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Galgano S, Kettle H, Free A, Houdijk JGM. Estimating the contribution of the porcine fecal core microbiota to metabolite production via mathematical modeling and in vitro fermentation. mSystems 2024; 9:e0036623. [PMID: 38059648 PMCID: PMC10805034 DOI: 10.1128/msystems.00366-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 11/03/2023] [Indexed: 12/08/2023] Open
Abstract
The swine gut microbiota is a complex ecosystem found throughout the gastrointestinal tract, with multiple exchanges with the host and whose composition is linked to both external and internal factors, such as diet or breed. Diet, probiotic, or prebiotic interventions have been designed to boost beneficial host-microbiota interactions, such as the production of anti-inflammatory molecules, or the fermentation of otherwise undigested resources. In parallel, a smaller microbial population, shared among the same host species, independent of external or internal factors, has been described and defined as the "core microbiota." Therapies targeting the core microbiota could possibly lead to more precise and long-lasting effects. However, the metabolic role of the porcine core microbiota, especially in relation to the rest of the microbial community, is currently missing. We present here the first dynamic model of the porcine core microbiota, which we used to estimate the core-microbiota metabolite production and to forecast the effect of a synbiotic intervention targeting the core genera of the core microbiota. We developed a community model in which a total of 17 microbial groups were established based on culture-based information of representative species. First, the model parameters were estimated, and the resulting model simulations were compared favorably with in vitro experimentation. The model was then used to predict the microbial dynamics of the core and non-core members under different experimental conditions. Therefore, it was able to theorize the main-metabolite core microbiota contribution, hypothesizing that it could be mainly responsible for acetate and propionate, but not for butyrate production.IMPORTANCECurrently, little information is present in the literature to describe the generic metabolic role of the porcine core microbiota or to inform on the effect of interventions targeting the core genera. Moreover, both in vitro and in vivo experimentations aiming to explore the core microbiota dynamics are technically demanding, expensive, or restricted by ethical considerations. Modeling approaches can be used as an initial exploratory tool to develop hypotheses for targeted experimentation. Our mathematical model provides initial information on the microbial and metabolite dynamics of the core microbiota in relation to diet and therapeutic intervention.
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Affiliation(s)
- Salvatore Galgano
- Monogastric Science Research Centre, Scotland's Rural College, Edinburgh, Scotland, United Kingdom
| | - Helen Kettle
- Biomathematics and Statistics Scotland, Edinburgh, Scotland, United Kingdom
| | - Andrew Free
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Jos G. M. Houdijk
- Monogastric Science Research Centre, Scotland's Rural College, Edinburgh, Scotland, United Kingdom
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Vanstokstraeten R, Callewaert E, Blotwijk S, Rombauts E, Crombé F, Emmerechts K, Soetens O, Vandoorslaer K, De Geyter D, Allonsius C, Vander Donck L, Blockeel C, Wybo I, Piérard D, Demuyser T, Mackens S. Comparing Vaginal and Endometrial Microbiota Using Culturomics: Proof of Concept. Int J Mol Sci 2023; 24:ijms24065947. [PMID: 36983020 PMCID: PMC10055768 DOI: 10.3390/ijms24065947] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
It is generally accepted that microorganisms can colonize a non-pathological endometrium. However, in a clinical setting, endometrial samples are always collected by passing through the vaginal-cervical route. As such, the vaginal and cervical microbiomes can easily cross-contaminate endometrial samples, resulting in a biased representation of the endometrial microbiome. This makes it difficult to demonstrate that the endometrial microbiome is not merely a reflection of contamination originating from sampling. Therefore, we investigated to what extent the endometrial microbiome corresponds to that of the vagina, applying culturomics on paired vaginal and endometrial samples. Culturomics could give novel insights into the microbiome of the female genital tract, as it overcomes sequencing-related bias. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy were included. An additional vaginal swab was taken from each participant right before hysteroscopy. Both endometrial biopsies and vaginal swabs were analyzed using our previously described WASPLab-assisted culturomics protocol. In total, 101 bacterial and two fungal species were identified among these 10 patients. Fifty-six species were found in endometrial biopsies and 90 were found in vaginal swabs. On average, 28 % of species were found in both the endometrial biopsy and vaginal swab of a given patient. Of the 56 species found in the endometrial biopsies, 13 were not found in the vaginal swabs. Of the 90 species found in vaginal swabs, 47 were not found in the endometrium. Our culturomics-based approach sheds a different light on the current understanding of the endometrial microbiome. The data suggest the potential existence of a unique endometrial microbiome that is not merely a presentation of cross-contamination derived from sampling. However, we cannot exclude cross-contamination completely. In addition, we observe that the microbiome of the vagina is richer in species than that of the endometrium, which contradicts the current sequence-based literature.
