Survey of laboratory-acquired infections around the world in biosafety level 3 and 4 laboratories

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.

Preparation for the next pandemic: challenges in strengthening surveillance

The devastating Coronavirus Disease 2019 (COVID-19) pandemic indicates that early detection of candidates with pandemic potential is vital. However, comprehensive metagenomic sequencing of the total microbiome is not practical due to the astronomical and rapidly evolving numbers and species of micro-organisms. Analysis of previous pandemics suggests that an increase in human-animal interactions, changes in animal and arthropod distribution due to climate change and deforestation, continuous mutations and interspecies jumping of RNA viruses, and frequent travels are important factors driving pandemic emergence. Besides measures mitigating these factors, surveillance at human-animal interfaces targeting animals with unusual tolerance to viral infections, sick heathcare workers, and workers at high biosafety level laboratories is crucial. Surveillance of sick travellers is important when alerted by an early warning system of a suspected outbreak due to unknown agents. These samples should be screened by multiplex nucleic acid amplification and subsequent unbiased next-generation sequencing. Novel viruses should be isolated in routine cell cultures, complemented by organoid cultures, and then tested in animal models for interspecies transmission potential. Potential agents are candidates for designing rapid diagnostics, therapeutics, and vaccines. For early detection of outbreaks, there are advantages in using event-based surveillance and artificial intelligence (AI), but high background noise and censorship are possible drawbacks. These systems are likely useful if they channel reliable information from frontline healthcare or veterinary workers and large international gatherings. Furthermore, sufficient regulation of high biosafety level laboratories, and stockpiling of broad spectrum antiviral drugs, vaccines, and personal protective equipment are indicated for pandemic preparedness.

Modifying Escherichia coli to mimic Shigella for medical microbiology laboratory teaching: a new strategy to improve biosafety in class

Introduction

Laboratory teaching of medical microbiology involves highly pathogenic microorganisms, thus posing potential biosafety risks to the students and the teacher. To address these risks, non/low-pathogenic microorganisms were modified to mimic highly pathogenic ones or highly pathogenic microorganisms were attenuated directly using the CRISPR/Cas9 technology. This study describes the modification of Escherichia coli DH5α to mimic Shigella and its evaluation as a safe alternative for medical laboratory teaching.

Methods

To generate E. coli DH5α△FliC△tnaA2a, the tnaA and FliC genes in E. coli DH5α were knocked out using CRISPR/Cas9 technology; a plasmid bearing the O-antigen determinant of S. flexneri 2a was then constructed and transformed. Acid tolerance assays and guinea pig eye tests were used to assess the viability and pathogenicity, respectively. Questionnaires were used to analyze teaching effectiveness and the opinions of teachers and students.

Results

The survey revealed that most teachers and students were inclined towards real-time laboratory classes than virtual classes or observation of plastic specimens. However, many students did not abide by the safety regulations, and most encountered potential biosafety hazards in the laboratory. E. coli DH5α△FliC△tnaA2a was biochemically and antigenically analogous to S. flexneri 2a and had lower resistance to acid than E. coli. There was no toxicity observed in guinea pigs. Most of teachers and students were unable to distinguish E. coli DH5α△FliC△tnaA2a from pure S. flexneri 2a in class. Students who used E. coli DH5α△FliC△tnaA2a in their practice had similar performance in simulated examinations compared to students who used real S. flexneri 2a, but significantly higher than the virtual experimental group.

Discussion

This approach can be applied to other high-risk pathogenic microorganisms to reduce the potential biosafety risks in medical laboratory-based teaching and provide a new strategy for the development of experimental materials.

A review of coxiellosis (Q fever) and brucellosis in goats and humans: Implications for disease control in smallholder farming systems in Southeast Asia

Coxiella burnetii and Brucella spp. are pathogenic bacteria that can cause large-scale outbreaks in livestock. Furthermore, these infectious agents are capable of causing zoonotic infections and therefore pose a risk to the close relationship between farm households and their livestock, especially goats. A review of seroprevalence studies of Coxiella burnetii and Brucella spp. in domestic goats demonstrated large differences in the total number of samples tested in different regions and countries. This review aims to provide information on coxiellosis (Q fever in humans) and brucellosis in goats concerning the characteristics of the causative agent, surveillance, and available prevention and control measures at a global level. Implications for Coxiella burnetii and Brucella spp. infections in domesticated goats in Southeast Asia are discussed.

The Biosafety Research Road Map: The Search for Evidence to Support Practices in the Laboratory-Bacillus anthracis and Brucella melitensis

Introduction

Brucella melitensis and Bacillus anthracis are zoonoses transmitted from animals and animal products. Scientific information is provided in this article to support biosafety precautions necessary to protect laboratory workers and individuals who are potentially exposed to these pathogens in the workplace or other settings, and gaps in information are also reported. There is a lack of information on the appropriate effective concentration for many chemical disinfectants for this agent. Controversies related to B. anthracis include infectious dose for skin and gastrointestinal infections, proper use of personal protective equipment (PPE) during the slaughter of infected animals, and handling of contaminated materials. B. melitensis is reported to have the highest number of laboratory-acquired infections (LAIs) to date in laboratory workers.

Methods

A literature search was conducted to identify potential gaps in biosafety and focused on five main sections including the route of inoculation/modes of transmission, infectious dose, LAIs, containment releases, and disinfection and decontamination strategies.

Results

Scientific literature currently lacks information on the effective concentration of many chemical disinfectants for this agent and in the variety of matrices where it may be found. Controversies related to B. anthracis include infectious dose for skin and gastrointestinal infections, proper use of PPE during the slaughter of infected animals, and handling contaminated materials.

Discussion

Clarified vulnerabilities based on specific scientific evidence will contribute to the prevention of unwanted and unpredictable infections, improving the biosafety processes and procedures for laboratory staff and other professionals such as veterinarians, individuals associated with the agricultural industry, and those working with susceptible wildlife species.

