, East Tallinn Central Hospital, Tallinn, Estonia
| | - Hiie Soeorg
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Jelena Štšepetova
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kai Truusalu
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Sigrid Vorobjov
- Department of Risk Behaviour Studies, National Institute of Health Development, Tallinn, Estonia
| | - Irja Lutsar
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Tuuli Metsvaht
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Paediatric and Neonatal Intensive Care Unit, Clinic of Anaesthesiology and Intensive Care, Tartu University Hospital, Tartu, Estonia
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3
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Mikelsaar M, Stsepetova J, Mikelsaar RH, Truusalu K, Smidt I, Hütt P, Rätsep M, Songisepp E. Polyamines of human strain Lactobacillus plantarum Inducia induce modulation of innate immune markers. J Funct Foods 2020. [DOI: 10.1016/j.jff.2020.104064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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4
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Bichele R, Kärner J, Truusalu K, Smidt I, Mändar R, Conti HR, Gaffen SL, Peterson P, Laan M, Kisand K. IL-22 neutralizing autoantibodies impair fungal clearance in murine oropharyngeal candidiasis model. Eur J Immunol 2018; 48:464-470. [PMID: 29150834 PMCID: PMC5844855 DOI: 10.1002/eji.201747209] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/31/2017] [Accepted: 11/14/2017] [Indexed: 12/30/2022]
Abstract
Protection against mucocutaneous candidiasis depends on the T helper (Th)17 pathway, as gene defects affecting its integrity result in inability to clear Candida albicans infection on body surfaces. Moreover, autoantibodies neutralizing Th17 cytokines have been related to chronic candidiasis in a rare inherited disorder called autoimmune polyendocriopathy candidiasis ectodermal dystrophy (APECED) caused by mutations in autoimmune regulator (AIRE) gene. However, the direct pathogenicity of these autoantibodies has not yet been addressed. Here we show that the level of anti-IL17A autoantibodies that develop in aged Aire-deficient mice is not sufficient for conferring susceptibility to oropharyngeal candidiasis. However, patient-derived monoclonal antibodies that cross-react with murine IL-22 increase the fungal burden on C. albicans infected mucosa. Nevertheless, the lack of macroscopically evident infectious pathology on the oral mucosa of infected mice suggests that additional susceptibility factors are needed to precipitate a clinical disease.
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MESH Headings
- Animals
- Antibodies, Neutralizing/immunology
- Autoantibodies/immunology
- Candida albicans/immunology
- Candidiasis, Chronic Mucocutaneous/immunology
- Candidiasis, Chronic Mucocutaneous/microbiology
- Candidiasis, Oral/immunology
- Candidiasis, Oral/microbiology
- Colony Count, Microbial
- Cross Reactions
- Disease Models, Animal
- Disease Susceptibility
- Female
- Humans
- Interleukin-17/immunology
- Interleukins/immunology
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Mice, Knockout
- Polyendocrinopathies, Autoimmune/immunology
- Th17 Cells/immunology
- Transcription Factors/deficiency
- Transcription Factors/genetics
- Transcription Factors/immunology
- AIRE Protein
- Interleukin-22
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Affiliation(s)
- Rudolf Bichele
- Department of Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Estonia
| | - Jaanika Kärner
- Department of Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Estonia
| | - Kai Truusalu
- Department of Microbiology, Institute of Biomedical and Translational Medicine, University of Tartu, Estonia
| | - Imbi Smidt
- Department of Microbiology, Institute of Biomedical and Translational Medicine, University of Tartu, Estonia
| | - Reet Mändar
- Department of Microbiology, Institute of Biomedical and Translational Medicine, University of Tartu, Estonia
| | - Heather R. Conti
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
- University of Toledo, Toledo, Ohio
| | - Sarah L. Gaffen
- Division of Rheumatology and Clinical Immunology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Pärt Peterson
- Department of Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Estonia
| | - Martti Laan
- Department of Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Estonia
| | - Kai Kisand
- Department of Molecular Pathology, Institute of Biomedical and Translational Medicine, University of Tartu, Estonia
