Clinical
Microbiology
N e w s l e t
CMN
Vol. 40, No. 9
May 1, 2018
www.cmnewsletter.com
I n Th is Issu e
69 The Canary in the
Coal Mine: Clinical and
Public Health Laboratories
74 Streptobacillus
moniliformis Native
Valve Endocarditis
A case report
Corresponding author: Michael
A. Pentella, Ph.D., D(ABMM),
University of Iowa College of
Public Health, CPH 433, 145
N. Riverside Dr., Room S433
CPHB, Iowa City, IA 52242.
Tel.: 319-384-1573. E-mail:
michael-pentella@uiowa.edu
0196-4399/©2018 Elsevier Inc.
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The Canary in the Coal Mine: Clinical and Public
Health Laboratories Respond to Biosafety Risks
Michael A. Pentella, Ph.D., D(ABMM), University of Iowa, Iowa City, Iowa
Abstract
Biosafety is important to all laboratories, as any clinical specimen has the potential to harbor an infec-
tious agent. The rate at which infectious diseases have spread globally in recent years has only heighted
awareness of laboratory safety and the assessment of biosafety risk. This article presents an overview of
responses to recent events and provides resources for laboratories that can be utilized to prepare and
improve their biosafety programs.
Introduction from infected patients, bacteriologists identified
In 2014, when clinical laboratories faced the Haemophilus influenzae in many specimens and
erroneously concluded that it was the causative
potential of receiving specimens from patients
suspected of being infected with the Ebola virus, agent of the pandemic. Only after the work of
many were unprepared. This sentinel event led to Richard Shope in 1930 was it recognized that
the recognition of the critical value of supporting “hog flu” was due to a virus and not the bacte-
a strong culture of biosafety in clinical and public rium H. influenzae [3]. In 1933, Shope worked
health laboratories. Performing a risk assessment with researchers in the United Kingdom, using
identifies how laboratorians are vulnerable to the ferret model to establish the pathogenicity
exposures and what steps to take to mitigate the of human influenza virus. Many new strains of
risk. Risk assessment is part of the biorisk man- influenza virus have emerged since 1918, and
agement system that needs to be in place in every another new strain can emerge at any time. For
laboratory [1]. It includes mitigation, evaluation, example, in 2009, a new strain of influenza virus
and continuous improvement. Biorisk manage- A H1N1 arose in Mexico and Southern Califor-
ment is now recognized as an important compo- nia and spread throughout the world. The 100th
nent of the quality management system. anniversary of the 1918 influenza pandemic is
an excellent opportunity to reflect on the risk of
Lessons Learned working with specimens from patients infected
This year marks the 100th anniversary of the with an unknown deadly agent that was posed to
1918 influenza pandemic, when an emerging scientists at the time. There is no documentation
influenza virus killed more people than World of fear associated with working with the speci-
mens and pathogen in 1918, but James Barry in
War I. Estimates are that 675,000 Americans died
in the 1918 pandemic [2]. The mortality rate was his book The Great Influenza [2] describes their
2.5%, compared to 0.1% in a typical influenza actions as “heroic.” We know that there was fear
season [2]. While the deadly disease was spread- of influenza in the community, and it probably
ing, medical scientists were at a loss to identify extended to the scientists in bacteriology labo-
the cause, let alone a vaccine or therapeutic agent. ratories, as well. It would be over a dozen years
Microbiology at that time was essentially focused before the cause of the pandemic was recognized.
on bacteriology, as viruses were not yet com- In 1918, the scientists did not have critical tools,
monly recognized. Through culturing of sputa risk assessment, or same level of laboratory or
Clinical Microbiology Newsletter 40:9,2018 | ©2018 Elsevier 69
personal protective equipment (PPE) we have today to help pro-
tect them from a laboratory-acquired infection (LAI). Emerging
and reemerging pathogens will always be a threat to public health;
the risk assessment process is the best tool to protect scientists in
the workplace.
