Laboratory-associated infections and biosafety

Molecular evidence of sporadic Coxiella burnetii excretion in sheep milk, central Portugal

Coxiella burnetii is the etiologic agent of Q fever, a worldwide zoonosis. Cattle, sheep and goats are considered the main reservoirs of the disease. Transmission to humans occurs mainly through the inhalation of infectious aerosols from milk, faeces, urine, and birth products from infected ruminants. In this study, a 2-year longitudinal approach was performed to ascertain the excretion of C. burnetii in bulk tank milk samples of sheep from a mountain plateau in central Portugal, with sampling conducted during the years 2015 and 2016. From a total of 156 bulk tank milk samples tested by qPCR, only one showed to be positive for C. burnetii (1.28% [95%CI: 0.03-6.94]), from 2015, the first year of collection. Bidirectional sequencing and phylogenetic analysis of IS1111 transposase partial region confirmed the presence of C. burnetii DNA. The presence of C. burnetii in raw milk samples highlights the necessity for additional research to determine if raw milk is a potential source for human infection. Animal health surveillance and prevention measures against this zoonotic disease should be considered.

Comparison of galactomannan lateral flow assay and enzyme immunoassay to identify Aspergillus spp. in bronchoalveolar lavage fluid

Aspergillus species can colonize and infect immunocompetent and immunocompromised hosts. Conventional fungal identification depends on microscopic analysis and microorganism medium growth. Other diagnostic methods, non-growth dependent, to invasive fungal infections, are the biomarkers that detect circulating polysaccharides, for example, 1-3-β-d-Glucan and galactomannan. Both are polysaccharides present on the external layer of fungi cell wall and can be detected in clinical samples during the growth of the fungus in the patient. This study aimed to compare the galactomannan detection of Lateral Flow Assay and Enzyme Immunoassay methods in Bronchoalveolar Lavage Fluid. The galactomannan antigen in Bronchoalveolar Lavage Fluid was measured using Enzyme Immunoassay according to the manufacturer's instructions (PLATELIA ASPERGILLUS™ BioRad) and, using a Lateral Flow Assay according to the manufacturer's instructions (Galactomannan LFA IMMY©). The 71 samples were Bronchoalveolar Lavage Fluid of patients hospitalized at Unicamp Clinical Hospital between 2019 and 2021; of these samples 12/71 (16.9 %) resulted in positive Galactomannan-Lateral Flow Assay. In contrast, Galactomannan-Enzyme Immunoassay resulted as positive in 9/71 (12.6 %) samples, a difference that showed not significant statistically (p-value = 0.36) Comparing both assays' results identified 8 divergences between them, about 11 % of the total sample. The Sensitivity (73.3 %), Specificity (92.35 %), Positive Predictive Value (62.85 %) and Negative Predictive Value (95.15 %) of Lateral Flow Assay were calculated using the Galactomannan Enzyme Immunoassay as standard. The Lateral Flow Assay demonstrated good results when compared with the Enzyme Immunoassay.

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.

Assessment and verification of chemical inactivation of peste des petits ruminants virus by virus isolation following virus capture using Nanotrap magnetic virus particles

IMPORTANCE

Research including diagnosis on highly contagious viruses at the molecular level such as PCR and next-generation sequencing requires complete inactivation of the virus to ensure biosafety and biosecurity so that any accidental release of the virus does not compromise the safety of the susceptible population and the environment. In this work, peste des petits ruminants virus (PPRV) was inactivated with chemical agents, and the virus inactivation was confirmed by virus isolation (VI) using Vero cells. Since the chemical agents are cytotoxic, inactivated virus (PPRV) was diluted 1:100 to neutralize cytotoxicity, and the residual viruses (if any) were captured using Nanotrap magnetic virus particles (NMVPs). The NMVPs and the captured viruses were subjected to VI. No CPE was observed, indicating complete inactivation, and the results were further supported by real-time RT-PCR. This new protocol to verify virus inactivation can be applicable to other viruses.

Best practices for implementing biosafety inspections in a clinical laboratory: Evidence from a multi-site experimental study

OBJECTIVES

To explore the key components when designing best practice inspection interventions, so as to induce high compliance with safety guidelines for laboratory workers.

METHODS

Five key components of an inspection intervention, identified from a focus group discussion, were used as the attributes of a discrete choice experiment (DCE). In the DCE, participants were presented with two hypothetical scenarios and asked to choose the scenario in which they were more willing to comply with the laboratory safety guidelines. Data were collected from 35 clinical laboratories in seven healthcare institutes located in Chengdu, China. In total, 188 laboratory workers completed the DCE. The collected data were analyzed using conditional logit regression and latent class analysis.

RESULTS

Five key attributes were identified as the most important ones to best ensure laboratory safety: the inspector, the inspection frequency, the inspection timing, the communication of the inspection outcome, and a follow-up with either a reward or a punishment. By investigating the laboratory workers' responses to the attributes, properly implementing the five attributes could improve the workers' compliance from 25.86% (at the baseline case) to 74.54%. Compliance could be further improved with the consideration of the laboratory workers' heterogeneous reactions. In this study, two classes of workers, A and B, were identified. Compliance percentages for Classes A and B would be improved to 85.48% and 81.84%, respectively, when the key attributes were properly implemented for each class. The employment type and the size of the laboratory could be used to predict class membership.

CONCLUSION

The findings indicate the importance of an employee-centered approach in encouraging a worker's compliance. This approach also supports the design of tailored interventions by considering the laboratory workers' heterogeneous responses to the interventions.

A practical approach to render tuberculosis samples safe for application of tuberculosis molecular bacterial load assay in clinical settings without a biosafety level 3 laboratory

BACKGROUND

Mycobacterium tuberculosis is a category B infectious pathogen requiring level-3-containment laboratories for handling. We assessed the efficacy of heat and Guanidine thiocyanate (GTC) to inactivate M. tuberculosis prior to performance of tuberculosis Molecular Bacterial Load Assay (TB-MBLA).

METHOD

We performed in vitro experiments using M.tb, H37Rv reference strain and replicated in sputum specimens. A 0.5 MacFarland standard of M. tuberculosis was serially diluted to 1x10¹ CFU/mL and pooled sputum was homogenised prior to serial dilutions and Xpert MTB/RIF Ultra. Three replicates for each containing 1 mL for M. tuberculosis and sputum were inactivated at 80 °C for 20 min and with GTC for 15 min. Inactivated samples were processed for culture and TB-MBLA.