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5
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Rätsep M, Kõljalg S, Sepp E, Smidt I, Truusalu K, Songisepp E, Stsepetova J, Naaber P, Mikelsaar RH, Mikelsaar M. A combination of the probiotic and prebiotic product can prevent the germination of Clostridium difficile spores and infection. Anaerobe 2017; 47:94-103. [PMID: 28465256 DOI: 10.1016/j.anaerobe.2017.03.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 03/23/2017] [Accepted: 03/28/2017] [Indexed: 12/17/2022]
Abstract
Clostridium difficile infection (CDI) is one of the most prevalent healthcare associated infections in hospitals and nursing homes. Different approaches are used for prevention of CDI. Absence of intestinal lactobacilli and bifidobacteria has been associated with C. difficile colonization in hospitalized patients. Our aim was to test a) the susceptibility of C. difficile strains of different origin and the intestinal probiotic Lactobacillus plantarum Inducia (DSM 21379) to various antimicrobial preparations incl. metronidazole, vancomycin; b) the susceptibility of C. difficile strains to antagonistic effects of the probiotic L. plantarum Inducia, prebiotic xylitol (Xyl) and their combination as a synbiotic (Syn) product; c) the suppression of germination of C. difficile spores in vitro and in vivo in animal model of C. difficile infection with Inducia, Xyl and Syn treatment. The VPI strain 10463 (ATCC 43255), epidemic strain (M 13042) and clinical isolates (n = 12) of C. difficile from Norway and Estonia were susceptible and contrarily L. plantarum Inducia resistant to vancomycin, metronidazole and ciprofloxacin. The intact cells of Inducia, natural and neutralized cell free supernatant inhibited in vitro the growth of tested C. difficile reference strain VPI and Estonian and Norwegian clinical isolates of C. difficile after co-cultivation. This effect against C. difficile sustained in liquid media under ampicillin (0.75 μg/ml) and Xyl (5%) application. Further, incubation of Inducia in the media with 5% Xyl fully stopped germination of spores of C. difficile VPI strain after 48 h. In infection model the 48 hamsters were administered ampicillin (30 mg/kg) and 10-30 spores of C. difficile VPI strain. They also received five days before and after the challenge a pretreatment with a synbiotic (single daily dose of L. plantarum Inducia 1 ml of 1010 CFU/ml and 20% xylitol in 1 ml by orogastric gavage). The survival rate of hamsters was increased to 78% compared to 13% (p = 0.003) survival rate of hamsters who received no treatment. When administered Xyl the survival rate of hamsters reached 56% vs.13% (p = 0.06). In both Syn (6/9, p = 0.003) and Xyl (3/9, p = 0.042) groups the number of animals not colonized with C. difficile significantly increased. In conclusion, the combination of xylitol with L. plantarum Inducia suppresses the germination of spores and outgrowth into vegetative toxin producing cells of C. difficile and reduces the colonization of gut with the pathogen. Putative therapeutical approach includes usage of the synbiotic during antimicrobial therapy for prevention of CDI and its potential to reduce recurrences of CDI.
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Affiliation(s)
- M Rätsep
- Institute of Biomedicine and Translational Medicine, University of Tartu, EE 50411, Estonia; Bio-Competence Centre of Healthy Dairy Products LLC, EE 51014, Estonia
| | - S Kõljalg
- Institute of Biomedicine and Translational Medicine, University of Tartu, EE 50411, Estonia
| | - E Sepp
- Institute of Biomedicine and Translational Medicine, University of Tartu, EE 50411, Estonia
| | - I Smidt
- Institute of Biomedicine and Translational Medicine, University of Tartu, EE 50411, Estonia
| | - K Truusalu
- Institute of Biomedicine and Translational Medicine, University of Tartu, EE 50411, Estonia
| | - E Songisepp
- Bio-Competence Centre of Healthy Dairy Products LLC, EE 51014, Estonia
| | - J Stsepetova
- Institute of Biomedicine and Translational Medicine, University of Tartu, EE 50411, Estonia
| | - P Naaber
- Institute of Biomedicine and Translational Medicine, University of Tartu, EE 50411, Estonia
| | - R H Mikelsaar
- Institute of Biomedicine and Translational Medicine, University of Tartu, EE 50411, Estonia
| | - M Mikelsaar
- Institute of Biomedicine and Translational Medicine, University of Tartu, EE 50411, Estonia; Bio-Competence Centre of Healthy Dairy Products LLC, EE 51014, Estonia.