Characterization of SARS-CoV-2 Distribution and Microbial Succession in a Clinical Microbiology Testing Facility during the SARS-CoV-2 Pandemic

The exchange of microbes between humans and the built environment is a dynamic process that has significant impact on health. Most studies exploring the microbiome of the built environment have been predicated on improving our understanding of pathogen emergence, persistence, and transmission. Previous studies have demonstrated that SARS-CoV-2 presence significantly correlates with the proportional abundance of specific bacteria on surfaces in the built environment. However, in these studies, SARS-CoV-2 originated from infected patients. Here, we perform a similar assessment for a clinical microbiology lab while staff were handling SARS-CoV-2 infected samples. The goal of this study was to understand the distribution and dynamics of microbial population on various surfaces within different sections of a clinical microbiology lab during a short period of 2020 Coronavirus disease (COVID-19) pandemic. We sampled floors, benches, and sinks in 3 sections (bacteriology, molecular microbiology, and COVID) of an active clinical microbiology lab over a 3-month period. Although floor samples harbored SARS-CoV-2, it was rarely identified on other surfaces, and bacterial diversity was significantly greater on floors than sinks and benches. The floors were primarily colonized by bacteria common to natural environments (e.g., soils), and benchtops harbored a greater proportion of human-associated microbes, including Staphylococcus and Streptococcus. Finally, we show that the microbial composition of these surfaces did not change over time and remained stable. Despite finding viruses on the floors, no lab-acquired infections were reported during the study period, which suggests that lab safety protocols and sanitation practices were sufficient to prevent pathogen exposures. IMPORTANCE For decades, diagnostic clinical laboratories have been an integral part of the health care systems that perform diagnostic tests on patient's specimens in bulk on a regular basis. Understanding their microbiota should assist in designing and implementing disinfection, and cleaning regime in more effective way. To our knowledge, there is a lack of information on the composition and dynamics of microbiota in the clinical laboratory environments, and, through this study, we have tried to fill that gap. This study has wider implications as understanding the makeup of microbes on various surfaces within clinical laboratories could help identify any pathogenic bacterial taxa that could have colonized these surfaces, and might act as a potential source of laboratory-acquired infections. Mapping the microbial community within these built environments may also be critical in assessing the reliability of laboratory safety and sanitation practices to lower any potential risk of exposures to health care workers.

A pseudo-outbreak of MRSA due to laboratory contamination related to MRSA carriage of a laboratory staff member

BACKGROUND

Methicillin resistant Staphylococcus aureus (MRSA) is a major burden for hospitals globally. However, in the Netherlands, the MRSA prevalence is relatively low due to the 'search and destroy' policy. Routine multiple-locus variable-number of tandem repeat analysis (MLVA) of MRSA isolates supports outbreak detection. However, whole genome multiple locus sequence typing (wgMLST) is superior to MLVA in identifying (pseudo-)outbreaks with MRSA. The present study describes a pseudo-outbreak of MRSA at the bacteriology laboratory of a large Dutch teaching hospital.

METHODS

All staff members of the bacteriology laboratory of the Elisabeth-TweeSteden hospital were screened for MRSA carriage, after a laboratory contamination with MRSA was suspected. Clonal relatedness between the index isolate and the MRSA isolates from laboratory staff members and all previous MRSA isolates from the Elisabeth-TweeSteden hospital with the same MLVA-type as the index case was examined based on wgMLST using whole genome sequencing.

RESULTS

One of the staff members was identified as the probable source of the laboratory contamination, because of carriage of a MRSA possessing the same MLVA-type as the index case. Eleven other isolates with the same molecular characteristics were found in the database, of which seven were retrospectively suspected of contamination. Clonal relatedness was found between ten isolates, including the isolate found in the staff member and the MRSA found in the index patient with a maximum of eleven alleles difference. All isolates were epidemiologically linked through the laboratory staff member, who had worked on all these cultures.

CONCLUSIONS

The present study describes a MRSA pseudo-outbreak over a 2.5-year period due to laboratory contamination caused by a MRSA carrying laboratory staff member involving nine patients. In case of unexpected bacteriological findings, the possibility of a laboratory contamination should be considered.

Safety Procedures to Work with West Nile Virus in Biosafety Level 3 Facilities

West Nile virus (WNV) can cause severe and sometimes fatal disease, but we do not have treatments or therapeutics to manage these outcomes. Since its introduction to the USA in 1999, WNV has been handled in a biosafety level 3 laboratory to decrease risk to researchers, requiring strict safety protocols and important considerations with planning experiments. Recent changes in US guidelines suggest that WNV can be handled at a lower biosafety level due to its endemicity in the USA and generally minor symptoms, but some research still requires the use of the agent at biosafety level 3. This chapter will briefly discuss the considerations of biosafety when working with WNV.

Motivating Proactive Biorisk Management

Scholars and practitioners of biosafety and biosecurity (collectively, biorisk management or BRM) have argued that life scientists should play a more proactive role in monitoring their work for potential risks, mitigating harm, and seeking help as necessary. However, most efforts to promote proactive BRM have focused on training life scientists in technical skills and have largely ignored the extent to which life scientists wish to use them (ie, their motivation). In this article, we argue that efforts to promote proactive BRM would benefit from a greater focus on life scientists' motivation. We review relevant literature on life scientists' motivation to practice BRM, offer examples of successful interventions from adjacent fields, and outline ideas for possible interventions to promote proactive BRM, along with strategies for iterative development, testing, and scaling.

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.

Concepts to Bolster Biorisk Management

The rapid increase in the power of the life sciences has not been accompanied by a proportionate increase in the sophistication of biorisk management. Through conversations with thought leaders in biosafety and biosecurity, we have identified 19 concepts that are critical for biorisk management to continue to ensure the responsible and safe conduct of the life sciences in the future. Our work is not meant to be a comprehensive list, but rather a collection of topics that we hope will spark dialogue in the policy, research, and biorisk management communities.

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.

