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Article: Comparasion of five gene loci (rnpB, 16S rRNA, 16S-23S rRNA, sodA and dnaJ) to aid the molecular identification of viridans-group streptococci and pneumococci.

Maeda, Y / Goldsmith, C E / Coulter, W A / Mason, C / Dooley, J S G / Lowery, C J / Millar, B C / Moore, J E

2012 Volume 68, Issue 4, Page(s) 190–196

Abstract: Viridans-group streptococci (VGS) consist of several taxa which historically have been highly diverse. However, at times it may become necessary to have a reliable scheme for the identification of these organisms to the species level. The aim of this ... ...

Abstract	Viridans-group streptococci (VGS) consist of several taxa which historically have been highly diverse. However, at times it may become necessary to have a reliable scheme for the identification of these organisms to the species level. The aim of this study is to compare the ability of five gene loci, namely rnpB, 16S rRNA, 16S-23S rRNA, sodA and dnaJ, to speciate such organisms through a sequence typing-based approach. Reference organisms consisting of six VGS species were compared based on sequence typing, followed by comparison of 31 wild-type respiratory isolates, and showed that employment of sequence typing using the rnpB gene locus was the most specific and reliable. Therefore, the use of rnpB sequencing for the identification of VGS to species level is a reliable and feasible option, based on a single gene target.
MeSH term(s)	Genes, Bacterial/genetics ; Humans ; Phylogeny ; Pneumococcal Infections/diagnosis ; Pneumococcal Infections/microbiology ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 23S/genetics ; Stomatitis/diagnosis ; Stomatitis/microbiology ; Streptococcal Infections/diagnosis ; Streptococcal Infections/microbiology ; Streptococcus pneumoniae/classification ; Streptococcus pneumoniae/genetics ; Streptococcus pneumoniae/isolation & purification ; Viridans Streptococci/classification ; Viridans Streptococci/genetics ; Viridans Streptococci/isolation & purification
Chemical Substances	RNA, Ribosomal, 16S ; RNA, Ribosomal, 23S
Language	English
Publishing date	2012-01-18
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1152119-3
ISSN	0967-4845
ISSN	0967-4845
DOI	10.1080/09674845.2011.11730349
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Article: Prevalence of clustered regulatory interspaced short palindromic repeat (CRISPR)-like sequences in mitis-group streptococci.

Maeda, Y / Goldsmith, C E / Coulter, W A / Mason, C / Dooley, J S G / Lowery, C J / Snelling, W J / Moore, J E

British journal of biomedical science

2011 Volume 68, Issue 2, Page(s) 65–68

Abstract: Clustered regulatory interspaced short palindromic repeats (CRISPRs) have been discovered in many bacteria and archaea. Many CRISPR-like sequences have been identified in an increasing number of studies on the function of CRISPRs. One CRISPR-like ... ...

Abstract	Clustered regulatory interspaced short palindromic repeats (CRISPRs) have been discovered in many bacteria and archaea. Many CRISPR-like sequences have been identified in an increasing number of studies on the function of CRISPRs. One CRISPR-like sequence of approximately 240 base pairs has been found to be highly conserved within 11 genome sequences of Streptococcus pneumoniae. A specific CRISPR-like polymerase chain reaction (PCR) assay was designed with the novel primers CRISPR 5F (forward primer) 5'-CTA ATY TCA TAA CCA TAR GAA TC-3' and CRISPR 3R (reverse primer) 5'-GAT AAR ATC CTY TAA WCT TCT AG-3' to detect the presence of this CRISPR-like sequence in pneumococci, as well as in viridans-group streptococci (VGS). This study investigates the prevalence of this CRISPR-like sequence in S. pneumoniae and 12 viridans-group streptococcal species and shows its existence to be shared by the majority of S. pneumoniae and, to a lesser extent, S. mitis. This CRISPR-like sequence was also found in S. australis and it is highly conserved among these strains, suggesting possible biological functional differences from true CRISPR because this CRISPR-like sequence has relatively few repeat numbers, and adjacent homology of CRISPR-associated (cas) genes was absent. The sharing of this CRISPR-like sequence between pneumococci, the mitis group and other VGS, as well as its high sequence homology, may suggest close evolutionary emergence of this sequence between these species.
MeSH term(s)	Base Sequence ; DNA, Bacterial/genetics ; Humans ; Inverted Repeat Sequences/genetics ; Molecular Sequence Data ; Sequence Alignment ; Species Specificity ; Streptococcus mitis/genetics ; Streptococcus pneumoniae/genetics
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2011-06-21
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1152119-3
ISSN	0967-4845
ISSN	0967-4845
DOI	10.1080/09674845.2011.11730325
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Article: Photocatalytic inactivation of Cryptosporidium parvum on nanostructured titanium dioxide films.