RESULTS

No M. tuberculosis growth was observed in MGIT for GTC or heat treated H37Rv cultures. All untreated H37Rv dilutions were MGIT positive except the most diluted specimens. Heat and GTC treatment of H37Rv reduced TB-MBLA load by 2.1log₁₀ (P = 0.7) and 1.8log₁₀ (P = 0.7) respectively, compared to controls. In contrast, heat treated sputum had TB-MBLA bacterial load of 3.47 ± 3.53 log₁₀ compared to 5.4 ± 3.1 log₁₀ eCFU/mL for GTC (p = 0.57). All heat and GTC treated sputum were culture negative.

CONCLUSION

Heat or GTC renders M. tuberculosis non-viable and eliminates the need for BSL3 laboratory for performing TB-MBLA in routine healthcare settings.

On-demand, remote and lossless manipulation of biofluid droplets

The recent global outbreaks of epidemics and pandemics have shown us that we are severely under-prepared to cope with infectious agents. Exposure to infectious agents present in biofluids (e.g., blood, saliva, urine etc.) poses a severe risk to clinical laboratory personnel and healthcare workers, resulting in hundreds of millions of hospital-acquired and laboratory-acquired infections annually. Novel technologies that can minimize human exposure through remote and automated handling of infectious biofluids will mitigate such risk. In this work, we present biofluid manipulators, which allow on-demand, remote and lossless manipulation of virtually any liquid droplet. Our manipulators are designed by integrating thermo-responsive soft actuators with superomniphobic surfaces. Utilizing our manipulators, we demonstrate on-demand, remote and lossless manipulation of biofluid droplets. We envision that our biofluid manipulators will not only reduce manual operations and minimize exposure to infectious agents, but also pave the way for developing inexpensive, simple and portable robotic systems, which can allow point-of-care operations, particularly in developing nations.

Enteric Pathogens Risk Factors Associated with Household Drinking Water: A Case Study in Ugu District Kwa-Zulu Natal Province, South Africa

The occurrence of diarrheal infections depends on the level of water and sanitation services available to households of immunocompromised individuals and children of less than five years old. It is therefore of paramount importance for immunocompromised individuals to be supplied with safe drinking water for better health outcomes. The current study aimed at ascertaining the probability of infection that Escherichia coli, Salmonella typhimurium, Shigella dysenteriae, Vibrio cholerae, and rotavirus might cause to rural dwellers as compared to urban dwellers. Both culture-based and molecular-based methods were used to confirm the presence of target microorganisms in drinking water samples, while Beta-Poisson and exponential models were used to determine the health risk assessment. Results revealed the presence of all targeted organisms in drinking water. The estimated health risks for single ingestion of water for the test pathogens were as follows: 1.6 × 10⁻⁷ for S. typhimurium, 1.79 × 10⁻⁴ for S. dysenteriae, 1.03 × 10⁻³ for V. cholerae, 2.2 × 10⁻⁴ for E. coli O157:H7, and 3.73 × 10⁻² for rotavirus. The general quantitative risk assessment undertaken in this study suggests that constant monitoring of household container-stored water supplies is vital as it would assist in early detection of microbial pathogens. Moreover, it will also allow the prompt action to be taken for the protection of public health, particularly for immunocompromised individuals and children who are prone to higher risk of infections.

Proportions of Pathogenic Bacteria Isolated from Door Locks and Working Benches in Clinical Laboratory: A Laboratory Based Study

Background

Numerous studies have revealed the association of the door handle and contamination of pathogenic bacteria. Door handles of clinical and research laboratories have higher chances of contamination with pathogenic bacteria during closing and opening with contaminated gloves on, or sometimes after visiting the toilets without the use of disinfectant materials. There is limited epidemiological data regarding bacteria cross contamination of door locks of the Clinical laboratory at Kilimanjaro Christian Medical Centre. This study aimed at providing the proportions of bacteria contaminating medical laboratory doors.

Methods

A cross section laboratory-based study was conducted and it involved collection of swab samples from doors and working benches in the clinical laboratory.

Results

Prevalence of Staphylococcus aureus, Escherichia coli, Coagulase Negative Staphylococcus, Bacillus spp., Pseudomonas aeroginosa and coliforms were (26%, 22%, 18%, 8%, 4% and 4% respectively.

Conclusion

This study has reported high proportion of pathogenic bacteria. The results entails that, internal and external environments are responsible for laboratory door contamination.

Building the evidence for hepatitis B vaccination programs for students and researchers working with biological samples in Indian Institutes of Higher Education

BACKGROUND

Individuals working with biological samples in Indian universities are at risk for occupational exposure to hepatitis B virus (HBV) and may not be vaccinated.

AIM

We documented the need for HBV vaccination in students and others, developed an institutional HBV vaccination program, delivered HBV vaccines, and then assessed the determinants of vaccine uptake.

METHODS

Over a year, we conducted a prospective cohort study documenting the need for HBV vaccination in people working with biological materials in a major Indian institution, developed a HBV vaccination program, delivered HBV vaccines, and assessed determinants of vaccine uptake. In August 2018, a needs assessment determined exposure to blood, body fluids, and other potentially infectious material in the research setting, followed in September by a cross-sectional survey on HBV vaccination status. Institutional approval for vaccination followed in October, and vaccine clinics began in February 2019. In September, a follow-up survey investigated determinants of vaccine uptake.

RESULTS

A total of 185 people participated in the baseline HBV vaccination status survey. Only 26% of students, staff, and faculty were fully vaccinated for HBV. Over 70% of the target group came forward for vaccination and >90% completed all doses. Getting vaccinated with peers strongly influenced vaccine uptake, as did availability of free vaccine, onsite clinics, and reminders.

CONCLUSION

HBV vaccination programs for individuals at occupational risk are needed in Indian academic institutions beyond medical schools as part of institutional biosafety programs.

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.

Occupational Histoplasmosis: Epidemiology and Prevention Measures

In areas where Histoplasma is endemic in the environment, occupations involving activities exposing workers to soil that contains bird or bat droppings may pose a risk for histoplasmosis. Occupational exposures are frequently implicated in histoplasmosis outbreaks. In this paper, we review the literature on occupationally acquired histoplasmosis. We describe the epidemiology, occupational risk factors, and prevention measures according to the hierarchy of controls.

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.

Evaluation of the Risk of Laboratory Microbial Contamination during Routine Testing in Automated Clinical Chemistry and Microbiology Laboratories

BACKGROUND

Every clinical specimen is potentially infectious, but data regarding risk for contamination of the laboratory environment during routine testing are scarce. We assessed contamination during routine sample analysis in automated clinical chemistry and microbiology laboratories.

