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  • 1
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    Simultaneous detection of micro‐organisms in water samples for future chip applications: coliform bacteria, non‐mandatory bacteria, hepatitis A virus and noroviruses
    Wiley ; 2009
    In:  physica status solidi c Vol. 6, No. 10 ( 2009-10), p. 2184-2189
    Details
    In: physica status solidi c, Wiley, Vol. 6, No. 10 ( 2009-10), p. 2184-2189
    Abstract: The use of surveillance systems demonstrates that waterborne pathogens are responsible for several diseases associated either with consuming of contaminated drinking water or contacting polluted recreational waters. To assure water quality not only mandatory microorganisms should be screened for. Emergent pathogens that represent danger to public health should also be analysed. Culture methods used routinely in water microbiology (bacteriology) laboratories are long time consumable. Moreover some of the emergent pathogens are not represented by conventional indicator bacteria, which limit the screening power of the current methodology. The present study aims at developing a rapid method to simultaneously detect several microorganisms (bacteria, protozoa, and virus) in water samples by the use of a DNA chip (AQUACHIP). Species specific DNA probes were developed based on the data available at public genomes databases. The probes were validated against the tested microorganism and artificial contaminated waters. Validation data shows that the probes may be useful to quickly evaluate water quality. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
    Type of Medium: Online Resource
    ISSN: 1862-6351 , 1610-1642
    URL: Issue
    URL: Article
    DOI: 10.1002/pssc.v6:10
    DOI: 10.1002/pssc.200881703
    Language: English
    Publisher: Wiley
    Publication Date: 2009
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  • 2
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    Genome Sequencing Reveals a Phage in Helicobacter pylori
    American Society for Microbiology ; 2011
    In:  mBio Vol. 2, No. 6 ( 2011-12-30)
    Details
    In: mBio, American Society for Microbiology, Vol. 2, No. 6 ( 2011-12-30)
    Abstract: Helicobacter pylori chronically infects the gastric mucosa in more than half of the human population, and while most of the infected individuals do not develop disease, H. pylori infection doubles the risk of developing gastric cancer. An abundance and diversity of viruses (phages) infect microbial populations in most environments and are important mediators of microbial diversity. Our finding of a 24.6-kb prophage integrated inside an H. pylori genome and the observation of circular integrase gene-containing DNA and phage-like particles inside cells upon UV treatment demonstrate that we have discovered a viable H. pylori phage. The additional finding of integrase genes in a large proportion of screened isolates of diverse geographic origins indicates that the prevalence of prophages may have been underestimated in H. pylori . Since phages are important drivers of microbial evolution, the discovery should be important for understanding and predicting genetic diversity in H. pylori .
    Type of Medium: Online Resource
    ISSN: 2161-2129 , 2150-7511
    URL: Article
    DOI: 10.1128/mBio.00239-11
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2011
    detail.hit.zdb_id: 2557172-2
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  • 3
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    Iridovirus-Like Viruses in Erythrocytes of Lacertids from Portugal
    Oxford University Press (OUP) ; 2013
    In:  Microscopy and Microanalysis Vol. 19, No. 5 ( 2013-10), p. 1183-1189
    Details
    In: Microscopy and Microanalysis, Oxford University Press (OUP), Vol. 19, No. 5 ( 2013-10), p. 1183-1189
    Abstract: Icosahedral nucleo-cytoplasmic large DNA viruses (NCLDV)-like viruses, which form inclusions in the erythrocyte cytoplasm of reptiles, were previously presented as candidates for a new genus of the Iridoviridae family. The present work describes the distribution of infected lizard hosts and ultrastructural characteristics of the viral inclusions of NCLDV-like viruses from Portugal and adjacent locations in Spain. Giemsa-stained blood smears of 235 Lacerta schreiberi from Portugal and Spain, 571 Lacerta monticola from the mountain Serra da Estrela (Portugal), 794 Podarcis hispanica from several localities in Portugal and Spain, and 25 Lacerta dugesii from Madeira Island, were studied. Infection in L. schreiberi was only found in mountain populations, up to 30% in Serra da Estrela and 9–11% elsewhere. It was absent in lizards from lowlands. Prevalence of infection among L. monticola in Serra da Estrela was 10%; infected lizards were found during March to July and October but not in August and September. Infection in P. hispanica was below 3.3%. Only one infected specimen of L. dugesii was identified by light microscopy. Ultrastructural examination of infected samples revealed that the inclusions are virus assembly sites of icosahedral cytoplasmic iridovirus-like virions. Virions from different host species have different ultrastructural features and probably represent different related viruses.