A Quick Laboratory Method for Assessment of Blood Penetration and Splash Resistance of PPE Fabrics During the COVID-19 Pandemic Situation

In the current outbreak of COVID-19, healthcare facilities are hit by a shortage of supply of Personal Protective Equipments (PPE) owing to extensive local and global demands and restrictions on their import or export. To circumvent this, trials with several indigenous materials suitable to qualify for PPEs and sterilization techniques for their reuse are being carried out. Prior to their commercialisation, it is imperative to evaluate the resistance of the PPE fabrics against penetration of synthetic blood under applied pressure, 40–300 mmHg as per test standards. Generally, two types of tests are recommended, Penetration Test and Splash Resistance Test, the former being more stringent. While the final certification of PPEs is carried out by authorised agencies, a first impression quick estimate of the choice of fabric can be made using a simple laboratory set-up. This study describes setups developed in the laboratory to carry out these tests. Evaluation of the fabrics, post-gamma irradiation, was also carried out. Microscopic examinations were performed to investigate radiation-induced structural changes in fabrics showing degraded performance. This set-up is useful for selection of fabrics and to assess the feasibility of reuse of PPEs, which is the need of the hour in this pandemic situation.

Biorisk Management for SARS-CoV-2 Research in a Biosafety Level-3 Core Facility

The emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents hazards to researchers and other laboratory personnel in research settings where the live virus is stored and handled. The Biosafety Level-3 (BSL-3) Core Facility (CF) at Yong Loo Lin School of Medicine in National University of Singapore (NUS Medicine) has implemented a biorisk management (BRM) system to ensure that biorisk to employees, the public, or the environment are consistently minimized to an acceptable level while working with SARS-CoV-2. This chapter summarizes how a BRM system can be implemented in academic institutions based on international standards in the context of existing local legislations/regulations and institutional policies/guidelines to minimize the risk of laboratory-acquired infections and deliberate misuse of the newly emerged virus, SARS-CoV-2 in BSL-3 laboratories. The BRM programs prioritize performing risk assessments prior to implementation of work processes and reassessing the risk portfolio of the facilities from time to time, determining root causes and prevention of recurrences. Focusing on awareness-raising and educating the laboratory users in biosafety and biosecurity, and identifying opportunities for improvement are the other key factors for a sustainable and successful BRM system in the NUS Medicine BSL-3 CF.

Risk Assessment for Activity Regulated Under the Human Tissue Act: A Single Institution Experience

Risk assessment represents one of the requirements for all activities involving human tissues within the premises. Although a variety of procedures are available to prepare risk assessments in general, there are no published examples of risks associated with the use of human samples in research. To cover this gap and to give an overview of the evaluation performed in our institution, we summarized the potential risks for the use of human samples in research identified in the projects under the remit of the UCL/UCLH Biobank. The procedures of acquisition, transportation, storage, use, and disposal of human samples, and security of the premises were analyzed. From our experience, there are governance-related risks associated with the process of consenting the patients, with the donor confidentiality, with mislabeling of samples and with the ethical approval associated with the project, and they generally do not compromise the integrity of the samples. On the other hand, samples' integrity is more at risk during collection, storage, transport, and use of the sample. Adequate training and having appropriate standard procedures in place and available for all staff seem to be the most effective control measures to prevent any issue. In addition, appropriate equipment maintenance, contingency plans, and strict regulation and monitoring of the facility security should always be in place. In summary, an appropriate evaluation of the risks associated with the use of human samples in research is one of the requirements for the use of human samples in research and it is fundamental for the protection of staff, students, the institution itself, and the patients. Supporting biobanking, implementing a culture of biosafety in the life sciences, and raising awareness in the scientific and regulatory communities are key ways to anticipate future problems associated with biological and governance risks.

Results of a 2020 Survey on Reporting Requirements and Practices for Biocontainment Laboratory Accidents

Biosafety laboratory accidents are a normal part of laboratory science, but the frequency of such accidents is unclear due to current reporting standards and processes. To better understand accident reporting, a survey was created, with input from ABSA International, which included a series of questions about standards, requirements, and likely motivations for reporting or nonreporting. A total of 60 biosafety officers completed the survey. Respondents reported working with more than 5,000 people in laboratories, including more than 40 biosafety level 3 or animal biosafety level 3 laboratories, which work with higher-risk pathogens. Most of the respondents were located in the United States, Canada, or New Zealand, or did not identify their location. Notable results included that 97% of surveyed biosafety officers oversee laboratories that require reporting exposure to at least some pathogens. However, 63% relayed that the reports are not usually sent outside of the institution where they occurred. A slight majority (55%) stated that paper reports were used, with the rest reporting they used a variety of computer systems. Even in laboratories that used paper-based reporting systems, 67% relayed that these reports were used alongside, or entered into, a digital system. While 82% of these biosafety officers agreed that workers understood the importance of reporting for their own safety, 82% also agreed that a variety of disincentives prevent laboratory workers from reporting incidents, including concerns about job loss and loss of funding.

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.

Supercritical fluid extraction-supercritical fluid chromatography of saliva: Single-quadrupole mass spectrometry monitoring of caffeine for gastric emptying studies†

Saliva is an attractive sampling matrix for measuring various endogenous and exogeneous substances but requires sample treatment prior to chromatographic analysis. Exploiting supercritical CO₂ for both extraction and chromatography simplifies sample preparation, reduces organic solvent consumption, and minimizes exposure to potentially infectious samples, but has not yet been applied to oral fluid. Here, we demonstrate the feasibility and benefits of online supercritical fluid extraction coupled to supercritical fluid chromatography and single-quadrupole mass spectrometry for monitoring the model salivary tracer caffeine. A comparison of ¹³ C- and ³² S-labeled internal standards with external standard calibration confirmed the superiority of stable isotope-labeled caffeine over nonanalogous internal standards. As proof of concept, the validated method was applied to saliva from a magnetic resonance imaging study of gastric emptying. After administration of 35 mg caffeine via ice capsule, salivary levels correlated with magnetic resonance imaging data, corroborating caffeine's usefulness as tracer of gastric emptying (R²  = 0.945). In contrast to off-line methods, online quantification required only minute amounts of organic solvents and a single manual operation prior to online bioanalysis of saliva, thus demonstrating the usefulness of CO₂ -based extraction and separation techniques for potentially infective biomatrices.