METHODS

A fluorescent marker was applied to specimen container exteriors to assess the impact of gross contamination. Nonpathogenic MS2 virus was added to remnant blood, urine, and ESwab matrices as a biomarker of cross-contamination. Samples were processed and analyzed using Roche Cobas 8100 and ISE, c502, e602, and c702 modules (blood) and BD Kiestra total laboratory automation (blood, urine, ESwabs) over 3 experiments. Fluorescence transfer to laboratory surfaces and personnel was visualized using ultraviolet light. Surfaces were swabbed and assessed for MS2 cross-contamination by RT-PCR. Adherence to standard precautions by laboratory staff was assessed by observation.

RESULTS

Fluorescence was observed on 49 of 165 (30%) laboratory surfaces and personnel and 21 of 93 (23%) total laboratory automation instruments. Fluorescence transferred most frequently to gloves (31/40), computer accessories (9/18), and specimen loading racks (12/12). None of 123 areas swabbed were positive for MS2. Improper personal protective equipment use occurred at a rate of 0.36 and 0.15 events per staff per hour in the chemistry and microbiology laboratories, respectively. Hand-washing compliance was observed for 61 of 132 (46%) staff members evaluated.

CONCLUSIONS

Analysis of grossly contaminated specimens on automated chemistry and microbiology equipment elicits a low likelihood of instrument contamination. However, handling contaminated specimen containers can result in contamination of environmental laboratory surfaces, representing a source of risk that is heightened by low adherence to appropriate personal protective equipment.

Evaluation of a New Histoplasma spp. Quantitative RT-PCR Assay

Laboratory diagnosis of histoplasmosis is based on various methods, including microscopy, culture, antigen, and DNA detection of Histoplasma capsulatum var. capsulatum or Histoplasma capsulatum var. duboisii. To improve sensitivity of existing real-time quantitative PCR (qPCR) assays, we developed a new RT-qPCR assay that allows amplification of whole nucleic acids of Histoplasma spp. validated on suspected cases. The limit of detection was 20 copies, and the specificity against 114 fungal isolates/species was restricted to Histoplasma spp. Whole nucleic acids of 1319 prospectively collected consecutive samples from 907 patients suspected of having histoplasmosis were tested routinely between May 2015 and May 2019 in parallel with standard diagnostic procedures performed in parallel. Forty-four had proven histoplasmosis attributable to H. capsulatum var. capsulatum (n = 40) or H. capsulatum var. duboisii (n = 4) infections. The results of RT-qPCR were positive in 43 of 44 patients (97.7% sensitivity) in at least one specimen. Nine of 863 cases (99% specificity) were RT-qPCR positive and therefore classified as possible cases. RT-qPCR was positive in 13 of 30 (43.3%) blood samples tested in proven cases. A positive RT-qPCR result in blood was significantly associated with H. capsulatum var. capsulatum progressively disseminated histoplasmosis with a positive RT-qPCR result in 92.3% of the immunocompromised patients with disseminated disease. This new Histoplasma RT-qPCR assay enabling amplification of H. capsulatum var. capsulatum and H. capsulatum var. duboisii is highly sensitive and allows the diagnosis of histoplasmosis advantageously from blood and bronchoalveolar lavage fluid.

Isolation of Streptococcus cuniculi from corneal lesion in laboratory-raised mice

Corneal lesions appearing as white mass beneath intact epithelium, with ocular discharge in one mouse, was observed in a batch of laboratory-raised BALB/c mice (n=9 of 56). The affected mice remained active, well-groomed and had normal appetite. Isolates recovered from swab cultures of the external and internal contents of the eye had partial 16S rRNA gene sequence of 99.1% similarity to Streptococcus cuniculi. No previous report of S. cuniculi infection in laboratory rodents has been presented. The isolate was susceptible to all antibiotics tested. We suggest S. cuniculi is an opportunistic bacteria in laboratory mice but are uncertain of its source. Our findings revealed that S. cuniculi is able to colonize laboratory mice and should be considered when mice present with eye lesion or ocular discharge.

Two discrete choice experiments on laboratory safety decisions and practices

INTRODUCTION

The path toward enhancing laboratory safety requires a thorough understanding of the factors that influence the safety-related decision making of laboratory personnel.

METHOD

We developed and administered a web-based survey to assess safety-related decision making of laboratory personnel of a government research organization. The survey included two brief discrete choice experiments (DCEs) that allowed for quantitative analysis of specific factors that potentially influence safety-related decisions and practices associated with two different hypothetical laboratory safety scenarios. One scenario related to reporting a laboratory spill, and the other scenario involved changing protective gloves between laboratory rooms. The survey also included several brief self-report measures of attitude, perception, and behavior related to safety practices.

RESULTS

Risk perception was the most influential factor in safety-related decision making in both scenarios. Potential negative consequences and effort associated with reporting an incident and the likelihood an incident was detected by others also affected reporting likelihood. Wearing gloves was also affected somewhat by perceived exposure risk, but not by other social or work-related factors included in the scenarios.

CONCLUSIONS

The study demonstrated the promise of DCEs in quantifying the relative impact of several factors on safety-related choices of laboratory workers in two hypothetical but realistic scenarios. Participants were faced with hypothetical choice scenarios with realistic features instead of traditional scaling techniques that ask about attitudes and perceptions. The methods are suitable for addressing many occupational safety concerns in which workers face tradeoffs in their safety-related decisions and behavior. Practical Application: Safety-related decisions regarding laboratory practices such as incident reporting and use of PPE were influenced primarily by workers' perceptions of risk of exposure and severity of risks to health and safety. This finding suggests the importance of providing laboratory workers with adequate and effective education and training on the hazards and risks associated with their work. DCEs are a promising research method for better understanding the relative influences of various personal, social, and organizational factors that shape laboratory safety decisions and practices. The information gained from DCEs may lead to more targeted training materials and interventions.