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Smidt I, Kiiker R, Oopkaup H, Lapp E, Rööp T, Truusalu K, Štšepetova J, Truu J, Mändar R. Comparison of detection methods for vaginal lactobacilli. Benef Microbes 2015; 6:747-51. [PMID: 25869280 DOI: 10.3920/bm2014.0154] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Vaginal lactobacilli offer protection against microbiota imbalance and genitourinary tract infections. We compared vaginal lactobacilli in 50 Estonian women of child-bearing age applying culture-based methods, quantitative PCR and next-generation sequencing (NGS). The culture-based methods found three different lactobacilli: Lactobacillus crispatus, Lactobacillus jensenii and Lactobacillus gasseri. Using NGS revealed the presence of L. crispatus in 76%, Lactobacillus iners in 52%, L. jensenii in 47% and L. gasseri in 33% of the samples. According to qPCR, L. iners was present in 67% and L. crispatus in 64% of the samples. The proportions of L. crispatus revealed by qPCR and NGS were in good correlation (R=0.79, P<0.001), while that of L. iners correlated poorly (R=0.13, P>0.05). Good concordance for L. crispatus was also found between the results of the culture-based method and qPCR. Finally, good overlap between the results of the culture-based method and NGS was revealed: in case of a positive NGS result for L. crispatus, the same species was isolated in 95% of samples. The corresponding percentages were 82% for L. jensenii and 86% for L. gasseri. Our data indicate fairly general concordance of the three methods for detecting vaginal lactobacilli, except for L. iners. This points out the importance of standardisation of techniques, and the respective studies should involve cultures applying a medium suitable for the fastidious L. iners.
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Affiliation(s)
- I Smidt
- 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.,2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia
| | - R Kiiker
- 2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia.,3 Faculty of Science and Technology, University of Tartu, Ravila 19, Tartu 50411, Estonia
| | - H Oopkaup
- 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia
| | - E Lapp
- 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.,2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia
| | - T Rööp
- 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.,2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia
| | - K Truusalu
- 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia
| | - J Štšepetova
- 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.,2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia
| | - J Truu
- 2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia.,3 Faculty of Science and Technology, University of Tartu, Ravila 19, Tartu 50411, Estonia
| | - R Mändar
- 1 Department of Microbiology, Faculty of Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia.,2 Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia
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7
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Kõljalg S, Truusalu K, Stsepetova J, Pai K, Vainumäe I, Sepp E, Mikelsaar M. TheEscherichia coliphylogenetic group B2 with integrons prevails in childhood recurrent urinary tract infections. APMIS 2013; 122:452-8. [DOI: 10.1111/apm.12167] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 07/27/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Siiri Kõljalg
- Department of Microbiology; University of Tartu; Tartu
| | - Kai Truusalu
- Department of Microbiology; University of Tartu; Tartu
| | | | - Kristiine Pai
- Department of Microbiology; University of Tartu; Tartu
| | - Inga Vainumäe
- Department ofPediatrics; University of Tartu; Tartu Estonia
| | - Epp Sepp
- Department of Microbiology; University of Tartu; Tartu
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Songisepp E, Hütt P, Rätsep M, Shkut E, Kõljalg S, Truusalu K, Stsepetova J, Smidt I, Kolk H, Zagura M, Mikelsaar M. Safety of a probiotic cheese containing Lactobacillus plantarum Tensia according to a variety of health indices in different age groups. J Dairy Sci 2012; 95:5495-509. [PMID: 22863096 DOI: 10.3168/jds.2011-4756] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 05/22/2012] [Indexed: 01/20/2023]
Abstract
