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Article ; Online: Nasopharyngeal Swabs vs. Nasal Aspirates for Respiratory Virus Detection

Matthew F. Flynn / Martin Kelly / James S. G. Dooley

Pathogens, Vol 10, Iss 1515, p

A Systematic Review

2021 Volume 1515

Abstract: Nasal pathogen detection sensitivities can be as low as 70% despite advances in molecular diagnostics. This may be linked to the choice of sampling method. A diagnostic test accuracy review for sensitivity was undertaken to compare sensitivity of ... ...

Abstract	Nasal pathogen detection sensitivities can be as low as 70% despite advances in molecular diagnostics. This may be linked to the choice of sampling method. A diagnostic test accuracy review for sensitivity was undertaken to compare sensitivity of swabbing to the nasopharynx and extracting nasal aspirates, using the PRISMA protocol, Cochrane rapid review methodology, and QUADAS-2 risk of bias tools, with meta-analysis of included studies. Sensitivities were calculated by a consensus standard of positivity by either method as the ‘gold standard.’ Insufficient sampling methodology, cross sectional study designs, and studies pooling samples across anatomical sites were excluded. Of 13 subsequently eligible studies, 8 had ‘high’ risk of bias, and 5 had ‘high’ applicability concerns. There were no statistical differences in overall sensitivities between collection methods for eight different viruses, and this did not differ with use of PCR, immunofluorescence, or culture. In one study alone, Influenza H1N1(2009) favored nasopharyngeal swabs, with aspirates having 93.3% of the sensitivity of swabs ( p > 0.001). Similarly equivocal sensitivities were noted in reports detecting bacteria. The chain of sampling, from anatomical site to laboratory results, features different potential foci along which sensitivity may be lost. A fair body of evidence exists that use of a different sampling method will not yield more respiratory pathogens.
Keywords	respiratory ; virus ; bacteria ; nasopharyngeal ; microbiome ; infection ; Medicine ; R
Subject code	310
Language	English
Publishing date	2021-11-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A Novel Biofilm Model System to Visualise Conjugal Transfer of Vancomycin Resistance by Environmental Enterococci

Michael Conwell / James S. G. Dooley / Patrick J. Naughton

Microorganisms, Vol 9, Iss 789, p

2021 Volume 789

Abstract: Enterococci and biofilm-associated infections are a growing problem worldwide, given the rise in antibiotic resistance in environmental and clinical settings. The increasing incidence of antibiotic resistance and its propagation potential within ... ...

Abstract	Enterococci and biofilm-associated infections are a growing problem worldwide, given the rise in antibiotic resistance in environmental and clinical settings. The increasing incidence of antibiotic resistance and its propagation potential within enterococcal biofilm is a concern. This requires a deeper understanding of how enterococcal biofilm develops, and how antibiotic resistance transfer takes place in these biofilms. Enterococcal biofilm assays, incorporating the study of antibiotic resistance transfer, require a system which can accommodate non-destructive, real-time experimentation. We adapted a Gene Frame ® combined with fluorescence microscopy as a novel non-destructive platform to study the conjugal transfer of vancomycin resistance in an established enterococcal biofilm.A multi-purpose fluorescent in situ hybridisation (FISH) probe, in a novel application, allowed the identification of low copy number mobile elements in the biofilm. Furthermore, a Hoechst stain and ENU 1470 FISH probe identified Enterococcus faecium transconjugants by excluding Enterococcus faecalis MF06036 donors. Biofilm created with a rifampicin resistant E. faecalis (MW01105 Rif ) recipient had a transfer efficiency of 2.01 × 10 −3 double that of the biofilm primarily created by the donor (E. faecalis MF06036). Conjugation in the mixed enterococcal biofilm was triple the efficiency of donor biofilm. Double antibiotic treatment plus lysozyme combined with live/dead imaging provided fluorescent micrographs identifying de novo enterococcal vancomycin resistant transconjugants inside the biofilm. This is a model system for the further study of antibiotic resistance transfer events in enterococci. Biofilms promote the survival of enterococci and reduce the effectiveness of drug treatment in clinical settings, hence giving enterococci an advantage. Enterococci growing in biofilms exchange traits by means of horizontal gene transfer, but currently available models make study difficult. This work goes some way to providing a ...
Keywords	enterococci ; biofilm ; model ; antibiotic resistance ; FISH ; Biology (General) ; QH301-705.5
Subject code	616
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Biofilm regulation in Clostridioides difficile

Megan G Taggart / William J Snelling / Patrick J Naughton / Roberto M La Ragione / James S G Dooley / Nigel G Ternan

PLoS Pathogens, Vol 17, Iss 9, p e

Novel systems linked to hypervirulence.