Assessment of the Biosafety and Biosecurity in the Reference Veterinary Laboratory of Parakou in Benin

Optimal biosafety and biosecurity are major requirements of global health security. This study assessed the biorisk management in the reference veterinary laboratory of Parakou (Benin). The study was cross-sectional, descriptive, and evaluative. The non-probability sampling method with the reasoned choice was used. The Food and Agriculture Organization laboratory mapping tool-safety was used to collect information from the laboratory team. Group discussion, working environment observation, and document exploitation were the data collection techniques. The biorisk management was rated good if the average indicator of the laboratory reached at least 80%. Otherwise, the biorisk management was rated insufficient. The overall laboratory biosafety and biosecurity score was insufficient (42.4%). Per area, the scores were 26.7% for engineering, 33.3% for administration, 53.8% for personal protective equipment, and 62.3% for the operational. There was no area or category score that reached 80%. Containment, waste disposal, and personal protective equipment disposal were the best performing categories with a score above 60%. The laboratory has no biosafety and accident prevention program. Its premises require renovation. The standard operating procedures for biosafety are not yet finalized, and the training mechanism is not optimal. Therefore, strong advocacy and implementation of a biorisk management improvement plan appear as urgent corrective actions which are required to help the reference veterinary laboratory of Parakou in its task to protect the livestock and, ultimately, the people of Benin from dangerous diseases and emerging pathogens.

COVID-19 Management at IHU Méditerranée Infection: A One-Year Experience

BACKGROUND

The Hospital-University Institute (IHU) Méditerranée Infection features a 27,000 square meter building hosting 700 employees and 75 hospitalized patients in the center of Marseille, France.

METHOD

Previous preparedness in contagious disease management allowed the IHU to manage the COVID-19 outbreak by continuing adaptation for optimal diagnosis, care and outcome. We report here the output of this management.

RESULTS

From 5 March 2020, and 26 April 2021, 608,313 PCR tests were provided for 424,919 patients and 44,089 returned positive. A total of 23,390 patients with COVID-19 were followed at IHU with an overall case fatality ratio of 1.7%. Of them 20,270 were followed as outpatients with an overall CFR of 0.17%. We performed 24,807 EKG, 5759 low dose CT Scanner, and 18,344 serology. Of the 7643 nasopharyngeal samples inoculated in cell cultures 3317 (43.3%) yielded SARS-Cov-2 isolates. Finally, 7370 SARS-Cov-2 genomes were analyzed, allowing description of the first genetic variants and their implication in the epidemiologic curves. Continuous clinical care quality evaluation provided the opportunity for 155 publications allowing a better understanding of the disease and improvement of care and 132 videos posted on the IHU Facebook network, totaling 60 million views and 390,000 followers, and dealing with COVID-19, outbreaks, epistemology, and ethics in medicine.

CONCLUSIONS

During this epidemic, IHU Méditerranée Infection played the role for which it has been created; useful clinical research to guarantee a high-quality diagnostic and care for patient and a recognized expertise.

Update on Potentially Zoonotic Viruses of European Bats

Bats have been increasingly gaining attention as potential reservoir hosts of some of the most virulent viruses known. Numerous review articles summarize bats as potential reservoir hosts of human-pathogenic zoonotic viruses. For European bats, just one review article is available that we published in 2014. The present review provides an update on the earlier article and summarizes the most important viruses found in European bats and their possible implications for Public Health. We identify the research gaps and recommend monitoring of these viruses.

Clinical Laboratory Biosafety Gaps: Lessons Learned from Past Outbreaks Reveal a Path to a Safer Future

Patient care and public health require timely, reliable laboratory testing. However, clinical laboratory professionals rarely know whether patient specimens contain infectious agents, making ensuring biosafety while performing testing procedures challenging. The importance of biosafety in clinical laboratories was highlighted during the 2014 Ebola outbreak, where concerns about biosafety resulted in delayed diagnoses and contributed to patient deaths. This review is a collaboration between subject matter experts from large and small laboratories and the federal government to evaluate the capability of clinical laboratories to manage biosafety risks and safely test patient specimens. We discuss the complexity of clinical laboratories, including anatomic pathology, and describe how applying current biosafety guidance may be difficult as these guidelines, largely based on practices in research laboratories, do not always correspond to the unique clinical laboratory environments and their specialized equipment and processes. We retrospectively describe the biosafety gaps and opportunities for improvement in the areas of risk assessment and management; automated and manual laboratory disciplines; specimen collection, processing, and storage; test utilization; equipment and instrumentation safety; disinfection practices; personal protective equipment; waste management; laboratory personnel training and competency assessment; accreditation processes; and ethical guidance. Also addressed are the unique biosafety challenges successfully handled by a Texas community hospital clinical laboratory that performed testing for patients with Ebola without a formal biocontainment unit. The gaps in knowledge and practices identified in previous and ongoing outbreaks demonstrate the need for collaborative, comprehensive solutions to improve clinical laboratory biosafety and to better combat future emerging infectious disease outbreaks.

Contagion Management at the Méditerranée Infection University Hospital Institute

The Méditerranée Infection University Hospital Institute (IHU) is located in a recent building, which includes experts on a wide range of infectious disease. The IHU strategy is to develop innovative tools, including epidemiological monitoring, point-of-care laboratories, and the ability to mass screen the population. In this study, we review the strategy and guidelines proposed by the IHU and its application to the COVID-19 pandemic and summarise the various challenges it raises. Early diagnosis enables contagious patients to be isolated and treatment to be initiated at an early stage to reduce the microbial load and contagiousness. In the context of the COVID-19 pandemic, we had to deal with a shortage of personal protective equipment and reagents and a massive influx of patients. Between 27 January 2020 and 5 January 2021, 434,925 nasopharyngeal samples were tested for the presence of SARS-CoV-2. Of them, 12,055 patients with COVID-19 were followed up in our out-patient clinic, and 1888 patients were hospitalised in the Institute. By constantly adapting our strategy to the ongoing situation, the IHU has succeeded in expanding and upgrading its equipment and improving circuits and flows to better manage infected patients.

Assessment of biorisk management systems in high containment laboratories, 18 countries in Europe, 2016 and 2017

Europe-wide activities to improve biosafety and biosecurity performed within the frameworks of the European Union (EU)-funded Joint Actions EMERGE and QUANDHIP led to the development of an Integrated European Checklist for Laboratory Biorisk Management (ECL).

