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Dion MB, Shah SA, Deng L, Thorsen J, Stokholm J, Krogfelt KA, Schjørring S, Horvath P, Allard A, Nielsen DS, Petit MA, Moineau S. Escherichia coli CRISPR arrays from early life fecal samples preferentially target prophages. ISME J 2024; 18:wrae005. [PMID: 38366192 PMCID: PMC10910852 DOI: 10.1093/ismejo/wrae005] [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] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/18/2024]
Abstract
CRISPR-Cas systems are defense mechanisms against phages and other nucleic acids that invade bacteria and archaea. In Escherichia coli, it is generally accepted that CRISPR-Cas systems are inactive in laboratory conditions due to a transcriptional repressor. In natural isolates, it has been shown that CRISPR arrays remain stable over the years and that most spacer targets (protospacers) remain unknown. Here, we re-examine CRISPR arrays in natural E. coli isolates and investigate viral and bacterial genomes for spacer targets using a bioinformatics approach coupled to a unique biological dataset. We first sequenced the CRISPR1 array of 1769 E. coli isolates from the fecal samples of 639 children obtained during their first year of life. We built a network with edges between isolates that reflect the number of shared spacers. The isolates grouped into 34 modules. A search for matching spacers in bacterial genomes showed that E. coli spacers almost exclusively target prophages. While we found instances of self-targeting spacers, those involving a prophage and a spacer within the same bacterial genome were rare. The extensive search for matching spacers also expanded the library of known E. coli protospacers to 60%. Altogether, these results favor the concept that E. coli's CRISPR-Cas is an antiprophage system and highlight the importance of reconsidering the criteria use to deem CRISPR-Cas systems active.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
| | - Ling Deng
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Jonathan Thorsen
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Ledreborg Alle 34, 2820 Gentofte, Denmark
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Universitetsvej 1, 4000 Roskilde, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300S Copenhagen, Denmark
| | - Philippe Horvath
- IFF Danisco, Health & Biosciences, Dangé-Saint-Romain 86220, France
| | - Antoine Allard
- Département de physique, de génie physique et d’optique, Université Laval, Québec, QC G1V 0A6, Canada
- Centre interdisciplinaire en modélisation mathématique, Université Laval, Québec, QC G1V 0A6, Canada
| | - Dennis S Nielsen
- Food Science, University of Copenhagen, Rolighedsvej 26, 1958 Frederiksberg, Denmark
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Micalis, Jouy-en-Josas 78350, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
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Halbedel S, Sperle I, Lachmann R, Kleta S, Fischer MA, Wamp S, Holzer A, Lüth S, Murr L, Freitag C, Espenhain L, Stephan R, Pietzka A, Schjørring S, Bloemberg G, Wenning M, Al Dahouk S, Wilking H, Flieger A. Large Multicountry Outbreak of Invasive Listeriosis by a Listeria monocytogenes ST394 Clone Linked to Smoked Rainbow Trout, 2020 to 2021. Microbiol Spectr 2023; 11:e0352022. [PMID: 37036341 PMCID: PMC10269727 DOI: 10.1128/spectrum.03520-22] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 03/17/2023] [Indexed: 04/11/2023] Open
Abstract
Whole-genome sequencing (WGS) has revolutionized surveillance of infectious diseases. Disease outbreaks can now be detected with high precision, and correct attribution of infection sources has been improved. Listeriosis, caused by the bacterium Listeria monocytogenes, is a foodborne disease with a high case fatality rate and a large proportion of outbreak-related cases. Timely recognition of listeriosis outbreaks and precise allocation of food sources are important to prevent further infections and to promote public health. We report the WGS-based identification of a large multinational listeriosis outbreak with 55 cases that affected Germany, Austria, Denmark, and Switzerland during 2020 and 2021. Clinical isolates formed a highly clonal cluster (called Ny9) based on core genome multilocus sequence typing (cgMLST). Routine and ad hoc investigations of food samples identified L. monocytogenes isolates from smoked rainbow trout filets from a Danish producer grouping with the Ny9 cluster. Patient interviews confirmed consumption of rainbow trout as the most likely infection source. The Ny9 cluster was caused by a MLST sequence type (ST) ST394 clone belonging to molecular serogroup IIa, forming a distinct clade within molecular serogroup IIa strains. Analysis of the Ny9 genome revealed clpY, dgcB, and recQ inactivating mutations, but phenotypic characterization of several virulence-associated traits of a representative Ny9 isolate showed that the outbreak strain had the same pathogenic potential as other serogroup IIa strains. Our report demonstrates that international food trade can cause multicountry outbreaks that necessitate cross-border outbreak collaboration. It also corroborates the relevance of ready-to-eat smoked fish products as causes for listeriosis. IMPORTANCE Listeriosis is a severe infectious disease in humans and characterized by an exceptionally high case fatality rate. The disease is transmitted through consumption of food contaminated by the bacterium Listeria monocytogenes. Outbreaks of listeriosis often occur but can be recognized and stopped through implementation of whole-genome sequencing-based pathogen surveillance systems. We here describe the detection and management of a large listeriosis outbreak in Germany and three neighboring countries. This outbreak was caused by rainbow trout filet, which was contaminated by a L. monocytogenes clone belonging to sequence type ST394. This work further expands our knowledge on the genetic diversity and transmission routes of an important foodborne pathogen.
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Affiliation(s)
- Sven Halbedel
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
- Institute for Medical Microbiology and Hospital Hygiene, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - Ida Sperle
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
- Postgraduate Training for Applied Epidemiology (PAE), Robert Koch Institute, Berlin, Germany
- ECDC Fellowship Program, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Raskit Lachmann
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Sylvia Kleta
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Martin A. Fischer
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Wamp
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
| | - Alexandra Holzer
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Stefanie Lüth
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Larissa Murr
- State Institute for Food, Food Hygiene and Cosmetics, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Christin Freitag
- Institute for Food of Animal Origin, Rhineland–Palatinate State Investigation Office, Koblenz, Germany
| | - Laura Espenhain
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Roger Stephan
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Graz, Austria
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Guido Bloemberg
- Swiss National Center for Enteropathogenic Bacteria and Listeria, Institute for Food Safety and Hygiene, University of Zurich, Switzerland
| | - Mareike Wenning
- State Institute for Food, Food Hygiene and Cosmetics, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Sascha Al Dahouk
- National Reference Laboratory for Listeria monocytogenes, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Hendrik Wilking
- FG35–Division for Gastrointestinal Infections, Zoonoses and Tropical Infections, Robert Koch Institute, Berlin, Germany
| | - Antje Flieger
- FG11–Division of Enteropathogenic bacteria and Legionella, Consultant Laboratory for Listeria, Robert Koch Institute, Wernigerode, Germany
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Torpdahl M, White ED, Schjørring S, Søby M, Engberg J, Engsbro AL, Holt HM, Lemming L, Lützen L, Olesen B, Coia JE, Kjelsø C, Müller L. Imported spring onions related to the first recorded outbreak of enteroinvasive Escherichia coli in Denmark, November to December 2021. Euro Surveill 2023; 28. [PMID: 37052680 PMCID: PMC10103548 DOI: 10.2807/1560-7917.es.2023.28.15.2200572] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Between November and December 2021, the first ever recorded outbreak of enteroinvasive Escherichia coli in Denmark occurred at national scale. We describe the investigation of this outbreak, which was initially recognised in early December 2021. A total of 88 cases (58 female; 30 male) with a median age of 52 years (range: 0-91) were detected by PCR-based diagnostic methods. Case ascertainment was complicated by current culture-free diagnostic procedures, with only 34 cases confirmed by culture, serotyping and whole genome sequencing. Isolates from cases grouped into two serotypes (O136:H7 and O96:H19), which was supported by whole-genome-sequence-phylogeny, also yielding two clusters. Interviews of 42 cases and traceback investigation pointed towards consumption of ready-to-eat salads as the outbreak cause. While the ready-to-eat salads comprised different vegetables, imported spring onions were the only common ingredient and thus the likely source. Environmental investigations failed to recover outbreak strains. This report highlights the value of fast typing (here O-typing) to confirm cases in an outbreak situation. Timely communication and data sharing are also important, and were facilitated by the national collaboration between relevant laboratories, the public health institute and the veterinary and food administration. High hygiene standards for imported fresh vegetables intended for ready-to-eat products are essential.
