Environmental surveillance of norovirus in Argentina revealed distinct viral diversity patterns, seasonality and spatio-temporal diffusion processes

Fernández, María Dolores Blanco; Torres, Carolina; Poma, Hugo Ramiro; Riviello-López, G.; Martı́nez, Laura C.; Cisterna, Daniel; Rajal, Verónica Beatriz; Nates, Silvia; Mbayed, Viviana Andrea

doi:10.1016/j.scitotenv.2012.08.033

Cited by 33 publications

(21 citation statements)

References 42 publications

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“…These fractions were efficiently recovered in the sample concentrates and very likely led to RT-qPCR inhibition. In previous studies (7,9,12), an ultrafiltration (UF) membrane with a molecular mass cutoff of 30 to 50 kDa was used as a secondary concentration method to detect viruses in environmental samples. The high-molecular-mass fractions observed in this study were probably what remained in the UF concentrate.…”

Section: Discussionmentioning

confidence: 99%

“…In the worst case, the concentrations of viruses were underestimated by 3 to 4 log 10 units due to the interference (3, 7). To overcome the RT-PCR inhibition problems, a virus concentration method based on adsorption-elution with an electronegative membrane has been developed and used widely (7,(11)(12)(13)(14). This method can exclude polyvalent cations and does not require beef extract.…”

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confidence: 99%

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Organic Substances Interfere with Reverse Transcription-Quantitative PCR-Based Virus Detection in Water Samples

Hata

Katayama

Furumai

2015

Appl Environ Microbiol

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bReverse transcription (RT)-PCR-based virus detection from water samples is occasionally hampered by organic substances that are coconcentrated during virus concentration procedures. To characterize these organic substances, samples containing commercially available humic acid, which is known to inhibit RT-PCR, and river water samples were subjected to adsorption-elution-based virus concentration using an electronegative membrane. In this study, the samples before, during, and after the concentration were analyzed in terms of organic properties and virus detection efficiencies. Two out of the three humic acid solutions resulted in RT-quantitative PCR (qPCR) inhibition that caused >3-log 10 -unit underestimation of spiked poliovirus. Over 60% of the organics contained in the two solutions were recovered in the concentrate, while over 60% of the organics in the uninhibited solution were lost during the concentration process. River water concentrates also caused inhibition of RT-qPCR. Organic concentrations in the river water samples increased by 2.3 to 3.9 times after the virus concentration procedure. The inhibitory samples contained organic fractions in the 10-to 100-kDa size range, which are suspected to be RT-PCR inhibitors. According to excitation-emission matrices, humic acid-like and protein-like fractions were also recovered from river water concentrates, but these fractions did not seem to affect virus detection. Our findings reveal that detailed organic analyses are effective in characterizing inhibitory substances. Human enteric viruses are etiological agents that can cause clinical symptoms, such as diarrhea and vomiting. Feces and vomit from infected individuals contain a substantial amount of viruses that contaminate the water environment. Consumption of improperly treated drinking water or contaminated environmental water during recreational activity leads to waterborne infections (1, 2).Quantitative detection of viruses present in water has been carried out worldwide in studies on the fate of viruses in the environment and potential viral infection risk (3-5). The detection of viruses in a water sample is commonly carried out using a PCR assay following virus concentration and nucleic acid extraction steps due to its superior rapidity, specificity, and sensitivity. However, the reliability of the PCR-based assay occasionally has come into question, as substances present in original samples or additives used during sample processing interfere with the nucleic acid extraction and reverse transcription (RT)-PCR (6-8). Even though several virus concentration methods have been developed, none of them can exclude the inhibitory substances completely (9).Polyvalent cations and some organic substances, such as beef extract constituents and humic acids, are known to inhibit RT-PCR (8, 10). Often, the virus detection efficiency is determined by spiking a known amount of viruses or nucleic acids in a sample and recovering them (6, 7, 11). In the worst case, the concentrations of viruses were underestimated by...