To better understand different approaches shaping biorisk management (BRM) systems on an operational level in high containment laboratories, the ECL was used to map the implementation of BRM in 32 high containment laboratories in 18 countries in Europe. The results suggest that the BRM elements referring to standard microbiological working practices and the handling of infectious material were fulfilled particularly well. The elements safety exercises involving internal and external emergency responders, and appropriate decommissioning plans were not fulfilled particularly well. BRM in Biosafety Level (BSL) 4 laboratories handling Risk Group (RG) 4 viruses appear to vary among each other less than BSL3 laboratories handling RG 3 bacteria. It is important to agree on comparable regulations in Europe as high containment laboratories are indispensable for a safe, quick and effective response to public health threats. As high containment laboratories may also present a public health risk it is crucial to have robust BRM on organisational and operational levels.

Current status and future prospect of management of biosafety laboratories for emerging infectious diseases

In recent years, there have been several outbreaks of infectious diseases around the world, including severe acute respiratory syndrome, Ebola virus disease, Middle East respiratory syndrome, and corona virus disease 2019. Experience suggests that the detection and research of emergent infectious diseases play a crucial role in the process of responding to the epidemic, which also brings great challenges to biosafety laboratories. In the face of unknown biological risk factors, the non-standard biosafety protection measures have a serious impact on the life safety of laboratory staff and the research of infectious diseases, which stresses the necessity of safety protection in biosafety laboratories. This article will briefly review the current status and future prospect of management of biosafety laboratories both in China and other countries in terms of safety protection measures during new sudden infectious disease incidents.

Biosafety threats of the rapidly established labs for SARS-CoV-2 tests in China

To increase the capacity of identifying coronavirus disease 2019 (COVID-19) infection, many Biosafety Level 2 (BSL-2) labs have been established in a short period of time for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid tests all over the world. However, their biosafety has not been evaluated, which could have been the first gateway to SARS-CoV-2 transmission. During 9-11 March 2020, the first comprehensive evaluation of the biosafety in all 89 labs qualified for conducting SARS-CoV-2 tests in Sichuan Province of China was conducted. The degree of compliance with 39 criteria in five categories was evaluated: biosafety requirements for lab activities (14 criteria), sample transfer, acceptance and management (6 criteria), waste management (9 criteria), personnel training and protection (4 criteria), and lab environmental disinfection, emergency plans and accident handling (6 criteria). Our results revealed that, although an overall median compliance rate of 94.6% for 39 criteria, only four of 89 labs met all of them. Criteria in personnel training and protection have been most satisfactorily met, followed by lab environmental disinfection, emergency plans and accident handling. The most severe risk was the lack of automatic doors at the main entrance or in core operation areas, especially among labs in CDC and hospitals. This risk, together with failure for keeping pressure in the core operation areas 25 ± 5 Pa (mainly among labs in the third-party testing agencies), may cause accidental exposure to biological agents from lab activities. Other severe risk included failure for standard labeling of SARS-CoV-2 wastes and lacking regular monitoring of sterilization effects. Our findings would provide experiences and lessons for strengthening lab biosafety in other Chinese provinces, and also serve as an important reference for many other countries where such labs are being or will be quickly built for fighting the COVID-19. The information of lab safety should be considered to be internally linked to the national intelligent syndromic surveillance system (NISSS), for better improving the safety of the labs at the greatest need and facilitating more comprehensive surveillance of risk for disease outbreak.

Tuberculosis and Other Airborne Microbes in Occupational Health and Safety

Airborne pathogens and non-malignant infectious diseases such as tuberculosis are highly contagious and can have severe effects on healthcare workers. The symptoms of these diseases take time to manifest, which can prevent workers from noticing that they have been exposed until symptoms appear. The current paper sought to assess the occupational safety and preventative measures taken in laboratories in Spain, and to compare these measures with those reported by other studies worldwide. A cross-sectional study of workers (35–50 years old) was conducted using a web survey (N = 30), and a bibliometric analysis was carried out in the Scopus database (92 documents were selected). The occupational safety and health measures were inadequate, according to the opinions of the workers. The training (p < 0.01), the amount of work (p < 0.05), and how the workers followed their protocols (p < 0.001) were linked to incidents and exposure to airborne pathogens. The most significant previous publication was a report (848 citations) stating that the previous variables linked to exposure are vital for prevention. Most works focused on countries like the U.S.A. (p = 0.009) were reviews, with a limited number of studies focused on occupational safety.

Disposal of the large volume of sputum positive for Mycobacterium tuberculosis by using microwave sterilisation technology as an alternative to traditional autoclaving in a tertiary respiratory care hospital in Delhi, India

Background

Everyday, tuberculosis hospitals collect enormous amount of sputum containing viable Mycobacterium tuberculosis bacilli, the disposal of which is a challenging task. Chemical (5% phenol) and physical (autoclaving) disinfection methods involve cost, space and cause further environmental degradation. Over the years, use of microwave for sterilisation of biomedical waste has become widespread. However, its efficacy to sterilise large volume of M. tuberculosis positive sputum has never been investigated.

Aim

To evaluate the effectiveness of microwave in sterilising large volumes of M. tuberculosis positive sputum samples.

Methods

226 sputum samples positive for M. tuberculosis were checked by Ziehl-Neelsen staining and liquid culture (MGIT ™) both before and after microwaving. χ² test was performed, and p-value <0.05 was considered significant.

Findings

Before microwaving, samples containing acid fast bacilli (AFB) and live M. tuberculosis bacilli were 93.8% and 95% (≈94.7%) respectively; which came down to 14.2% (32) and <1% (≈0.9%) in post microwave. In the 32 post-microwave AFB positive samples, bacilli appeared apoptotic, decreased in size, fragmented, loosely arranged and were easily missed as stain artefacts. Their beaded appearance was not appreciable. Background pus cells were of smaller size, did not take up methylene blue stain properly, and multilobed nuclear material was missing.