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Affiliation(s)
| | | | | | - Malene Søby
- Danish Veterinary and Food Administration, Glostrup, Denmark
| | - Jørgen Engberg
- Department of Clinical Microbiology, Zealand University Hospital, Slagelse, Denmark
| | - Anne Line Engsbro
- Department of Clinical Microbiology, Copenhagen University Hospital, Hvidovre, Denmark
| | - Hanne M Holt
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Lars Lemming
- Department of Clinical Microbiology, Aarhus University Hospital, Aarhus, Denmark
| | - Lisbeth Lützen
- Department of Clinical Microbiology, Lillebaelt Hospital, Vejle, Denmark
| | - Bente Olesen
- Department of Clinical Microbiology, Copenhagen University Hospital, Herlev and Gentofte, Denmark
| | - John E Coia
- Department of Clinical Diagnostics, Hospital South West Jutland, Esbjerg, Denmark
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Piras F, Spanu V, Siddi G, Gymoese P, Spanu C, Cibin V, Schjørring S, De Santis E, Scarano C. Whole-genome sequencing analysis of highly prevalent Salmonella serovars in wild boars from a national park in Sardinia. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.108247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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5
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Michlmayr D, de Sousa LA, Müller L, Jokelainen P, Ethelberg S, Vestergaard LS, Schjørring S, Mikkelsen S, Jensen CW, Rasmussen LD, Stensvold CR. Incubation period, spore shedding duration, and symptoms of Enterocytozoon bieneusi genotype C infection in a foodborne outbreak in Denmark, 2020. Clin Infect Dis 2021; 75:468-475. [PMID: 34791090 PMCID: PMC9427152 DOI: 10.1093/cid/ciab949] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
Background Microsporidia are rarely reported to cause outbreaks of diarrhea. We describe a foodborne outbreak of microsporidiosis from a workplace canteen in November 2020 in Denmark. Methods A probable case was defined as any person using the canteen between 4 November and 13 December 2020, reporting at least one gastrointestinal symptom, whereas a confirmed case also had an Enterocytozoon bieneusi positive stool sample. A web-based questionnaire was used to collect clinical, epidemiological, and food exposure data. We performed a retrospective cohort study and tested stool samples from affected individuals for bacterial, viral, and parasitic pathogens, including E. bieneusi. Results Altogether, 195 individuals completed the questionnaire. We identified 52 cases (65% male; median age 45 years [range 25–65]). Diarrhea (90%), fatigue (83%), and abdominal pain (79%) were the most commonly reported symptoms. Eight cases were laboratory-confirmed and had E. bieneusi genotype C. The incubation period was between 5 and 12 days, and polymerase chain reaction (PCR)-detectable spore shedding occurred up to 43 days after symptom onset. Disease was associated with consuming food from the workplace canteen on 4 November 2020 (relative risk [RR[, 2.8 [95% confidence interval [CI]: 1.4 – 5.4]) and lunchboxes containing open sandwiches (RR, 3.2 [95% CI: 1.4 – 7.2]) served that day. Conclusions This is the second documented foodborne outbreak of E. bieneusi genotype C-associated diarrhea worldwide. Epidemiological findings advocated an open sandwiches lunchbox from 4 November 2020, as a likely source. E. bieneusi may be an under-reported cause of outbreaks of diarrhea, and testing for it might be useful in foodborne outbreak investigations.
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Affiliation(s)
- Daniela Michlmayr
- Department of Bacteria, Parasites and Fungi, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark.,European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Luís Alves de Sousa
- Department of Infectious Disease Epidemiology and Prevention, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark.,European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | - Luise Müller
- Department of Infectious Disease Epidemiology and Prevention, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Pikka Jokelainen
- Department of Bacteria, Parasites and Fungi, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark.,Department of Public Health, Global Health Section, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Skafte Vestergaard
- Department of Bacteria, Parasites and Fungi, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark.,Department of Infectious Disease Epidemiology and Prevention, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Sarah Mikkelsen
- Danish Veterinary Food Administration (DVFA), Copenhagen, Denmark
| | | | - Lasse Dam Rasmussen
- Department of Virus & Microbiological Special Diagnostics, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Christen Rune Stensvold
- Department of Bacteria, Parasites and Fungi, Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
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6
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Joensen KG, Schjørring S, Gantzhorn MR, Vester CT, Nielsen HL, Engberg JH, Holt HM, Ethelberg S, Müller L, Sandø G, Nielsen EM. Whole genome sequencing data used for surveillance of Campylobacter infections: detection of a large continuous outbreak, Denmark, 2019. ACTA ACUST UNITED AC 2021; 26. [PMID: 34085631 PMCID: PMC8176674 DOI: 10.2807/1560-7917.es.2021.26.22.2001396] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Background Campylobacter is one of the most frequent causes of bacterial gastroenteritis. Campylobacter outbreaks are rarely reported, which could be a reflection of a surveillance without routine molecular typing. We have previously shown that numerous small outbreak-like clusters can be detected when whole genome sequencing (WGS) data of clinical Campylobacter isolates was applied. Aim Typing-based surveillance of Campylobacter infections was initiated in 2019 to enable detection of large clusters of clinical isolates and to match them to concurrent retail chicken isolates in order to react on ongoing outbreaks. Methods We performed WGS continuously on isolates from cases (n = 701) and chicken meat (n = 164) throughout 2019. Core genome multilocus sequence typing was used to detect clusters of clinical isolates and match them to isolates from chicken meat. Results Seventy-two clusters were detected, 58 small clusters (2–4 cases) and 14 large clusters (5–91 cases). One third of the clinical isolates matched isolates from chicken meat. One large cluster persisted throughout the whole year and represented 12% of all studied Campylobacter cases. This cluster type was detected in several chicken samples and was traced back to one slaughterhouse, where interventions were implemented to control the outbreak. Conclusion Our WGS-based surveillance has contributed to an improved understanding of the dynamics of the occurrence of Campylobacter strains in chicken meat and the correlation to clusters of human cases.
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Affiliation(s)
| | - Susanne Schjørring
- Statens Serum Institut, Department of Bacteria, Parasites and Fungi, Copenhagen, Denmark
| | | | | | - Hans Linde Nielsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark.,Department of Clinical Microbiology, Aalborg University Hospital, Aalborg, Denmark
| | | | - Hanne Marie Holt
- Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark
| | - Steen Ethelberg
- Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Copenhagen, Denmark
| | - Luise Müller
- Statens Serum Institut, Department of Infectious Disease Epidemiology and Prevention, Copenhagen, Denmark
| | - Gudrun Sandø
- Danish Veterinary and Food Administration, Glostrup, Denmark
| | - Eva Møller Nielsen
- Statens Serum Institut, Department of Bacteria, Parasites and Fungi, Copenhagen, Denmark
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Ahluwalia TS, Eliasen AU, Sevelsted A, Pedersen CET, Stokholm J, Chawes B, Bork-Jensen J, Grarup N, Pedersen O, Hansen T, Linneberg A, Sharma A, Weiss ST, Evans MD, Jackson DJ, Morin A, Krogfelt KA, Schjørring S, Mortensen PB, Hougaard DM, Bybjerg-Grauholm J, Bækvad-Hansen M, Mors O, Nordentoft M, Børglum AD, Werge T, Agerbo E, Gern JE, Lemanske RF, Ober C, Pedersen AG, Bisgaard H, Bønnelykke K. FUT2-ABO epistasis increases the risk of early childhood asthma and Streptococcus pneumoniae respiratory illnesses. Nat Commun 2020; 11:6398. [PMID: 33328473 PMCID: PMC7744576 DOI: 10.1038/s41467-020-19814-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
Asthma with severe exacerbation is the most common cause of hospitalization among young children. We aim to increase the understanding of this clinically important disease entity through a genome-wide association study. The discovery analysis comprises 2866 children experiencing severe asthma exacerbation between ages 2 and 6 years, and 65,415 non-asthmatic controls, and we replicate findings in 918 children from the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC) birth cohorts. We identify rs281379 near FUT2/MAMSTR on chromosome 19 as a novel risk locus (OR = 1.18 (95% CI = 1.11-1.25), Pdiscovery = 2.6 × 10-9) as well as a biologically plausible interaction between functional variants in FUT2 and ABO. We further discover and replicate a potential causal mechanism behind this interaction related to S. pneumoniae respiratory illnesses. These results suggest a novel mechanism of early childhood asthma and demonstrates the importance of phenotype-specificity for discovery of asthma genes and epistasis.