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

Organic Substances Interfere with Reverse Transcription-Quantitative PCR-Based Virus Detection in Water Samples

Hata

Katayama

Furumai

2015

Appl Environ Microbiol

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“…On the other hand, in sewage polluted rivers in the region of Buenos Aires city, Argentina, GII.4 was also the most prevalent (Fernández et al . ). Considering the size of the population in each city it was not evidenced a clear difference in the diversity of NoV genotypes.…”

Section: Discussionmentioning

confidence: 97%

Norovirus molecular detection in Uruguayan sewage samples reveals a high genetic diversity and GII.4 variant replacement along time

et al. 2016

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“…Therefore sewage from health care institutes is now viewed as a significant cause of environmental contamination and as a marker for tracing the origin of resistance [31,32]. Globally hospital sewage sampling is an attractive option over direct patient sampling for surveillance because it is representative of a large population and requires no consent with respect to ethical concerns [33][34][35][36]. The coexistence of integron and bla NDM genes in the sewage and environment is worth attention and is relevant in the context of antimicrobial resistance emergence across the globe [37].…”

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confidence: 99%

Detection of New Delhi metallo-beta-lactamase enzyme gene bla NDM-1 associated with the Int-1 gene in Gram-negative bacteria collected from the effluent treatment plant of a tuberculosis care hospital in Delhi, India

Aggarwal

Bhalla

Fatima

2020

Access Microbiology

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Background. Organisms possessing the bla NDM-1 gene (responsible for carbapenem resistance) with a class-1 integron can acquire many other antibiotic resistance genes from the community sewage pool and become multidrug-resistant superbugs. In this regard, hospital sewage, which contains a large quantity of residual antibiotics, metals and disinfectants, is being recognized as a significant cause of antimicrobial resistance (AMR) origination and spread across the major centres of the world and is thus routinely investigated as a marker for tracing the origin of drug resistance. Therefore, in this study, an attempt has been made to identify and characterize the carbapenem-resistant microbes associated with integron genes amongst the organisms isolated from the effluent treatment plant (ETP) installed in a tertiary respiratory care hospital in Delhi, India. Methods. One hundred and thirty-eight organisms belonging to Escherichia , Klebsiella , Pseudomonas and Acinetobacter spp. were collected from the incoming and outgoing sewage lines of the ETP. Carbapenem sensitivity and characterization was performed by the imipenem and imipenem-EDTA disc diffusion method. Later DNA extraction and PCR steps were performed for the Int-1 and bla NDM-1 genes. Results. Of the 138 organisms, 86 (62.3 %) were imipenem-resistant (P<0.05). One hundred and twenty-four (89.9 %) organisms had one or both of the genes. Overall, the bla NDM-1 gene (genotypic resistance) was present in 71 % (98/138) of organisms. 53.6 % (74/138) organisms were double gene-positive (bla NDM-1 + Int-1), of which 40 were producing the metallo-beta-lactamase enzyme, making up almost 28.9 % (40/138) of the collected organisms. Conclusion. The current study strengthens the hypothesis that Carbapenem resistant organisms are in a high-circulation burden through the human gut and hospital ETPs are providing an environment for resistance origination and amplification.

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Environmental surveillance of norovirus in Argentina revealed distinct viral diversity patterns, seasonality and spatio-temporal diffusion processes

Cited by 33 publications

References 42 publications

Organic Substances Interfere with Reverse Transcription-Quantitative PCR-Based Virus Detection in Water Samples

Organic Substances Interfere with Reverse Transcription-Quantitative PCR-Based Virus Detection in Water Samples

Norovirus molecular detection in Uruguayan sewage samples reveals a high genetic diversity and GII.4 variant replacement along time

Detection of New Delhi metallo-beta-lactamase enzyme gene bla NDM-1 associated with the Int-1 gene in Gram-negative bacteria collected from the effluent treatment plant of a tuberculosis care hospital in Delhi, India

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