2021 Volume 1009817

Abstract: Clostridiodes difficile (C. difficile) was ranked an "urgent threat" by the Centers for Disease Control and Prevention (CDC) in 2019. C. difficile infection (CDI) is the most common healthcare-associated infection (HAI) in the United States of America as ...

Abstract	Clostridiodes difficile (C. difficile) was ranked an "urgent threat" by the Centers for Disease Control and Prevention (CDC) in 2019. C. difficile infection (CDI) is the most common healthcare-associated infection (HAI) in the United States of America as well as the leading cause of antibiotic-associated gastrointestinal disease. C. difficile is a gram-positive, rod-shaped, spore-forming, anaerobic bacterium that causes infection of the epithelial lining of the gut. CDI occurs most commonly after disruption of the human gut microflora following the prolonged use of broad-spectrum antibiotics. However, the recurrent nature of this disease has led to the hypothesis that biofilm formation may play a role in its pathogenesis. Biofilms are sessile communities of bacteria protected from extracellular stresses by a matrix of self-produced proteins, polysaccharides, and extracellular DNA. Biofilm regulation in C. difficile is still incompletely understood, and its role in disease recurrence has yet to be fully elucidated. However, many factors have been found to influence biofilm formation in C. difficile, including motility, adhesion, and hydrophobicity of the bacterial cells. Small changes in one of these systems can greatly influence biofilm formation. Therefore, the biofilm regulatory system would need to coordinate all these systems to create optimal biofilm-forming physiology under appropriate environmental conditions. The coordination of these systems is complex and multifactorial, and any analysis must take into consideration the influences of the stress response, quorum sensing (QS), and gene regulation by second messenger molecule cyclic diguanosine monophosphate (c-di-GMP). However, the differences in biofilm-forming ability between C. difficile strains such as 630 and the "hypervirulent" strain, R20291, make it difficult to assign a "one size fits all" mechanism to biofilm regulation in C. difficile. This review seeks to consolidate published data regarding the regulation of C. difficile biofilms in order to ...
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-09-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The Fate of Foodborne Pathogens in Manure Treated Soil

Zoe Black / Igori Balta / Lisa Black / Patrick J. Naughton / James S. G. Dooley / Nicolae Corcionivoschi

Frontiers in Microbiology, Vol

2021 Volume 12

Abstract: The aim of this review was to provide an update on the complex relationship between manure application, altered pathogen levels and antibiotic resistance. This is necessary to protect health and improve the sustainability of this major farming practice ... ...

Abstract	The aim of this review was to provide an update on the complex relationship between manure application, altered pathogen levels and antibiotic resistance. This is necessary to protect health and improve the sustainability of this major farming practice in agricultural systems based on high levels of manure production. It is important to consider soil health in relation to environment and land management practices in the context of the soil microflora and the introduction of pathogens on the health of the soil microbiome. Viable pathogens in manure spread on agricultural land may be distributed by leaching, surface run-off, water source contamination and contaminated crop removal. Thus it is important to understand how multiple pathogens can persist in manures and on soil at farm-scale and how crops produced under these conditions could be a potential transfer route for zoonotic pathogens. The management of pathogen load within livestock manure is a potential mechanism for the reduction and prevention of outbreaks infection with Escherichia coli, Listeria Salmonella, and Campylobacter. The ability of Campylobacter, E. coli, Listeria and Salmonella to combat environmental stress coupled with their survival on food crops and vegetables post-harvest emphasizes the need for further study of these pathogens along with the emerging pathogen Providencia given its link to disease in the immunocompromised and its’ high levels of antibiotic resistance. The management of pathogen load within livestock manure has been widely recognized as a potential mechanism for the reduction and prevention of outbreaks infection but any studies undertaken should be considered as region specific due to the variable nature of the factors influencing pathogen content and survival in manures and soil. Mediocre soils that require nutrients could be one template for research on manure inputs and their influence on soil health and on pathogen survival on grassland and in food crops.
Keywords	manure ; bacterial pathogens ; soil ; agriculture ; pathogen persistence ; zoonotic pathogens ; Microbiology ; QR1-502
Subject code	630
Language	English
Publishing date	2021-12-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: A review of new and existing non-extractive techniques for monitoring marine protected areas

Ryan McGeady / Robert M. Runya / James S. G. Dooley / John A. Howe / Clive J. Fox / Andrew J. Wheeler / Gerard Summers / Alexander Callaway / Suzanne Beck / Louise S. Brown / Gerard Dooly / Chris McGonigle

Frontiers in Marine Science, Vol

2023 Volume 10

Abstract: Ocean biodiversity loss is being driven by several anthropogenic threats and significant efforts are required to halt losses and promote healthy marine ecosystems. The establishment of a network of Marine Protected Areas (MPAs) can help restrict damaging ...