Overview of National Biosafety Efforts
The U.S. Centers for Disease Control and Prevention (CDC) has
provided national leadership to public health and clinical labora-
tories regarding biosafety issues. In 2007, the Trans-Federal Task
Force on Optimizing Biosafety and Biocontainment Oversight
was convened [4]. As an outcome of the Trans-Federal Task Force,
in 2008, the CDC convened the Biosafety Blue Ribbon Panel. In
2012, the Morbidity and Mortality Weekly Report (MMWR) “Guide-
lines for safe work practices in human and animal medical diagnos-
tic laboratories” was published [5]. Competencies are an excellent
way to build knowledge and improve biosafety practices. In 2011,
the MMWR “Guidelines for Biosafety Laboratory Competen-
cies” was published based on a collaborative effort of the CDC
and the Association of Public Health Laboratories (APHL) [6]. In
2015, the White House published plans for enhancing biosafety
and biosecurity at infectious disease laboratories [7]. The admin-
istration performed a comprehensive evaluation of biosafety and
biosecurity practices and identified best practices.
Despite the availability of these resources and activities to promote
biosafety, clinical and public health laboratories had not focused
on biosafety and biosecurity practices and were unprepared for
the potential to encounter Ebola virus in 2014. Since then, funds
have been provided through the CDC to improve biosafety and
biosecurity in both public health and clinical laboratories. This
funding, which was made available starting in 2015 for a three-year
term, provides a full time biosafety officer/official for all 62 funded
public health laboratories. These include the 50 state public health
laboratories, Pacific islands and larger metropolitan public health
laboratories. The focus of the efforts supported by the funds has
been to make every public health and clinical laboratory able to
conduct a risk assessment. Conducting risk assessments and ana-
lyzing the biosafety program in every laboratory ensures that the
laboratories can safely handle and dispose of Ebola virus and other
highly infectious agents. The funding provides technical assistance
through the BSOs to strengthen biosafety practices in local clinical
laboratories. During the first year of the 3-year funding period, the
work of the BSOs was to enhance biosafety capabilities in public
health laboratories. In years 2 and 3, the focus moved to clinical
laboratories. By now, all clinical laboratories in the United States
should have been contacted by their state or local public health
laboratories about ways to improve biosafety practices.
The CDC has engaged the APHL, a membership organization in
the U.S. representing the laboratories that protect the health and
safety of the public, to serve as subject matter experts. The APHL’s
primary role assigned by the CDC is providing biosafety/biosecu-
rity expertise and training to the public health laboratories. In turn,
public health laboratories are charged with connecting with clinical
laboratories in their jurisdictions to improve biosafety practices.
70 Clinical Microbiology Newsletter 40:9,2018 | ©2018 Elsevier
Table 1. BBC key priorities
Priority no. Details
I Serve as subject matter expert to public health and
clinical laboratories
II Build a toolbox for biosafety and biosecurity preparation
III Develop a COP for BSOs
IV Design and deliver a core curriculum and training for
biosafety and biosecurity
V Encourage a culture of biosafety and biosecurity
VI Engage professional organizations and regulatory groups
in supporting biosafety and biosecurity efforts
The APHL has established the Biosafety and Biosecurity Commit-
tee (BBC) to address the resources needed to develop materials to
assist those laboratories with outreach and training for the clini-
cal laboratories in their jurisdictions. The BBC membership con-
sists of experts in biosafety and biosecurity from APHL member
laboratories, the CDC, and other professional organizations. The
BBC identifies its purpose as providing leadership and guidance
on policies and practices that impact biosafety and biosecurity in
state and local governmental, as well as clinical, laboratories. In
turn, the BBC vision is that every laboratory performing clinical
testing on human and animal specimens should be prepared to
safely handle specimens for any emerging disease threat.
At the outset of organizing, the BBC established 6 key priorities
(Table 1) with the goal of organizing a national effort for the public
health laboratory BSOs to work collaboratively. The first priority
of the BBC is to serve as a subject matter expert for public health
and clinical laboratories. This includes providing guidance and
support to public health laboratories and resources for outreach to
strengthen biosafety practices at clinical laboratories. Ultimately,
the purpose of the BSO is to serve as an expert resource for both
clinical and public health laboratories by developing training
courses, risk assessment templates, and other biosafety/biosecurity
tools that can be applied to clinical laboratories. The APHL Lab
Biosafety and Biosecurity Resource Website is available to every-
one at no cost, and past webinars are also available at no cost [8].