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Affiliation(s)
- Robin Vanstokstraeten
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ellen Callewaert
- Department of Pharmaceutical Sciences, Entity of In Vitro Toxicology, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Susanne Blotwijk
- Biostatistics and Medical Informatics Research Group (BISI), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Eleni Rombauts
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Florence Crombé
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Kristof Emmerechts
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Deborah De Geyter
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Camille Allonsius
- Department of Bioscience Engineering, University of Antwerp (UA), 2020 Antwerp, Belgium
| | - Leonore Vander Donck
- Department of Bioscience Engineering, University of Antwerp (UA), 2020 Antwerp, Belgium
| | - Christophe Blockeel
- Brussels IVF, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
- AIMS Lab, Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Shari Mackens
- Brussels IVF, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
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Gregorczyk-Maga I, Fiema M, Kania M, Jachowicz-Matczak E, Romaniszyn D, Gerreth K, Klupa T, Wójkowska-Mach J. Oral Microbiota-One Habitat or Diverse Niches? A Pilot Study of Sampling and Identification of Oral Bacterial and Fungal Biota in Patients with Type I Diabetes Mellitus Treated with Insulin Pump. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2252. [PMID: 36767617 PMCID: PMC9914992 DOI: 10.3390/ijerph20032252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVE The oral microbiota is a very complex and dynamic microbial ecosystem. Alterations of its balance can result in oral and systemic diseases. We aimed to characterize the microbiota in particular niches of the oral cavity in adult type 1 diabetes patients treated with continuous infusion of insulin with insulin pump (IP). In addition, we aimed to determine optimal sites of oral microbiota sampling in studies of large research groups of patients with DM I. DESIGN In this pilot study, we sampled the buccal and soft palate mucosa, tongue, palatal and buccal dental surfaces and gingival pockets of adult DM I patients treated with IP. RESULTS In total, 23 patients were recruited. The oral microbiota was dominated by Streptococus and Neisseria, with a low incidence of cariogenic S. mutans and Lactobacillus, as well as periodontal pathogens such as Prevotella. There were significant differences in overall CFU counts of all strains, Gram-positive, Staphylococci, Streptococci and S. oralis strains between mucosal and dental surface sites. The overall CFU counts of all strains and Gram-positive strains were higher in dental sites vs. mucosal sites (both p < 0.001). CFU counts of S. oralis were significantly higher in dental sites vs. gingival pocket sites (p = 0.013). Candida species were rare. The mucosal sites on the buccae presented lower diversity and bacterial counts. CONCLUSIONS In the study group of adult DM I patients treated with IP, the microbiota in particular niches of the oral cavity was significantly different. Three distinct and optimally appropriate sampling sites for oral microflora were identified: buccal and palatal mucosa, dental surface and gingival pockets. The results of this study may be the basis for further studies of large groups of patients with DM I.