Strategies for managing N95 mask shortages at water resource recovery facilities during pandemics: a review

As the numbers of COVID-19 cases grew globally, the severe shortages of health care respiratory protective equipment impacted the ability of water resource recovery facilities (WRRFs) to acquire N95 masks for worker protection. While the Occupational Safety and Health Administration (OSHA) encourages WRRFs to conduct job safety assessments to mitigate risks from bioaerosols, it does not provide clear guidance on respiratory protection requirements, leaving the use of N95 masks across the industry non-standardized and difficult to justify. Strategies need to be developed to cope with shortages during pandemics, and these should take into consideration a WRRF's size and disinfection equipment available. Our objective is to provide an overview of respiratory protection-related practices recommended for health care professionals that apply to WRRFs (e.g., elimination, substitution, extended use, reuse, disinfection). Reviewed N95 mask disinfection strategies included using hydrogen peroxide, autoclaving, moist heat, dry heat, ultraviolet germicidal irradiation (UVGI), ethylene oxide, chlorine and ethanol. Of these, dry heat, autoclaving and UVGI present the most promise for WRRFs, with UVGI being limited to larger utilities. We recommend that WRRFs work closely with disinfection technology manufacturers, mask providers, health and safety staff and inspectors to develop suitable programs to cope with N95 mask shortages during pandemics.

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.

Occupational Respiratory Infections

Occupational respiratory infections can be caused by bacterial, viral, and fungal pathogens. Transmission in occupational settings can occur from other humans, animals, or the environment, and occur in various occupations and industries. In this article, we describe 4 occupationally acquired respiratory infections at the focus of NIOSH investigations over the last decade: tuberculosis (TB), influenza, psittacosis, and coccidioidomycosis. We highlight the epidemiology, clinical manifestations, occupational risk factors, and prevention measures.

Effect of equipment layout on bioaerosol temporal-spatial distribution and deposition in one BSL-3 laboratory

Reasonable equipment layout is essential for creating a healthy and safe environment, especially in a three-level biosafety laboratory with high potential risk factors of infection. Since 2019, COVID-19, an emerging infection has swept the world and caused severe losses. Biosafety laboratories are mandatory sites for detecting high-risk viruses, so related research is urgently needed to prevent further laboratory-acquired infections of operators. This study investigated the effects of obstacles on exposure infection of staff in a biosafety laboratory with related experimental equipment. The numerical simulation results are highly verified by the measured results. The results indicate that although the equipment layout does not affect the bioaerosol removal time, nearly 17% of the pollutant particles in the actual laboratory cannot be discharged effectively compared with the ideal situation. These particles lingered in the lower space under the influence of vortex, which would increase the respiratory risk of operators. In addition, after the experiment a large part of bioaerosol particles would be captured by equipment and floor, and the deposition rate per unit area is 0.45%/m² and 0.8%/m², respectively. Although the results show that the equipment layout could reduce the pollution on the floor, the disinfection is still an important link, especially on the surfaces of equipment. Meanwhile, the result also indicates that the action should be light and slow when operating in BSL-3 laboratory, so as to avoid the secondary suspension pollution of bioaerosol particles on the equipment surface and floor.

Comparative pathology study of Venezuelan, eastern, and western equine encephalitis viruses in non-human primates

Venezuelan, eastern, and western equine encephalitis viruses (VEEV, EEEV, and WEEV) are mosquito-borne viruses in the Americas that cause central nervous system (CNS) disease in humans and equids. In this study, we directly characterized the pathogenesis of VEEV, EEEV, and WEEV in cynomolgus macaques following subcutaneous exposure because this route more closely mimics natural infection via mosquito transmission or by an accidental needle stick. Our results highlight how EEEV is significantly more pathogenic compared to VEEV similarly to what is observed in humans. Interestingly, EEEV appears to be just as neuropathogenic by subcutaneous exposure as it was in previously completed aerosol exposure studies. In contrast, subcutaneous exposure of cynomolgus macaques with WEEV caused limited disease and is contradictory to what has been reported for aerosol exposure. Several differences in viremia, hematology, or tissue tropism were noted when animals were exposed subcutaneously compared to prior aerosol exposure studies. This study provides a more complete picture of the pathogenesis of the encephalitic alphaviruses and highlights how further defining the neuropathology of these viruses could have important implications for the development of medical countermeasures for the neurovirulent alphaviruses.

The utility of real-time polymerase chain reaction in detecting Coccidioides immitis among clinical specimens in the Central California San Joaquin Valley

Coccidioidomycosis, the fungal infection caused by dimorphic Coccidioides species, is typically diagnosed by histopathologic identification of spherules, by culture, or by serology. These tests are reliable but time-intensive, delaying diagnosis and treatment. Rapid real-time polymerase chain reaction (RT-PCR) can be performed and was validated to identify Coccidioides immitis using an in-house developed assay for the Becton Dickinson molecular instrument (BD MAXTM). These studies were performed using patient samples that had been shown to be positive on previously set up fungal cultures. To evaluate this new RT-PCR test in the clinical setting, we conducted a retrospective chart review of patients (N = 1160) who underwent Coccidioides PCR (Cocci PCR) on clinical samples between March 1, 2014, and Dec 31, 2016. We abstracted clinical, microbiologic, serologic, radiographic, treatment, and follow-up data. Specimens of cerebrospinal fluid (CSF), bronchioalveolar lavage fluid (BAL), lung tissue biopsy (LTB), sputum, and pleural fluid were evaluated to determine sensitivity and specificity. Of the 113 specimens that tested positive for Cocci PCR, all had clinical disease defined by traditional clinical criteria, yielding 100% specificity. Overall sensitivity was 74% versus 46% for fungal culture and was available in 4 hours rather than 1-2 weeks. Sensitivities varied by source material and clinical setting. CSF had a sensitivity of 59%, BAL for acute pneumonia 91%, sputum for acute pneumonia 94%, pleural fluid 86%, but LTB for lung nodules only 44%. Overall positive predictive value (PPV) was 100%, while negative predictive value (NPV) was 96%, but again this varied by specimen and clinical setting. Our experience with clinical testing of >1160 specimens over 2-3 years shows we can utilize this technology to improve our ability to diagnose disease but that the sensitivity varies by specimen source and clinical setting.

Survey of Suspected Laboratory-Acquired Infections and Biosafety Practices in Research, Clinical, and Veterinary Laboratories in Karachi, Pakistan

Laboratory-acquired infections (LAIs), an occupational illness, are defined as all infections acquired through laboratory or laboratory-related activities. A report published in 1898 described an LAI resulting from Corynebacterium diphtheriae being transmitted through mouth pipetting. Despite all efforts, LAIs continue, especially in developing countries like Pakistan, which has been fighting to curb many infectious diseases. As reflected in the published literature, the biosafety culture is severely lacking in many laboratories, and there are no data available from Pakistan on LAIs. Our objective was to ascertain the frequency and rate of LAIs in various labs with versatile portfolios in relation to biosafety and biosecurity practices in Karachi. Ours is a descriptive multicenter cross-sectional study conducted in 30 laboratories located in Karachi from November 2017 to April 2018. Data were collected from laboratories including the university hospital labs, research labs, animal labs, and biomedical labs. Out of 30 facilities, half (n = 15) were clinical/biomedical laboratories, 16.6% (n = 5) were university hospital laboratories, 26.6% (n = 8) were R&D laboratories, and 6.6% (n = 2) were animal laboratories. Needle stick was found to be the most common injury, followed by animal bite/scratch, cut on mucous membrane, falling of personnel, and burn injury.