Sunnotel, O / Verdoold, R / Dunlop, P S M / Snelling, W J / Lowery, C J / Dooley, J S G / Moore, J E / Byrne, J A

Journal of water and health

2010 Volume 8, Issue 1, Page(s) 83–91

Abstract: Control of waterborne gastrointestinal parasites represents a major concern to water industries worldwide. In developed countries, pathogens in drinking water supplies are normally removed by sand filtration followed by chemical disinfection. ... ...

Abstract	Control of waterborne gastrointestinal parasites represents a major concern to water industries worldwide. In developed countries, pathogens in drinking water supplies are normally removed by sand filtration followed by chemical disinfection. Cryptosporidium spp. are generally resistant to common disinfection techniques and alternative control strategies are being sought. In the current study, the photocatalytic inactivation of C. parvum oocysts was shown to occur in buffer solution (78.4% after 180 min) and surface water (73.7% after 180 min). Viability was assessed by dye exclusion, excystation, direct examination of oocysts and a novel gene expression assay based on lactate dehydrogenase 1 (LDH1) expression levels. Collectively, this confirmed the inactivation of oocysts and scanning electron microscopy (SEM) confirmed cleavage at the suture line of oocyst cell walls, revealing large numbers of empty (ghost) cells after exposure to photocatalytic treatment.
MeSH term(s)	Cryptosporidium parvum/radiation effects ; Disinfection/instrumentation ; Nanostructures ; Oocysts/radiation effects ; Photolysis ; RNA, Protozoan ; Titanium ; Water Purification/instrumentation ; Water Purification/methods
Chemical Substances	RNA, Protozoan ; titanium dioxide (15FIX9V2JP) ; Titanium (D1JT611TNE)
Language	English
Publishing date	2010-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2123845-5
ISSN	1996-7829 ; 1477-8920
ISSN (online)	1996-7829
ISSN	1477-8920
DOI	10.2166/wh.2009.204
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Article: Molecular characterisation of the quinolone resistance-determining regions (QRDR) including gyrA, gyrB, parC and parE genes in Streptococcus pneumoniae.

Kakinuma, Y / Maeda, Y / Mason, C / Goldsmith, C E / Coulter, W A / Matsuda, M / Dooley, J S G / Lowery, C J / Moore, J E

British journal of biomedical science

2012 Volume 69, Issue 3, Page(s) 123–125

Abstract: Streptococcus pneumoniae is the leading cause of community-acquired pneumonia (CAP). Currently, empirical treatment with quinolones is being used due to the emergence of beta-lactam and macrolide resistance in S. pneumonaie. Although the prevalence of ... ...

