Application of next generation sequencing technology on contamination monitoring in microbiology laboratory

Abstract

The surveillance and prevention of pathogenic microbiological contamination are the most important tasks of biosafety management in the lab. There is an urgent need to establish an effective and unbiased method to evaluate and monitor such contamination. This study aims to investigate the utility of next generation sequencing (NGS) method to detect possible contamination in the microbiology laboratory. Environmental samples were taken at multiple sites at the lab including the inner site of centrifuge rotor, the bench used for molecular biological tests, the benches of biosafety cabinets used for viral culture, clinical sample pre-treatment and nucleic acids extraction, by scrubbing the sites using sterile flocked swabs. The extracted total nucleic acids were used to construct the libraries for deep sequencing according to the protocol of Ion Torrent platform. At least 1G raw data was obtained for each sample. The reads of viruses and bacteria accounted for 0.01 ± 0.02%, and 77.76 ± 12.53% of total reads respectively. The viral sequences were likely to be derived from gene amplification products, the nucleic acids contaminated in fetal bovine serum. Reads from environmental microorganisms were also identified. Our results suggested that NGS method was capable of monitoring the nucleic acids contaminations from different sources in the lab, demonstrating its promising utility in monitoring and assessing the risk of potential laboratory contamination. The risk of contamination from reagents, remnant DNA and environment should be considered in data analysis and results interpretation.

Metagenomic identification of viral sequences in laboratory reagents

“…In sum, this study further highlights the extent of viral sequences in commonly used laboratory reagents [9], and the power of mNGS to monitor contamination in microbiological laboratories [53]. Although the source of these contaminants is unknown and needs further scrutiny, we tentatively suggest that viral vectors (for example, in the Lentiviridae ) represent a likely source.…”

“…Although the novel reagent-associated lenti-like virus was genetically distinct from known EIAV sequences, care should obviously be taken to ensure that any EIAV-like virus is a true viral infection rather than a reagent contaminant. In sum, this study further highlights the extent of viral sequences in commonly used laboratory reagents [9], and the power of mNGS to monitor contamination in microbiological laboratories [53]. Although the source of these contaminants is unknown and needs further scrutiny, we tentatively suggest that viral vectors (for example, in the Lentiviridae) represent a likely source.…”

COVID-19 and environmental concerns: A rapid review

“…So far, not much of the literature has dealt with the success of public health [ 177 ] infection prevention and control measures (IPC) for the management of COVID-19 transmission during the current outbreak. Literature on the modes of COVID-19 virus transmission from clinical samples [ 51 , 178 , 179 ], can further assist in identifying priority IPC measures in preventing and reducing the transmission of the pandemic. Literature observes that the monitoring clinics and laboratories for providing information on public health and upcoming potential hazards are not sufficient [ 152 ].…”

Diversity of RNA viruses in agricultural insects

“…Given the inherent nature of indiscriminately sequencing viral contaminants alongside actual viruses presented in the sample, prudence is imperative when interpreting the results derived from NGS. Viral contaminants can be introduced across the various stages of sample preparation, ranging from sample collection and RNA extraction to the sequencing [135] , [148] , [149] , [150] . Therefore, careful consideration of experimental design is essential to avoid potential sources of contamination [2] .…”