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.

Creating a Library of Random Transposon Mutants in Leptospira

Generation of a random transposon mutant library is advantageous in Leptospira as site-directed mutagenesis remains a challenge, especially in pathogenic species. This procedure is typically completed by transformation of Leptospira with a Himar1 containing plasmid via conjugation with Escherichia coli as a donor cell. Here we describe the methodology to generate random transposon mutants in the saprophyte Leptospira biflexa via conjugation of plasmid pSW29T-TKS2 harbored in E. coli β2163. Determination of transposon insertion site by semi-random nested PCR will also be described. A similar methodology may be employed to generate Tn mutants of pathogenic Leptospira species.

Antibody Response Following Pre-Exposure Immunization Against Rabies in High-Risk Professionals

Vaccination against rabies and routine antibody testing of subjects participating in programs for the surveillance and control of rabies in animals is strongly recommended. The scope of this study is to describe the antibody level as measured by a commercial enzyme-linked immunosorbent assay (ELISA) after primary and booster intramuscular vaccination with a purified vero-cell rabies vaccine (PVRV) in high-risk professionals and to determine the influence of an array of factors on antibody level, that is, time elapsed since primary immunization series and booster dose, sex, age, pathologic conditions, high-risk occupation, and peak antibody level after initial scheme and booster dose. A primary series of three doses of PVRV was administered and a commercial ELISA was recommended 14 days postimmunization with continuous repetition at 6 months and yearly intervals for the laboratory personnel and the rest of the professionals, respectively. The protective antibody titer was defined as a minimum of 0.5 equivalent units/mL (EU/mL) (seroconvertion) and a booster dose was applied if the titer was determined nonprotective. The seroconversion rate (SCR) after primary vaccination was 100%, with a geometric mean titer (GMT) of 2.90 EU/mL (interquartile range [IQR]: 1.85-3.45). After booster vaccination due to nonprotective titer, the SCR was 100% and the GMT increased by 678% (95% confidence interval [CI]: 514-887) reaching 4.25 EU/mL (IQR: 4.00-4.60), 2.5 times higher than the GMT elicited by the primary vaccine scheme in the respective recipients. The titer dropped by 1.20% per month (95% CI: 0.52-1.89) regardless of booster administration or any other factor. Women had 51% higher titer compared with men (95% CI: 6-116). High-risk professionals should be verified for adequate antibody titers, but routine administration of a single booster dose of PVRV 1 year after the primary series could be considered; more evidence is needed to support the benefit in terms of immunity and logistics.

Characterization of Brain Inflammation, Apoptosis, Hypoxia, Blood-Brain Barrier Integrity and Metabolism in Venezuelan Equine Encephalitis Virus (VEEV TC-83) Exposed Mice by In Vivo Positron Emission Tomography Imaging

Traditional pathogenesis studies of alphaviruses involves monitoring survival, viremia, and pathogen dissemination via serial necropsies; however, molecular imaging shifts this paradigm and provides a dynamic assessment of pathogen infection. Positron emission tomography (PET) with PET tracers targeted to study neuroinflammation (N,N-diethyl-2-[4-phenyl]-5,7-dimethylpyrazolo[1,5-a]pyrimidine-3-acetamide, [¹⁸F]DPA-714), apoptosis (caspase-3 substrate, [¹⁸F]CP-18), hypoxia (fluormisonidazole, [¹⁸F]FMISO), blood–brain barrier (BBB) integrity ([¹⁸F]albumin), and metabolism (fluorodeoxyglucose, [¹⁸F]FDG) was performed on C3H/HeN mice infected intranasally with 7000 plaque-forming units (PFU) of Venezuelan equine encephalitis virus (VEEV) TC-83. The main findings are as follows: (1) whole-brain [¹⁸F]DPA-714 and [¹⁸F]CP-18 uptake increased three-fold demonstrating, neuroinflammation and apoptosis, respectively; (2) [¹⁸F]albumin uptake increased by 25% across the brain demonstrating an altered BBB; (3) [¹⁸F]FMISO uptake increased by 50% across the whole brain indicating hypoxic regions; (4) whole-brain [¹⁸F]FDG uptake was unaffected; (5) [¹⁸F]DPA-714 uptake in (a) cortex, thalamus, striatum, hypothalamus, and hippocampus increased through day seven and decreased by day 10 post exposure, (b) olfactory bulb increased at day three, peaked day seven, and decreased day 10, and (c) brain stem and cerebellum increased through day 10. In conclusion, intranasal exposure of C3H/HeN mice to VEEV TC-83 results in both time-dependent and regional increases in brain inflammation, apoptosis, and hypoxia, as well as modest decreases in BBB integrity; however, it has no effect on brain glucose metabolism.

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

Background

The Laboratory Incident Notification Canada (LINC) surveillance system monitors laboratory incidents reported under the Human Pathogens and Toxins Act. The year 2018 marks the third complete year of data.

Objective

To describe the laboratory exposure and laboratory-acquired infection incidents that occurred in Canada in 2018 compared to previous years, and then by sector, human pathogens and toxins involved, number of affected persons, incident type and root causes.

Methods

Laboratory incidents that occurred in 2018 were reported through the LINC system. The number of laboratory incidents, people exposed and laboratory-acquired infections were compared to previous years, then the incidents were analyzed by sector, human pathogen or toxin involved, the type of incident, people exposed, route of exposure and root causes. Microsoft Excel 2016 was used for descriptive analysis.

Results

In 2018, there were 89 exposure incidents to human pathogens and 235 people were exposed. There were five suspected and one confirmed laboratory-acquired infections. This was approximately twice the number of exposure incidents that were reported in 2017 (n=44) and 2016 (n=46). The highest number of exposure incidents occurred in the academic and hospital sectors, and the ratio of incidence to licences was the lowest in the private sector. The majority of incidents (n=50; 56%) involved Risk Group 2 human pathogens that were manipulated in a Containment Level 2 laboratory. Most exposures were related to sharps or procedures and the most common people exposed were laboratory technicians. Human interaction and standard operating procedures were the leading root causes.