The BBC established a second priority, to build a repository for
biosafety and biosecurity tools and also make them available at
no cost to public health and clinical laboratories. The repository
includes risk assessment templates, sample risk assessment, and
checklists, available at the APHL Lab Biosafety and Biosecurity
Resources website [8]. Providing resources, such as checklists and
templates, serves to standardize processes and educate users. To
that end, the BBC set out to prepare tools, materials, and train-
ing documents and posted them on the web page for anyone’s use.
Prior to posting, the documents were vetted through expert review.
The third priority of the BBC is to provide advice and assistance in
the development of a “community of practice” (COP) for BSOs in
public health laboratories. The BBC recognized that by connect-
ing the BSOs, a system of mutual support, sharing of experiences,
providing expert resources, and collaboration would form. To facil-
itate communication for the COP, a listserv was made available.
The listserv, which is restricted to only BSO’s, has grown to 140
members and serves to connect colleagues from across the coun-
try and territories to share information, experiences, suggestions,
etc. Typical topics include potential exposures, decontamination
and disinfection concerns, issues surrounding personal protective
equipment, laboratory procedures to support biosafety activities,
and training efforts. In-person workshops also served to build the
COP, which has proven to be an excellent resource for BSOs to
rely on to receive expert opinion and share experiences.
The fourth priority, designing a core curriculum for biosafety and
biosecurity, delivering training materials, and convening work-
shops, was important because the BSOs did not have the same
level of expertise. The BBC determined that a BSO must have
competencies in safety, security, workforce training, microbiology,
communications, emergency management and response, quality
management systems, and general laboratory practices. Finding
individuals with expertise in all these areas is difficult. Most of the
BSOs hired for the positions lacked some of the necessary com-
petencies. In order to build the competencies, APHL convened
workshops for BSOs in six regions throughout the U.S. to assist
BSOs in building the skills and competencies needed to perform
the functions of the role. These 2.5-day workshops included train-
ing sessions on risk assessment, risk mitigation strategies, com-
petency assessment, incident response, and other topics related
to building a culture of safety in the laboratory. The in-person
workshops further enhance the development of the COP. In addi-
tion to the workshops, another opportunity of knowledge building
and skill development is peer networking, where a BSO from one
state visits a BSO from another state for 2 or 3 days. These visits
are well-structured events where the BSOs have the opportunity
to observe and discuss biosafety issues in another laboratory. A
less experienced BSO is partnered with an experienced BSO who
has significant expertise. After the initial visit, the experienced
BSO then travels to the other laboratory to further exchange
ideas and mentor another BSO. An additional means of building
BSO competency is the Bio360 BSO Leadership Program, which
is an online course, presented by Sean Kaufman, CEO of Behav-
ioral Based Improvements Solutions. Such courses are offered to
all BSOs.
Other educational opportunities include webinars, which are
archived and available on the APHL Biosafety website [8]. The
webinar topics include Clinical Laboratory training materials and
“Fundamentals of Biosafety and Biosecurity.” When the “Funda-
mentals of Biosafety and Biosecurity” webinar was first provided,
there were 781 participants from 138 sites. A second webinar,
“Public Health Laboratory Competencies,” originally had 205
participants from 54 sites. A third webinar is “Biosecurity in
Public Health Laboratories: More than Locking Doors,” which
originally had 115 participants from 43 sites. A fourth webinar
is “Public Health Laboratories Outreach to Clinical Labora-
tories: Challenges and Solutions.” This webinar was originally
presented to 160 participants from 50 sites. The fifth webinar is
“Case Studies in Biosafety and Biosecurity,” which was originally
viewed by 61 sites.
