Identifications of pathogens—a bioinformatic point of view

Christen, Richard

doi:10.1016/j.copbio.2008.04.003

Cited by 16 publications

(10 citation statements)

References 49 publications

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“…3C). This genus is ubiquitous in natural and man-made aquatic environments (9,11,12,15,17,21,35,46), and finding sequences of this genus does not automatically indicate pathogenesis. To conclude whether the identified Legionella species in the shower water poses a threat to hospital patients, isolation (by culturing) and characterization of the strain are necessary.…”

Section: Discussionmentioning

confidence: 99%

Potentially Pathogenic Bacteria in Shower Water and Air of a Stem Cell Transplant Unit

Perkins

Mayfield

Fraser

et al. 2009

Appl Environ Microbiol

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Potential pathogens from shower water and aerosolized shower mist (i.e., shower aerosol) have been suggested as an environmental source of infection for immunocompromised patients. To quantify the microbial load in shower water and aerosol samples, we used culture, microscopic, and quantitative PCR methods to investigate four shower stalls in a stem cell transplant unit at Barnes-Jewish Hospital in St. Louis, MO. We also tested membrane-integrated showerheads as a possible mitigation strategy. In addition to quantification, a 16S rRNA gene sequencing survey was used to characterize the abundant bacterial populations within shower water and aerosols. The average total bacterial counts were 2.2 ؋ 10 7 cells/liter in shower water and 3.4 ؋ 10 4 cells/m 3 in shower aerosol, and these counts were reduced to 6.3 ؋ 10 4 cells/liter (99.6% efficiency) and 8.9 ؋ 10 3 cells/m 3 (82.4% efficiency), respectively, after membrane-integrated showerheads were installed. Potentially pathogenic organisms were found in both water and aerosol samples from the conventional showers. Most notable was the presence of Mycobacterium mucogenicum (99.5% identity) in the water and Pseudomonas aeruginosa (99.3% identity) in the aerosol samples. Membrane-integrated showerheads may protect immunocompromised patients from waterborne infections in a stem cell transplant unit because of efficient capture of vast numbers of potentially pathogenic bacteria from hospital water. However, an in-depth epidemiological study is necessary to investigate whether membrane-integrated showerheads reduce hospital-acquired infections. The microbial load in shower aerosols with conventional showerheads was elevated compared to the load in HEPA-filtered background air in the stem cell unit, but it was considerably lower than typical indoor air. Thus, in shower environments without HEPA filtration, the increase in microbial load due to shower water aerosolization would not have been distinguishable from anticipated variations in background levels.

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Section: Discussionmentioning

confidence: 99%

Potentially Pathogenic Bacteria in Shower Water and Air of a Stem Cell Transplant Unit

Perkins

Mayfield

Fraser

et al. 2009

Appl Environ Microbiol

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“…These primers amplify the 16S rRNA gene region from positions 313 to 332 to positions 889 to 908 based on the 16S rRNA gene reference sequence of M. haemofelis (accession no. AF178677) (37,72). Based on our in silico PCR analysis (72) of these universal primers against the different mycoplasma 16S rRNA gene sequences available in the GenBank database, it was demonstrated that depending on the target Mycoplasma spp., these primers produce PCR fragments with sizes of 595 to 620 bp.…”

Section: Methodsmentioning

confidence: 99%

Prevalence, Genotype Richness, and Coinfection Patterns of Hemotropic Mycoplasmas in Raccoons (Procyon lotor) on Environmentally Protected and Urbanized Barrier Islands