Abstract	Streptococcus pneumoniae is the leading cause of community-acquired pneumonia (CAP). Currently, empirical treatment with quinolones is being used due to the emergence of beta-lactam and macrolide resistance in S. pneumonaie. Although the prevalence of quinolone-resistant S. pneumoniae remains low, increasing numbers of resistant isolates are being seen. Genetic mechanisms leading to fluoroquinolone resistance in pneumococci are complex. This study aims to use molecular methods to characterise all isolates through sequence analysis of their QRDR regions. Thirty-two S. pneumoniae isolates were obtained from nasal swabs from adult and paediatric patients attending local general practices in Northern Ireland. Phenotypic minimum inhibitory concentration (MIC) was determined for Clinical and Laboratory Standards Institute (CLSI) broth microdilution against ciprofloxacin, levofloxacin and norfloxacin. Simultaneously, the QRDR regions of gyrA, gyrB, parC and parE were analysed by sequence typing for all pneumococci obtained. Only one isolate (3.1%) showed reduced susceptibility to ciprofloxacin and levofloxacin. Two amino acid positions were discordant in the S. pneumoniae R6 strain and eight (25%) and 23 (71.9%) isolates contained the mutations Ile460Val in gyrA and Lys137Asn in parC (deposited in GenBank, accession numbers GQ999587-GQ999589), respectively. No mutations were found in either the gyrB or parE loci. In conclusion, the study demonstrated increased fluoroquinolone resistance which could not be accounted for simply through QRDR mutations, and, reciprocally, that mutations in the QRDR region do not necessarily result in overt phenotypic resistance.
MeSH term(s)	Adult ; Cell Survival/drug effects ; Cell Survival/genetics ; Child ; DNA Gyrase/genetics ; DNA Topoisomerase IV/genetics ; Drug Resistance, Bacterial/drug effects ; Drug Resistance, Bacterial/genetics ; Humans ; Microbial Sensitivity Tests ; Mutation ; Quinolones/pharmacology ; Streptococcus pneumoniae/drug effects ; Streptococcus pneumoniae/genetics
Chemical Substances	Quinolones ; DNA Topoisomerase IV (EC 5.99.1.-) ; DNA Gyrase (EC 5.99.1.3)
Language	English
Publishing date	2012
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1152119-3
ISSN	0967-4845
ISSN	0967-4845
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Article: Effectiveness of standard UV depuration at inactivating Cryptosporidium parvum recovered from spiked Pacific oysters (Crassostrea gigas).

Sunnotel, O / Snelling, W J / McDonough, N / Browne, L / Moore, J E / Dooley, J S G / Lowery, C J

Applied and environmental microbiology

2007 Volume 73, Issue 16, Page(s) 5083–5087

Abstract: When filter-feeding shellfish are consumed raw, because of their ability to concentrate and store waterborne pathogens, they are being increasingly associated with human gastroenteritis and have become recognized as important pathogen vectors. In the ... ...

Abstract	When filter-feeding shellfish are consumed raw, because of their ability to concentrate and store waterborne pathogens, they are being increasingly associated with human gastroenteritis and have become recognized as important pathogen vectors. In the shellfish industry, UV depuration procedures are mandatory to reduce pathogen levels prior to human consumption. However, these guidelines are based around more susceptible fecal coliforms and Salmonella spp. and do not consider Cryptosporidium spp., which have significant resistance to environmental stresses. Thus, there is an urgent need to evaluate the efficiency of standard UV depuration against the survival of Cryptosporidium recovered from shellfish. Our study found that in industrial-scale shellfish depuration treatment tanks, standard UV treatment resulted in a 13-fold inactivation of recovered, viable C. parvum oocysts from spiked (1 x 10(6) oocysts liter (-1)) Pacific oysters. Depuration at half power also significantly reduced (P < 0.05; ninefold) the number of viable oocysts recovered from oysters. While UV treatment resulted in significant reductions of recovered viable oocysts, low numbers of viable oocysts were still recovered from oysters after depuration, making their consumption when raw a public health risk. Our study highlights the need for increased periodic monitoring programs for shellfish harvesting sites, improved depuration procedures, and revised microbial quality control parameters, including Cryptosporidium assessment, to minimize the risk of cryptosporidiosis.
MeSH term(s)	Animals ; Cryptosporidium parvum/growth & development ; Cryptosporidium parvum/radiation effects ; Oocysts/growth & development ; Oocysts/radiation effects ; Ostreidae/parasitology ; Seafood/parasitology ; Seafood/standards ; Ultraviolet Rays
Language	English
Publishing date	2007-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
DOI	10.1128/AEM.00375-07
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Article: Effectiveness of Standard UV Depuration at Inactivating Cryptosporidium parvum Recovered from Spiked Pacific Oysters (Crassostrea gigas)

Sunnotel, O / Snelling, W.J / McDonough, N / Browne, L / Moore, J.E / Dooley, J.S.G / Lowery, C.J