    Type of Medium: Online Resource
    ISSN: 1431-9276 , 1435-8115
    URL: Article
    DOI: 10.1017/S1431927613001773
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2013
    detail.hit.zdb_id: 1481716-0
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  • 4
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    Helicobacter pylori Phage Screening
    Oxford University Press (OUP) ; 2008
    In:  Microscopy and Microanalysis Vol. 14, No. S3 ( 2008-09), p. 150-151
    Details
    In: Microscopy and Microanalysis, Oxford University Press (OUP), Vol. 14, No. S3 ( 2008-09), p. 150-151
    Abstract: Helicobacter pylori is a helical shaped Gram-negative bacterium that colonizes the human stomach. It is associated with several human pathologies, such as gastritis, peptic ulcer, and gastric cancer. The standard first-line treatment is a one week triple therapy: the association of two antibiotics, most frequently amoxicillin and clarithromycin, and a proton pump inhibior. Despite the evolution of the treatment strategy, quadruple therapy, there is an increasing percentage of failure of the antibiotic therapy, due to antibiotics resistance. Phage therapy is the therapeutic use of lytic bacteriophages to treat pathogenic bacterial infections and H. pylori is a good target. However there are no available phage collections, and H. pylori phages description is diminutive on literature.
    Type of Medium: Online Resource
    ISSN: 1431-9276 , 1435-8115
    URL: Article
    DOI: 10.1017/S1431927608089721
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2008
    detail.hit.zdb_id: 1481716-0
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  • 5
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    Design and preliminary results of a DNA chip for the detection of microorganisms in water samples
    Wiley ; 2010
    In:  physica status solidi c Vol. 7, No. 11-12 ( 2010-11), p. 2751-2754
    Details
    In: physica status solidi c, Wiley, Vol. 7, No. 11-12 ( 2010-11), p. 2751-2754
    Abstract: Waterborne pathogens are responsible for several diseases, either due to the consumption of contaminated drinking water or due to the contact with polluted recreational waters. There is an increasing awareness that emergent and viral pathogens should also be monitored for determining water quality. Conventional detection methodologies present several shortcomings, such as reliance in indicator species, low throughput and increasing resources as more species are to be detected. DNA chips have the potential to serve as surveillance systems for the simultaneous detection of pathogens, overcoming these limitations. In the present study, a rapid method for the detection of multiple waterborne pathogens (bacteria and viruses) was developed, using a DNA chip (AQUACHIP®). Species and group specific probes were implemented on a DNA chip, both for mandatory and non‐mandatory microorganisms. Considerations regarding the AQUACHIP® design (probe layout, replicates and dilutions), DNA labelling and amplification, and preliminary results of the application of the chip for the detection of E. coli DNA are presented (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
    Type of Medium: Online Resource
    ISSN: 1862-6351 , 1610-1642
    URL: Issue
    URL: Article
    DOI: 10.1002/pssc.v7.11/12
    DOI: 10.1002/pssc.200983799
    Language: English
    Publisher: Wiley
    Publication Date: 2010
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  • 6
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    Recent “omics” advances in Helicobacter pylori
    Wiley ; 2016
    In:  Helicobacter Vol. 21, No. S1 ( 2016-09), p. 14-18
    Details
    In: Helicobacter, Wiley, Vol. 21, No. S1 ( 2016-09), p. 14-18
    Abstract: The development of high‐throughput whole genome sequencing ( WGS ) technologies is changing the face of microbiology, facilitating the comparison of large numbers of genomes from different lineages of a same organism. Our aim was to review the main advances on Helicobacter pylori “omics” and to understand how this is improving our knowledge of the biology, diversity and pathogenesis of H. pylori . Since the first H. pylori isolate was sequenced in 1997, 510 genomes have been deposited in the NCBI archive, providing a basis for improved understanding of the epidemiology and evolution of this important pathogen. This review focuses on works published between April 2015 and March 2016. Helicobacter “omics” is already making an impact and is a growing research field. Ultimately these advances will be translated into a routine clinical laboratory setting in order to improve public health.