Volokhov

Hwang

Chizhikov

et al. 2017

Appl Environ Microbiol

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Raccoons (Procyon lotor) are successful urban adapters and hosts to a number of zoonotic and nonzoonotic pathogens, yet little is known about their hemoplasma infections and how prevalence varies across habitat types. This study identifies hemotropic Mycoplasma species infection in raccoons from urban and undisturbed habitats and compares hemoplasma infection in sympatric urban cats (Felis catus) from the same geographic region. We collected blood from raccoons (n ϭ 95) on an urban coastal island (n ϭ 37) and an undisturbed coastal island (n ϭ 58) and from sympatric urban cats (n ϭ 39) in Georgia, USA. Based on 16S rRNA gene amplification, 62.1% (59/95) of raccoons and 17.9% (7/39) of feral cats were positive for hemoplasma. There was a greater percentage of hemoplasma-infected raccoons on the undisturbed island (79.3% [46/58]) than on the urban island (35.1% [13/37]; 2 ϭ 16.9, df ϭ 1, P ϭ 0.00004). Sequencing of the full-length 16S rRNA gene amplicons revealed six hemoplasma genotypes in raccoons, including five novel genotypes that were distinct from three known hemoplasma species identified in the sympatric cats. In addition, the hemoplasma genotypes detected in raccoons were not identified in sympatric cats or vice versa. Although all six hemoplasma genotypes were found in raccoons from urban and undisturbed islands, coinfection patterns differed between sites and among individuals, with the proportion of coinfected raccoons being greater in the undisturbed site. This study shows that raccoons are hosts for several novel hemoplasmas and that habitat type influences infection patterns.IMPORTANCE This study provides information about novel hemoplasmas identified in raccoons (Procyon lotor), which can be used for assessments of the prevalence of these hemoplasmas in raccoon populations and for future studies on the potential pathogenic impacts of these hemoplasmas on raccoon health. Raccoons from the undisturbed habitat had a higher prevalence of hemoplasma infection than urban raccoons. There does not appear to be cross-species transmission of hemotropic mycoplasmas between urban raccoons and feral cats. Raccoons appear to be hosts for several novel hemoplasmas, and habitat type influences infection patterns.KEYWORDS raccoons, Procyon lotor, feral cats, Felis catus, hemoplasmas, wildlife, 16S rRNA gene, phylogenetic analysis, hemoplasma U rbanization is a strong ecological driver that causes significant changes in the composition of wildlife communities and in various intra-and interspecies interactions (1). Ecological responses to urbanization can lead to changes in the dynamics

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“…Thus, at this moment, the only way to collect every sequence of a given gene is to combine keyword retrieval and a search by similarity (15). Keyword analysis often allows an estimation of the proportion of false positives and false negatives from a similarity method.…”

Section: Methodsmentioning

confidence: 99%

<i>In Silico</i> Analyses of Primers Used to Detect the Pathogenicity Genes of <i>Vibrio cholerae</i>

2012

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In Vibrio cholerae, the etiological agent of cholera, most of the virulence genes are located in two pathogenicity islands, named TCP (Toxin-Co-regulated Pilus) and CTX (Cholera ToXins). For each V. cholerae pathogenicity gene, we retrieved every primer published since 1990 and every known allele in order to perform a complete in silico survey and assess the quality of the PCR primers used for amplification of these genes. Primers with a melting temperature in the range 55–60°C against any target sequence were considered valid. Our survey clearly revealed that two thirds of the published primers are not able to properly detect every genetic variant of the target genes. Moreover, the quality of primers did not improve with time. Their lifetime, i.e. the number of times they were cited in the literature, is also not a factor allowing the selection of valid primers. We were able to improve some primers or design new primers for the few cases where no valid primer was found. In conclusion, many published primers should be avoided or improved for use in molecular detection tests, in order to improve and perfect specificity and coverage. This study suggests that bioinformatic analyses are important to validate the choice of primers.

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Identifications of pathogens—a bioinformatic point of view

Cited by 16 publications

References 49 publications

Potentially Pathogenic Bacteria in Shower Water and Air of a Stem Cell Transplant Unit

Potentially Pathogenic Bacteria in Shower Water and Air of a Stem Cell Transplant Unit

Prevalence, Genotype Richness, and Coinfection Patterns of Hemotropic Mycoplasmas in Raccoons (Procyon lotor) on Environmentally Protected and Urbanized Barrier Islands

<i>In Silico</i> Analyses of Primers Used to Detect the Pathogenicity Genes of <i>Vibrio cholerae</i>

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