Applied and environmental microbiology AEM. 2007 Aug. 15, v. 73, no. 16

2007

Abstract	When filter-feeding shellfish are consumed raw, because of their ability to concentrate and store waterborne pathogens, they are being increasingly associated with human gastroenteritis and have become recognized as important pathogen vectors. In the shellfish industry, UV depuration procedures are mandatory to reduce pathogen levels prior to human consumption. However, these guidelines are based around more susceptible fecal coliforms and Salmonella spp. and do not consider Cryptosporidium spp., which have significant resistance to environmental stresses. Thus, there is an urgent need to evaluate the efficiency of standard UV depuration against the survival of Cryptosporidium recovered from shellfish. Our study found that in industrial-scale shellfish depuration treatment tanks, standard UV treatment resulted in a 13-fold inactivation of recovered, viable C. parvum oocysts from spiked (1 x 10⁶ oocysts liter ⁻¹) Pacific oysters. Depuration at half power also significantly reduced (P < 0.05; ninefold) the number of viable oocysts recovered from oysters. While UV treatment resulted in significant reductions of recovered viable oocysts, low numbers of viable oocysts were still recovered from oysters after depuration, making their consumption when raw a public health risk. Our study highlights the need for increased periodic monitoring programs for shellfish harvesting sites, improved depuration procedures, and revised microbial quality control parameters, including Cryptosporidium assessment, to minimize the risk of cryptosporidiosis.
Keywords	Crassostrea gigas ; Cryptosporidium parvum ; Salmonella ; coliform bacteria ; cryptosporidiosis ; gastroenteritis ; guidelines ; harvesting ; humans ; industry ; microbiological quality ; monitoring ; oocysts ; oysters ; pathogens ; public health ; quality control ; raw shellfish ; risk ; shellfish ; stress tolerance ; tanks
Language	English
Dates of publication	2007-0815
Size	p. 5083-5087.
Publishing place	American Society for Microbiology
Document type	Article
ZDB-ID	223011-2
ISSN	1098-5336 ; 0099-2240
ISSN (online)	1098-5336
ISSN	0099-2240
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Article: PCR-IMS detection and molecular typing of Cryptosporidium parvum recovered from a recreational river source and an associated mussel (Mytilus edulis) bed in Northern Ireland.

Lowery, C J / Nugent, P / Moore, J E / Millar, B C / Xiru, X / Dooley, J S

Epidemiology and infection

2002 Volume 127, Issue 3, Page(s) 545–553

Abstract: PCR-IMS was used to detect Cryptosporidium spp. in environmental water samples in Northern Ireland which had previously tested negative by a conventional IFA staining method. Oocysts of C. parvum detected in river water and final treated sewage effluent ... ...

Abstract	PCR-IMS was used to detect Cryptosporidium spp. in environmental water samples in Northern Ireland which had previously tested negative by a conventional IFA staining method. Oocysts of C. parvum detected in river water and final treated sewage effluent collected from various sites along the river Lagan were identified as genotype 2 (animal origin) based on polymorphisms observed at the thrombospondin related adhesion protein gene locus. Similarly, genotype 1 (human origin) oocysts of C. parvum were detected in the marine filter feeder mussel, Mytilus edulis, collected from the shores of Belfast Lough. Detection of the human genotype of Cryptosporidium in mussels destined for human consumption identifies the organism's serious potential as a foodborne pathogen. This work highlights the possible value of monitoring filter feeder systems, in conjunction with specific molecular epidemiological tools, as an alternative monitoring system for the parasite within the aquatic environment.
MeSH term(s)	Animals ; Bivalvia/parasitology ; Cryptosporidium parvum/genetics ; Cryptosporidium parvum/isolation & purification ; Cryptosporidium parvum/pathogenicity ; Environmental Monitoring ; Fresh Water ; Genotype ; Molecular Epidemiology ; Northern Ireland ; Polymerase Chain Reaction ; Polymorphism, Restriction Fragment Length ; Water Microbiology
Language	English
Publishing date	2002-01-24
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	632982-2
ISSN	1469-4409 ; 0950-2688
ISSN (online)	1469-4409
ISSN	0950-2688
DOI	10.1017/s0950268801006276
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Article: Rapid and sensitive detection of single cryptosporidium oocysts from archived glass slides.

Sunnotel, O / Snelling, W J / Xiao, L / Moule, K / Moore, J E / Millar, B Cherie / Dooley, J S G / Lowery, C J

Journal of clinical microbiology

2006 Volume 44, Issue 9, Page(s) 3285–3291

Abstract: In this study we report on the development and application of a novel method for efficiently extracting and detecting single Cryptosporidium oocysts from archived glass slides. Laser capture microscopy was used to extract low numbers of oocysts from ... ...

