Surveillance of laboratory exposures to human pathogens and toxins: Canada 2018

Persistent pollution of genetic materials in a typical laboratory environment

From the onset of coronavirus disease (COVID-19) pandemic, there are concerns regarding the disease spread and environmental pollution of biohazard since studies on genetic engineering flourish and numerous genetic materials were used such as the nucleic acid test of the severe acute respiratory syndrome coronavirus (SARS-CoV-2). In this work, we studied genetic material pollution in an institute during a development cycle of plasmid, one of typical genetic materials, with typical laboratory settings. The pollution source, transmission routes, and pollution levels in laboratory environment were examined. The Real-Time quantitative- Polymerase Chain Reaction results of all environmental mediums (surface, aerosol, and liquid) showed that a targeted DNA segment occurred along with routine experimental operations. Among the 79 surface and air samples collected in the genetic material operation, half of the environment samples (38 of 79) are positive for nucleic acid pollution. Persistent nucleic acid contaminations were observed in all tested laboratories and spread in the public area (hallway). The highest concentration for liquid and surface samples were 1.92 × 108 copies/uL and 5.22 × 107 copies/cm2, respectively. Significant amounts of the targeted gene (with a mean value of 74 copies/L) were detected in the indoor air of laboratories utilizing centrifuge devices, shaking tables, and cell homogenizers. Spills and improper disposal of plasmid products were primary sources of pollution. The importance of establishing designated experimental zones, employing advanced biosafety cabinets, and implementing highly efficient cleaning systems in laboratories with lower biosafety levels is underscored. SYNOPSIS: STATEMENT. Persistent environmental pollutions of genetic materials are introduced by typical experiments in laboratories with low biosafety level.

Laboratory-acquired infections and pathogen escapes worldwide between 2000 and 2021: a scoping review

Laboratory-acquired infections (LAIs) and accidental pathogen escape from laboratory settings (APELS) are major concerns for the community. A risk-based approach for pathogen research management within a standard biosafety management framework is recommended but is challenging due to reasons such as inconsistency in risk tolerance and perception. Here, we performed a scoping review using publicly available, peer-reviewed journal and media reports of LAIs and instances of APELS between 2000 and 2021. We identified LAIs in 309 individuals in 94 reports for 51 pathogens. Eight fatalities (2·6% of all LAIs) were caused by infection with Neisseria meningitidis (n=3, 37·5%), Yersinia pestis (n=2, 25%), Salmonella enterica serotype Typhimurium (S Typhimurium; n=1, 12·5%), or Ebola virus (n=1, 12·5%) or were due to bovine spongiform encephalopathy (n=1, 12·5%). The top five LAI pathogens were S Typhimurium (n=154, 49·8%), Salmonella enteritidis (n=21, 6·8%), vaccinia virus (n=13, 4·2%), Brucella spp (n=12, 3·9%), and Brucella melitensis (n=11, 3·6%). 16 APELS were reported, including those for Bacillus anthracis, SARS-CoV, and poliovirus (n=3 each, 18·8%); Brucella spp and foot and mouth disease virus (n=2 each, 12·5%); and variola virus, Burkholderia pseudomallei, and influenza virus H5N1 (n=1 each, 6·3%). Continual improvement in LAI and APELS management via their root cause analysis and thorough investigation of such incidents is essential to prevent future occurrences. The results are biased due to the reliance on publicly available information, which emphasises the need for formalised global LAIs and APELS reporting to better understand the frequency of and circumstances surrounding these incidents.

Surveillance of laboratory exposures to human pathogens and toxins, Canada, 2021

Background

The Laboratory Incident Notification Canada surveillance system monitors laboratory incidents that are mandated to be reported under the Human Pathogens and Toxins Act and the Human Pathogens and Toxins Regulations. This article describes laboratory exposure incidents that occurred in Canada in 2021 and individuals affected in these incidents.

Methods

We extracted all laboratory incidents occurring in licensed Canadian laboratories in 2021 from the Laboratory Incident Notification Canada system and analyzed them using the software R. We calculated the rate of exposure incidents and performed descriptive statistics by sector, root cause, activity, occurrence type and type of pathogen/toxin. Analysis of the education level, route of exposure, sector, role and laboratory experience of the affected persons was also conducted. We conducted seasonality analysis to compare the median monthly occurrence of exposure incidents between 2016 and 2020 to monthly incidents in 2021.