Safety of the probiotic Lactobacillus plantarum strain Tensia (DSM 21380) was tested in vitro, in semihard Edam-type cheese, in an animal model and after consumption of the probiotic cheese in double-blind randomized placebo-controlled human intervention studies with different age groups. The susceptibility of L. plantarum Tensia to 8 antibiotics, and the presence of tetracycline (tet M, S, O, K, L) genes and class 1 integron was assessed by applying epsilometer-test and PCR-based methods. Production of biogenic amines by the probiotic strain in decarboxylation medium containing 1% of l-histidine, l-glutamine, l-ornithine, l-arginine, or l-lysine and in cheese was tested by gas chromatography. The biosafety of L. plantarum Tensia was evaluated on National Institutes of Health-line mice fed cheese containing Tensia at a concentration of 9.6 log cfu/g for 30 consecutive days. In human intervention trials in adults and the elderly, the effects of different doses of Edam-type cheese and the probiotic bacterium on BW, gut functionality indices, and host metabolism were evaluated. The strain L. plantarum Tensia was susceptible to all tested antibiotics and did not possess the tetracycline resistance-determining genes tet(L), tet(S) and tet(O), nor did it contain the integron (Int1) gene. However, the strain was tet(K) and tet(M) positive. Lactobacillus plantarum Tensia did not produce potentially harmful biogenic amines, such as histamine or cadaverine. The amount of tyramine produced in the cheese environment during ripening and after 15 wk of storage was below the clinically significant content. In the animal model, no translocation of the administered strain or other microbes into the blood or organs of mice was detected. No harmful effect was observed on body mass index, inflammatory markers, or serum lipidograms during human intervention trials with different age groups at a daily dose of 10.3 or 8.17 log cfu/serving for 3 wk. No negative effect on gastrointestinal welfare was observed, but the consumption of 100g/d for 3 wk caused hard stools from the second week of the trial. The content of total lactobacilli increased in feces, and the presence of the ingested probiotic strain was confirmed after the consumption of cheese. Thus, L. plantarum strain Tensia is suitable for generally recognized as safe (GRAS) and qualified presumption of safety (QPS) criteria because it did not have any undesirable characteristics. The regular semihard Edam-type cheese (fat content of 26%) with the probiotic additive at a daily dose of 50 g or in excess (100g) and with a probiotic daily dose of 10 log cfu for 3 wk was safe.
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Affiliation(s)
- E Songisepp
- Bio-Competence Centre of Healthy Dairy Products LLC, Kreutzwaldi Str. 1, 51014 Tartu, Estonia.
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Kõll P, Mändar R, Smidt I, Hütt P, Truusalu K, Mikelsaar RH, Shchepetova J, Krogh-Andersen K, Marcotte H, Hammarström L, Mikelsaar M. Screening and evaluation of human intestinal lactobacilli for the development of novel gastrointestinal probiotics. Curr Microbiol 2010; 61:560-6. [PMID: 20443005 DOI: 10.1007/s00284-010-9653-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2009] [Accepted: 04/17/2010] [Indexed: 02/07/2023]
Abstract
The aim of this study was to screen intestinal lactobacilli strains for their advantageous properties to select those that could be used for the development of novel gastrointestinal probiotics. Ninety-three isolates were subjected to screening procedures. Fifty-nine percent of the examined lactobacilli showed the ability to auto-aggregate, 97% tolerated a high concentration of bile (2% w/v), 50% survived for 4 h at pH 3.0, and all strains were unaffected by a high concentration of pancreatin (0.5% w/v). One Lactobacillus buchneri strain was resistant to tetracycline. None of the tested strains caused lysis of human erythrocytes. Six potential probiotic strains were selected for safety evaluation in a mouse model. Five of 6 strains caused no translocation, and were considered safe. In conclusion, several strains belonging to different species and fermentation groups were found that have properties required for a potential probiotic strain. This study was the first phase of a multi-phase study aimed to develop a novel, safe and efficient prophylactic and therapeutic treatment system against gastrointestinal infections using genetically modified probiotic lactobacilli.