Abstract	In this study we report on the development and application of a novel method for efficiently extracting and detecting single Cryptosporidium oocysts from archived glass slides. Laser capture microscopy was used to extract low numbers of oocysts from archived glass slides. Highly sensitive real-time PCR methods were then developed to enable the rapid detection and identification of Cryptosporidium oocysts from these samples. The method was applied to fecal smears stained with a variety of standard oocyst stains and water samples. This application, with samples derived from both public health and water service laboratories, highlighted the strong potential of this method to be used as a rapid high-throughput screening tool for the routine monitoring of Cryptosporidium and other medically important pathogens from clinical, veterinary, and environmental water samples. Importantly, the application of our protocol could be used to type Cryptosporidium and other pathogens from stored archived glass slides in public health and water service laboratories, providing vital epidemiological updates and helping to identify and trace pathogens and their routes of infection and ultimately improve their control.
MeSH term(s)	Animals ; Cryptosporidium/classification ; Cryptosporidium/genetics ; Cryptosporidium/growth & development ; Cryptosporidium/isolation & purification ; DNA, Protozoan/analysis ; DNA, Protozoan/isolation & purification ; Feces/parasitology ; Glass ; Humans ; Microscopy, Confocal/methods ; Molecular Sequence Data ; Oocysts/isolation & purification ; Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Time Factors ; Water Supply
Chemical Substances	DNA, Protozoan
Language	English
Publishing date	2006-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/JCM.00541-06
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Article: Cryptosporidium.

Sunnotel, O / Lowery, C J / Moore, J E / Dooley, J S G / Xiao, L / Millar, B C / Rooney, P J / Snelling, W J

Letters in applied microbiology

2006 Volume 43, Issue 1, Page(s) 7–16

Abstract: This review discusses characteristics of the genus Cryptosporidium and addresses the pathogenesis, reservoirs, public health significance and current applications for the detection and typing of this important pathogen. By increasing knowledge in key ... ...

Abstract	This review discusses characteristics of the genus Cryptosporidium and addresses the pathogenesis, reservoirs, public health significance and current applications for the detection and typing of this important pathogen. By increasing knowledge in key areas of Cryptosporidium research such as aetiology, epidemiology, transmission and host interactions, the numbers of cases of human cryptosporidiosis should be reduced.
MeSH term(s)	Animals ; Cattle ; Cryptosporidiosis/epidemiology ; Cryptosporidiosis/parasitology ; Cryptosporidiosis/prevention & control ; Cryptosporidiosis/transmission ; Cryptosporidium/classification ; Cryptosporidium/isolation & purification ; Cryptosporidium/pathogenicity ; Dogs ; Guinea Pigs ; Host-Parasite Interactions ; Humans ; Public Health
Language	English
Publishing date	2006-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	632584-1
ISSN	1472-765X ; 0266-8254
ISSN (online)	1472-765X
ISSN	0266-8254
DOI	10.1111/j.1472-765X.2006.01936.x
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Article: Rapid and Sensitive Detection of Single Cryptosporidium Oocysts from Archived Glass Slides

Sunnotel, O / Snelling, W.J / Xiao, L / Moule, K / Moore, J.E / Millar, B. Cherie / Dooley, J.S.G / Lowery, C.J

Journal of clinical microbiology JCM. 2006 Sept., v. 44, no. 9

2006

Abstract	In this study we report on the development and application of a novel method for efficiently extracting and detecting single Cryptosporidium oocysts from archived glass slides. Laser capture microscopy was used to extract low numbers of oocysts from archived glass slides. Highly sensitive real-time PCR methods were then developed to enable the rapid detection and identification of Cryptosporidium oocysts from these samples. The method was applied to fecal smears stained with a variety of standard oocyst stains and water samples. This application, with samples derived from both public health and water service laboratories, highlighted the strong potential of this method to be used as a rapid high-throughput screening tool for the routine monitoring of Cryptosporidium and other medically important pathogens from clinical, veterinary, and environmental water samples. Importantly, the application of our protocol could be used to type Cryptosporidium and other pathogens from stored archived glass slides in public health and water service laboratories, providing vital epidemiological updates and helping to identify and trace pathogens and their routes of infection and ultimately improve their control.
Language	English
Dates of publication	2006-09
Size	p. 3285-3291.
Publishing place	American Society for Microbiology
Document type	Article
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
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