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Affiliation(s)
- Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Department of Biology, The Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
| | - Anders U Eliasen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Astrid Sevelsted
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Casper-Emil T Pedersen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael D Evans
- Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | - Andreanne Morin
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Preben B Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- NCRR, The National Center for Register-based research, Business and Social Sciences, Aarhus University, Aarhus C, Denmark
- CIRRAU-Center for Integrated Register-Based Research at Aarhus University, Aarhus C, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Mental Health Center Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department of Biomedicine and iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus C, Denmark
- Center for Genomics and Personalized Medicine, Central Region Denmark, Aarhus C, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Mental Health Center Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- NCRR, The National Center for Register-based research, Business and Social Sciences, Aarhus University, Aarhus C, Denmark
- CIRRAU-Center for Integrated Register-Based Research at Aarhus University, Aarhus C, Denmark
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | | | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Anders G Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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Christensen ED, Thorsen J, Stokholm J, Pedersen TM, Brix S, Krogfelt KA, Schjørring S, Chawes B, Bønnelykke K, Bisgaard H, Rasmussen MA. Early life bacterial airway colonization, local immune mediator response and risk of otitis media. J Med Microbiol 2020; 69:1124-1131. [PMID: 32597749 DOI: 10.1099/jmm.0.001227] [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] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Acute otitis media (AOM) is the most common bacterial infection in early childhood, but the underlying mechanisms making some children more susceptible are poorly understood.Aim. To examine the associations between bacterial airway colonization in early life and the risk of AOM and tympanostomy tube insertion (TTI), and whether such associations are modulated by an insufficient local immune mediator response to bacterial colonization.Methodology. Bacterial cultures from hypopharyngeal samples were obtained at 1 week, 1 month and 3 months of age in the Copenhagen Prospective Studies on Asthma in Childhood 2010 (COPSAC2010) cohort comprising 700 children. Twenty immune mediators were quantified from airway mucosal lining fluid sampled at 1 month. AOM symptoms were registered in a daily diary until 3 years. Information on TTI in the first 3 years was obtained from national registers.Results. Children colonized with Streptococcus pneumoniae at 1 month of age had increased incidence of AOM [aIRR 2.43 (1.14-5.21)] and children colonized with Moraxella catarrhalis at 1 month or Haemophilus influenzae at 3 months had an increased risk of TTI [aHR 1.45 (1.00-2.10) and 1.73 (1.10-2.71)]. There were no associations between the local immune mediator response to colonization and risk of AOM or TTI.Conclusion. Pathogenic bacterial airway colonization in early life was found to be associated with an increased risk of otitis media, albeit not consistently. These associations were independent of the local immune response to colonization.
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Affiliation(s)
- Emil Dalgaard Christensen
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark.,Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jonathan Thorsen
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark.,Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark.,Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Tine Marie Pedersen
- Department of Pediatrics, Slagelse Hospital, Slagelse, Denmark.,Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Brix
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | | | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Bo Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Morten Arendt Rasmussen
- Department of Food Science, University of Copenhagen, Frederiksberg, Denmark.,Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
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9
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Schjørring S, Jepsen MT, Sørensen CA, Valentiner-Branth P, Kantsø B, Petersen RF, Skovgaard O, Krogfelt KA. Laboratory Diagnostics of Rickettsia Infections in Denmark 2008-2015. Biology (Basel) 2020; 9:biology9060133. [PMID: 32575502 PMCID: PMC7345066 DOI: 10.3390/biology9060133] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 11/30/2022]
Abstract
Rickettsiosis is a vector-borne disease caused by bacterial species in the genus Rickettsia. Ticks in Scandinavia are reported to be infected with Rickettsia, yet only a few Scandinavian human cases are described, and rickettsiosis is poorly understood. The aim of this study was to determine the prevalence of rickettsiosis in Denmark based on laboratory findings. We found that in the Danish individuals who tested positive for Rickettsia by serology, the majority (86%; 484/561) of the infections belonged to the spotted fever group. In contrast, we could confirm 13 of 41 (32%) PCR-positive individuals by sequencing and identified all of these as R. africae, indicating infections after travel exposure. These 13 samples were collected from wound/skin material. In Denmark, approximately 85 individuals test positive for Rickettsia spp. annually, giving an estimated 26% (561/2147) annual prevalence among those suspected of rickettsiosis after tick bites. However, without clinical data and a history of travel exposure, a true estimation of rickettsiosis acquired endemically by tick bites cannot be made. Therefore, we recommend that both clinical data and specific travel exposure be included in a surveillance system of Rickettsia infections.
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Affiliation(s)
- Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300 Copenhagen, Denmark; (S.S.); (M.T.J.); (R.F.P.)
- European Program for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), 27180 Solnar, Sweden
| | - Martin Tugwell Jepsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300 Copenhagen, Denmark; (S.S.); (M.T.J.); (R.F.P.)
- Scandtick Innovation, Project Group, InterReg, 551 11 Jönköping, Sweden;
| | - Camilla Adler Sørensen
- Scandtick Innovation, Project Group, InterReg, 551 11 Jönköping, Sweden;
- Virus and Microbiological Special Diagnostics, Statens Serum Institut (SSI), 2300 Copenhagen, Denmark;
| | - Palle Valentiner-Branth
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut (SSI), 2300 Copenhagen, Denmark;
| | - Bjørn Kantsø
- Virus and Microbiological Special Diagnostics, Statens Serum Institut (SSI), 2300 Copenhagen, Denmark;
| | - Randi Føns Petersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300 Copenhagen, Denmark; (S.S.); (M.T.J.); (R.F.P.)
- Virus and Microbiological Special Diagnostics, Statens Serum Institut (SSI), 2300 Copenhagen, Denmark;
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Correspondence: (O.S.); (K.A.K.)
| | - Karen A. Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300 Copenhagen, Denmark; (S.S.); (M.T.J.); (R.F.P.)
- Scandtick Innovation, Project Group, InterReg, 551 11 Jönköping, Sweden;
- Virus and Microbiological Special Diagnostics, Statens Serum Institut (SSI), 2300 Copenhagen, Denmark;
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
- Correspondence: (O.S.); (K.A.K.)
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10
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Mathieu A, Dion M, Deng L, Tremblay D, Moncaut E, Shah SA, Stokholm J, Krogfelt KA, Schjørring S, Bisgaard H, Nielsen DS, Moineau S, Petit MA. Virulent coliphages in 1-year-old children fecal samples are fewer, but more infectious than temperate coliphages. Nat Commun 2020; 11:378. [PMID: 31953385 PMCID: PMC6969025 DOI: 10.1038/s41467-019-14042-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 12/10/2019] [Indexed: 01/08/2023] Open
Abstract
Bacteriophages constitute an important part of the human gut microbiota, but their impact on this community is largely unknown. Here, we cultivate temperate phages produced by 900 E. coli strains isolated from 648 fecal samples from 1-year-old children and obtain coliphages directly from the viral fraction of the same fecal samples. We find that 63% of strains hosted phages, while 24% of the viromes contain phages targeting E. coli. 150 of these phages, half recovered from strain supernatants, half from virome (73% temperate and 27% virulent) were tested for their host range on 75 E. coli strains isolated from the same cohort. Temperate phages barely infected the gut strains, whereas virulent phages killed up to 68% of them. We conclude that in fecal samples from children, temperate coliphages dominate, while virulent ones have greater infectivity and broader host range, likely playing a role in gut microbiota dynamics. The impact of bacteriophages in the human gut microbiome remains poorly understood. Here, the authors characterize coliphages isolated from a large cohort of 1-year-old infants and show that temperate coliphages dominate, while virulent ones have greater infectivity and broader host range.
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Affiliation(s)
- Aurélie Mathieu
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Moïra Dion
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Ling Deng
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Denise Tremblay
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Elisabeth Moncaut
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Shiraz A Shah
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej5, 2300S, Copenhagen, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej5, 2300S, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Herlev-Gentofte, Ledreborg Allé 34, DK-2820, Gentofte, Denmark
| | - Dennis S Nielsen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France.