Conclusion

The study shows efficacy of microwave as an alternative sterilisation method for large volume sputum samples containing M. tuberculosis bacilli. Microwave can become an effective sterilisation method, especially for isolated tuberculosis care centres in countries which struggle for disposal of sputum, the biomedical waste.

Establishment of the key Technical Indicators of Positive Pressure Biological Protective Clothing

Objective

Trying to establish the key technical indicators related to positive pressure biological protective clothing (PPBPC), providing technical support for the establishment of PPBPC standards in the future.

Method

We examined the protection standard systems established by the major standards organizations in China and other developed countries. We also analyzed the technical indicators of the gas-tight chemical protective clothing and ventilated protective clothing against particulate radioactive contamination which closely related to PPBPC. And tested the performance of a set of imported dual-purpose PPBPC to verify the fit of its technical indicators with the standards. We aimed to identify the status of China’s standards in the area of personnel protection and put forward feasible suggestions for the production of PPBPC in China.

Results

Developed countries in Europe and North America have a complete system of standard protective clothing. China should also strengthen the construction of standard protective clothing, especially PPBPC.

Conclusion

With the improvements in infectious disease prevention and control on a global scale, the demand for PPBPC continues to increase and consideration should be given to the establishment of standards for this.

Development of Improved Devices for Handling and Restraining Experimental Laboratory Mice

Introduction

Most animal handling procedures are associated with injuries among veterinary staff and laboratory animal researchers. However, much of the currently available animal handling equipment is inadequate, limiting access to the treated animal or making workflow cumbersome. Moreover, restraining animals to perform procedures, such as blood collection or injection, elicits stress in both the animal and the worker. Herein, we present 4 home-built restraint and blood collection devices in extensive use in our institute.

Methods

Animal laboratory workers and experienced veterinarians regularly using the devices (n = 14) were asked to complete a survey ranking the contribution of the devices to worker safety and procedural efficiency.

Results

The overwhelming majority of responders (≥75%) associated all 4 devices with substantial improvements in worker safety and procedural efficiency. There were no reports of impaired workflow or safety when using the devices.

Discussion

Infection and exposure control may be implemented on various levels, including use of safer procedures, such as injection and blood collection devices. The presented intuitive handling and restraint devices allow the animal worker/researcher to perform various procedures safely and efficiently while eliciting less animal and worker stress. The devices can be easily adjusted to accommodate animal size and disease status.

Conclusion

The current devices will serve as prototypes for design of devices for larger laboratory animals.

Imported biologicals: unforeseen biosecurity risks in the laboratory

Imported biological products are ubiquitous necessities of modern life that can pose significant biosecurity risks to Australia. Products produced using animal material are used everywhere from enzymes in cleaning products, to cell lines and bacterial cultures used to produce vaccines and medicines. This article highlights adventitious agents of biologicals and provides an overview of the considerations and regulatory tools administered under the Biosecurity Act 2015 (Commonwealth) to manage these biosecurity risks whilst still facilitating imports of biologicals.

Effective methods for the inactivation of Francisella tularensis

Francisella tularensis (F. tularensis) is highly pathogenic to humans and must be handled under biosafety level 3 conditions. Samples used for the diagnosis and experimental analysis must be completely inactivated, although methods for the inactivation of F. tularensis are limited. In this study, effective methods for the inactivation of F. tularensis SCHU P9 and five other strains were determined by comparisons of colony-forming units between treated and control samples. The results showed that F. tularensis SCHU P9 was denatured by heat treatment (94°C for 3 min and 56°C for 30 min), filtration with a 0.22 μm filter, and the use of various solutions (i.e. >70% ethanol, methanol, acetone, and 4% paraformaldehyde). F. tularensis SCHU P9 remained viable after treatment with 50% ethanol for 1 min, filtration with a 0.45 μm filter, and treatments with detergents (i.e. 1% lithium dodecyl sulfate buffer, 1% Triton X-100 and 1% Nonidet P-40) at 4°C for 24 h. Additionally, F. tularensis SCHU P9 suspended in fetal bovine serum in plastic tubes was highly resistant to ultraviolet radiation compared to suspensions in water and chemically defined medium. The methods for inactivation of F. tularensis SCHU P9 was applicable to the other five strains of F. tularensis. The data presented in this study could be useful for the establishment of guidelines and standard operating procedures (SOP) to inactivate the contaminated samples in not only F. tularensis but also other bacteria.

Modified Efficient and Simple Method for Biological Spill Cleanup

INTRODUCTION

Spill response procedures are an important aspect of laboratories where infectious materials are handled. The decades-old conventional method of spill cleanup uses paper towels to cover the spill. It requires 2 staff and involves a considerable amount of bending and squatting and being able to balance in those positions while wearing personal protective equipment (PPE). In this article, we describe a method that simplifies spill cleanup and compares it to the conventional method. The simplified method can be easily conducted by 1 person, takes about half the time, generates less waste, and reduces the amount of time spent in contaminated areas.

OBJECTIVE

The objective is to describe a modified, simple method of spill cleanup.

METHODS

A mock spill was created and a spill response initiated per the institution's procedure. The simplified procedure uses a pail filled with decontaminant and a household mop dripping with the decontaminant. Mopping is done from the noncontaminated area toward the contaminated area so the spill does not spread. Mopping is done more than once, and all the materials used, including the mop(s), are disposed as biohazardous material.

RESULTS

The simplified spill cleanup process described here can be performed by just one person and does not require bending and squatting while wearing PPE. The kit is very simple, consisting of a pail and a mop, which are common household tools familiar to most people.

CONCLUSION

The mop-and-pail methodology is simple, requires only one staff member, generates less biological waste, and requires less training and practice while effectively cleaning the spill.