Conclusion

Although overall the annual incidence of laboratory exposures in Canada remains relatively low, the incidence was higher in 2018 than in previous years. Whether this is a true increase in incidence or an increase in reporting is not known at this time as baseline estimates are still being established.

Autochthonous Transmission of Coccidioides in Animals, Washington, USA

We report 5 cases of coccidioidomycosis in animals that were acquired within Washington, USA, and provide further evidence for the environmental endemicity of Coccidioides immitis within the state. Veterinarians should consider coccidioidomycosis in animals with compatible clinical signs that reside in, or have traveled to, south central Washington.

Rapid Inactivation of Non-Endospore-Forming Bacterial Pathogens by Heat Stabilization is Compatible with Downstream Next-Generation Sequencing

Introduction:

Heat stabilization treatment preserves the in vivo state of biological samples by rapidly inactivating enzymes that cause degradation of proteins and nucleic acids. Historically, proteomics studies used this technique as an alternative to chemical fixation. More recently, microbiologists discovered that heat stabilization treatment rapidly inactivates pathogens present in tissue samples and preserves deoxyribonucleic acid (DNA) in the tissue. However, these recent studies did not investigate the inactivation of high-density bacterial suspensions and the quality of bacterial DNA.

Methods and Results:

High-density suspensions of Escherichia coli (>109cfu/mL) were completely inactivated by heat stabilization treatment using the Denator Stabilizor T1 instrument at 72°C and 95°C for 45 seconds. Using the heat stabilization instrument, a panel of 30 species, 20 Gram-negative and 10 non-endospore-forming Gram-positive species, were fully inactivated by treatment (95°C for 45 seconds). DNA was isolated from bacterial suspensions of Gram-negative bacteria, including E. albertii, E. coli, Shigella dysenteriae, and S. flexneri, following inactivation via heat stabilization treatment and without treatment. DNA isolated following heat stabilization treatment was fully compatible with all downstream molecular applications tested, including next-generation sequencing, pulsed-field gel electrophoresis, multiplex polymerase chain reaction (PCR), and real-time PCR.

Conclusions and Discussion:

Heat stabilization treatment of Gram-negative and non-endospore-forming Gram-positive pathogens completely inactivates high-density bacterial suspensions. This treatment is compatible with downstream DNA molecular assays, including next-generation sequencing, pulsed-field gel electrophoresis, and PCR. Inactivation by heat stabilization is a rapid process that may increase safety by decreasing risks for laboratory-associated infections and risks associated with transportation of infectious materials.

The Fate of Osteoblast-Like MG-63 Cells on Pre-Infected Bactericidal Nanostructured Titanium Surfaces

Biomaterials that have been newly implanted inside the body are the substratum targets for a "race for the surface", in which bacterial cells compete against eukaryotic cells for the opportunity to colonize the surface. A victory by the former often results in biomaterial-associated infections, which can be a serious threat to patient health and can undermine the function and performance of the implant. Moreover, bacteria can often have a 'head start' if implant contamination has taken place either prior to or during the surgery. Current prevention and treatment strategies often rely on systemic antibiotic therapies, which are becoming increasingly ineffective due to a growing prevalence of antibiotic-resistant bacteria. Nanostructured surfaces that kill bacteria by physically rupturing bacterial cells upon contact have recently emerged as a promising solution for the mitigation of bacterial colonization of implants. Furthermore, these nanoscale features have been shown to enhance the adhesion and proliferation of eukaryotic cells, which is a key to, for example, the successful osseointegration of load-bearing titanium implants. The bactericidal activity and biocompatibility of such nanostructured surfaces are often, however, examined separately, and it is not clear to what extent bacterial cell-surface interactions would affect the subsequent outcomes of host-cell attachment and osseointegration processes. In this study, we investigated the ability of bactericidal nanostructured titanium surfaces to support the attachment and growth of osteoblast-like MG-63 human osteosarcoma cells, despite them having been pre-infected with pathogenic bacteria. MG-63 is a commonly used osteoblastic model to study bone cell viability, adhesion, and proliferation on the surfaces of load-bearing biomaterials, such as titanium. The nanostructured titanium surfaces used here were observed to kill the pathogenic bacteria, whilst simultaneously enhancing the growth of MG-63 cells in vitro when compared to that occurring on sterile, flat titanium surfaces. These results provide further evidence in support of nanostructured bactericidal surfaces being used as a strategy to help eukaryotic cells win the "race for the surface" against bacterial cells on implant materials.

Isolation of Complete Equine Encephalitis Virus Genome from Human Swab Specimen, Peru

While studying respiratory infections in Peru, we identified Venezuelan equine encephalitis virus (VEEV) in a nasopharyngeal swab, indicating that this alphavirus can be present in human respiratory secretions. Because VEEV may be infectious when aerosolized, our finding is relevant for the management of VEEV-infected patients and for VEEV transmission studies.

Red Fluorescent Chlamydia trachomatis Applied to Live Cell Imaging and Screening for Antibacterial Agents

In this study, we describe the application of a transformed Chlamydia trachomatis strain constitutively expressing the red fluorescent protein mCherry, to allow real-time monitoring of the infection cycle and screening for agents that block replication of C. trachomatis. The red fluorescent C. trachomatis strain was detected autonomously without antibody staining and was equally susceptible to doxycycline as the wild type strain. A high-throughput screening assay was developed using the transformed strain and automated fluorescence microscopy. The assay was used in a pilot screen of a 349 compound library containing natural products from Australian flora and fauna. Compounds with anti-chlamydial activity were tested for dose response and toxicity to host cells and two non-toxic compounds had 50% effective concentration (EC₅₀) values in the low micromolar range. Natural products are valuable sources for drug discovery and the identified Chlamydia growth inhibition may be starting points for future drug development. Live cell imaging was used to visualize growth of the red fluorescent C. trachomatis strain over time. The screening assay reduced workload and reagents compared to an assay requiring immunostaining and could further be used to monitor the development of Chlamydia inclusions and anti-chlamydial effect in real time.

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.

Surveillance of laboratory exposures to human pathogens and toxins: Canada 2017

Background

Under Canada's Human Pathogens and Toxins Act and Human Pathogens and Toxins Regulations, the Public Health Agency of Canada (PHAC) is mandated with monitoring laboratory incident notifications through the Laboratory Incident Notification Canada (LINC) surveillance system. The year 2017 marks the second complete year of data.

Objective

To describe the laboratory exposure and laboratory-acquired infection incidents that occurred in Canada in 2017 by sector, human pathogens and toxins involved, number of affected persons, incident type and root causes.