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11
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Gupta S, Mortensen MS, Schjørring S, Trivedi U, Vestergaard G, Stokholm J, Bisgaard H, Krogfelt KA, Sørensen SJ. Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing. Commun Biol 2019; 2:291. [PMID: 31396571 PMCID: PMC6683184 DOI: 10.1038/s42003-019-0540-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022] Open
Abstract
Next-Generation Sequencing (NGS) of 16S rRNA gene is now one of the most widely used application to investigate the microbiota at any given body site in research. Since NGS is more sensitive than traditional culture methods (TCMs), many studies have argued for them to replace TCMs. However, are we really ready for this transition? Here we compare the diagnostic efficiency of the two methods using a large number of samples (n = 1,748 fecal and n = 1,790 hypopharyngeal), among healthy children at different time points. Here we show that bacteria identified by NGS represented 75.70% of the unique bacterial species cultured in each sample, while TCM only identified 23.86% of the bacterial species found by amplicon sequencing. We discuss the pros and cons of both methods and provide perspective on how NGS can be implemented effectively in clinical settings.
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Affiliation(s)
- Shashank Gupta
- 1Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Martin S Mortensen
- 1Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Susanne Schjørring
- 2Department of Bacterial, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen S, Denmark
| | - Urvish Trivedi
- 1Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Gisle Vestergaard
- 1Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, Copenhagen, Denmark
| | - Karen A Krogfelt
- 2Department of Bacterial, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen S, Denmark
- 4Virus and Microbiological diagnostics, Statens Serum Institut, 2300 Copenhagen S, Denmark
| | - Søren J Sørensen
- 1Section of Microbiology, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
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12
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Rahman Fink N, Chawes BL, Thorsen J, Stokholm J, Krogfelt KA, Schjørring S, Kragh M, Bønnelykke K, Brix S, Bisgaard H. Neonates colonized with pathogenic bacteria in the airways have a low-grade systemic inflammation. Allergy 2018; 73:2150-2159. [PMID: 29672858 DOI: 10.1111/all.13461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND AND OBJECTIVES The development of childhood asthma is associated with neonatal colonization with pathogenic bacteria in hypopharynx. Furthermore, established asthma is associated with systemic low-grade inflammation. We here report on the association between neonatal colonization with pathogenic bacteria in hypopharynx and the development of systemic low-grade inflammation. METHODS Bacterial colonization of the hypopharynx with Moraxella catharralis, Haemophilus influenzae, and/or Streptococcus pneumoniae was assessed in asymptomatic children from the Copenhagen Prospective Studies on Asthma in Childhood2000 (COPSAC2000 ) cohort at age 1 month by culturing technique (N = 238) and by quantitative polymerase chain reaction (qPCR) technique (N = 249) and in the COPSAC2010 cohort by culturing at age 1 month (N = 622) and again at age 3 months (N = 613). Systemic low-grade inflammation was determined in both cohorts at age 6 months by measuring plasma levels of high-sensitivity C-reactive protein (hs-CRP), tumor necrosis factor-α (TNF-α), and interleukin-6 (lL-6). RESULTS In both cohorts, bacterial colonization was associated with increased levels of hs-CRP: COPSAC2000 , 1 month culturing (geometric mean ratio of colonized/noncolonized [95% CI]), 1.39 [0.97-2.01], P = .08; 1 month qPCR, 1.55 [1.14-2.10], P < .01; COPSAC2010 , 1 month, 1.52 [1.23-1.87], P < .01; and 3 month, 1.57 [1.30-1.90], P < .01. A multiparametric principal component analysis incorporating hs-CRP, TNF-α, and IL-6 confirmed a systemic inflammatory profile in children colonized with M. catharralis, H. influenzae. and/or S. pneumoniae in the hypopharynx compared to noncolonized children (P-values < .05). CONCLUSION The composition of the upper airway microbiome in early life may cause systemic low-grade inflammation.
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Affiliation(s)
- N. Rahman Fink
- COPSAC; Copenhagen Prospective Studies on Asthma in Childhood; Herlev and Gentofte Hospital; University of Copenhagen; Copenhagen Denmark
| | - B. L. Chawes
- COPSAC; Copenhagen Prospective Studies on Asthma in Childhood; Herlev and Gentofte Hospital; University of Copenhagen; Copenhagen Denmark
| | - J. Thorsen
- COPSAC; Copenhagen Prospective Studies on Asthma in Childhood; Herlev and Gentofte Hospital; University of Copenhagen; Copenhagen Denmark
| | - J. Stokholm
- COPSAC; Copenhagen Prospective Studies on Asthma in Childhood; Herlev and Gentofte Hospital; University of Copenhagen; Copenhagen Denmark
| | - K. A. Krogfelt
- Bacterial Infections; Department of Bacteria; Parasites and Fungi; Statens Serum Institut; Copenhagen Denmark
| | - S. Schjørring
- Bacterial Infections; Department of Bacteria; Parasites and Fungi; Statens Serum Institut; Copenhagen Denmark
| | - M. Kragh
- Disease Systems Immunology; Department of Biotechnology and Biomedicine; Technical University of Denmark; Lyngby Denmark
| | - K. Bønnelykke
- COPSAC; Copenhagen Prospective Studies on Asthma in Childhood; Herlev and Gentofte Hospital; University of Copenhagen; Copenhagen Denmark
| | - S. Brix
- Disease Systems Immunology; Department of Biotechnology and Biomedicine; Technical University of Denmark; Lyngby Denmark
| | - H. Bisgaard
- COPSAC; Copenhagen Prospective Studies on Asthma in Childhood; Herlev and Gentofte Hospital; University of Copenhagen; Copenhagen Denmark
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13
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Schjørring S, Gillesberg Lassen S, Jensen T, Moura A, Kjeldgaard JS, Müller L, Thielke S, Leclercq A, Maury MM, Tourdjman M, Donguy MP, Lecuit M, Ethelberg S, Nielsen EM. Cross-border outbreak of listeriosis caused by cold-smoked salmon, revealed by integrated surveillance and whole genome sequencing (WGS), Denmark and France, 2015 to 2017. ACTA ACUST UNITED AC 2018; 22. [PMID: 29258647 PMCID: PMC5743096 DOI: 10.2807/1560-7917.es.2017.22.50.17-00762] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In August 2017, an outbreak of six listeriosis cases in Denmark was traced to cold-smoked salmon, using epidemiological investigations and whole-genome sequencing (WGS) analyses. Exchange of genome sequences allowed identification in France of a food isolate from a salmon-derived product and a human isolate from 2016 within the same cgMLST cluster as the Danish isolates (L2-SL8-ST8-CT771). The salmon product came from a third European Union country. WGS can rapidly link human cases and food isolates across Europe.
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Affiliation(s)
- Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Gillesberg Lassen
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Tenna Jensen
- The Danish Veterinary and Food Administration, Copenhagen, Denmark
| | - Alexandra Moura
- Institut Pasteur, National Reference Centre and WHO collaborating Center for Listeria, Biology of Infection Unit, Paris, France
| | - Jette S Kjeldgaard
- National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Luise Müller
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Stine Thielke
- The Danish Veterinary and Food Administration, Copenhagen, Denmark
| | - Alexandre Leclercq
- Institut Pasteur, National Reference Centre and WHO collaborating Center for Listeria, Biology of Infection Unit, Paris, France
| | - Mylene M Maury
- Institut Pasteur, National Reference Centre and WHO collaborating Center for Listeria, Biology of Infection Unit, Paris, France
| | - Mathieu Tourdjman
- Santé Publique France, the French Public Health Agency, Saint-Maurice, France
| | | | - Marc Lecuit
- Paris Descartes University, Sorbonne Paris Cité, Division of Infectious Diseases, Necker-Enfants Malades University Hospital, Institut Imagine, F-75743 Paris, France
.,Institut Pasteur, National Reference Centre and WHO collaborating Center for Listeria, Biology of Infection Unit, Paris, France
| | - Steen Ethelberg
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Eva M Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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14
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Schjørring S, Stegger M, Kjelsø C, Lilje B, Bangsborg JM, Petersen RF, David S, Uldum SA. Genomic investigation of a suspected outbreak of Legionella pneumophila ST82 reveals undetected heterogeneity by the present gold-standard methods, Denmark, July to November 2014. ACTA ACUST UNITED AC 2017; 22:30558. [PMID: 28662761 PMCID: PMC5490456 DOI: 10.2807/1560-7917.es.2017.22.25.30558] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 07/04/2016] [Accepted: 09/16/2016] [Indexed: 12/20/2022]
Abstract
Between July and November 2014, 15 community-acquired cases of Legionnaires´ disease (LD), including four with Legionella pneumophila serogroup 1 sequence type (ST) 82, were diagnosed in Northern Zealand, Denmark. An outbreak was suspected. No ST82 isolates were found in environmental samples and no external source was established. Four putative-outbreak ST82 isolates were retrospectively subjected to whole genome sequencing (WGS) followed by phylogenetic analyses with epidemiologically unrelated ST82 sequences. The four putative-outbreak ST82 sequences fell into two clades, the two clades were separated by ca 1,700 single nt polymorphisms (SNP)s when recombination regions were included but only by 12 to 21 SNPs when these were removed. A single putative-outbreak ST82 isolate sequence segregated in the first clade. The other three clustered in the second clade, where all included sequences had < 5 SNP differences between them. Intriguingly, this clade also comprised epidemiologically unrelated isolate sequences from the UK and Denmark dating back as early as 2011. The study confirms that recombination plays a major role in L. pneumophila evolution. On the other hand, strains belonging to the same ST can have only few SNP differences despite being sampled over both large timespans and geographic distances. These are two important factors to consider in outbreak investigations.
