Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity

Autor: Elke De Wachter, Denis Pierard, Jeroen Wagemans, Jean-Paul Pirnay, Rob Lavigne, Vera van Noort, Anca Boeras, Matthieu Thimmesch, Fedoua Echahidi, Marijke Proesmans, Charlotte Peeters, Cédric Lood, Katrien Lagrou, Evelien De Canck, Quentin Lamy-Besnier, Daniel De Vos, Peter Vandamme
Přispěvatelé: Navarre, William, Microbiology and Infection Control, Clinical Biology, Supporting clinical sciences, Clinical sciences, Physiotherapy, Human Physiology and Anatomy, Pediatrics
Jazyk: angličtina
Rok vydání: 2021
Předmět:
Bacterial Diseases
Male
Cystic Fibrosis
Pulmonology
Endemic Diseases
Physiology
Epidemiology
Single Nucleotide Polymorphisms
Pathology and Laboratory Medicine
Genome
Cystic fibrosis
Medical Conditions
Medicine and Health Sciences
Biology (General)
Child
Genetics
0303 health sciences
biology
Burkholderia multivorans
Burkholderia Infections
Genomics
Bacterial Pathogens
Body Fluids
3. Good health
Infectious Diseases
Genetic Diseases
Medical Microbiology
Child
Preschool
Female
Pathogens
Anatomy
Research Article
Microbiology (medical)
Adult
Burkholderia
QH301-705.5
Immunology
Single-nucleotide polymorphism
Microbiology
Burkholderia Cepacia Complex
03 medical and health sciences
Autosomal Recessive Diseases
Microbial Control
Virology
medicine
Humans
Microbial Pathogens
Molecular Biology
Prophage
030304 developmental biology
Pharmacology
Clinical Genetics
Bacteria
030306 microbiology
Organisms
Sputum
Biology and Life Sciences
RC581-607
biology.organism_classification
medicine.disease
Fibrosis
Mucus
Burkholderia cepacia complex
Parasitology
Genetic Loci
Antibiotic Resistance
Burkholderia Infection
Antimicrobial Resistance
Immunologic diseases. Allergy
Developmental Biology
Zdroj: PLoS Pathogens, Vol 17, Iss 3, p e1009418 (2021)
PLOS PATHOGENS
PLoS Pathogens
ISSN: 1553-7374
1553-7366
Popis: Burkholderia multivorans is a member of the Burkholderia cepacia complex (Bcc), notorious for its pathogenicity in persons with cystic fibrosis. Epidemiological surveillance suggests that patients predominantly acquire B. multivorans from environmental sources, with rare cases of patient-to-patient transmission. Here we report on the genomic analysis of thirteen isolates from an endemic B. multivorans strain infecting four cystic fibrosis patients treated in different pediatric cystic fibrosis centers in Belgium, with no evidence of cross-infection. All isolates share an identical sequence type (ST-742) but whole genome analysis shows that they exhibit peculiar patterns of genomic diversity between patients. By combining short and long reads sequencing technologies, we highlight key differences in terms of small nucleotide polymorphisms indicative of low rates of adaptive evolution within patient, and well-defined, hundred kbps-long segments of high enrichment in mutations between patients. In addition, we observed large structural genomic variations amongst the isolates which revealed different plasmid contents, active roles for transposase IS3 and IS5 in the deactivation of genes, and mobile prophage elements. Our study shows limited within-patient B. multivorans evolution and high between-patient strain diversity, indicating that an environmental microdiverse reservoir must be present for this endemic strain, in which active diversification is taking place. Furthermore, our analysis also reveals a set of 30 parallel adaptations across multiple patients, indicating that the specific genomic background of a given strain may dictate the route of adaptation within the cystic fibrosis lung.
Author summary In many countries, Burkholderia multivorans is the most prevalent species within the Burkholderia cepacia complex (Bcc) found infecting the lungs of patients with cystic fibrosis (CF). Its positive identification is of immediate concern to the health of the patient as it is notoriously hard to eradicate using antibiotics and can cause necrosis of the lung tissues (cepacia syndrome). Infection control measures reduced the prevalence of B. cenocepacia in CF wards, but patients continue to acquire infections by B. multivorans from environmental sources. In most reported cases, the infecting strains are unique except in rare cases in which cross-infection is observed between patients. We report here an endemic strain of B. multivorans with sequence type ST-742 that has been infecting multiple patients, without evidence for cross-infection. We investigated the epidemiology and genomics of this ST-742 strain and show that it is microdiverse, as isolates between-patients exhibit numerous genomic differences, at scales that have not been observed previously when looking at evolutionary trajectories within-patients. Additionally, we found that the specific genomic background of a given strain may dictate the strategy of adaptation within the CF lung.
Databáze: OpenAIRE
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