Dataset Information

Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.

ABSTRACT: Thanks to huge advances in sequencing technologies, genomic resources are increasingly being generated and shared by the scientific community. The quality of such public resources are therefore of critical importance. Errors due to contamination are particularly worrying; they are widespread, propagate across databases, and can compromise downstream analyses, especially the detection of horizontally-transferred sequences. However we still lack consistent and comprehensive assessments of contamination prevalence in public genomic data. Here we applied a standardized procedure for foreign sequence annotation to 43 published arthropod genomes from the widely used Ensembl Metazoa database. This method combines information on sequence similarity and synteny to identify contaminant and putative horizontally-transferred sequences in any genome assembly, provided that an adequate reference database is available. We uncovered considerable heterogeneity in quality among arthropod assemblies, some being devoid of contaminant sequences, whereas others included hundreds of contaminant genes. Contaminants far outnumbered horizontally-transferred genes and were a major confounder of their detection, quantification and analysis. We strongly recommend that automated standardized decontamination procedures be systematically embedded into the submission process to genomic databases.

SUBMITTER: Francois CM

PROVIDER: S-EPMC7003083 | biostudies-literature | 2020 Feb

REPOSITORIES: biostudies-literature

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Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.

Francois Clementine M CM Durand Faustine F Figuet Emeric E Galtier Nicolas N

G3 (Bethesda, Md.) 20200206 2

Thanks to huge advances in sequencing technologies, genomic resources are increasingly being generated and shared by the scientific community. The quality of such public resources are therefore of critical importance. Errors due to contamination are particularly worrying; they are widespread, propagate across databases, and can compromise downstream analyses, especially the detection of horizontally-transferred sequences. However we still lack consistent and comprehensive assessments of contamin ...[more]

PMID: 31862787

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Project description:BackgroundStudies in different parts of the world have implicated money as a vehicle for transmission of pathogens. Such information which is necessary to facilitate infection control strategies is lacking in many sub-Saharan countries including Cameroon. This study analyzed the Franc de la Communauté Financiere d'Afrique (Franc CFA), the currency used in Cameroon and other countries in the Central African sub-region, as a potential vehicle for transmission of pathogenic bacteria and fungi, particularly drug-resistant strains, to generate findings which could create awareness on currency contamination and serve as a guide when formulating health policies on currency.MethodsTwo hundred and thirteen currency samples representing various denominations of notes and coins randomly collected from diverse sources in Buea, Cameroon were analyzed for bacteria and fungi. The sensitivity of bacterial isolates to antibiotics was tested using the disc diffusion method. The relationship between contamination and physical state, source or denomination of currency was assessed using the χ2 test. All statistics were discussed at 0.05 significance level.ResultsTwo hundred (93.9%) samples were contaminated with notes (96.6%) showing higher contamination than coins (88.2%). Uncirculated (mint) samples showed no contamination. There was a significant difference (P<0.05) in contamination with respect to currency denomination, physical state and source. All samples from butchers and patients/personnel in hospitals were contaminated. Lower denominations showed significantly higher (P = 0.008) levels of contamination than higher denominations. Dirty currency was more contaminated than clean currency. Nine bacterial species were isolated. Coagulase-negative Staphylococcus (CoNS) (54.9%) and Staphylococcus aureus (20.1%) predominated. Among the fungi detected, Aspergillus sp (17.3%) and Penicillium sp (15.9%) showed higher frequency of occurrence. Bacteria were susceptible (100%) to ceftriaxone, gentamicin, norfloxacin and ofloxacin. Susceptibility to amoxicillin, penicillin, ampicillin, vancomycin and cotrimoxazole was low. Staphylococci were resistant (100%) to vancomycin, penicillin G, and amoxicillin. CoNS in addition showed resistance (100%) to cotrimoxazole.ConclusionsThe CFA franc circulating in Buea could serve as a vehicle for transmission of drug resistant pathogenic or potential organisms and contamination could be due to currency usage and handling as mint notes were not contaminated. Hygiene practices during or after handling currency is greatly encouraged to prevent infection.

Project description:To incorporate genomics data into environmental assessments a mechanistic perspective of interactions between chemicals and induced biological processes needs to be developed. Since chemical compounds with structural similarity often induce comparable biological responses in exposed animals, gene expression signatures can serve as a starting point for the assessment of chemicals and their toxicity, but only when relevant and stable gene panels are available. To design such a panel, we isolated differentially expressed gene fragments from the soil arthropod Folsomia candida, a species often used for ecotoxicological testing. Animals were exposed to two chemically distinct compounds, being a metal (cadmium) and a polycyclic aromatic hydrocarbon (phenanthrene). We investigated the affected molecular responses resulting from either treatment and developed and validated 44 qPCR assays for their responses using a high throughput nano-liter RT-qPCR platform for the analysis of the samples.Suppressive subtractive hybridization (SSH) was used to retrieve stress-related gene fragments. SSH libraries revealed pathways involved in mitochondrial dysfunction and protein degradation for cadmium and biotransformation for phenanthrene to be overrepresented. Amongst a small cluster of SSH-derived cadmium responsive markers were an inflammatory response protein and an endo-glucanase. Conversely, cytochrome P450 family 6 or 9 was specifically induced by phenanthrene. Differential expressions of these candidate biomarkers were also highly significant in the independently generated test sample set. Toxicity levels in different training samples were not reflected by any of the markers' intensity of expressions. Though, a model based on partial least squares differential analysis (PLS-DA) (with RMSEPs between 9 and 22% and R(2)s between 0.82 and 0.97) using gene expressions of 25 important qPCR assays correctly predicted the nature of exposures of test samples.For the application of molecular bio-indication in environmental assessments, multivariate analyses obviously have an added value over univariate methods. Our results suggest that compound discrimination can be achieved by PLS-DA, based on a hard classification of the within-class rankings of samples from a test set. This study clearly shows that the use of high throughput RT-qPCR could be a valuable tool in ecotoxicology combining high throughput with analytical sensitivity.

Dataset Information

Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.

Publications

Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies.

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