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Affiliation(s)
- Piret Kõll
- Department of Microbiology, University of Tartu, Tartu, Estonia
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Sepp E, Stsepetova J, Lõivukene K, Truusalu K, Kõljalg S, Naaber P, Mikelsaar M. The occurrence of antimicrobial resistance and class 1 integrons among commensal Escherichia coli isolates from infants and elderly persons. Ann Clin Microbiol Antimicrob 2009; 8:34. [PMID: 19995422 PMCID: PMC2794839 DOI: 10.1186/1476-0711-8-34] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 12/08/2009] [Indexed: 11/17/2022] Open
Abstract
Background The aim of our study was to compare the presence of the intI1 gene and its associations with the antibiotic resistance of commensal Escherichia coli strains in children with/without previous antibiotic treatments and elderly hospitalized/healthy individuals. Methods One-hundred-and-fifteen intestinal E. coli strains were analyzed: 30 strains from 10 antibiotic-naive infants; 27 from 9 antibiotic-treated outpatient infants; 30 from 9 healthy elderly volunteers; and 28 from 9 hospitalized elderly patients. The MIC values of ampicillin, cefuroxime, cefotaxime, gentamicin, ciprofloxacin, and sulfamethoxazole were measured by E-test and IntI1 was detected by PCR. Results Out of the 115 strains, 56 (49%) carried class 1 integron genes. Comparing persons without medical interventions, we found in antibiotic-naive children a significantly higher frequency of integron-bearing strains and MIC values than in healthy elderly persons (53% versus 17%; p < 0.01). Evaluating medical interventions, we found a higher resistance and frequency of integrons in strains from hospitalized elderly persons compared with non-hospitalized ones. Children treated with antibiotics had strains with higher MIC values (when compared with antibiotic-naive ones), but the integron-bearing in strains was similar. In most cases, the differences in resistance between the groups (integron-positive and negative strains separately) were higher than the differences between integron-positive and negative strains within the groups. Conclusion The prevalence of integrons in commensal E. coli strains in persons without previous medical intervention depended on age. The resistance of integron-carrying and non-carrying strains is more dependent on influencing factors (hospitalization and antibiotic administration) in particular groups than merely the presence or absence of integrons.
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Affiliation(s)
- Epp Sepp
- Department of Microbiology, University of Tartu, Ravila 19, 50411 Tartu, Estonia.
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Truusalu K, Naaber P, Kullisaar T, Tamm H, Mikelsaar RH, Zilmer K, Rehema A, Zilmer M, Mikelsaar M. The influence of antibacterial and antioxidative probiotic lactobacilli on gut mucosa in a mouse model ofSalmonellainfection. Microbial Ecology in Health and Disease 2009. [DOI: 10.1080/08910600410021783] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Kai Truusalu
- Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Paul Naaber
- Department of Microbiology, University of Tartu, Tartu, Estonia
| | - Tiiu Kullisaar
- Department of Biochemistry, University of Tartu, Tartu, Estonia
| | - Hannes Tamm
- Department of Pathology and Forensic Medicine, Medical Faculty, University of Tartu, Tartu, Estonia
| | - Raik-hiio Mikelsaar
- Department of Pathology and Forensic Medicine, Medical Faculty, University of Tartu, Tartu, Estonia
| | - Kersti Zilmer
- Department of Biochemistry, University of Tartu, Tartu, Estonia
| | - Aune Rehema
- Department of Biochemistry, University of Tartu, Tartu, Estonia
| | - Mihkel Zilmer
- Department of Biochemistry, University of Tartu, Tartu, Estonia
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Truusalu K, Mikelsaar RH, Naaber P, Karki T, Kullisaar T, Zilmer M, Mikelsaar M. Eradication of Salmonella Typhimurium infection in a murine model of typhoid fever with the combination of probiotic Lactobacillus fermentum ME-3 and ofloxacin. BMC Microbiol 2008; 8:132. [PMID: 18680567 PMCID: PMC2518159 DOI: 10.1186/1471-2180-8-132] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Accepted: 08/04/2008] [Indexed: 12/24/2022] Open
Abstract
Background The aim of the study was to detect whether in experimental Salmonella enterica Typhimurium infection the probiotic Lactobacillus fermentum ME-3 in combination with fluoroquinolone therapy would eradicate S. Typhimurium, prevent the development of liver and spleen granulomas and improve the indices of oxidative stress in the ileum mucosa. The selected bacteriological, histological and biochemical methods were applied. Results Combined treatment with L. fermentum ME-3 and ofloxacin eradicated Salmonella Typhimurium from blood, ileum and liver, decreased the number of animals with liver and spleen granulomas and reduced the value of lipid peroxides in the ileum mucosa. Higher total counts of intestinal lactobacilli in all experimental groups were associated with the absence of liver granulomas. Conclusion The antimicrobial and antioxidative probiotic L. fermentum ME-3 combined with ofloxacin enhances the eradication of experimental S. Typhimurium infection. These observations on probiotic and antimicrobial co-action may serve as basis to develop new strategies for treatment of invasive bacterial infections of the gut.