Methods

The incidents included in the analysis occurred between January 1 and December 31, 2017. They were reported by laboratories with active licences to PHAC through the LINC surveillance system. Microsoft Excel 2010 was used for basic descriptive statistics.

Results

A total of 44 exposure and laboratory-acquired infection incidents were reported to the LINC in 2017. Compared by sector and their respective shares of licences, the number of incidents was highest in the academic and hospital sectors compared with government laboratories and private industry. Altogether 118 people were exposed for an average of 2.7 people per incident (range of 1-29). There were no reports of secondary exposure. Six exposure incidents (14%) led to "suspected" (n=5) or confirmed (n=1) cases of laboratory-acquired infection. Although overall, risk group (RG)2 human pathogens and toxins were involved in the majority of incidents (n=23; 52%), Francisella tularensis (n=4; 9%) and Coccidioides immitis (n=3; 7%) were the most frequently involved in reported exposure incidents. These two pathogens are both RG3 and security-sensitive biological agents (SSBAs). An average of 2.3 root causes were identified per incident (n=101). Problems with standard operating procedures (SOPs) and human error were the two most common causes.

Conclusion

The incidence of laboratory exposure incidents was relatively low in 2017. The most common route of exposure was through inhalation and the most common root causes were problems with SOPs and human error. Since this is a new surveillance system, baseline estimates are still being established.

Auxotrophy to Xeno-DNA: an exploration of combinatorial mechanisms for a high-fidelity biosafety system for synthetic biology applications

BACKGROUND

Biosafety is a key aspect in the international Genetically Engineered Machine (iGEM) competition, which offers student teams an amazing opportunity to pursue their own research projects in the field of Synthetic Biology. iGEM projects often involve the creation of genetically engineered bacterial strains. To minimize the risks associated with bacterial release, a variety of biosafety systems were constructed, either to prevent survival of bacteria outside the lab or to hinder horizontal or vertical gene transfer.

MAIN BODY

Physical containment methods such as bioreactors or microencapsulation are considered the first safety level. Additionally, various systems involving auxotrophies for both natural and synthetic compounds have been utilized by iGEM teams in recent years. Combinatorial systems comprising multiple auxotrophies have been shown to reduced escape frequencies below the detection limit. Furthermore, a number of natural toxin-antitoxin systems can be deployed to kill cells under certain conditions. Additionally, parts of naturally occurring toxin-antitoxin systems can be used for the construction of 'kill switches' controlled by synthetic regulatory modules, allowing control of cell survival. Kill switches prevent cell survival but do not completely degrade nucleic acids. To avoid horizontal gene transfer, multiple mechanisms to cleave nucleic acids can be employed, resulting in 'self-destruction' of cells. Changes in light or temperature conditions are powerful regulators of gene expression and could serve as triggers for kill switches or self-destruction systems. Xenobiology-based containment uses applications of Xeno-DNA, recoded codons and non-canonical amino acids to nullify the genetic information of constructed cells for wild type organisms. A 'minimal genome' approach brings the opportunity to reduce the genome of a cell to only genes necessary for survival under lab conditions. Such cells are unlikely to survive in the natural environment and are thus considered safe hosts. If suitable for the desired application, a shift to cell-free systems based on Xeno-DNA may represent the ultimate biosafety system.

CONCLUSION

Here we describe different containment approaches in synthetic biology, ranging from auxotrophies to minimal genomes, which can be combined to significantly improve reliability. Since the iGEM competition greatly increases the number of people involved in synthetic biology, we will focus especially on biosafety systems developed and applied in the context of the iGEM competition.

Frequency of Instrument, Environment, and Laboratory Technologist Contamination during Routine Diagnostic Testing of Infectious Specimens

Laboratory testing to support the care of patients with highly infectious diseases may pose a risk for laboratory workers. However, data on the risk of virus transmission during routine laboratory testing conducted using standard personal protective equipment (PPE) are sparse. Our objective was to measure laboratory contamination during routine analysis of patient specimens. Remnant specimens were spiked with the nonpathogenic bacteriophage MS2 at 1.0 × 10⁷ PFU/ml, and contamination was assessed using reverse transcriptase PCR (RT-PCR) for MS2. Specimen containers were exteriorly coated with a fluorescent powder to enable the visualization of gross contamination using UV light. Testing was performed by two experienced laboratory technologists using standard laboratory PPE and sample-to-answer instrumentation. Fluorescence was noted on the gloves, bare hands, and laboratory coat cuffs of the laboratory technologist in 36/36 (100%), 13/36 (36%), and 4/36 (11%) tests performed, respectively. Fluorescence was observed in the biosafety cabinet (BSC) in 8/36 (22%) tests, on test cartridges/devices in 14/32 (44%) tests, and on testing accessory items in 29/32 (91%) tests. Fluorescence was not observed on or in laboratory instrumentation or adjacent surfaces. In contrast to fluorescence detection, MS2 detection was infrequent (3/286 instances [1%]) and occurred during test setup for the FilmArray instrument and on FilmArray accessory equipment. The information from this study may provide opportunities for the improvement of clinical laboratory safety practices so as to reduce the risk of pathogen transmission to laboratory workers.

Comparative Review of Antimicrobial Resistance in Humans and Nonhuman Primates

Antimicrobial resistance (AMR) presents serious threats to human and animal health. Although AMR of pathogens is often evaluated independently between humans and animals, comparative analysis of AMR between humans and animals is necessary for zoonotic pathogens. Major surveillance systems monitor AMR of zoonotic pathogens in humans and food animals, but comprehensive AMR data in veterinary medicine is not diligently monitored for most animal species with which humans commonly contact, including NHP. The objective of this review is to provide a complete report of the prevalences of AMR among zoonotic bacteria that present the greatest threats to NHP, occupational, and public health. High prevalences of AMR exist among Shigella, Campylobacter, and Yersinia, including resistance to antimicrobials important to public health, such as macrolides. Despite improvements in regulations, standards, policies, practices, and zoonotic awareness, occupational exposures to and illnesses due to zoonotic pathogens continue to be reported and, given the documented prevalences of AMR, constitute an occupational and public health risk. However, published literature is sparse, thus indicating the need for veterinarians to proactively monitor AMR in dangerous zoonotic bacteria, to enable veterinarians to make more informed decisions to maximize antimicrobial therapy and minimize occupational risk.