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Affiliation(s)
- Iwona Gregorczyk-Maga
- Institute of Dentistry, Faculty of Medicine, Jagiellonian University Medical College, 31-155 Krakow, Poland
| | - Mateusz Fiema
- Department of Endocrinology, University Hospital, 30-688 Krakow, Poland
| | - Michal Kania
- Doctoral School of Medicine and Health Sciences, Jagiellonian University Medical College, 31-008 Krakow, Poland
- Department of Metabolic Diseases, Center of Advanced Technologies in Diabetes, Faculty of Medicine, Jagiellonian University Medical College, 30-688 Krakow, Poland
| | - Estera Jachowicz-Matczak
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Dorota Romaniszyn
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
| | - Karolina Gerreth
- Department of Risk Group Dentistry, Chair of Pediatric Dentistry, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| | - Tomasz Klupa
- Department of Metabolic Diseases, Center of Advanced Technologies in Diabetes, Faculty of Medicine, Jagiellonian University Medical College, 30-688 Krakow, Poland
| | - Jadwiga Wójkowska-Mach
- Department of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, 31-121 Krakow, Poland
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Gregorczyk-Maga I, Fiema M, Kania M, Kędzierska J, Jachowicz E, Romaniszyn D, Wójkowska-Mach J. Cultivable oral bacteriota dysbiosis in mechanically ventilated COVID-19 patients. Front Microbiol 2022; 13:1013559. [PMID: 36386658 PMCID: PMC9651008 DOI: 10.3389/fmicb.2022.1013559] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/12/2022] [Indexed: 11/29/2022] Open
Abstract
Potential interactions between the SARS-CoV-2 virus and the human oral microbiota are currently investigated widely. Patients with COVID-19 requiring mechanical ventilation in an intensive care unit (ICU) setting are at high risk of developing severe complications, including ventilator-associated pneumonia, thus making oral health management important. The aim of this study was to evaluate the oral health status and assess the dysbiosis of cultivable oral bacteriota in COVID-19 patients hospitalized in an ICU with acute respiratory distress within 36 h following intubation. In this prospective cohort study, we recruited 56 adult COVID-19 patients that qualified for mechanical ventilation in the Temporary ICU for COVID-19 Patients of the University Hospital in Krakow. On admission to the ICU, oral health of patients was assessed using the modified Beck Oral Assessment Score (BOAS). Four oral habitats were sampled, namely the buccal mucosa, tongue, buccal dental surface and gingival pocket. Microorganisms were identified by MALDI/TOF mass spectrometry. The mean age of the study population was 66.5 ± 12.7 years, there were 24 (42.9%) females. All patients included in this study were intubated and ventilated in the ICU, with a corresponding high mortality rate (76.8%). On admission to ICU, 76.8% subjects scored 11–20 on the BOAS scale (median 12 [IQR 10–14]), indicating moderate or severe dysfunction of oral health. Potentially pathogenic bacteria were identified in the oral microbiota samples, including Acinetobacter baumannii, Enterococcus faecalis, Escherichia coli and Klebsiella pneumoniae in 23.2%, 39.3%, 17.9%, and 19.6% of patients, respectively. Lactobacillus spp. were present in 57.1% subjects. The mean CFU counts of all bacteria strains in dental brushes were 9.3E+5 (1.4E+6) and in gingival pockets 7.6E+5 (1.4E+6). The highest CFU counts were observed for Enterococcus spp. and, Lactobacillus spp., although these did not differ significantly from CFU counts of Streptococcus spp. and Staphylococcus spp. In this report we comprehensively characterized the oral health condition and cultivable oral bacteriota in COVID-19 patients hospitalized in an ICU with acute respiratory distress within 36 h following intubation. The oral bacteriota showed significant qualitative and quantitative dysbiosis. Hospitalization in an ICU and mechanical ventilation are important factors leading to oral dysbiosis in SARS-CoV-2 patients.