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Affiliation(s)
- Kai Truusalu
- Department of Microbiology, University of Tartu, Estonia.
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Truusalu K, Sepp E, Shchepetova J, Koljalg S, Vainumäe I, Stroo K, Sepp K, Mikelsaar M. P1023 Clonality and presence of antibiotic resistance genes of E. coli isolated in recurrent urinary tract infections. Int J Antimicrob Agents 2007. [DOI: 10.1016/s0924-8579(07)70864-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Truusalu K, Naaber P, Kullisaar T, Tamm H, Mikelsaar RH, Zilmer K, Rehema A, Zilmer M, Mikelsaar M. The Influence of Antibacterial and Antioxidative Probiotic Lactobacilli on Gut Mucosa in a Mouse Model of SalmonellaInfection. Microbial Ecology in Health & Disease 2004. [DOI: 10.3402/mehd.v16i4.7924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Karki T, Truusalu K, Vainumäe I, Mikelsaar M. Antibiotic susceptibility patterns of community- and hospital-acquired Staphylococcus aureus and Escherichia coli in Estonia. Scand J Infect Dis 2002; 33:333-8. [PMID: 11440217 DOI: 10.1080/003655401750173904] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
This study compares the susceptibility patterns of Staphylococcus aureus and Escherichia coli isolated from patients with hospital-acquired and outpatient infections. A total of 902 isolates of S. aureus and 1,114 of E. coli were collected in five different Estonian medical centers between January 1997 and November 1997. Strains were grouped into two different categories, depending on whether they had been obtained from inpatients or outpatients. Compared to S. aureus strains isolated from inpatients, the strains from outpatients were significantly more resistant to erythromycin (25.3% vs. 17.9%), tetracycline (33.5% vs. 22.4%) and trimethoprim-sulfamethoxazole (13.9% vs. 7.9%). The overall prevalence of oxacillin-resistant S. aureus was 10.4%, with no significant differences noted between isolates recovered from inpatients and outpatients. In the case of E. coli, significantly more isolates from inpatients (42.8%) than from outpatients (34.4%) were ampicillin-resistant. Inpatient isolates of E. coli were also more resistant to cefotaxime (9.3%) and nitrofurantoin (11.2%) than outpatient strains (0% and 3.1%, respectively). Analysis showed remarkable co-resistance among both inpatient and outpatient strains of S. aureus and E. coli. Multiple resistant S. aureus and E. coli strains represented 15.1% and 17.3%, respectively of the organisms examined in this study. With respect to E. coli, significantly more multiresistant isolates were found in inpatient than outpatient isolates (20.4% vs. 8.9%). Our results indicate that the distinction between community-acquired and hospital infections due to S. aureus and E. coli may not be valid in Estonia.
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Affiliation(s)
- T Karki
- Department of Microbiology, University of Tartu, Estonia
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