A Review of Laboratory-Acquired Infections in the Asia-Pacific: Understanding Risk and the Need for Improved Biosafety for Veterinary and Zoonotic Diseases

A rapid review was performed to determine (1) the number and causes of reported laboratory-acquired infections (LAI) in the Asia-Pacific region; (2) their significance and threat to the community; (3) the primary risk factors associated with LAIs; (4) the consequences in the event of a LAI or pathogen escape; and (5) to make general recommendations regarding biosafety practices for diagnosis and research in the Asia-Pacific region. A search for LAI and zoonoses in the Asia-Pacific region using online search engines revealed a relatively low number of reports. Only 27 LAI reports were published between 1982 and 2016. The most common pathogens associated with LAIs were dengue virus, Arthroderma spp., Brucella spp., Mycobacterium spp., Rickettsia spp., and Shigella spp. Seventy-eight percent (21 out of 27 LAI reports) occurred in high-income countries (i.e., Australia, Japan, South Korea, Singapore, and Taiwan) where laboratories were likely to comply with international biosafety standards. Two upper-middle income countries (China (2), and Malaysia (2)) and one lower-middle income country (India (2)) reported LAI incidents. The majority of the reports (fifty-two percent (14/27)) of LAIs occurred in research laboratories. Five LAI reports were from clinical or diagnostic laboratories that are considered at the frontier for zoonotic disease detection. Governments and laboratories in the Asia-Pacific region should be encouraged to report LAI cases as it provides a useful tool to monitor unintended release of zoonotic pathogens and to further improve laboratory biosafety. Non-reporting of LAI events could pose a risk of disease transmission from infected laboratory staff to communities and the environment. The international community has an important and continuing role to play in supporting laboratories in the Asia-Pacific region to ensure that they maintain the safe working environment for the staff and their families, and the wider community.

Epidemiological Review of Francisella Tularensis: A Case Study in the Complications of Dual Diagnoses

INTRODUCTION

Tularemia is a rare but potentially fatal disease that develops in numerous wild and domestic animals, including lagomorphs, rodents, cats, and humans.  Francisella tularensis bacterium, the causative agent of tularemia, was identified by veterinary personnel at Fort Riley, Kansas during a routine post-mortum evaluation of a domestic feline. However, before formal diagnosis was confirmed, the sample was sent and prepared for rabies testing at the Department of Defense (DoD) U.S. Army Public Health Command Central (PHC-C), Food Analysis and Diagnostic Laboratory (FADL).  This case report provides insight on how veterinarian staff and laboratory personnel can clinically manage esoteric, unexplained, or post-mortum examinations.  The epidemiologic characteristics of tularemia, F. tularensis as an organism of military interest, potential laboratory management of F. tularensis, and clinical findings on a case of feline tularemia are discussed. It further raises questions as to whether or not dead animals should be treated as sentinels and be pre-screened for select agents, especially in instances of dual diagnoses.

METHODS

A necropsy was performed on the cat by the Fort Riley veterinarian, DNA extraction and PCR analyses were conducted by FADL microbiologists, histology and immunohistology analyses were conducted by the Kansas State Veterinary Diagnostic Laboratory, and feline tissue and blood were sent to the U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID) for confirmatory testing and strain identification of tularemia.

RESULTS

Tularemia was identified in the spleen of the cat by the Fort Riley veterinarian and during the histological sampling of the spleen by the Kansas State Veterinary Diagnostic Laboratory.  A specific subsequent real-time polymerase chain reaction (RT-PCR) in vitro diagnostic detection of target DNA sequences of F. tularensis was conducted by the FADL microbiologists using a Joint Biological Agent Identification and Diagnostic System (JBAIDS) Tularemia Detection Kit to detect a presumptive qualitative result to detect tularemia in feline and blood samples.   USAMRIID also performed RT-PCR and identified genomic DNA from F. tularensis Type A, (SPL15.013.02), thus confirming the FADL's initial presumptive result of F. tularensis.  USAMRIID attempted to culture F. tularensis from three samples (swab, feline tissue, and transfer pipette tip), but no growth consistent with F. tularensis was observed on the cysteine heart agar with sheep blood and antibiotics (CHAB) and chocolate (CHOC) plates.

DISCUSSIONS

Our case study of a dual diagnosis of presumptive F. tularensis and possible rabies exposure transmission from a pet cat to its owner provides insight on how veterinarian staff and laboratory personnel can clinically manage esoteric, unexplained, or post-mortum examinations.  Our case study also demonstrates the obligation for cooperation between animal health, human health, and public health professionals in the management of zoonotic diseases.

Practical Guidance for Clinical Microbiology Laboratories: Laboratory Diagnosis of Parasites from the Gastrointestinal Tract

This Practical Guidance for Clinical Microbiology document on the laboratory diagnosis of parasites from the gastrointestinal tract provides practical information for the recovery and identification of relevant human parasites. The document is based on a comprehensive literature review and expert consensus on relevant diagnostic methods. However, it does not include didactic information on human parasite life cycles, organism morphology, clinical disease, pathogenesis, treatment, or epidemiology and prevention. As greater emphasis is placed on neglected tropical diseases, it becomes highly probable that patients with gastrointestinal parasitic infections will become more widely recognized in areas where parasites are endemic and not endemic. Generally, these methods are nonautomated and require extensive bench experience for accurate performance and interpretation.

The Global Threats from Naturally Occurring Infectious Diseases

Biological risk relates to a broad spectrum of possible scenarios, that can be classified in three categories: natural occurring, unintended and deliberate. The prevention and management of such events require dedicated measures at national and international level, in terms of biosafety and biosecurity: an optimized intervention can minimize the probability of occurrence, but also adverse short-term (i.e.: number of casualties, population reaction…) and long-term (i.e.: chronic illnesses, ecological changes, trades drop…) consequences. Natural scenarios include common, emerging/re-emerging and chronic infectious diseases: they are caused by biological agents, which can be normally present in the communities, as acute or chronic pathologies, or suddenly appear, causing new or uncommon syndromes. In particular, a lot of environmental and human factors can influence emerging and re-emerging diseases: for example, urbanization and people mobility facilitate microorganisms spread, while climate changes are likely to induce a relocation of pathogens vectors. Unintended events are usually due to research and diagnostic activities: laboratories are the places where biological agents are handled and a lack in Biosafety measures or negligence can result in accidental release; the so called Laboratory Acquired Infections represent the main consequence, since they cause pathologies in the laboratory workers, but could be also transmitted in the population. Deliberate use of biological agents is strictly related to terroristic activities: microorganisms are very suitable for this purpose, since they are hidden and can easily spread. The present chapter summarizes the main characteristics of biological agents related events, taking in account their origin and the principal consequences on the community.

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.