Development and implementation of evidence-based laboratory safety management tools for a public health laboratory

We developed an evidence-based continuous quality improvement (CQI) cycle for laboratory safety as a method of utilizing survey data to improve safety in a public health laboratory setting. • Expert Opinion: The CQI cycle begins with the solicitation of laboratory staff input via an annual survey addressing potential chemical, physical and radiological hazards associated with multiple laboratory activities. The survey collects frequency, severity and exposure data related to these activities in the context of the most pathogenic organisms handled at least weekly. • Gap Analysis: Step 2 of the CQI cycle used survey data to identify areas needing improvement. Typically, the traditional two-dimensional risk assessment matrix is used to prioritize mitigations. However, we added an additional dimension - frequency of exposure - to create three-dimensional risk maps to better inform and communicate risk priorities. • Mitigation Measures: Step 3 of the CQI cycle was to use these results to develop mitigations. This included evaluating the identified risks to determine what risk control measures (elimination, substitution, engineering, administrative or PPE) were needed. In the 2016 iteration of the CQI cycle described here, all mitigations were based on administrative controls. • Evaluation and Feedback: The last step of the CQI cycle was to evaluate the inferred effects of interventions through subsequent surveys, allowing for qualitative assessment of intervention effectiveness while simultaneously restarting the cycle by identifying new hazards. Here we describe the tools used to drive this CQI cycle, including the survey tool, risk analysis method, design of interventions and inference of mitigation effectiveness.

Improved Biosafety and Biosecurity Measures and/or Strategies to Tackle Laboratory-Acquired Infections and Related Risks

Herein, we reviewed laboratory-acquired infections (LAIs) along with their health-related biological risks to provide an evidence base to tackle biosafety/biosecurity and biocontainment issues. Over the past years, a broad spectrum of pathogenic agents, such as bacteria, fungi, viruses, parasites, or genetically modified organisms, have been described and gained a substantial concern due to their profound biological as well as ecological risks. Furthermore, the emergence and/or re-emergence of life-threatening diseases are of supreme concern and come under the biosafety and biosecurity agenda to circumvent LAIs. Though the precise infection risk after an exposure remains uncertain, LAIs inspections revealed that Brucella spp., Mycobacterium tuberculosis, Salmonella spp., Shigella spp., Rickettsia spp., and Neisseria meningitidis are the leading causes. Similarly, the human immunodeficiency virus (HIV) as well as hepatitis B (HBV) and C viruses (HCV), and the dimorphic fungi are accountable for the utmost number of viral and fungal-associated LAIs. In this context, clinical laboratories at large and microbiology, mycology, bacteriology, and virology-oriented laboratories, in particular, necessitate appropriate biosafety and/or biosecurity measures to ensure the safety of laboratory workers and working environment, which are likely to have direct or indirect contact/exposure to hazardous materials or organisms. Laboratory staff education and training are indispensable to gain an adequate awareness to handle biologically hazardous materials as per internationally recognized strategies. In addition, workshops should be organized among laboratory workers to let them know the epidemiology, pathogenicity, and human susceptibility of LAIs. In this way, several health-related threats that result from the biologically hazardous materials can be abridged or minimized and controlled by the correct implementation of nationally and internationally certified protocols that include proper microbiological practices, containment devices/apparatus, satisfactory facilities or resources, protective barriers, and specialized education and training of laboratory staffs. The present work highlights this serious issue of LAIs and associated risks with suitable examples. Potential preventive strategies to tackle an array of causative agents are also discussed. In this respect, the researchers and scientific community may benefit from the lessons learned in the past to anticipate future problems.

Evaluating interest in an influenza A(H5N1) vaccine among laboratory workers who work with highly-pathogenic avian influenza viruses in the United States

•

Highly pathogenic avian influenza viruses pose an occupational risk to laboratorians.

•

The majority of survey respondents were interested in the Q-Pan H5N1 vaccine.

•

Interest in vaccination varied by role in the laboratory and time spent with HPAI viruses.

•

Q-Pan H5N1 vaccine could be used in tandem with current biosafety practices for HPAI laboratorians.

Background

Highly pathogenic avian influenza A (HPAI) viruses found in poultry and wild birds occasionally infect humans and can cause serious disease. In 2014, the Advisory Committee on Immunization Practices (ACIP) reviewed data from one licensed ASO3-adjuvanted influenza A(H5N1) vaccine for consideration of use during inter-pandemic periods among persons with occupational exposure. To guide vaccine policy decisions, we conducted a survey of laboratory workers to assess demand for HPAI vaccination.

Methods

We designed an anonymous web survey (EpiInfo 7.0) to collect information on demographics, type of work and time spent with HPAI viruses, and interest in HPAI vaccination. Eligible participants were identified from 42 entities registered with United States Department of Agriculture’s Agricultural Select Agent program in 2016 and emailed electronic surveys. Personnel with Biosafety Level 3 enhanced (BSL-3E) laboratory access were surveyed. Descriptive analysis was performed.

Results

Overall, 131 responses were received from 33 principal investigators, 26 research scientists, 24 technicians, 15 postdoctoral fellows, 6 students, and 27 others. The estimated response rate was 15% among the laboratory personnel of responding principal investigators. One hundred respondents reported working in a BSL-3E area where HPAI experiments occurred with a mean time of 5.1–11.7 h per week. Overall, 49% were interested in receiving an A(H5N1) vaccine. By role, interest was highest among students (80%) and among those who spent >50% of their time in a BSL-3E area (64%). Most (61%) of those who said they might be or were not interested in vaccine believed it would not provide additional protection to current safety practices.

Conclusions

Half of responding laboratory workers was interested in receiving an influenza A(H5N1) vaccine. HPAI vaccination of laboratory workers at risk of occupational exposure could be used along with existing safety practices to protect this population.

