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Qasmi 2019
Qasmi 2019
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.
Shamsul Arfin Qasmi, PhD, is a Professor, Department of Pathology, Fazaia Ruth Pfau Medical College, Karachi, Pakistan. Bilal
Ahmed Khan, MPhil, is an Assistant Professor, Department of Molecular Pathology, Dow University of Health Sciences, Karachi,
Pakistan.
372
QASMI AND KHAN
conducted a survey in 2006, which reported 2 LAIs from tion of the data and statistics to generate the numeric de-
Listeria monocytogenes and Brucella melitensis. This was fol- scription of the data. Bar graphs and pie charts show the
lowed by another survey in Belgium from 2007 to 2012, which relative number of participants in each category (by re-
reported 140 LAIs.6 porting the percentages/counts within each category). The
Laboratory-acquired infections can occur by exposure to graphs were made to provide visual comparisons between
or inhalation of an agent, contact with mucous membrane, or the different variables. A descriptive analysis provides a de-
percutaneous inoculation, but in most cases, the actual cause tailed report of the percentages and frequencies of all the
remains uncertain. Therefore, the significant increase in work categorical variables in the study.
with pathogenic organisms and the emergence of infectious
diseases make LAIs a global health security concern.
Since an infected laboratory worker can be an index pa- Results
tient for a new epidemic,7 many biosafety guidelines have
been developed as well as sophisticated containment equip- Laboratory Affiliations
ment to prevent LAIs.8 Despite these efforts, LAIs continue Of the 30 facilities that were included in the survey, 50%
to occur and cannot be ignored, especially in developing (n = 15) were clinical/biomedical laboratories, 16.6% (n = 5)
countries like Pakistan, which has been fighting to curb in- were university hospital laboratories, 26.6% (n = 8) were
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fectious diseases. As reflected in the published literature, the research and development (R&D) laboratories, and 6.6%
biosafety culture is severely lacking in many laboratories,9-11 (n = 2) were animal laboratories. Clinical and biomedical
and no data are available from Pakistan on this topic. laboratories have the same status, while university hospital
Therefore, this study was conducted to identify and as- laboratories are associated with inhouse healthcare labora-
certain the incidence of LAIs, to develop indigenous data, tories whose main patients are inpatients in the hospital.
and to review protocols followed in response to incidents
in research, veterinary, and clinical laboratories. This study
will serve as a starting point to understanding the spectrum Biosafety Levels Surveyed
of problems; to designing and implementing policies and In cross tabulation analyses, the survey team found that
training programs that can mitigate risks in handing, most laboratories were designated as biosafety level 2 (BSL-
transportation, and storage of infectious pathogens; and to 2), across the 4 types of facilities surveyed. Among clinical/
propagating a culture of safety in Pakistan. biomedical labs, 6.7% were BSL-1, 73.3% were BSL-2,
6.7% were BSL-3, and 13.3% of the facilities have both
BSL-2 and -3 labs. In university hospital labs, 80% were
Methodology BSL-2, and 20% of the facilities have both BSL-2 and -3
laboratories. All of the animal laboratories were BSL-2,
A comprehensive questionnaire composed of 64 questions was keeping in mind the risk groups with their biosafety and
designed under the guidance of technical experts in microbi- biosecurity challenges. In R&D laboratories, 87.5% of the
ology and biorisk management from Pakistan and the United facilities were BSL-2, and 12.5% were BSL-3 (Table 1).
States. The questionnaire was formulated to assess the biosafety
measures in place, compliance with standard operating proce- Table 1. Biosafety Level of Laboratories Surveyed:
dures (SOPs) and international guidelines, microorganisms Cross Tabulation
or toxins handled, availability and use of personal protective
equipment (PPE) and other containment measures, emergency Biosafety Level (BSL)
preparedness, suspected LAIs, and possible route of exposure in
laboratories with diverse portfolios. The survey was conducted BSL-1 BSL-2 BSL-3 BSL-2 and -3 Total
1 11 1 2 15
by a research associate under the supervision of the principal
6.7% 73.3% 6.7% 13.3% 100.0%
investigator among the 30 laboratories in Karachi, Pakistan.
100.0% 45.8% 50.0% 66.7% 50.0%
The laboratories were selected by a cluster random sampling 0 4 0 1 5
method. The data were obtained from laboratory staff and 0.0% 80.0% 0.0% 20.0% 100.0%
recorded by the research associate under the supervision of the 0.0% 16.7% 0.0% 33.3% 16.7%
principal investigator. Data were then entered and statistically 0 2 0 0 2
analyzed using SPSS version 20 by a biostatistician. 0.0% 100.0% 0.0% 0.0% 100.0%
The data consisted of categorical variables, mostly of the 0.0% 8.3% 0.0% 0.0% 6.7%
nominal and ordinal type. Each category in the variable was 0 7 1 0 8
separated from the other. Descriptive statistics were recorded 0.0% 87.5% 12.5% 0.0% 100.0%
in percentages and frequencies for categorical data. Cross 0.0% 29.2% 50.0% 0.0% 26.7%
1 24 2 3 30
tabulations were done between different categorical vari-
3.3% 80.0% 6.7% 10.0% 100.0%
ables for finding comparisons between different variables.