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Affiliation(s)
- Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.,European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Charlotte Kjelsø
- Department of Infectious Disease Epidemiology and prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Berit Lilje
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jette M Bangsborg
- Department of Clinical Microbiology, Herlev Hospital, University of Copenhagen, Denmark
| | - Randi F Petersen
- Department of Virus and Microbiological Special Diagnostics; Statens Serum Institut, Copenhagen, Denmark
| | - Sophia David
- Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Søren A Uldum
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
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15
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Jensen MBF, Schjørring S, Björkman JT, Torpdahl M, Litrup E, Nielsen EM, Niskanen T. External quality assessment for molecular typing of Salmonella 2013-2015: performance of the European national public health reference laboratories. Eur J Clin Microbiol Infect Dis 2017; 36:1923-1932. [PMID: 28573470 PMCID: PMC5602099 DOI: 10.1007/s10096-017-3015-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 05/12/2017] [Indexed: 11/24/2022]
Abstract
We report the results of three consecutive External Quality Assessments (EQAs) for molecular subtyping of Salmonella to assess the performance of the European national public health reference laboratories (NPHRLs). The EQA included the molecular typing methods used for European enhanced surveillance of human Salmonella infections: pulsed field gel electrophoresis (PFGE), including gel analysis by the use of the software BioNumerics, and 5-locus multiple locus variable number of tandem repeat analysis (MLVA) for serovar Typhimurium. The participation in the PFGE laboratory part was higher (27/35) than in the gel analysis (19/35) and MLVA (15/35), suggestive of the need for capacity building in methods requiring specialized equipment (MLVA) or software (gel analysis). The majority (25/27) of the participating NPHRLs produced inter-laboratory comparable PFGE gel(s). Two laboratories continued to produce low-quality gels and should have additional technical assistance in the future. In particular, two gel quality evaluation parameters, measuring "image acquisition and running conditions" and "bands", were identified to cause gel quality problems throughout the EQAs. Despite the high number of laboratories participating in the PFGE laboratory part, the participation in gel analysis was low, although increasing. In the MLVA part, the NPHRLs correctly assigned 96% (405/420) allelic profiles according to the nomenclature. In conclusion, the EQAs identified critical parameters for unsuccessful performance and helped to offer assistance to those laboratories that needed it most. The assessments supported the development of quality in molecular typing and promoted the harmonization of subtyping methods used for EU/EEA-wide surveillance of human Salmonella infections.
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Affiliation(s)
- M B F Jensen
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - S Schjørring
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
- European Programme for Public Health Microbiology Training, European Centre for Disease Prevention and Control (ECDC), Granits väg 8, 171 65, Solna, Stockholm, Sweden
| | - J T Björkman
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - M Torpdahl
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - E Litrup
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark
| | - E M Nielsen
- Unit of Foodborne Infections, Statens Serum Institut, 2300, Copenhagen, Artillerivej 5, Denmark.
| | - T Niskanen
- European Centre for Disease Prevention and Control (ECDC), Granits väg 8, 171 65, Solna, Stockholm, Sweden
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16
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Holm-Hansen C, Midgley S, Schjørring S, Fischer T. The importance of enterovirus surveillance in a Post-polio world. Clin Microbiol Infect 2017; 23:352-354. [DOI: 10.1016/j.cmi.2017.02.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/03/2017] [Accepted: 02/07/2017] [Indexed: 11/24/2022]
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Schjørring S, Niskanen T, Torpdahl M, Björkman JT, Nielsen EM. Evaluation of molecular typing of foodborne pathogens in European reference laboratories from 2012 to 2013. ACTA ACUST UNITED AC 2017; 21:30429. [PMID: 28006653 PMCID: PMC5291138 DOI: 10.2807/1560-7917.es.2016.21.50.30429] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 10/05/2016] [Indexed: 11/20/2022]
Abstract
In 2012, the European Centre for Disease Prevention and Control (ECDC) initiated external quality assessment (EQA) schemes for molecular typing including the National Public Health Reference Laboratories in Europe. The overall aim for these EQA schemes was to enhance the European surveillance of food-borne pathogens by evaluating and improving the quality and comparability of molecular typing. The EQAs were organised by Statens Serum Institut (SSI) and included Salmonella enterica subsp. enterica, verocytotoxin-producing Escherichia coli (VTEC) and Listeria monocytogenes. Inter-laboratory comparable pulsed-field gel electrophoresis (PFGE) images were obtained from 10 of 17 of the participating laboratories for Listeria, 15 of 25 for Salmonella, but only nine of 20 for VTEC. Most problems were related to PFGE running conditions and/or incorrect use of image acquisition. Analysis of the gels was done in good accordance with the provided guidelines. Furthermore, we assessed the multilocus variable-number tandem repeat analysis (MLVA) scheme for S. Typhimurium. Of 15 laboratories, nine submitted correct results for all analysed strains, and four had difficulties with one strain only. In conclusion, both PFGE and MLVA are prone to variation in quality, and there is therefore a continuous need for standardisation and validation of laboratory performance for molecular typing methods of food-borne pathogens in the human public health sector.
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Affiliation(s)
- Susanne Schjørring
- Unit of foodborne infections, Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark.,European Programme for Public Health Microbiology Training (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Taina Niskanen
- Food and Waterborne Diseases and Zoonoses Programme, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Mia Torpdahl
- Unit of foodborne infections, Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Jonas T Björkman
- Unit of foodborne infections, Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Eva Møller Nielsen
- Unit of foodborne infections, Department of Microbiology and Infection Control, Statens Serum Institut (SSI), Copenhagen, Denmark
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Stokholm J, Thorsen J, Chawes BL, Schjørring S, Krogfelt KA, Bønnelykke K, Bisgaard H. Cesarean section changes neonatal gut colonization. J Allergy Clin Immunol 2016; 138:881-889.e2. [PMID: 27045582 DOI: 10.1016/j.jaci.2016.01.028] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 12/18/2015] [Accepted: 01/06/2016] [Indexed: 11/25/2022]
Abstract
BACKGROUND Delivery by means of cesarean section has been associated with increased risk of childhood immune-mediated diseases, suggesting a role of early bacterial colonization patterns for immune maturation. OBJECTIVE We sought to describe the influence of delivery method on gut and airway colonization patterns in the first year of life in the Copenhagen Prospective Studies on Asthma in Childhood2010 (COPSAC2010) birth cohort. METHODS Seven hundred children from the COPSAC2010 birth cohort participated in this analysis. Fecal samples were collected at age 1 week, 1 month, and 1 year, and hypopharyngeal aspirates were collected at age 1 week, 1 month, and 3 months and cultured for bacteria. Detailed information on delivery method, intrapartum antibiotics, and lifestyle factors was obtained by personal interviews. RESULTS Seventy-eight percent of the children were born by means of natural delivery, 12% by means of emergency cesarean section, and 9% by means of elective cesarean section. Birth by means of cesarean section was significantly associated with colonization of the intestinal tract by Citrobacter freundii, Clostridium species, Enterobacter cloacae, Enterococcus faecalis, Klebsiella oxytoca, Klebsiella pneumoniae, and Staphylococcus aureus at age 1 week, whereas colonization by Escherichia coli was associated with natural birth. At age 1 month, these differences were less prominent, and at age 1 year, they were not apparent, which was confirmed by means of multivariate data-driven partial least squares analyses. The initial airway microbiota was unaffected by birth method. CONCLUSION Delivery by means of cesarean section was associated with early colonization patterns of the neonatal gut but not of the airways. The differences normalized within the first year of life. We speculate that microbial derangements, as indicated in our study, can demonstrate a possible link between delivery by means of cesarean section and immune-mediated disease.