Results

Forty-three exposure incidents involving 72 individuals were reported to Laboratory Incident Notification Canada in 2021. There were two confirmed laboratory-acquired infections and one suspected infection. The annual incident exposure rate was 4.2 incidents per 100 active licenses. Most exposure incidents involved non-Security Sensitive Biological Agents (n=38; 86.4%) and human risk group 2 (RG2) pathogens (n=27; 61.4%), with bacteria (n=20; 45.5%) and viruses (n=16; 36.4%) as the most implicated agent types. Microbiology was the most common activity associated with these incidents (n=18; 41.9%) and most incidents were reported by the academic sector (n=20; 46.5%). Sharps-related (n=12; 22.2%) incidents were the most common, while human interaction (e.g. workload constraints/pressures/demands, human error) (n=29, 28.2%) was the most common root cause. Most affected individuals were exposed through inhalation (n=38; 52.8%) and worked as technicians or technologists (n=51; 70.8%). Seasonality analyses revealed that the number of exposure incidents reported in 2021 were highest in September and May.

Conclusion

The rate of laboratory incidents was slightly lower in 2021 than in 2020. The most common occurrence type was sharps-related while issues with human interaction was the most cited root cause.

Zika Virus Infection During Research Vaccine Development: Investigation of the Laboratory-Acquired Infection via Nanopore Whole-Genome Sequencing

Zika virus (ZIKV) emerged as a serious public health problem since the first major outbreak in 2007. Current ZIKV diagnostic methods can successfully identify known ZIKV but are impossible to track the origin of viruses and pathogens other than known ZIKV strains. We planned to determine the ability of Whole Genome Sequencing (WGS) in clinical epidemiology by evaluating whether it can successfully detect the origin of ZIKV in a suspected case of laboratory-acquired infection (LAI). ZIKV found in the patient sample was sequenced with nanopore sequencing technology, followed by the production of the phylogenetic tree, based on the alignment of 38 known ZIKV strains with the consensus sequence. The closest viral strain with the consensus sequence was the strain used in the laboratory, with a percent identity of 99.27%. We think WGS showed its time-effectiveness and ability to detect the difference between strains to the level of a single base. Additionally, to determine the global number of LAIs, a literature review of articles published in the last 10 years was performed, and 53 reports of 338 LAIs were found. The lack of a universal reporting system was worrisome, as in the majority of cases (81.1%), the exposure route was unknown.

Surveillance of laboratory exposures to human pathogens and toxins, Canada 2020

BACKGROUND

The Laboratory Incident Notification Canada surveillance system monitors laboratory incidents reported under the Human Pathogens and Toxins Act and the Human Pathogens and Toxins Regulations. The objective of this report is to describe laboratory exposures that were reported in Canada in 2020 and the individuals who were affected.

METHODS

Laboratory incident exposures occurring in licensed Canadian laboratories in 2020 were analyzed. The exposure incident rate was calculated and the descriptive statistics were performed. Exposure incidents were analyzed by sector, activity type, occurrence type, root cause and pathogen/toxin. Affected persons were analyzed by education, route of exposure sector, role and laboratory experience. The time between the incident and the reporting date was also analyzed.

RESULTS

Forty-two incidents involving 57 individuals were reported to Laboratory Incident Notification Canada in 2020. There were no suspected or confirmed laboratory acquired infections. The annual incident exposure rate was 4.2 incidents per 100 active licenses. Most exposure incidents occurred during microbiology activities (n=22, 52.4%) and/or were reported by the hospital sector (n=19, 45.2%). Procedural issues (n=16, 27.1%) and sharps-related incidents (n=13, 22.0%) were the most common occurrences. Most affected individuals were exposed via inhalation (n=28, 49.1%) and worked as technicians or technologists (n=36, 63.2%). Issues with standard operating procedures was the most common root cause (n=24, 27.0%), followed by human interactions (n=21, 23.6%). The median number of days between the incident and the reporting date was six days.

CONCLUSION

The rate of laboratory incidents were lower in 2020 than 2019, although the ongoing pandemic may have contributed to this decrease because of the closure of non-essential workplaces, including laboratories, for a portion of the year. The most common occurrence type was procedural while issues with not complying to standard operating procedures and human interactions as the most cited root causes.