Abstract	Ocean biodiversity loss is being driven by several anthropogenic threats and significant efforts are required to halt losses and promote healthy marine ecosystems. The establishment of a network of Marine Protected Areas (MPAs) can help restrict damaging activities and have been recognised as a potential solution to aid marine conservation. When managed correctly they can deliver both ecological and socio-economic benefits. In recent times, MPA designations have increased rapidly while many countries have set future MPA targets for the decades ahead. An integral element of MPA management is adequate monitoring that collects data to assess if conservation objectives are being achieved. Data acquired by monitoring can vary widely as can the techniques employed to collect such data. Ideally, non-destructive and non-invasive methods are preferred to prevent damage to habitats and species, though this may rule out a number of traditional extractive sampling approaches such as dredges and trawls. Moreover, advances in ocean observation technologies enable the collection of large amounts of data at high resolutions, while automated data processing is beginning to make analyses more logistically feasible and less time-consuming. Therefore, developments to existing marine monitoring techniques and new emerging technologies have led to a diverse array of options when choosing to implement an MPA monitoring programme. Here, we present a review of new and existing non-extractive techniques which can be applied to MPA monitoring. We summarise their capabilities, applications, advantages, limitations and possible future developments. The review is intended to aid MPA managers and researchers in determining the suitability of available monitoring techniques based on data requirements and site conditions.
Keywords	monitoring ; marine protected area ; management ; marine ; conservation ; biodiversity ; Science ; Q ; General. Including nature conservation ; geographical distribution ; QH1-199.5
Subject code	333
Language	English
Publishing date	2023-07-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Transfer of antibiotic resistance genes between Enterococcus faecalis strains in filter feeding zooplankton Daphnia magna and Daphnia pulex

Olanrewaju, Temilola O / Mary McCarron / James S.G. Dooley / Joerg Arnscheidt

Science of the total environment. 2019 Apr. 01, v. 659

2019

Abstract: Antibiotic resistant bacteria from faecal pollution sources are pervasive in aquatic environments. A facilitating role for the emergence of waterborne, multi-drug resistant bacterial pathogens has been attributed to biofiltration but had not yet been ... ...

Abstract	Antibiotic resistant bacteria from faecal pollution sources are pervasive in aquatic environments. A facilitating role for the emergence of waterborne, multi-drug resistant bacterial pathogens has been attributed to biofiltration but had not yet been substantiated. This study investigated the effect of filtration and gut passage in Daphnia spp. on conjugal transfer of resistance genes in Enterococcus faecalis. In vivo conjugation experiments involved a vancomycin-resistant donor strain bearing a plasmid-borne vanA resistance gene, and two vancomycin-susceptible and rifampicin-resistant recipient strains in the presence of Daphnia magna or Daphnia pulex. Results showed successful transfer of the vanA resistance gene from donor to recipient; gene identity was confirmed by PCR and DNA sequencing. There was no significant difference in the number of transconjugants recovered from D. magna and D. pulex. However, transconjugant numbers differed by one order of magnitude between recipient strains. Transconjugant numbers from D. magna were also significantly different between treatments with ingestion of individual phytoplankton species before filtration of bacteria. The highest transfer efficiency calculated from excreted transconjugants was 2.5 × 10−6. This proof of concept for facilitation of horizontal gene transfer by a filter feeding organism provides evidence that Daphnia can disseminate antibiotic resistant transconjugants in the environment.
Keywords	Daphnia magna ; Daphnia pulex ; Enterococcus faecalis ; antibiotic resistance ; antibiotic resistance genes ; aquatic environment ; bacteria ; biofiltration ; digestive system ; ingestion ; multiple drug resistance ; pathogens ; phytoplankton ; pollution ; polymerase chain reaction ; sequence analysis ; zooplankton
Language	English
Dates of publication	2019-0401
Size	p. 1168-1175.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2018.12.314
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Competent but complex communication

Amy J Sterling / William J Snelling / Patrick J Naughton / Nigel G Ternan / James S G Dooley

PLoS Pathogens, Vol 16, Iss 4, p e

The phenomena of pheromone-responsive plasmids.

2020 Volume 1008310

Abstract: Enterococci are robust gram-positive bacteria that are found in a variety of surroundings and that cause a significant number of healthcare-associated infections. The genus possesses a high-efficiency pheromone-responsive plasmid (PRP) transfer system ... ...

