A comparison of two informative SNP-based strategies for typing Pseudomonas aeruginosa isolates from patients with cystic fibrosis

Syrmis, Melanie W.; Kidd, Timothy J.; Moser, Ralf; Ramsay, Kay A.; Gibson, Kristen M; Anuj, S.N.; Bell, Scott C.; Wainwright, Claire; Grimwood, Keith; Nissen, Michael D.; Sloots, Theo P.; Whiley, David M.

doi:10.1186/1471-2334-14-307

Cited by 23 publications

(31 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…No dominant Australian shared CF P. aeruginosa strains (e.g. AUST‐01, AUST‐02 and AUST‐06) were observed. In contrast, our analysis demonstrated that 20 (67%) participants had infection with P. aeruginosa strains, with genotype profiles that showed close genetic relationships to locally derived genotypes found in the environment, animals and other non‐CF clinical presentations .…”

Section: Resultsmentioning

confidence: 98%

“…A hole‐correction factor was applied to account for possible ‘stacking’ of bacterial colonies on the agar plates inside the ACI . All confirmed P. aeruginosa isolates underwent genotyping using an iPLEX20SNP assay (Sequenom, San Diego, CA, USA) as previously published …”

Section: Methodsmentioning

confidence: 99%

“…Purified presumptive P. aeruginosa isolates representing different colonial morphotypes from each specimen (where possible) were selected and stored at −80°C, with identification subsequently confirmed by real‐time PCR . All confirmed P. aeruginosa isolates underwent iPLEX20SNP genotyping . The genotyping results were evaluated using a database of multilocus sequence profiles from local environmental, animal and CF‐ and non‐CF‐associated clinical isolates .…”

Section: Methodsmentioning

confidence: 99%

“…27 All confirmed P. aeruginosa isolates underwent genotyping using an iPLEX20SNP assay (Sequenom, San Diego, CA, USA) as previously published. 28 Genotyping study Sputum microbiology Sputa were collected from 30 eligible participants with a recent history of P. aeruginosa infection (bronchiectasis, n = 29; COPD, n = 1) and cultured in an accredited clinical microbiological laboratory in accordance with local protocols (Pathology Queensland). Longitudinal sputum samples were included for analysis where available.…”

Section: Microbiologymentioning

confidence: 99%

“…28 The genotyping results were evaluated using a database of multilocus sequence profiles from local environmental, animal and CF-and non-CF-associated clinical isolates. 6,28 Fourteen isolates (from nine participants) had indistinguishable iPLEX20SNP profiles and subsequently underwent enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis 29 (200 kb ladder was used for comparison and the gel was run at 80 V for 5 h). ERIC-PCR banding patterns were visually analysed, with isolates showing a variance of ≥1 band allocated to a different rep-PCR type.…”

Section: Genotypingmentioning

confidence: 99%

See 4 more Smart Citations

Transmission of bacteria in bronchiectasis and chronic obstructive pulmonary disease: Low burden of cough aerosols

et al. 2019

View full text Add to dashboard Cite

Background and objective Aerosol transmission of Pseudomonas aeruginosa has been suggested as a possible mode of respiratory infection spread in patients with cystic fibrosis (CF); however, whether this occurs in other suppurative lung diseases is unknown. Therefore, we aimed to determine if (i) patients with bronchiectasis (unrelated to CF) or chronic obstructive pulmonary disease (COPD) can aerosolize P. aeruginosa during coughing and (ii) if genetically indistinguishable (shared) P. aeruginosa strains are present in these disease cohorts. Methods People with bronchiectasis or COPD and P. aeruginosa respiratory infection were recruited for two studies. Aerosol study: Participants (n = 20) underwent cough testing using validated cough rigs to determine the survival of P. aeruginosa aerosols in the air over distance and duration. Genotyping study: P. aeruginosa sputum isolates (n = 95) were genotyped using the iPLEX20SNP platform, with a subset subjected to the enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC‐PCR) assay to ascertain their genetic relatedness. Results Aerosol study: Overall, 7 of 20 (35%) participants released P. aeruginosa cough aerosols during at least one of the cough aerosol tests. These cough aerosols remained viable for 4 m from the source and for 15 min after coughing. The mean total aerosol count of P. aeruginosa at 2 m was two colony‐forming units. Typing study: No shared P. aeruginosa strains were identified. Conclusion Low viable count of P. aeruginosa cough aerosols and a lack of shared P. aeruginosa strains observed suggest that aerosol transmission of P. aeruginosa is an unlikely mode of respiratory infection spread in patients with bronchiectasis and COPD.

show abstract

Section: Resultsmentioning

confidence: 98%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Microbiologymentioning

confidence: 99%

Section: Genotypingmentioning

confidence: 99%

See 3 more Smart Citations

Transmission of bacteria in bronchiectasis and chronic obstructive pulmonary disease: Low burden of cough aerosols

et al. 2019

View full text Add to dashboard Cite

show abstract

Feasibility of mini-sequencing schemes based on nucleotide polymorphisms for microbial identification and population analyses

Araújo

Eusébio

Caramalho

2015

Appl Microbiol Biotechnol

View full text Add to dashboard Cite

Practical schemes based on single nucleotide polymorphisms (SNP) have been proposed as alternatives to simplify and replace the molecular methodologies based on the extensive sequencing analysis of genes. SNaPshot mini-sequencing has been progressively experienced during the last decade and represents a fast and robust strategy to analyze critical polymorphisms. Such assays have been proposed to characterize some bacteria and microbial eukaryotes, and its feasibility was now reviewed in the present manuscript. The mini-sequencing schemes showed high discriminatory power and competence for identification of microorganisms, but some specificity errors were still found, particularly for species of the Burkholderia cepacia complex and mycobacteria. SNP assays designed for other goals, e.g., comparison of strains, detection of serotypes, virulence, epidemic, and phylogenetic-related subgroups of isolates, can be very useful by facilitating the investigation of large collections of isolates. The next-generation of SNP assays might consider the inclusion of large number of markers to fully characterize microbial taxonomy and strains; nevertheless, these new technologies are still prone to errors and can largely benefit from integration with well-established mini-sequencing assays. Newly proposed molecular tools should be systematically tested in collections of isolates with high indexes of diversity and guarantee interlaboratorial validation.

show abstract

Emergence and impact of oprD mutations in Pseudomonas aeruginosa strains in cystic fibrosis

Sherrard

Wee

Duplancic

et al. 2022

Journal of Cystic Fibrosis

Self Cite

View full text Add to dashboard Cite

show abstract

A comparison of two informative SNP-based strategies for typing Pseudomonas aeruginosa isolates from patients with cystic fibrosis

Cited by 23 publications

References 19 publications

Transmission of bacteria in bronchiectasis and chronic obstructive pulmonary disease: Low burden of cough aerosols

Transmission of bacteria in bronchiectasis and chronic obstructive pulmonary disease: Low burden of cough aerosols

Feasibility of mini-sequencing schemes based on nucleotide polymorphisms for microbial identification and population analyses

Emergence and impact of oprD mutations in Pseudomonas aeruginosa strains in cystic fibrosis

Contact Info

Product

Resources

About