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Affiliation(s)
- Iwona Gregorczyk-Maga
- Faculty of Medicine, Institute of Dentistry, Jagiellonian University Medical College, Krakow, Poland
| | - Mateusz Fiema
- Department of Endocrinology, University Hospital, Krakow, Poland
| | - Michal Kania
- Doctoral School of Medicine and Health Sciences, Jagiellonian University Medical College, Krakow, Poland
- Chair of Metabolic Diseases, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
- *Correspondence: Michal Kania,
| | | | - Estera Jachowicz
- Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Dorota Romaniszyn
- Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
| | - Jadwiga Wójkowska-Mach
- Chair of Microbiology, Faculty of Medicine, Jagiellonian University Medical College, Krakow, Poland
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Vanstokstraeten R, Mackens S, Callewaert E, Blotwijk S, Emmerechts K, Crombé F, Soetens O, Wybo I, Vandoorslaer K, Mostert L, De Geyter D, Muyldermans A, Blockeel C, Piérard D, Demuyser T. Culturomics to Investigate the Endometrial Microbiome: Proof-of-Concept. Int J Mol Sci 2022; 23:12212. [PMID: 36293066 PMCID: PMC9602868 DOI: 10.3390/ijms232012212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/03/2022] [Accepted: 10/09/2022] [Indexed: 08/29/2023] Open
Abstract
The microbiome of the reproductive tract has been associated with (sub)fertility and it has been suggested that dysbiosis reduces success rates and pregnancy outcomes. The endometrial microbiome is of particular interest given the potential impact on the embryo implantation. To date, all endometrial microbiome studies have applied a metagenomics approach. A sequencing-based technique, however, has its limitations, more specifically in adequately exploring low-biomass settings, such as intra-uterine/endometrial samples. In this proof-of-concept study, we demonstrate the applicability of culturomics, a high-throughput culturing approach, to investigate the endometrial microbiome. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy, as part of their routine work-up at Brussels IVF, were included after their informed consent. Biopsies were used to culture microbiota for up to 30 days in multiple aerobic and anaerobic conditions. Subsequent WASPLab®-assisted culturomics enabled a standardized methodology. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA sequencing was applied to identify all of bacterial and fungal isolates. Eighty-three bacterial and two fungal species were identified. The detected species were in concordance with previously published metagenomics-based endometrial microbiota analyses as 77 (91%) of them belonged to previously described genera. Nevertheless, highlighting the added value of culturomics to identify most isolates at the species level, 53 (62.4%) of the identified species were described in the endometrial microbiota for the first time. This study shows the applicability and added value of WASPLab®-assisted culturomics to investigate the low biomass endometrial microbiome at a species level.
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Affiliation(s)
- Robin Vanstokstraeten
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Shari Mackens
- Brussels IVF, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ellen Callewaert
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Susanne Blotwijk
- Biostatistics and Medical Informatics Research Group (BISI), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Kristof Emmerechts
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Florence Crombé
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Laurence Mostert
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Deborah De Geyter
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Astrid Muyldermans
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Christophe Blockeel
- Brussels IVF, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
- Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
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Gao J, Chen Q, Peng Y, Jiang N, Shi Y, Ying C. Copan Walk Away Specimen Processor (WASP) Automated System for Pathogen Detection in Female Reproductive Tract Specimens. Front Cell Infect Microbiol 2021; 11:770367. [PMID: 34869072 PMCID: PMC8635742 DOI: 10.3389/fcimb.2021.770367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Objective Automation is increasingly being applied in clinical laboratories; however, preanalytical processing for microbiology tests and screening is still largely performed using manual methods owing to the complex procedures involved. To promote automation of clinical microbiology laboratories, it is important to assess the performance of automated systems for different specimen types separately. Therefore, the aim of this study was to explore the potential clinical application of the Copan Walk Away Specimen Processor (WASP) automated preanalytical microbiology processing system in the detection of pathogens in female reproductive tract specimens and its feasibility in optimizing diagnostic procedures. Methods Female reproductive tract specimens collected from pregnant women at their first obstetric check-up were inoculated into culture media using