Abstract	Enterococci are robust gram-positive bacteria that are found in a variety of surroundings and that cause a significant number of healthcare-associated infections. The genus possesses a high-efficiency pheromone-responsive plasmid (PRP) transfer system for genetic exchange that allows antimicrobial-resistance determinants to spread within bacterial populations. The pCF10 plasmid system is the best characterised, and although other PRP systems are structurally similar, they lack exact functional homologues of pCF10-encoded genes. In this review, we provide an overview of the enterococcal PRP systems, incorporating functional details for the less-well-defined systems. We catalogue the virulence-associated elements of the PRPs that have been identified to date, and we argue that this reinforces the requirement for elucidation of the less studied systems.
Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2020-04-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Microbial water quality

Teri Bigham / Charnete Casimero / James S.G. Dooley / Nigel G. Ternan / William J. Snelling / James Davis

Electrochemistry Communications, Vol 101, Iss , Pp 99-

Voltammetric detection of coliforms based on riboflavin–ferrocyanide redox couples

2019 Volume 103

Abstract: The ability to screen water for the presence of faecal contamination is a pressing need for rural communities dependent upon local purification systems. While there are a multitude of coliform detection assays based on the activity of β-galactosidase, ... ...

Abstract	The ability to screen water for the presence of faecal contamination is a pressing need for rural communities dependent upon local purification systems. While there are a multitude of coliform detection assays based on the activity of β-galactosidase, this report details the adaptation of a voltammetric pH sensing strategy which could offer rapid analysis. The approach exploits the bacterial metabolism of lactose via pyruvate to lactate with the subsequent decrease in pH measured by examining the peak separation of a riboflavin (sensing) – ferrocyanide (reference) couple. Disposable carbon fibre electrodes were used as in situ sensors in Escherichia coli cultures (103–107 cfu/mL) with detection times of 4 h enabling confirmation of coliform activity. The bacterial compatibility of the riboflavin–ferrocyanide system in combination with the simplicity of the detection methodology, stand in marked contrast to many existing coliform assays and could open new avenues through which voltammetric pH sensing could be employed. Keywords: Galactosidase, pH, Riboflavin, Coliform, Water quality, Sensor
Keywords	Industrial electrochemistry ; TP250-261 ; Chemistry ; QD1-999
Subject code	600
Language	English
Publishing date	2019-04-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing

Syed A. K. Shifat Ahmed / Michelle Rudden / Sabrina M. Elias / Thomas J. Smyth / Roger Marchant / Ibrahim M. Banat / James S. G. Dooley

Scientific Reports, Vol 11, Iss 1, Pp 1-

2021 Volume 15

Abstract: Abstract Pseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl- ... ...

Abstract	Abstract Pseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than ...
Keywords	Medicine ; R ; Science ; Q
Subject code	572
Language	English
Publishing date	2021-03-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Array based detection of antibiotic resistance genes in Gram negative bacteria isolated from retail poultry meat in the UK and Ireland

McNeece, Grainne / James S.G. Dooley / Martin J. Woodward / Patrick J. Naughton / Violetta Naughton

International journal of food microbiology. 2014 June 02, v. 179

2014

Abstract: The use of antibiotics in birds and animals intended for human consumption within the European Union (EU) and elsewhere has been subject to regulation prohibiting the use of antimicrobials as growth promoters and the use of last resort antibiotics in an ... ...

Abstract	The use of antibiotics in birds and animals intended for human consumption within the European Union (EU) and elsewhere has been subject to regulation prohibiting the use of antimicrobials as growth promoters and the use of last resort antibiotics in an attempt to reduce the spread of multi-resistant Gram negative bacteria. Given the inexorable spread of antibiotic resistance there is an increasing need for improved monitoring of our food. Using selective media, Gram negative bacteria were isolated from retail chicken of UK-Intensively reared (n=27), Irish-Intensively reared (n=19) and UK-Free range (n=30) origin and subjected to an oligonucleotide based array system for the detection of 47 clinically relevant antibiotic resistance genes (ARGs) and two integrase genes. High incidences of β-lactamase genes were noted in all sample types, acc (67%), cmy (80%), fox (55%) and tem (40%) while chloramphenicol resistant determinants were detected in bacteria from the UK poultry portions and were absent in bacteria from the Irish samples. Denaturing Gradient Gel Electrophoresis (DGGE) was used to qualitatively analyse the Gram negative population in the samples and showed the expected diversity based on band stabbing and DNA sequencing. The array system proved to be a quick method for the detection of antibiotic resistance gene (ARG) burden within a mixed Gram negative bacterial population.
Keywords	antibiotic resistance ; beta-lactamase ; chickens ; chloramphenicol ; denaturing gradient gel electrophoresis ; European Union ; genes ; Gram-negative bacteria ; growth promotion ; monitoring ; oligonucleotides ; poultry meat ; rearing ; selective media ; sequence analysis ; Ireland ; United Kingdom
Language	English
Dates of publication	2014-0602
Size	p. 24-32.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	87122-9
ISSN	1879-3460 ; 0168-1605
ISSN (online)	1879-3460
ISSN	0168-1605
DOI	10.1016/j.ijfoodmicro.2014.03.019
Database	NAL-Catalogue (AGRICOLA)

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