100.0% 100.0% 100.0% 100.0% 100.0%
Bar graphs and pie charts were created as a visual presenta-
Table 2. Types of Services Provided by the Surveyed Facilities In 43.3% of the facilities, management has stated a com-
mitment but does not have clearly defined roles, while in
Services Frequency, No. (%)
10% of the facilities, management has not made a com-
Pathology /histopathology 13 (43.3) mitment to biosafety (Figure 1).
Virology 4 (13.3)
Molecular diagnostics 17 (56.7)
Clinical pathology (hematology/ 20 (66.7)
biochemistry) International Biosafety Guidelines
Cell culture 9 (30) Regarding biosafety policies and guidelines, 50% (n = 15) of
Bacteriology 25 (83.3) the laboratories follow World Health Organization (WHO)
Serology 22 (73.3) guidelines,12 26.7% (n = 8) follow Biosafety in Micro-
Toxicology 3 (10) biological and Biomedical Laboratories (BMBL) guide-
In vitro research 7 (23.3) lines,13 and 1 (3.3%) has its own policies; 16.7% (n = 5)
Other 3 (10)
do not follow any biosafety policies or guidelines (Figure 2). It
was interesting to find in cross tabs distribution that 80% of the
clinical/biomedical labs follow WHO laboratory biosafety
Laboratory-related Activities guidelines, while 20% do not follow any biosafety guidelines.
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Data regarding the type of services provided by the labo- Of the university hospital labs, 80% follow BMBL guidelines,
ratories revealed that 83.3% (n = 25) of the laboratories while the remaining 20% follow other guidelines (mostly
were doing bacteriology, 73.3% (n = 22) were doing se- WHO). Half of the animal labs follow the WHO biosafety
rology, 66.7% (n = 20) were doing clinical pathology, and manual, while 50% do not follow any specific guidelines. Of
56.7% (n = 17) were doing molecular diagnostics. Only the R&D labs, 25% follow WHO laboratory biosafety
13.3 % (n = 4) were dealing with virology, 30% (n = 9) with guidelines, 50% follow BMBL, 3.3% follow their own labo-
cell culture, and 10% (n = 3) with toxicology (Table 2). ratory’s SOPs, and 16.7% follow various biosafety policies or
did not have any prior knowledge of biosafety policies and
guidelines (Figure 2).
Safety Culture
To prevent exposure to potentially infectious material and
to prevent LAIs, it is important to determine the level of Biosafety Officer
biorisk management implementation. We found that The placement of a biosafety officer in a facility is important
46.6% of the facilities have clearly defined the roles and for safeguarding the employees, as it ensures labs adhere to
responsibilities for implementation of biosafety practices. biosafety practices. We found that 70% of the facilities have
assigned the responsibility of a biosafety officer in their insti- do not have any warning signs outside of their laboratories.
tute, while only 3.3% also have assigned responsibility to Regarding the availability and use of primary containment
different related personnel. While 80% of the facilities have biosafety cabinets (Class II), the questionnaire showed that
assigned the role of biosafety officer to laboratory managers and in 10% of the laboratories, primary containment biosafety
13.3% to a scientific manager, 86.7% of facilities have assigned cabinets did not exist at all, while in 30% of the laboratories
the role of biosafety officer to microbiologists, and 70% of the primary containment biosafety cabinets were present, but
facilities have given this role to pathologists (Table 3). The they were used only periodically; in 60% of the laborato-
biosafety officer is responsible for promoting a culture of safety ries, primary containment biosafety cabinets (Class II) were
according to his or her expertise in biosafety and biosecurity, used consistently (Figure 3). However, the proper annual
which enables a facility or institute to curb the unintentional or field certification for biosafety cabinets as per the NSF 49
intentional misuse or exposure of potentially infectious mate- standard were not done in the facilities, as NSF-certified
rial and to prevent incidents in the laboratory environment. professionals are not currently available and trained in
Pakistan. This function is currently performed by engineers
referred by the vendors of biosafety cabinets.
Biosafety Facilities
The study found that 86.6% (n = 26) of the laboratories
have posted biohazard signs, while 13.3% (n = 4) of the labs Personal Protective Equipment
Assessments regarding the compliance with biosafety
measures revealed that in 50% of the facilities there is strict
Table 3. Assignment of Roles and Responsibilities Related
to Biosafety and Biosecurity compliance with biosafety measures, while in 43.3% of the
facilities biosafety measures are often not put into practice,
Designated Personnel in and in 6.6% biosafety measures are not respected at all.
the Surveyed Institutes Frequency, No. (%) