1
|
Kristensen M, de Koff EM, Chu ML, Groendijk S, Tramper-Stranders GA, de Winter-de Groot KM, Janssens HM, Tiddens HA, van Westreenen M, Sanders EAM, Arets BHGM, van der Ent CK, Prevaes SMPJ, Bogaert D. 16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients. Microbiol Spectr 2023; 11:e0405722. [PMID: 37199622 PMCID: PMC10269535 DOI: 10.1128/spectrum.04057-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/21/2023] [Indexed: 05/19/2023] Open
Abstract
16S-based sequencing provides broader information on the respiratory microbial community than conventional culturing. However, it (often) lacks species- and strain-level information. To overcome this issue, we used 16S rRNA-based sequencing results from 246 nasopharyngeal samples obtained from 20 infants with cystic fibrosis (CF) and 43 healthy infants, which were all 0 to 6 months old, and compared them to both standard (blind) diagnostic culturing and a 16S-sequencing-informed "targeted" reculturing approach. Using routine culturing, we almost uniquely detected Moraxella catarrhalis, Staphylococcus aureus, and Haemophilus influenzae (42%, 38%, and 33% of samples, respectively). Using the targeted reculturing approach, we were able to reculture 47% of the top-5 operational taxonomical units (OTUs) in the sequencing profiles. In total, we identified 60 species from 30 genera with a median of 3 species per sample (range, 1 to 8). We also identified up to 10 species per identified genus. The success of reculturing the top-5 genera present from the sequencing profile depended on the genus. In the case of Corynebacterium being in the top 5, we recultured them in 79% of samples, whereas for Staphylococcus, this value was only 25%. The success of reculturing was also correlated with the relative abundance of those genera in the corresponding sequencing profile. In conclusion, revisiting samples using 16S-based sequencing profiles to guide a targeted culturing approach led to the detection of more potential pathogens per sample than conventional culturing and may therefore be useful in the identification and, consequently, treatment of bacteria considered relevant for the deterioration or exacerbation of disease in patients like those with CF. IMPORTANCE Early and effective treatment of pulmonary infections in cystic fibrosis is vital to prevent chronic lung damage. Although microbial diagnostics and treatment decisions are still based on conventional culture methods, research is gradually focusing more on microbiome and metagenomic-based approaches. This study compared the results of both methods and proposed a way to combine the best of both worlds. Many species can relatively easily be recultured based on the 16S-based sequencing profile, and it provides more in-depth information about the microbial composition of a sample than that obtained through routine (blind) diagnostic culturing. Still, well-known pathogens can be missed by both routine diagnostic culture methods as well as by targeted reculture methods, sometimes even when they are highly abundant, which may be a consequence of either sample storage conditions or antibiotic treatment at the time of sampling.
Collapse
Affiliation(s)
- Maartje Kristensen
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emma M. de Koff
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Spaarne Gasthuis Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands
| | - Mei Ling Chu
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Simone Groendijk
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Karin M. de Winter-de Groot
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Hettie M. Janssens
- Department of Pediatric Pulmonology and Allergology, Sophia Children’s Hospital, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Harm A. Tiddens
- Department of Pediatric Pulmonology and Allergology, Sophia Children’s Hospital, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mireille van Westreenen
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Elisabeth A. M. Sanders
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- National Institute for Public Health and the Environment, Centre for Infectious Disease Control, Bilthoven, The Netherlands
| | - Bert H. G. M. Arets
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Cornelis K. van der Ent
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sabine M. P. J. Prevaes
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Debby Bogaert
- Department of Pediatrics, Wilhelmina Children’s Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
2
|
Bogaert D, van Beveren GJ, de Koff EM, Lusarreta Parga P, Balcazar Lopez CE, Koppensteiner L, Clerc M, Hasrat R, Arp K, Chu MLJN, de Groot PCM, Sanders EAM, van Houten MA, de Steenhuijsen Piters WAA. Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites. Cell Host Microbe 2023; 31:447-460.e6. [PMID: 36893737 DOI: 10.1016/j.chom.2023.01.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [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: 10/07/2022] [Revised: 12/07/2022] [Accepted: 01/30/2023] [Indexed: 03/11/2023]
Abstract
Early-life microbiota seeding and subsequent development is crucial to future health. Cesarean-section (CS) birth, as opposed to vaginal delivery, affects early mother-to-infant transmission of microbes. Here, we assess mother-to-infant microbiota seeding and early-life microbiota development across six maternal and four infant niches over the first 30 days of life in 120 mother-infant pairs. Across all infants, we estimate that on average 58.5% of the infant microbiota composition can be attributed to any of the maternal source communities. All maternal source communities seed multiple infant niches. We identify shared and niche-specific host/environmental factors shaping the infant microbiota. In CS-born infants, we report reduced seeding of infant fecal microbiota by maternal fecal microbes, whereas colonization with breastmilk microbiota is increased when compared with vaginally born infants. Therefore, our data suggest auxiliary routes of mother-to-infant microbial seeding, which may compensate for one another, ensuring that essential microbes/microbial functions are transferred irrespective of disrupted transmission routes.
Collapse
Affiliation(s)
- Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK.
| | - Gina J van Beveren
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands
| | - Emma M de Koff
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands
| | - Paula Lusarreta Parga
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK
| | - Carlos E Balcazar Lopez
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK
| | - Lilian Koppensteiner
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK
| | - Melanie Clerc
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, EH16 4TJ Edinburgh, UK
| | - Raiza Hasrat
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands
| | - Kayleigh Arp
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands
| | - Pieter C M de Groot
- Department of Obstetrics and Gynaecology, Spaarne Gasthuis, 2035 RC Haarlem, the Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands
| | | | - Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, 3584 EA Utrecht, the Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, 3721 MA Bilthoven, the Netherlands.
| |
Collapse
|
3
|
de Steenhuijsen Piters WAA, Watson RL, de Koff EM, Hasrat R, Arp K, Chu MLJN, de Groot PCM, van Houten MA, Sanders EAM, Bogaert D. Early-life viral infections are associated with disadvantageous immune and microbiota profiles and recurrent respiratory infections. Nat Microbiol 2022; 7:224-237. [PMID: 35058634 DOI: 10.1038/s41564-021-01043-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [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: 06/30/2021] [Accepted: 12/06/2021] [Indexed: 12/17/2022]
Abstract
The respiratory tract is populated by a specialized microbial ecosystem, which is seeded during and directly following birth. Perturbed development of the respiratory microbial community in early-life has been associated with higher susceptibility to respiratory tract infections (RTIs). Given a consistent gap in time between first signs of aberrant microbial maturation and the observation of the first RTIs, we hypothesized that early-life host-microbe cross-talk plays a role in this process. We therefore investigated viral presence, gene expression profiles and nasopharyngeal microbiota from birth until 12 months of age in 114 healthy infants. We show that the strongest dynamics in gene expression profiles occurred within the first days of life, mostly involving Toll-like receptor (TLR) and inflammasome signalling. These gene expression dynamics coincided with rapid microbial niche differentiation. Early asymptomatic viral infection co-occurred with stronger interferon activity, which was related to specific microbiota dynamics following, including early enrichment of Moraxella and Haemophilus spp. These microbial trajectories were in turn related to a higher number of subsequent (viral) RTIs over the first year of life. Using a multi-omic approach, we found evidence for species-specific host-microbe interactions related to consecutive susceptibility to RTIs. Although further work will be needed to confirm causality of our findings, together these data indicate that early-life viral encounters could impact subsequent host-microbe cross-talk, which is linked to later-life infections.
Collapse
Affiliation(s)
- Wouter A A de Steenhuijsen Piters
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Rebecca L Watson
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - Emma M de Koff
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
| | - Raiza Hasrat
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Kayleigh Arp
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Mei Ling J N Chu
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Pieter C M de Groot
- Department of Obstetrics and Gynaecology, Spaarne Gasthuis, Hoofddorp and Haarlem, the Netherlands
| | - Marlies A van Houten
- Spaarne Gasthuis Academy, Hoofddorp and Haarlem, the Netherlands
- Department of Paediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, the Netherlands
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital/University Medical Center Utrecht, Utrecht, the Netherlands.
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, the Netherlands.
- Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
4
|
de Koff EM, van Houten MA, de Heij F, Berbers GAM, Bogaert D, Sanders EAM. Salivary antibody responses to ten-valent pneumococcal conjugate vaccination following two different immunization schedules in a healthy birth cohort. Vaccine 2021; 40:408-413. [PMID: 34961634 DOI: 10.1016/j.vaccine.2021.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/31/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 11/18/2022]
Abstract
Pneumococcal conjugate vaccines reduce pneumococcal colonization via serotype-specific immunoglobulin G (IgG) at mucosal surfaces. The infant immunization schedule with the ten-valent pneumococcal conjugate vaccine (PCV10) changed from a 3 + 1 schedule (2-3-4-11 months) to a 2 + 1 schedule (2-4-11 months) in The Netherlands in 2013. We compared anti-pneumococcal IgG concentrations in saliva between the schedules. IgG was measured using a fluorescent bead-based multiplex immunoassay at the ages of 6 (post-primary) and 12 (post-booster) months in 51 infants receiving the 3 + 1 schedule and 68 infants receiving the 2 + 1 schedule. Post-primary IgG geometric mean concentrations (GMCs) were comparable between schedules for all vaccine serotypes. Post-booster IgG GMCs were significantly lower after the 2 + 1 schedule for serotypes 4 (p = 0.035), 7F (p = 0.048) and 23F (p = 0.0056). This study shows small differences in mucosal IgG responses between a 3 + 1 and a 2 + 1 PCV10 schedule. Future studies should establish correlates of protection against pneumococcal colonization for mucosal antibodies.
Collapse
Affiliation(s)
- Emma M de Koff
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, Netherlands; Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, Netherlands
| | - Marlies A van Houten
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, Netherlands; Department of Paediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, Netherlands
| | - Femke de Heij
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Guy A M Berbers
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Debby Bogaert
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands; Medical Research Council and University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK.
| | - Elisabeth A M Sanders
- Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, Netherlands; Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| |
Collapse
|
5
|
de Koff EM, Euser SM, Badoux P, Sluiter-Post J, Eggink D, Sanders EAM, van Houten MA. Respiratory Pathogen Detection in Children: Saliva as a Diagnostic Specimen. Pediatr Infect Dis J 2021; 40:e351-e353. [PMID: 34260500 DOI: 10.1097/inf.0000000000003191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We compared pathogen detection between saliva, nasopharyngeal and oropharyngeal swabs in children with respiratory symptoms. The sensitivity in nasopharyngeal swabs was 93% (95% confidence interval [CI]: 78%-98%), in oropharyngeal swabs 79% (95% CI: 60%-90%), in saliva overall 76% (95% CI: 58%-88%) and in 18 saliva samples collected with drooling or sponges, 94% (95% CI: 74%-99%). Saliva could be a relevant specimen alternative.
Collapse
Affiliation(s)
- Emma M de Koff
- From the Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Sjoerd M Euser
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Paul Badoux
- Regional Public Health Laboratory Kennemerland, Haarlem, The Netherlands
| | - Judith Sluiter-Post
- From the Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
| | - Dirk Eggink
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Elisabeth A M Sanders
- Department of Pediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Marlies A van Houten
- From the Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
- Department of Pediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
| |
Collapse
|
6
|
de Koff EM, Man WH, van Houten MA, Vlieger AM, Chu MLJN, Sanders EAM, Bogaert D. Microbial and clinical factors are related to recurrence of symptoms after childhood lower respiratory tract infection. ERJ Open Res 2021; 7:00939-2020. [PMID: 34195257 PMCID: PMC8236756 DOI: 10.1183/23120541.00939-2020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/15/2020] [Accepted: 02/17/2021] [Indexed: 12/16/2022] Open
Abstract
Childhood lower respiratory tract infections (LRTI) are associated with dysbiosis of the nasopharyngeal microbiota, and persistent dysbiosis following the LRTI may in turn be related to recurrent or chronic respiratory problems. Therefore, we aimed to investigate microbial and clinical predictors of early recurrence of respiratory symptoms as well as recovery of the microbial community following hospital admission for LRTI in children. To this end, we collected clinical data and characterised the nasopharyngeal microbiota of 154 children (4 weeks–5 years old) hospitalised for a LRTI (bronchiolitis, pneumonia, wheezing illness or mixed infection) at admission and 4–8 weeks later. Data were compared to 307 age-, sex- and time-matched healthy controls. During follow-up, 66% of cases experienced recurrence of (mild) respiratory symptoms. In cases with recurrence of symptoms during follow-up, we found distinct nasopharyngeal microbiota at hospital admission, with higher levels of Haemophilus influenzae/haemolyticus, Prevotella oris and other gram-negatives and lower levels of Corynebacterium pseudodiphtheriticum/propinquum and Dolosigranulum pigrum compared with healthy controls. Furthermore, in cases with recurrence of respiratory symptoms, recovery of the microbiota was also diminished. Especially in cases with wheezing illness, we observed a high rate of recurrence of respiratory symptoms, as well as diminished microbiota recovery at follow-up. Together, our results suggest a link between the nasopharyngeal microbiota composition during LRTI and early recurrence of respiratory symptoms, as well as diminished microbiota recovery after 4–8 weeks. Future studies should investigate whether (speed of) ecological recovery following childhood LRTI is associated with long-term respiratory problems. Composition of nasopharyngeal microbiota during LRTI in children is related to recurring respiratory symptoms in the following months, and to incomplete microbiota recovery. Future research may pinpoint host and microbial predictors of clinical outcomes.https://bit.ly/3aInAwN
Collapse
Affiliation(s)
- Emma M de Koff
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands.,Dept of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Wing Ho Man
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands.,Dept of Paediatrics, Willem-Alexander Children's Hospital and Leiden University Medical Centre, Leiden, The Netherlands
| | - Marlies A van Houten
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands.,Dept of Paediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
| | - Arine M Vlieger
- Dept of Paediatrics, St Antonius Ziekenhuis, Nieuwegein, The Netherlands
| | - Mei Ling J N Chu
- Dept of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Elisabeth A M Sanders
- Dept of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Debby Bogaert
- Dept of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands.,Medical Research Council and University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
7
|
de Koff EM, Man WH, van Houten MA, Jansen NJG, Arp K, Hasrat R, Sanders EAM, Bogaert D. The respiratory microbiota during and following mechanical ventilation for respiratory infections in children. Eur Respir J 2020; 57:13993003.02652-2020. [PMID: 33303531 PMCID: PMC8012590 DOI: 10.1183/13993003.02652-2020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 07/06/2020] [Accepted: 11/14/2020] [Indexed: 11/30/2022]
Abstract
The lower respiratory tract (LRT) harbours distinct, dynamic low-density microbial communities, established through micro-aspiration from the upper respiratory tract (URT) [1–3]. However, during intubation and mechanical ventilation, the endotracheal tube temporarily alters the anatomical continuity between URT and LRT, and may provide a bridge for airborne microbes and a barrier for micro-aspiration. Shortly after intubation for a severe LRT infection (LRTI) in children, the microbiota of the nasopharynx and LRT were shown to be very similar [4]. However, it remains unknown how the respiratory microbial community develops while the child recovers from the infection under treatment with mechanical ventilation and antibiotics. We therefore analysed respiratory microbiota changes in children participating in our study on acute LRTIs and who were admitted to the paediatric intensive care unit (PICU) for mechanical ventilation [4]. During mechanical ventilation for an LRTI in children, the respiratory microbiota shifted from Haemophilus- and Moraxella-dominated profiles to profiles dominated by antibiotic-resistant Enterobacteriaceae, and Staphylococcus and Streptococcus species.https://bit.ly/3pGfvhQ
Collapse
Affiliation(s)
- Emma M de Koff
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands.,Dept of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Wing Ho Man
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands.,Dept of Paediatrics, Willem-Alexander Children's Hospital and Leiden University Medical Centre, Leiden, The Netherlands
| | - Marlies A van Houten
- Spaarne Academy, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands.,Dept of Paediatrics, Spaarne Gasthuis, Hoofddorp and Haarlem, The Netherlands
| | - Nicolaas J G Jansen
- Dept of Paediatric Intensive Care, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands.,Dept of Paediatrics, Beatrix Children's Hospital, University Medical Centre Groningen, Groningen, The Netherlands
| | - Kayleigh Arp
- Dept of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Raiza Hasrat
- Dept of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Elisabeth A M Sanders
- Dept of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Debby Bogaert
- Dept of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital and University Medical Centre Utrecht, Utrecht, The Netherlands .,Medical Research Council and University of Edinburgh Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
8
|
Watson RL, de Koff EM, Bogaert D. Characterising the respiratory microbiome. Eur Respir J 2019; 53:13993003.01711-2018. [PMID: 30487204 DOI: 10.1183/13993003.01711-2018] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/05/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Rebecca L Watson
- Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK.,Both authors contributed equally
| | - Emma M de Koff
- Dept of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands.,Spaarne Academy, Spaarne Gasthuis, Hoofddorp, The Netherlands.,Both authors contributed equally
| | - Debby Bogaert
- Center for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, Edinburgh, UK.,Dept of Pediatrics, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, The Netherlands
| |
Collapse
|