    Type of Medium: Online Resource
    ISSN: 1083-4389 , 1523-5378
    URL: Issue
    URL: Article
    DOI: 10.1111/hel.2016.21.issue-S1
    DOI: 10.1111/hel.12334
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2020336-6
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  • 7
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    The expression of Helicobacter pylori tfs plasticity zone cluster is regulated by pH and adherence, and its composition is associated with differential gastric IL ‐8 secretion
    Wiley ; 2017
    In:  Helicobacter Vol. 22, No. 4 ( 2017-08)
    Details
    In: Helicobacter, Wiley, Vol. 22, No. 4 ( 2017-08)
    Abstract: Helicobacter pylori virulence is associated with different clinical outcomes. The existence of an intact dupA gene from tfs4b cluster has been suggested as a predictor for duodenal ulcer development. However, the role of tfs plasticity zone clusters in the development of ulcers remains unclear. We studied several H. pylori strains to characterize the gene arrangement of tfs3 and tfs4 clusters and their impact in the inflammatory response by infected gastric cells. Methods The genome of 14 H. pylori strains isolated from Western patients, pediatric (n=10) and adult (n=4), was fully sequenced using the Illumina platform MiSeq, in addition to eight pediatric strains previously sequenced. These strains were used to infect human gastric cells, and the secreted interleukin‐8 ( IL ‐8) was quantified by ELISA . The expression of virB2 , dupA , virB8 , virB10 , and virB6 was assessed by quantitative PCR in adherent and nonadherent fractions of H. pylori during in vitro co‐infection, at different pH values. Results We have found that cagA ‐positive H. pylori strains harboring a complete tfs plasticity zone cluster significantly induce increased production of IL ‐8 from gastric cells. We have also found that the region spanning from virB2 to virB10 genes constitutes an operon, whose expression is increased in the adherent fraction of bacteria during infection, as well as in both adherent and nonadherent fractions at acidic conditions. Conclusions A complete tfs plasticity zone cluster is a virulence factor that may be important for the colonization of H. pylori and to the development of severe outcomes of the infection with cagA ‐positive strains.
    Type of Medium: Online Resource
    ISSN: 1083-4389 , 1523-5378
    URL: Issue
    URL: Article
    DOI: 10.1111/hel.2017.22.issue-4
    DOI: 10.1111/hel.12390
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020336-6
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  • 8
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    Two novel sequence types of Helicobacter pylori strains: The first report from Turkey
    Wiley ; 2022
    In:  Helicobacter Vol. 27, No. 4 ( 2022-08)
    Details
    In: Helicobacter, Wiley, Vol. 27, No. 4 ( 2022-08)
    Type of Medium: Online Resource
    ISSN: 1083-4389 , 1523-5378
    URL: Issue
    URL: Article
    DOI: 10.1111/hel.v27.4
    DOI: 10.1111/hel.12907
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2020336-6
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  • 9
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    Population genetic structure of Helicobacter pylori strains from Portuguese‐speaking countries
    Wiley ; 2017
    In:  Helicobacter Vol. 22, No. 4 ( 2017-08)
    Details
    In: Helicobacter, Wiley, Vol. 22, No. 4 ( 2017-08)
    Abstract: The human gastric colonizer Helicobacter pylori is useful to track human migrations given the agreement between the bacterium phylogeographic distribution and human migrations. As Portugal was an African and Brazilian colonizer for over 400 years, we hypothesized that Portuguese isolates were likely genetically closer with those from countries colonized by Portuguese in the past. We aimed to characterize the population structure of several Portuguese‐speaking countries, including Portugal, Brazil, Angola, and Cape Verde. Materials and Methods We included strains isolated in Portugal from Portuguese and from former Portuguese colonies. These strains were typed by multilocus sequence typing ( MLST ) for seven housekeeping genes. We also retrieved from Multi Locus Sequence Typing Web site additional housekeeping gene sequences, namely from Angola and Brazil. Results We provided evidence that strains from Portuguese belong to hpEurope and that the introgression of hpEurope in non‐European countries that speak Portuguese is low, except for Brazil and Cape Verde, where hpEurope accounted for one quarter and one half of the population, respectively. We found genetic similarity for all strains from Portuguese‐speaking countries that belong to hpEurope population. Moreover, these strains showed a predominance of ancestral Europe 2 ( AE 2) over ancestral Europe 1 ( AE 1), followed by ancestral Africa 1. Conclusions H. pylori is a useful marker even for relative recent human migration events and may become rapidly differentiated from founder populations. H. pylori from Portuguese‐speaking countries assigned to hpEurope appears to be a hybrid population resulting from the admixture of AE 1, AE 2 and ancestral hpAfrica1.
    Type of Medium: Online Resource
    ISSN: 1083-4389 , 1523-5378
    URL: Issue
    URL: Article
    DOI: 10.1111/hel.2017.22.issue-4
    DOI: 10.1111/hel.12382
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020336-6
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  • 10
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    Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates
    MDPI AG ; 2021
    In:  Microorganisms Vol. 9, No. 11 ( 2021-10-28), p. 2252-
    Details
    In: Microorganisms, MDPI AG, Vol. 9, No. 11 ( 2021-10-28), p. 2252-
    Abstract: Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the β-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy.
    Type of Medium: Online Resource
    ISSN: 2076-2607
    URL: Article
    DOI: 10.3390/microorganisms9112252
    Language: English
    Publisher: MDPI AG
    Publication Date: 2021
    detail.hit.zdb_id: 2720891-6
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