The fifth priority of the BBC is to encourage a culture of biosafety
and biosecurity within all laboratories. The APHL is an advocate
for a strong culture of safety in all laboratories. To highlight the
importance of biosafety and biosecurity, APHL members adopted
a position statement titled “Urging Laboratories To Enhance Bio-
safety Practices via Routine Risk Assessments and Standardized
Training, Identification of True Risk and Best Practices, Devel-
opment of Consensus Standards and Guidelines, and Improved
Reporting of Exposure Events.” The APHL conducted a survey
of public health laboratories at the outset of these efforts to deter-
mine the current status and to serve as a benchmark for progress.
The survey results were published in the 2016 APHL Biosafety and
Biosecurity Survey: Summary Data Report [9]. Fifty-seven of the 62
CDC-funded public health laboratories responded to the survey.
A year into the funding, 87.7% of the laboratories had completed
a risk assessment, 62% had identified gaps through the process,
and all had mitigated the risks identified. In the survey, the pub-
lic health laboratories indicated that 5,194 clinical laboratories
were in their jurisdictions. Those clinical laboratories would be
the focus of further outreach efforts. Another survey, planned for
2018, will focus on the connection with the clinical laboratories.
The sixth and final priority of the BBC is to engage other labora-
tory professional organizations and regulatory groups in support-
ing biosafety and biosecurity efforts. To achieve the objectives of
this priority, the APHL invited partners to send a representative
to a one-day in-person meeting hosted by the APHL to discuss
stakeholder priorities on biosafety and biosecurity in clinical and
public health laboratories. This meeting was named the Biosafety
and Biosecurity Partners Forum. At the conclusion of the meeting,
all of the attendees left with the assignment to bring the biosafety
priorities to the attention of their organization’s membership
and to consider ways to support this national effort. BBC mem-
bers have presented on biosafety related topics at several national
meetings, including ASM Microbe, the Clinical Laboratory Man-
agement Association national meeting, the American Biological
Safety Association annual meeting, and APHL annual meetings.
Presentations and trainings have focused on issues of mutual
importance to public health and clinical laboratories regarding
biosafety and biosecurity.
The APHL continues to reach out to the broader clinical labora-
tory community through the APHL Partners Forum, which meets
annually. The participating partners are from federal and non-gov-
ernmental organizations and discuss opportunities to strengthen
biosafety and biosecurity in clinical and public health laboratories.
The meeting serves to facilitate exchange of information and ideas
among stakeholders. The Partners Forum reviews priorities and
proposes directions for activities to improve biosafety and bios-
ecurity practices in clinical and public health laboratories. The
purpose is for the represented partners to bring the information
to their constituents and to adopt the biosafety and biosecurity
priorities that the APHL and the CDC are advocating.
Clinical Microbiology Newsletter 40:9,2018 | ©2018 Elsevier 71
The APHL has also worked to strengthen biosafety practices glob-
ally through partnership with CRDF Global to support global
fellowship programs, providing biological safety cabinet train-
ing and conducting reviews of biosafety practices and policies in
other countries.
Risk Assessment
A metric of the success of these efforts to improve biosafety prac-
tices in our nation’s laboratories has been the number of labora-
tories that have performed a risk assessment. For example, when
considering a laboratory’s readiness to handle infectious specimens
from a patient suspected of being infected with Ebola virus, the
first step a laboratory should begin is the risk assessment process.
Preventing LAIs starts with determining the risk of a biologi-
cal exposure to staff in the laboratory. The performance of a risk
assessment achieves two important goals. First, it provides infor-
mation regarding a particular risk, and second, it reduces the risk
to an acceptable level [10]. Therefore, the expectation that every
clinical laboratory should perform a risk assessment is a reason-
able performance measure.
The risk assessment should be based on the procedures that the
laboratory currently performs. This is done by defining the situ-
ation and asking specific questions, such as what work is occur-
ring, what can go wrong, how likely it is to happen, and what the
consequences are. There are tools available to help the clinical
laboratorian perform the risk assessment, but performing the
risk assessment is more than completing a checklist, it is a critical
analysis of procedures and protocols and determining what miti-
gation steps are appropriate.
There are essentially four steps to the risk assessment process:
(i) hazard identification, (ii) hazard evaluation or dose-response
assessment, (iii) exposure assessment, and (iv) risk characteriza-
tion. The hazard in the case of a biosafety risk assessment is the
microbial agent, i.e., a bacterium, virus, fungus, or protozoan. Each
laboratory needs to begin the risk assessment process by asking
what pathogens are likely to be encountered. Since the clinical
laboratory is rarely informed of what pathogen the physician sus-
pects, this question can be difficult to answer. However, the clinical
laboratory can make an educated assumption based on where the
laboratory is located, what pathogens are routinely encountered,
and what unusual pathogens have been encountered in the past.
To evaluate the hazard, the assessor must review the host range
for the identified likely pathogens, with special concern for human
pathogens. If the organism is pathogenic to humans, the assessor
must determine if it is a highly pathogenic agent or has a low level
of pathogenicity. Part of this assessment step is to determine if the
dose of the exposure matters for the specific pathogen being con-
sidered. For example, exposure to as few as 10 Mycobacterium tuber-
culosis organisms could result in disease [5]. As the list of organisms
is assembled and the pathogenicity is assessed, it is important to
review which of these pathogens have been reported as a cause of
LAI. Next, consideration must be given to the length of survival
of the pathogen if it were to contaminate a surface.
72 Clinical Microbiology Newsletter 40:9,2018 | ©2018 Elsevier
After identifying the organisms commonly and potentially
encountered in the facility, the assessor can proceed to perform
the exposure assessment by reviewing the activities performed
that may present a risk of exposure. This assessment should be a
collaborative effort between the assessor and staff working in the
laboratory section to determine how exposure could occur and
what routes of exposure are possible. By reviewing these issues,
the risk involved in working with the agent can be determined.
There are several portals of entry through which staff are vulner-
able to exposure to infectious agents, including intact skin and the
mucous membranes of the eyes, nose, and mouth. Intact skin is
an excellent barrier against nearly all agents, but sharps, such as
needles and broken glass, can easily puncture intact skin. Mucous
membranes of the eyes, nose, and mouth and breaks in the skin
provide portals of entry. Aerosols, splashes, and splatter can con-
taminate mucous membranes and serve as an excellent means of
entry. Protecting against splashes and splatter serves to protect
individuals from agents that infect through mucous membranes,
the gastrointestinal tract, and the skin. One portal of entry that
needs its own type of protection is the respiratory tract, since inha-
lation of aerosols is a risk.
Based on these results, the risk of exposure can be characterized.
Essentially, risk is characterized by considering the likelihood of
exposure and the consequence if an exposure occurs. In the prior
example of a sputum specimen, if the laboratory processes sputum
specimens from patients suspected of having tuberculosis, then
the likelihood of exposure is high. The consequence of exposure
is also high, because fewer than 10 organisms may cause disease.
The next consideration in the risk assessment process is mitiga-
tion [5], which is the combination of actions and control measures
that serve to reduce or eliminate the risks associated with biologi-
cal agents and toxins. There are several effective ways to mitigate
exposure risks. For example, working in a biosafety cabinet pro-
tects against splash, splatter, and aerosols. While the pathogens
typically found in a sputum culture dictate that a sputum speci-
men should be processed in a biosafety cabinet, the same cannot
be said for a urine culture. which can be safely processed on the
open bench. It is important to think through the process and to
use the mitigation tools to effectively mitigate the risk while not
imposing too much burden when the risk is not reasonable. There
is a hierarchy of mitigation [11]. At the apex are administrative
procedures, which are followed by containment equipment, such
as biosafety cabinets, laboratory practices, and PPE. Staff need to
recognize that PPE is the final and least effective mitigation tool.
Understanding how to use mitigation tools and effectively utiliz-
ing them is critical to a successful biosafety program.
In the above example, by mitigating the risk by using a biosafety
cabinet, the likelihood of exposure was reduced to low, but the
consequence of the exposure remained high. With additional
PPE requirements for an N95 respirator, the likelihood of expo-
sure from failure of the biosafety cabinet can be reduced to rare.
From consideration of the mitigation steps, the risk is reduced,
although some acceptable risk remains. The nature of the work
dictates that the risk cannot be eliminated totally. Even if every
available protection is taken, the risk will never be zero. There is
always the potential for human error or that exposure may occur
to someone who was not considered to be at risk.