the Copan WASP automated specimen processing system and were also cultured using a conventional manual inoculation method. After 48 h of culture, the growth of colonies was observed, and the types of bacteria, number of colonies, and efficiency in isolating single colonies were compared between the automated and manual groups. The specimens collected from the WASP system using the Copan-ESwab sample collection tubes were further analyzed for the presence of Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Ureaplasmaurealyticum (UU) via fluorescence quantitative polymerase chain reaction (qPCR) and an immunochromatographic assay to investigate the feasibility of this method in optimizing detection of these common pathogens of the female reproductive tract. Results Compared with the manual culture method, the Copan WASP microbiology automation system detected fewer bacterial types (P<0.001) and bacterial colonies (P<0.001) but had a higher detection rate of single colonies (P<0.001). There was no significant difference in the detection rates of common pathogens encountered in clinical obstetrics and gynecology, including group B Streptococcus (GBS) (P=0.575) and Candida (P=0.917), between the two methods. Specimens collected in the Copan-ESwab tubes could be used for screening of GBS and CT via fluorescence-based qPCR but not with immunochromatography. However, UU and NG were not detected in any sample with either method; thus, further validation is required to determine the feasibility of the Copan system for screening these pathogens. Conclusion The Copan WASP microbiology automation system could facilitate the optimization of diagnostic procedures for detecting common pathogens of the female reproductive system, thereby reducing associated costs.
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Affiliation(s)
- Jing Gao
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Qiujing Chen
- Institute of Cardiovascular Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yiqian Peng
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Nanyan Jiang
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Youhao Shi
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chunmei Ying
- Department of Clinical Laboratory, Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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7
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Wolf EA, Rettig HC, Lupatsii M, Schlüter B, Schäfer K, Friedrich D, Graspeuntner S, Rupp J. Culturomics Approaches Expand the Diagnostic Accuracy for Sexually Transmitted Infections. Int J Mol Sci 2021; 22:ijms221910815. [PMID: 34639153 PMCID: PMC8509341 DOI: 10.3390/ijms221910815] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 09/26/2021] [Accepted: 10/01/2021] [Indexed: 02/07/2023] Open
Abstract
Sexually transmitted infections (STIs) are a major health concern with clinical manifestations being acknowledged to cause severe reproductive impairment. Research in infectious diseases has been centered around the known major pathogens for decades. However, we have just begun to understand that the microbiota of the female genital tract is of particular importance for disease initiation, infection progression, and pathological outcome. Thus, we are now aware that many poorly described, partially not yet known, or cultured bacteria may pave the way for an infection and/or contribute to disease severity. While sequencing-based methods are an important step in diagnosing STIs, culture-based methods are still the gold-standard method in diagnostic routine, providing the opportunity to distinguish phenotypic traits of bacteria. However, current diagnostic culture routines suffer from several limitations reducing the content of information about vaginal microbiota. A detailed characterization of microbiota-associated factors is needed to assess the impact of single-bacterial isolates from the vaginal community on vaginal health and the containment of STIs. Here we provide current concepts to enable modern culture routines and create new ideas to improve diagnostic approaches with a conjunct usage of bioinformatics. We aim to enable scientists and physicians alike to overcome long-accepted limitations in culturing bacteria of interest to the human health. Eventually, this may improve the quality of culture-based diagnostics, facilitate a research interface, and lead to a broader understanding of the role of vaginal microbiota in reproductive health and STIs.
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Affiliation(s)
- Ellinor Anna Wolf
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Hannah Clara Rettig
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Mariia Lupatsii
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Britta Schlüter
- Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, 23538 Lübeck, Germany;
| | - Kathrin Schäfer
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Dirk Friedrich
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
| | - Simon Graspeuntner
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
| | - Jan Rupp
- Department of Infectious Diseases and Microbiology, University of Lübeck, 23538 Lübeck, Germany; (E.A.W.); (H.C.R.); (M.L.); (K.S.); (D.F.); (S.G.)