Laboratory Focus on Improving the Culture of Biosafety: Statewide Risk Assessment of Clinical Laboratories That Process Specimens for Microbiologic Analysis

The Wisconsin State Laboratory of Hygiene challenged Wisconsin laboratories to examine their biosafety practices and improve their culture of biosafety. One hundred three clinical and public health laboratories completed a questionnaire-based, microbiology-focused biosafety risk assessment. Greater than 96% of the respondents performed activities related to specimen processing, direct microscopic examination, and rapid nonmolecular testing, while approximately 60% performed culture interpretation. Although they are important to the assessment of risk, data specific to patient occupation, symptoms, and travel history were often unavailable to the laboratory and, therefore, less contributory to a microbiology-focused biosafety risk assessment than information on the specimen source and test requisition. Over 88% of the respondents complied with more than three-quarters of the mitigation control measures listed in the survey. Facility assessment revealed that subsets of laboratories that claim biosafety level 1, 2, or 3 status did not possess all of the biosafety elements considered minimally standard for their respective classifications. Many laboratories reported being able to quickly correct the minor deficiencies identified. Task assessment identified deficiencies that trended higher within the general (not microbiology-specific) laboratory for core activities, such as packaging and shipping, direct microscopic examination, and culture modalities solely involving screens for organism growth. For traditional microbiology departments, opportunities for improvement in the cultivation and management of highly infectious agents, such as acid-fast bacilli and systemic fungi, were revealed. These results derived from a survey of a large cohort of small- and large-scale laboratories suggest the necessity for continued microbiology-based understanding of biosafety practices, vigilance toward biosafety, and enforcement of biosafety practices throughout the laboratory setting.

Performance of materials used for biological personal protective equipment against blood splash penetration

For occupational safety, healthcare workers must select and wear appropriate personal protective equipment (PPE), protective clothing, and masks as countermeasures against exposure to infectious body fluids and blood splash. It is important for healthcare workers to ensure the protective performance of each PPE against penetration of pathogens. The International Standards Organization (ISO) 22609 test evaluates the effectiveness of medical facemasks to protect against penetration of splashed synthetic blood. However, in this method, the protective performance is determined only visually, without quantification of leaked liquid volume. Therefore, in this study, we modified the ISO 22609 test method to quantify the volume of leaked liquid and obtain a more accurate assessment of the protection performance. We tested non-woven and woven materials used for masks or protective clothing, and the performance of each material was classified using this new method. We found that the quantity of leaked synthetic blood was dependent on the structural characteristics of each material. These findings will allow healthcare workers to select the most appropriate PPE for a given situation or task.

Surveillance of laboratory exposures to human pathogens and toxins: Canada 2016

Background

Canada recently enacted legislation to authorize the collection of data on laboratory incidents involving a biological agent. This is done by the Public Health Agency of Canada (PHAC) as part of a comprehensive national program that protects Canadians from the health and safety risks posed by human and terrestrial animal pathogens and toxins.

Objective

To describe the first year of data on laboratory exposure incidents and/or laboratory-acquired infections in Canada since the Human Pathogens and Toxins Regulations came into effect.

Methods

Incidents that occurred between January 1 and December 31, 2016 were self-reported by federally-regulated parties across Canada using a standardized form from the Laboratory Incident Notification Canada (LINC) surveillance system. Exposure incidents were described by sector, frequency of occurrence, timeliness of reporting, number of affected persons, human pathogens and toxins involved, causes and corrective actions taken. Microsoft Excel 2010 was used for basic descriptive analyses.

Results

In 2016, 46 exposure incidents were reported by holders of 835 active licences in Canada representing 1,352 physical areas approved for work involving a biological agent, for an overall incidence of 3.4%. The number of incidents was highest in the academic (n=16; 34.8%) and hospital (n=12; 26.1%) sectors, while the number of reported incidents was relatively low in the private industry sector. An average of four to five incidents occurred each month; the month of September presented as an outlier with 10 incidents.​: A total of 100 people were exposed, with no reports of secondary exposure. Four incidents led to suspected (n=3) or confirmed (n=1) cases of laboratory-acquired infection. Most incidents involved pathogens classified at a risk group 2 level that were manipulated in a containment level 2 laboratory (91.3%). Over 22 different species of human pathogens and toxins were implicated, with bacteria the most frequent (34.8%), followed by viruses (26.1%). Eleven (23.9%) incidents involved a security sensitive biologic agent. Procedure breaches (n=15) and sharps-related incidents (n=14) were the most common antecedents to an exposure. In 10 (21.7%) cases, inadvertent possession (i.e., isolation of an unexpected biological agent during routine work) played a role. Possible improvements to standard operating procedures were cited in 71.7% of incidents. Improvements were also indicated for communication (26.1%) and management (23.9%).

Conclusions

The Laboratory Incident Notification Canada is one of the first surveillance systems in the world to gather comprehensive data on laboratory incidents involving human pathogens and toxins. Exposure incidents reported in the first year were relatively rare, occurring in less than 4% of containment zones within laboratory settings.

Critical Aspects for Detection of Coxiella burnetii

Coxiella burnetii is a globally distributed zoonotic γ-proteobacterium with an obligatory intracellular lifestyle. It is the causative agent of Q fever in humans and of coxiellosis among ruminants, although the agent is also detected in ticks, birds, and various other mammalian species. Requirements for intracellular multiplication together with the necessity for biosafety level 3 facilities restrict the cultivation of C. burnetii to specialized laboratories. Development of a novel medium formulation enabling axenic growth of C. burnetii has facilitated fundamental genetic studies. This review provides critical insights into direct diagnostic methods currently available for C. burnetii. It encompasses molecular detection methods, isolation, and propagation of the bacteria and its genetic characterization. Differentiation of C. burnetii from Coxiella-like organisms is an essential diagnostic prerequisite, particularly when handling and analyzing ticks.

Biosafety and Biosecurity in European Containment Level 3 Laboratories: Focus on French Recent Progress and Essential Requirements

Even if European Union (EU) Member States are obliged to implement EU Directives 2000/54/EC on the protection of workers from risks related to exposure to biological agents at work, national biosafety regulations and practices varied from country to country. In fact, EU legislation on biological agents and genetically modified microorganisms is often not specific enough to ensure harmonization leading to difficulties in implementation for most laboratories. In the same way, biosecurity is a relatively new concept and a few EU Member States are known to have introduced national laboratory biosecurity legislation. In France, recent regulations have reinforced biosafety/biosecurity in containment level 3 (CL-3) laboratories but they concern a specific list of pathogens with no correlation in other European Members States. The objective of this review was to summarize European biosafety/biosecurity measures concerning CL-3 facilities focusing on French specificities. Essential requirements needed to preserve efficient biosafety measures when manipulating risk group 3 biological agents are highlighted. In addition, International, European and French standards related to containment laboratory planning, operation or biosafety equipment are described to clarify optimal biosafety and biosecurity requirements.