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Affiliation(s)
- Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Pediatrics, Naestved Hospital, Naestved, Denmark
| | - Jonathan Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bo L Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Schjørring
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Karen A Krogfelt
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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Hebbelstrup Jensen B, Röser D, Andreassen BU, Olsen KEP, Nielsen HV, Roldgaard BB, Schjørring S, Mirsepasi-Lauridsen HC, Jørgensen SL, Mortensen EM, Petersen AM, Krogfelt KA. Childhood diarrhoea in Danish day care centres could be associated with infant colic, low birthweight and antibiotics. Acta Paediatr 2016; 105:90-5. [PMID: 26355526 DOI: 10.1111/apa.13209] [Citation(s) in RCA: 8] [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: 04/30/2015] [Revised: 08/13/2015] [Accepted: 09/07/2015] [Indexed: 12/11/2022]
Abstract
AIM Diarrhoea is very common in children attending day care centres. The aim of this study was to examine certain predisposing risk factors for an association with diarrhoea, including foreign travel, treatment with antibiotics, having household pets, infant colic, bottle feeding, using a pacifier and low birthweight. METHODS A dynamic one-year follow-up cohort study comprising 179 children from 36 day care centres was conducted from September 2009 to July 2013 in Copenhagen, Denmark. Questionnaires were sent to the children's parents or legal guardians every two months for a year, requesting information on gastrointestinal symptoms and exposure. A logistic regression was performed to identify the odds ratios of different risk factors for diarrhoea. RESULTS The odds ratios for diarrhoea were 1.97 (0.93-4.20) for children with a history of infant colic, 1.91 (0.90-4.04) for low birthweight children and 1.45 (0.74-2.82) for children who had used antibiotics. Having a pet in the household had a possible protective effect towards diarrhoeal events, with an odds ratio of 0.47 (0.20-1.09). CONCLUSION A history of infant colic, low birthweight, and to a lesser extent antibiotic use, possibly increased the risk of diarrhoea in Danish children in day care centres.
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Affiliation(s)
| | - Dennis Röser
- Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen Denmark
- Department of Paediatrics; Hvidovre University Hospital; Copenhagen Denmark
| | | | - Katharina E. P. Olsen
- Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen Denmark
| | - Henrik Vedel Nielsen
- Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen Denmark
| | - Bent Bjørn Roldgaard
- Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen Denmark
| | - Susanne Schjørring
- Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen Denmark
| | | | - Steffen L. Jørgensen
- Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen Denmark
| | - Esben Munk Mortensen
- Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen Denmark
| | - Andreas Munk Petersen
- Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen Denmark
- Department of Gastroenterology; Hvidovre University Hospital; Copenhagen Denmark
- Department of Clinical Microbiology; Hvidovre University Hospital; Copenhagen Denmark
| | - Karen Angeliki Krogfelt
- Department of Microbiology and Infection Control; Statens Serum Institut; Copenhagen Denmark
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Stokholm J, Chawes BL, Vissing NH, Bjarnadóttir E, Pedersen TM, Vinding RK, Schoos AMM, Wolsk HM, Thorsteinsdóttir S, Hallas HW, Arianto L, Schjørring S, Krogfelt KA, Fischer TK, Pipper CB, Bønnelykke K, Bisgaard H. Azithromycin for episodes with asthma-like symptoms in young children aged 1-3 years: a randomised, double-blind, placebo-controlled trial. Lancet Respir Med 2015; 4:19-26. [PMID: 26704020 PMCID: PMC7164820 DOI: 10.1016/s2213-2600(15)00500-7] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 11/18/2015] [Accepted: 11/20/2015] [Indexed: 12/20/2022]
Abstract
Background Bacteria and viruses are equally associated with the risk of acute episodes of asthma-like symptoms in young children, suggesting antibiotics as a potential treatment for such episodes. We aimed to assess the effect of azithromycin on the duration of respiratory episodes in young children with recurrent asthma-like symptoms, hypothesising that it reduces the duration of the symptomatic period. Methods In this randomised, double-blind, placebo-controlled trial, we recruited children aged 1–3 years, who were diagnosed with recurrent asthma-like symptoms from the Copenhagen Prospective Studies on Asthma in Childhood 2010 cohort; a birth cohort consisting of the general Danish population of Zealand, including Copenhagen. Exclusion criteria were macrolide allergy, heart, liver, neurological, and kidney disease, and, before each treatment, one or more clinical signs of pneumonia (respiratory frequency of ≥50 breaths per min; fever of ≥39°C; C-reactive protein concentration of ≥476·20 nmol/L [≥50 mg/L]). Each episode of asthma-like symptoms lasting at least 3 days was randomly allocated to a 3-day course of azithromycin oral solution of 10 mg/kg per day or placebo after thorough examination by a study physician at the Copenhagen Prospective Studies on Asthma research unit. Each episode was randomly allocated independently of previous treatment from a computer-generated list of random numbers in blocks of ten (generated at the Pharmacy of Glostrup). Investigators and children were masked until the youngest child turned 3 years of age and throughout the data validation and analysis phases. The primary outcome was duration of the respiratory episode after treatment, verified by prospective daily diaries and analysed with Poisson regression. Analyses were per protocol (excluding those without a primary outcome measure or who did not receive treatment). This trial is registered with ClinicalTrials.gov, number NCT01233297. Findings Between Nov 17, 2010, and Jan 28, 2014, we randomly allocated 158 asthma-like episodes in 72 children (79 [50%] to azithromycin and 79 [50%] to placebo). The mean duration of the episode after treatment was 3·4 days for children receiving azithromycin compared with 7·7 days for children receiving placebo. Azithromycin caused a significant shortening of the episode of 63·3% (95% CI 56·0–69·3; p<0·0001). The effect size increased with early initiation of treatment, showing a reduction in episode duration of 83% if treatment was initiated before day 6 of the episode compared with 36% if initiated on or after day 6 (p<0·0001). We noted no differences in clinical adverse events between the azithromycin (18 [23%] of 78 episodes included in final analysis) and placebo (24 [30%] of 79) groups (p=0·30), but we did not investigate bacterial resistance patterns after treatment. Interpretation Azithromycin reduced the duration of episodes of asthma-like symptoms in young children, suggesting that this drug could have a role in acute management of exacerbations. Further research is needed to disentangle the inflammatory versus antimicrobial aspects of this relation. Funding Lundbeck Foundation, Danish Ministry of Health, Danish Council for Strategic Research, Capital Region Research Foundation.