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23538 Lübeck, Germany
- Correspondence:
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Ikken Y, Charof R, Elouennass M, Sekhsokh Y. The novel biphasic medium for transport, culture and conservation at an ambient temperature of Neisseria meningitidis, Streptococcus pneumoniae and Haemophilus influenzae. World J Microbiol Biotechnol 2021; 37:187. [PMID: 34586515 DOI: 10.1007/s11274-021-03149-5] [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: 04/28/2021] [Accepted: 09/16/2021] [Indexed: 11/26/2022]
Abstract
Bacterial meningitis remains a very important disease worldwide, and the major causative pathogens were Neisseria meningitidis (N. meningitidis), Streptococcus pneumoniae (S. pneumoniae) and Haemophilus influenzae (H. influenzae). In our context, the technical difficulties encountered in the routine practice were associated with the fragility of these bacteria, the high rates of negative culture and the demanding transport conditions. That's why the need to look for a solution to its technical problems and to propose a new proper solution with the local situation. The aim of this study was to develop, perform and evaluate a novel biphasic medium used for the transport, culture and conservation at an ambient temperature of N. meningitidis, S. pneumoniae and H. influenzae. The results showed that this biphasic medium provided more, novels and easy nutriments through the addition of liquid phase and solid phase medium and it was found to be conducive to the growth and conservation of N. meningitidis, S. pneumoniae and H. influenzae at an ambient temperature of a minimum of 40 days. And the ingredients used in the medium are readily available at a low cost as well as the components prepared in large quantities, they could be stored at + 4 ± 1 °C for 2 years without significantly altering their growth and conservation supporting their potential. The survival and recovery for the fastidious bacteria on the biphasic medium and the other media used for comparison in this study were significantly different (P < 0.05). In addition, the Sensitivity, Specificity, Positive and Negative Predictive Value of biphasic medium showed highest among the three bacteria at least 40 days of storage at room temperature in this study. In conclusion, we found the biphasic medium to be low cost and suitable for previously mentioned bacteria from suspected meningitis patients, offering an optimal condition and an increase in the viability of the isolates at ambient temperature. And it was concluded that this biphasic medium could be used as a technical solution in laboratories for the management of meningitis.
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Affiliation(s)
- Youssef Ikken
- Biosafety Level 3 and Research Laboratory, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10 000, Rabat, Morocco.
- Laboratory of Medical Bacteriology, National Institute of Hygiene in Rabat, 27, Avenue Ibn Batouta, B.P. 769, 10 000, Rabat, Morocco.
| | - Réda Charof
- Laboratory of Medical Bacteriology, National Institute of Hygiene in Rabat, 27, Avenue Ibn Batouta, B.P. 769, 10 000, Rabat, Morocco
| | - Mostafa Elouennass
- Laboratory of Bacteriology, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10 000, Rabat, Morocco
| | - Yassine Sekhsokh
- Biosafety Level 3 and Research Laboratory, Mohammed V Military Teaching Hospital, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, 10 000, Rabat, Morocco
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Clinical Relevance of the Microbiome in Odontogenic Abscesses. BIOLOGY 2021; 10:biology10090916. [PMID: 34571794 PMCID: PMC8468448 DOI: 10.3390/biology10090916] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/30/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022]
Abstract
Simple Summary Odontogenic infections are very common. The course of disease ranges from mild to severe and sometimes even life-threatening infections. Optimal therapy is based on rapid abscess incision and, especially in severe cases, on adjuvant antibiotic therapy that ideally targets the culprit bacteria. In order to identify these bacteria, clinicians usually perform cultural analysis from smears of pus and aim for antibiotic susceptibility testing. In recent years, using new molecular methods, it has become possible to carry out a much more detailed analysis of the bacterial colonization of different parts of the human body by determining a microbiome. In our study, we have, for the first time, compared such a microbiome of odontogenic abscesses with cultural bacterial determination carried out in the clinical routine of a university hospital. The key finding of the study is not only that considerably more bacteria can be detected in the abscess in this way but also that easily cultivated bacteria dominate over the actual fastidious pathogenic bacteria. Thus, routine clinical culture probably only provides a distorted picture of reality and should be supplemented by molecular methods in the future. Abstract Odontogenic abscesses are usually caused by bacteria of the oral microbiome. However, the diagnostic culture of these bacteria is often prone to errors and sometimes fails completely due to the fastidiousness of the relevant bacterial species. The question arises whether additional pathogen diagnostics using molecular methods provide additional benefits for diagnostics and therapy. Experimental 16S rRNA gene analysis with next-generation sequencing (NGS) and bioinformatics was used to identify the microbiome of the pus in patients with severe odontogenic infections and was compared to the result of standard diagnostic culture. The pus microbiome was determined in 48 hospitalized patients with a severe odontogenic abscess in addition to standard cultural pathogen detection. Cultural detection was possible in 41 (85.42%) of 48 patients, while a pus-microbiome could be determined in all cases. The microbiomes showed polymicrobial infections in 46 (95.83%) cases, while the picture of a mono-infection occurred only twice (4.17%). In most cases, a predominantly anaerobic spectrum with an abundance of bacteria was found in the pus-microbiome, while culture detected mainly Streptococcus, Staphylococcus, and Prevotella spp. The determination of the microbiome of odontogenic abscesses clearly shows a higher number of bacteria and a significantly higher proportion of anaerobes than classical cultural methods. The 16S rRNA gene analysis detects considerably more bacteria than conventional cultural methods, even in culture-negative samples. Molecular methods should be implemented as standards in medical microbiology diagnostics, particularly for the detection of polymicrobial infections with a predominance of anaerobic bacteria.
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Comprehensive Wet-Bench and Bioinformatics Workflow for Complex Microbiota Using Oxford Nanopore Technologies. mSystems 2021; 6:e0075021. [PMID: 34427527 PMCID: PMC8407471 DOI: 10.1128/msystems.00750-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The advent of high-throughput sequencing techniques has recently provided an astonishing insight into the composition and function of the human microbiome. Next-generation sequencing (NGS) has become the gold standard for advanced microbiome analysis; however, 3rd generation real-time sequencing, such as Oxford Nanopore Technologies (ONT), enables rapid sequencing from several kilobases to >2 Mb with high resolution. Despite the wide availability and the enormous potential for clinical and translational applications, ONT is poorly standardized in terms of sampling and storage conditions, DNA extraction, library creation, and bioinformatic classification. Here, we present a comprehensive analysis pipeline with sampling, storage, DNA extraction, library preparation, and bioinformatic evaluation for complex microbiomes sequenced with ONT. Our findings from buccal and rectal swabs and DNA extraction experiments indicate that methods that were approved for NGS microbiome analysis cannot be simply adapted to ONT. We recommend using swabs and DNA extractions protocols with extended washing steps. Both 16S rRNA and metagenomic sequencing achieved reliable and reproducible results. Our benchmarking experiments reveal thresholds for analysis parameters that achieved excellent precision, recall, and area under the precision recall values and is superior to existing classifiers (Kraken2, Kaiju, and MetaMaps). Hence, our workflow provides an experimental and bioinformatic pipeline to perform a highly accurate analysis of complex microbial structures from buccal and rectal swabs. IMPORTANCE Advanced microbiome analysis relies on sequencing of short DNA fragments from microorganisms like bacteria, fungi, and viruses. More recently, long fragment DNA sequencing of 3rd generation sequencing has gained increasing importance and can be rapidly conducted within a few hours due to its potential real-time sequencing. However, the analysis and correct identification of the microbiome relies on a multitude of factors, such as the method of sampling, DNA extraction, sequencing, and bioinformatic analysis. Scientists have used different protocols in the past that do not allow us to compare results across different studies and research fields. Here, we provide a comprehensive workflow from DNA extraction, sequencing, and bioinformatic workflow that allows rapid and accurate analysis of human buccal and rectal swabs with reproducible protocols. This workflow can be readily applied by many scientists from various research fields that aim to use long-fragment microbiome sequencing.
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Tops SCM, Kolmus M, Wulms D, van Ingen J, Wertheim HFL, Kolwijck E. Recovery of aerobic gram-negative bacteria from the Copan Eswab transport system after long-term storage. Diagn Microbiol Infect Dis 2020; 98:115100. [PMID: 32622288 DOI: 10.1016/j.diagmicrobio.2020.115100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/27/2020] [Accepted: 05/29/2020] [Indexed: 10/24/2022]
Abstract
We evaluated the Copan Eswab transport system for the quantitative recovery of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa after 1, 2, 3, 5, and 7 days of storage at room and refrigerator temperatures, and 7 and 30 days of storage at -80 °C and -20 °C using mono- and polymicrobial samples. The study was based on Clinical and Laboratory Standards Institute (CLSI) M40-A2 standard procedures on the quality control of microbiological transport systems. Eswab met the CLSI standards at room and refrigerator temperatures for all (combinations of) bacterial strains tested. At room temperature, after 24 h, bacterial growth was observed. At -80 °C, bacterial viability was maintained in monomicrobial samples; however, in polymicrobial samples, P. aeruginosa recovery was compromised. Storage at -20 °C was unsuitable. We conclude that specimens collected using Eswab should be transported to the laboratory as soon as possible. If transport or processing is delayed, specimens should preferably be stored at refrigerator temperatures.
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Affiliation(s)
- Sofie C M Tops
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands.
| | - Marlien Kolmus
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands.
| | - Damy Wulms
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands.
| | - Jakko van Ingen
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands.
| | - Heiman F L Wertheim
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands.
| | - Eva Kolwijck
- Radboudumc Center for Infectious Diseases, Department of Medical Microbiology, Radboud university medical center, Nijmegen, The Netherlands.
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Ribeiro VST, Kraft L, Suss PH, Cieslinski J, Wollmann LC, Tuon FF. Anaerobic bioburden in transport solution of human cardiovascular tissues. J Microbiol Methods 2019; 166:105723. [PMID: 31526821 DOI: 10.1016/j.mimet.2019.105723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 09/10/2019] [Accepted: 09/11/2019] [Indexed: 11/26/2022]
Abstract
Although reports of infections caused by anaerobes after tissue transplantation are uncommon, contamination of allografts may result in substantial complications. Anaerobic incubation and testing of organ transport solution (TS) are not routine. The aim of this study was to determine the bioburden of strict anaerobic bacteria and oxygen tension of heart-TS. Forty TS from different donors were evaluated cultured using membrane filtration (MF), direct inoculation on broth and automated blood culture bottle (ABCB). Bacterial identification was performed by MALDI-TOF. The transport conditions were simulated to verify the bacterial recovery. A sterile bag fulfilled with 250 ml-1 of sterile saline was spiked with 100 CFU ml-1 of Clostridium perfringens and the fluid recovered 0 h, 1 h, 2 h, 6 h, 12 h, 24 h and 48 h for culture and oxygen measurement. Strict anaerobic bacteria were not isolated in heart-TS. The recovery of C.perfringens spiked in heart-TS was 100% using automated blood culture bottles. MF method detected >100 CFU only after 6 h of spiking. The manual culture was not able to recover C.perfringens after the process. The percentage of O2 measures varied from 77.6 to 87.9%. MF or ABCB are better than direct inoculation for recovery of anaerobes from heart-TS. Although all samples from heart donors were negative for anaerobes (probably due to low incidence of contamination), C.perfringens were all recovered in the simulated transport condition.
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Affiliation(s)
- Victoria Stadler Tasca Ribeiro
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80215-901, Brazil
| | - Letícia Kraft
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80215-901, Brazil
| | - Paula Hansen Suss
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80215-901, Brazil
| | - Juliette Cieslinski
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80215-901, Brazil
| | | | - Felipe Francisco Tuon
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80215-901, Brazil; Human Tissue Bank, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná 80215-901, Brazil.
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