The risk assessment process prescribes reviewing the procedures
performed, analyzing expected hazards that may be encountered,
and implementing mitigation processes that are reasonable. A
potential additional benefit of a risk assessment is that the find-
ings of the risk assessment could be the basis for justification for
space and equipment needs. Importantly, the risk assessment is
an opportunity for evaluation of emergency plans and potential
procedural changes.
Another important consideration is when to perform the risk
assessment. There are several events that should trigger the perfor-
mance of a risk assessment. First, before a new testing procedure
is being performed in the laboratory. Second, whenever there is a
move or renovation in the laboratory. Third, if there are signifi-
cant changes in personnel. Fourth, if there is a new or emerging
infectious agent that the laboratory is going to perform testing
to detect or if there are new reagents or equipment being used in
the laboratory. Risk assessments should be reviewed on an annual
basis and repeated when changes are made in reagents, practice,
employees, or facilities and when new pathogens emerge that may
be encountered in the laboratory.
Clearly, a knowledgeable assessor is vital to a successful risk assess-
ment. The assessor needs a good deal of practical experience and
good problem-solving skills. There is a wealth of diversity in opin-
ions in the microbiology community on biosafety issues. However,
many practices are not based on scientifically proven information.
Therefore, the assessor must be familiar with best practices in the
laboratory community that can be successfully implemented in the
clinical laboratory.
The assessment of laboratory activities must be protocol driven.
The assessor must consider the procedures and protocols com-
monly practiced in the laboratory while handling the infectious
agents. For example, how are suspensions of organisms made?
Are open tubes ever vortexed? If organisms are being cultured,
then this is an amplification step, and the risk of working on the
cultures may be greater than that of working on the specimens.
The risk assessment is successful and complete when the process
has identified the agent’s hazards, as well as the laboratory’s proce-
dure hazards; determined appropriate biosafety level and selected
additional precautions; evaluated staff competency, as well as the
performance of safety equipment; and the assessment is reviewed
with staff and management.
To avoid LAI and to protect staff, a clinical laboratory needs a
biosafety plan and an exposure control plan. Performing a risk
assessment can be the foundation for the development of both of
these plans and policies. Performing the risk assessment clearly
highlights what needs to be implemented in the biosafety plan with
regard to mitigation options, but it also highlights which infectious
agents staff may reasonably expect to be exposed to. This prepa-
ration allows laboratory management to plan medical follow-up
and to document the process in the exposure control plan. It is
necessary to have a document that defines exactly what happens
when an exposure occurs. These plans can save valuable time and
can be used as a training tool. Management and staff must agree
that risk will never be down to zero percent; in the effort to keep
everyone as safe as possible, there needs to be a strong culture of
safety that serves as the bedrock of the safety program. The culture
of safety is supported by the recognition that safety is ultimately
everyone’s responsibility.
Conclusion
Public health and clinical laboratories have many resources avail-
able to them to improve their biosafety programs. There are free
tools available on the internet to make the processes easier and
faster [8]. Direct consultation is available through the jurisdic-
tional public health laboratories to obtain expert advice. What
is needed is the time and institutional leadership to accomplish
the work. That must be supplied locally by the public health and
clinical laboratories. If laboratories are to be prepared for the next
emerging pathogen that poses a high risk to laboratory workers,
then every laboratory needs to perform a risk assessment. Not
just in the microbiology laboratory, but throughout all the sec-
tions of the laboratory in which there is a risk. While there are no
federal mandates or certification requirements, we know that we
need to do it to be prepared to do our jobs. The future vision for
biosafety in public health and clinical laboratories must include
active biosafety programs. These programs should come under
the umbrella of the laboratory quality management system. Over
time, quality indicators can be measured, for example, the num-
ber of risk assessments completed, the number of risk assessments
revised and the reasons for revision, the reduction in exposures,
and the number of laboratories that incorporate biosafety compe-
tencies into their quality management systems. With strong lead-
ership at the national and local levels, much can be accomplished
for the safety of staff, the good of the patient, and the security of
the nation [12,13].
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