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Affiliation(s)
- Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Pediatrics, Naestved Hospital, Naestved, Denmark
| | - Bo L Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Nadja H Vissing
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Elín Bjarnadóttir
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Pediatrics, Naestved Hospital, Naestved, Denmark
| | - Tine M Pedersen
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Pediatrics, Naestved Hospital, Naestved, Denmark
| | - Rebecca K Vinding
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark; Department of Pediatrics, Naestved Hospital, Naestved, Denmark
| | - Ann-Marie M Schoos
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Helene M Wolsk
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Sunna Thorsteinsdóttir
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Henrik W Hallas
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Lambang Arianto
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Susanne Schjørring
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Karen A Krogfelt
- Department of Microbiology and Infection Control, Statens Serum Institut, Copenhagen, Denmark
| | - Thea K Fischer
- Department of Microbiological Diagnostics and Virology, Statens Serum Institut, Copenhagen, Denmark
| | - Christian B Pipper
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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Midgley S, Trebbien R, Schjørring S, Christiansen C, Weismann Poulsen M, Fischer T. Diversity of enteroviruses in respiratory samples: Challenges for entero- and rhinovirus diagnostics and genotyping. J Clin Virol 2015. [DOI: 10.1016/j.jcv.2015.07.169] [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: 11/15/2022]
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Bisgaard H, Vissing NH, Carson CG, Bischoff AL, Følsgaard NV, Kreiner-Møller E, Chawes BLK, Stokholm J, Pedersen L, Bjarnadóttir E, Thysen AH, Nilsson E, Mortensen LJ, Olsen SF, Schjørring S, Krogfelt KA, Lauritzen L, Brix S, Bønnelykke K. Deep phenotyping of the unselected COPSAC2010 birth cohort study. Clin Exp Allergy 2014; 43:1384-94. [PMID: 24118234 PMCID: PMC4158856 DOI: 10.1111/cea.12213] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 07/19/2013] [Accepted: 09/04/2013] [Indexed: 01/05/2023]
Abstract
Background We hypothesize that perinatal exposures, in particular the human microbiome and maternal nutrition during pregnancy, interact with the genetic predisposition to cause an abnormal immune modulation in early life towards a trajectory to chronic inflammatory diseases such as asthma and others. Objective The aim of this study is to explore these interactions by conducting a longitudinal study in an unselected cohort of pregnant women and their offspring with emphasis on deep clinical phenotyping, exposure assessment, and biobanking. Exposure assessments focus on the human microbiome. Nutritional intervention during pregnancy in randomized controlled trials are included in the study to prevent disease and to be able to establish causal relationships. Methods Pregnant women from eastern Denmark were invited during 2008–2010 to a novel unselected ‘COPSAC2010’ cohort. The women visited the clinic during pregnancy weeks 24 and 36. Their children were followed at the clinic with deep phenotyping and collection of biological samples at nine regular visits until the age of 3 and at acute symptoms. Randomized controlled trials of high‐dose vitamin D and fish oil supplements were conducted during pregnancy, and a trial of azithromycin for acute lung symptoms was conducted in the children with recurrent wheeze. Results Seven hundred and thirty‐eight mothers were recruited from week 24 of gestation, and 700 of their children were included in the birth cohort. The cohort has an over‐representation of atopic parents. The participant satisfaction was high and the adherence equally high with 685 children (98%) attending the 1 year clinic visit and 667 children (95%) attending the 2 year clinic visit. Conclusions The COPSAC2010 birth cohort study provides longitudinal clinical follow‐up with highly specific end‐points, exposure assessments, and biobanking. The cohort has a high adherence rate promising strong data to elucidate the interaction between genomics and the exposome in perinatal life leading to lifestyle‐related chronic inflammatory disorders such as asthma.
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Affiliation(s)
- H Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte & Naestved, Denmark; Health Sciences, University of Copenhagen, Copenhagen, Denmark
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Stokholm J, Schjørring S, Pedersen L, Bischoff AL, Følsgaard N, Carson CG, Chawes BLK, Bønnelykke K, Mølgaard A, Krogfelt KA, Bisgaard H. Prevalence and predictors of antibiotic administration during pregnancy and birth. PLoS One 2013; 8:e82932. [PMID: 24340068 PMCID: PMC3858309 DOI: 10.1371/journal.pone.0082932] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/29/2013] [Indexed: 12/04/2022] Open
Abstract
Background Antibiotic treatment during pregnancy and birth is very common. In this study, we describe the estimated prevalence of antibiotic administration during pregnancy and birth in the COPSAC2010 pregnancy cohort, and analyze dependence on social and lifestyle-related factors. Methods 706 pregnant women from the novel unselected Copenhagen Prospective Study on Asthma in Childhood (COPSAC2010) pregnancy cohort participated in this analysis. Detailed information on oral antibiotic prescriptions during pregnancy filled at the pharmacy was obtained and verified longitudinally. Information on intrapartum antibiotics, social, and lifestyle-factors was obtained by personal interviews. Results The prevalence of antibiotic use was 37% during pregnancy and 33% intrapartum. Lower maternal age at birth; adjusted odds ratio (aOR) 0.94, 95% CI, [0.90-0.98], p = 0.003 and maternal smoking; aOR 1.97, 95% CI, [1.07-3.63], p = 0.030 were associated with use of antibiotics for urinary tract infection during pregnancy. Maternal educational level (low vs. high), aOR 2.32, 95% CI, [1.24-4.35], p = 0.011, maternal asthma; aOR 1.99, 95% CI, [1.33-2.98], p < 0.001 and previous childbirth; aOR 1.80, 95% CI, [1.21-2.66], p = 0.004 were associated with use of antibiotics for respiratory tract infection during pregnancy. Lower gestational age; aOR 0.72, 95% CI, [0.61-0.85], p < 0.001, maternal smoking; aOR 2.84, 95% CI, [1.33-6.06], p = 0.007, and nulliparity; aOR 1.79, 95% CI, [1.06-3.02], p = 0.030 were associated with administration of intrapartum antibiotics in women giving birth vaginally. Conclusion Antibiotic administration during pregnancy and birth may be influenced by social and lifestyle-factors. Understanding such risk factors may guide preventive strategies in order to avoid unnecessary use of antibiotics.
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Affiliation(s)
- Jakob Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Naestved Hospital, Naestved, Denmark
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Susanne Schjørring
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Louise Pedersen
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Naestved Hospital, Naestved, Denmark
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Anne Louise Bischoff
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Nilofar Følsgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Charlotte G. Carson
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Bo L. K. Chawes
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Anne Mølgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
| | - Karen A. Krogfelt
- Department of Microbiological Surveillance and Research, Statens Serum Institut, Copenhagen, Denmark
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Copenhagen University Hospital, Gentofte, Copenhagen, Denmark
- * E-mail:
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Stokholm J, Schjørring S, Eskildsen CE, Pedersen L, Bischoff AL, Følsgaard N, Carson CG, Chawes BLK, Bønnelykke K, Mølgaard A, Jacobsson B, Krogfelt KA, Bisgaard H. Antibiotic use during pregnancy alters the commensal vaginal microbiota. Clin Microbiol Infect 2013; 20:629-35. [PMID: 24118384 DOI: 10.1111/1469-0691.12411] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 09/18/2013] [Accepted: 09/23/2013] [Indexed: 11/26/2022]
Abstract
Antibiotics may induce alterations in the commensal microbiota of the birth canal in pregnant women. Therefore, we studied the effect of antibiotic administration during pregnancy on commensal vaginal bacterial colonization at gestational week 36. Six hundred and sixty-eight pregnant women from the novel unselected Copenhagen Prospective Studies on Asthma in Childhood (COPSAC2010 ) pregnancy cohort participated in this analysis. Detailed information on oral antibiotic prescriptions during pregnancy filled at the pharmacy was obtained and verified prospectively. Vaginal samples were obtained at pregnancy week 36 and cultured for bacteria. Women who received oral antibiotics during any pregnancy trimester had an increased rate of colonization by Staphylococcus species in the vaginal samples as compared with samples obtained from women without any antibiotic treatment during pregnancy (adjusted OR 1.63, 95% CI 1.06-2.52, p 0.028). Oral antibiotic administration in the third trimester were also associated with increased colonization by Staphylococcus species (adjusted OR 1.98, 95% CI 1.04-3.76, p 0.037). These bacteriological changes were associated with urinary tract infection antibiotics. Women treated in the third trimester of pregnancy were more often colonized by Escherichia coli than women without antibiotic treatment in the third trimester (adjusted OR 1.91, 95% CI 1.04-3.52, p 0.038). This change was associated with respiratory tract infection (RTI) antibiotics. We did not observe any significant changes in vaginal Streptococcus agalactiae (group B streptoccocus) or Staphylococcus aureus colonization following antibiotic treatment in pregnancy. Antibiotic administration during pregnancy leads to alterations in the vaginal microbiological ecology prior to birth, with potential morbidity, and long-term effects on the early microbial colonization of the neonate.
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Affiliation(s)
- J Stokholm
- Copenhagen Prospective Studies on Asthma in Childhood, Health Sciences, University of Copenhagen, Naestved Hospital, Naestved, Denmark; Department of Food Science, Faculty of Life Sciences, University of Copenhagen, Copenhagen, Denmark
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Følsgaard NV, Schjørring S, Chawes BL, Rasmussen MA, Krogfelt KA, Brix S, Bisgaard H. Pathogenic bacteria colonizing the airways in asymptomatic neonates stimulates topical inflammatory mediator release. Am J Respir Crit Care Med 2013; 187:589-95. [PMID: 23370914 DOI: 10.1164/rccm.201207-1297oc] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RATIONALE Bacterial colonization of neonatal airways with the pathogenic bacterial species, Moraxella catarrhalis, Streptococcus pneumoniae, and Haemophilus influenzae, is associated with later development of childhood asthma. OBJECTIVES To study a possible association between colonization with pathogenic bacterial strains and the immune signature of the upper airways in healthy neonates. METHODS A total of 20 cytokines and chemokines were quantified in vivo in the airway mucosal lining fluid of 662 neonates from the Copenhagen Prospective Study of Asthma in Childhood 2010 birth cohort. Colonization of the hypopharynx with M. catarrhalis, S. pneumoniae, H. influenzae, and Staphylococcus aureus was assessed simultaneously. The association between immune signatures and bacterial colonization or noncolonized controls was analyzed using conventional statistical methods supplemented by a multivariate approach for pattern identification. MEASUREMENTS AND MAIN RESULTS Colonization with M. catarrhalis and H. influenzae induced a mixed T helper cell (Th) type 1/Th2/Th17 response with high levels of IL-1β (M. catarrhalis, P = 2.2 × 10(-12); H. influenzae, P = 7.1 × 10(-10)), TNF-α (M. catarrhalis, P = 1.5 × 10(-9); H. influenzae, P = 5.9 × 10(-7)), and macrophage inflammatory protein-1β (M. catarrhalis, P = 1.6 × 10(-11); H. influenzae, P = 2.7 × 10(-7)). S. aureus colonization demonstrated a Th17-promoting profile with elevated IL-17 levels (P = 1.6 × 10(-24)). S. pneumoniae colonization was not significantly associated with any of the mediators. CONCLUSIONS M. catarrhalis and H. influenzae colonization of the airways of asymptomatic neonates is associated with an inflammatory immune response of the airway mucosa, which may result in chronic inflammation.
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Affiliation(s)
- Nilofar V Følsgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Copenhagen University Hospital, Gentofte, Ledreborg Allé 34, Gentofte, Copenhagen, Denmark
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Schjørring S, Struve C, Krogfelt KA. Transfer of antimicrobial resistance plasmids from Klebsiella pneumoniae to Escherichia coli in the mouse intestine. J Antimicrob Chemother 2008; 62:1086-93. [PMID: 18703526 PMCID: PMC2566516 DOI: 10.1093/jac/dkn323] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [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] [Indexed: 11/13/2022] Open
Abstract
Objectives and methods Klebsiella pneumoniae is a nosocomial pathogen and is considered the most common Gram-negative bacterium that exhibits multiple antimicrobial resistances. In this study, the transfer of antimicrobial resistance genes from the clinical multiresistant K. pneumoniae MGH75875 isolate was assessed in vitro and in vivo in an intestinal colonization animal model. The ability to colonize and transfer was tested under different antimicrobial treatments. The frequency of the horizontal gene transfer was also examined in vitro. Results The clinical isolate of K. pneumoniae colonized the intestine of mice at levels up to 109 cfu/g faeces in antimicrobial-treated mice. In mice without antimicrobial treatment, the strain quickly decreased to below the detection limit due to competitive exclusion by the indigenous mouse flora. Onset of antimicrobial treatment gave immediate rise to detectable levels of the strain in the faeces of up to 109 cfu/g faeces. The experiment clearly shows that the treatment selects resistant strains and gives advantages to colonize the gastrointestinal tract. Furthermore, high transfer frequency of different plasmids was observed during colonization of the mouse intestine. The blaSHV and blaTEM genotypes were transferred to both an indigenous recipient in the in vivo setting and to an MG1655 Escherichia coli recipient strain in vitro. Conclusions K. pneumoniae is an excellent colonizer of the intestine and is extremely promiscuous with respect to the transferability of its numerous plasmids. Antimicrobial treatment enhances the selection of resistant strains and results in an increase in the resistance gene pool, which ultimately raises the risk of spreading resistance genes.
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Affiliation(s)
- Susanne Schjørring
- Department of Bacteriology, Mycology and Parasitology, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen S, Denmark
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Lampkowska J, Feld L, Monaghan A, Toomey N, Schjørring S, Jacobsen B, van der Voet H, Andersen SR, Bolton D, Aarts H, Krogfelt KA, Wilcks A, Bardowski J. A standardized conjugation protocol to asses antibiotic resistance transfer between lactococcal species. Int J Food Microbiol 2008; 127:172-5. [PMID: 18675485 DOI: 10.1016/j.ijfoodmicro.2008.06.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2007] [Revised: 06/11/2008] [Accepted: 06/13/2008] [Indexed: 11/16/2022]
Abstract
Optimal conditions and a standardized method for conjugation between two model lactococcal strains, Lactococcus lactis SH4174 (pAMbeta1-containing, erythromycin resistant donor) and L. lactis Bu2-60 (plasmid-free, erythromycin sensitive recipient), were developed and tested in a inter-laboratory experiments involving five laboratories from different countries. The ultimate goal of the study was to assess the microbial potential of antibiotic resistance transfer among Lactic Acid Bacteria (LAB). The influence of culture age (various OD values) and ratios of donor and recipient cultures as well as filter, solid and liquid mating techniques, were examined in order to optimize the conjugation protocol. In the result of these studies, we concluded that the donor-to-recipient ratio appear to be important; the most efficient technique for conjugation was filter mating and the optimal conditions for gene transfer were observed when late logarithmic cultures of both donor and recipient were used. Comparison of conjugal transfer frequencies between five partner laboratories showed that results are sufficiently intra-laboratory repeatable and inter-laboratory comparable. This is the first study of this kind, in which a standardized protocol of conjugal mating for testing antibiotic resistance dissemination among LAB was established and validated.
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Affiliation(s)
- Joanna Lampkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
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Feld L, Schjørring S, Hammer K, Licht TR, Danielsen M, Krogfelt K, Wilcks A. Selective pressure affects transfer and establishment of a Lactobacillus plantarum resistance plasmid in the gastrointestinal environment. J Antimicrob Chemother 2008; 61:845-52. [PMID: 18238887 DOI: 10.1093/jac/dkn033] [Citation(s) in RCA: 84] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES AND METHODS A Lactobacillus plantarum strain recently isolated from French raw-milk cheese was tested for its ability to transfer a small plasmid pLFE1 harbouring the erythromycin resistance gene erm(B) to Enterococcus faecalis. Mating was studied in vitro and in different gastrointestinal environments using gnotobiotic rats as a simple in vivo model and streptomycin-treated mice as a more complex model. Transfer and establishment of transconjugants in the intestine were investigated with and without selective pressure. RESULTS Compared with the relatively low transfer frequency of approximately 5.7 x 10(-8) transconjugants/recipient obtained in vitro by filter mating, a surprisingly high number of transconjugants (10(-4) transconjugants/recipient) was observed in gnotobiotic rats even without antibiotic treatment. When erythromycin was administered, a transfer rate of approximately 100% was observed, i.e. the recipient population turned completely into transconjugants (3 x 10(9) cfu/g faeces). Additionally, the time to reach a stable transconjugant population level was much faster in the erythromycin-treated gnotobiotic rats (1 day) than in the untreated animals (4-5 days). Transconjugants persisted in the gut in relatively stable numbers at least 12 days after termination of antibiotic treatment. In the streptomycin-treated mice, no transfer was observed either with or without erythromycin treatment. CONCLUSIONS The overall results imply that the gastrointestinal tract may comprise a more favourable environment for antibiotic resistance transfer than conditions provided in vitro. However, the indigenous gut microbiota severely restricts transfer, thus minimizing the number of detectable transfer events. Treatment with erythromycin strongly favoured transfer and establishment of pLFE1.
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Affiliation(s)
- Louise Feld
- Department of Microbiology and Risk Assessment, National Food Institute, Technical University of Denmark, Mørkhøj Bygade 19, DK-2860 Søborg, Denmark
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Schjørring S, Gregersen J, Bregnballe T. Prospecting enhances breeding success of first-time breeders in the great cormorant, Phalacrocorax carbo sinensis. Anim Behav 1999; 57:647-654. [PMID: 10196055 DOI: 10.1006/anbe.1998.0993] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In many species of colonial seabirds, young birds visit colonies in the years before they start breeding. This prospecting behaviour may allow them to obtain information that could enhance their future breeding success. We examined the reproductive consequences of prospecting behaviour in the colonial great cormorant, and found support for this idea. New breeders that had been prospecting actively in the previous year obtained breeding sites of higher quality (i.e. closer to sites where conspecifics had fledged young in the previous year) and had higher breeding success than those that had been less active. Prospecting occurred mostly late in the breeding season, and coincided with the time when the majority of the eggs had hatched but before the chicks started fledging, that is, when breeding success in the colony reflected habitat suitability. These results are thus consistent with the use of conspecific reproductive performance as a cue for the quality of a breeding habitat as expected from the 'performance-based conspecific attraction hypothesis'. Copyright 1999 The Association for the Study of Animal Behaviour.
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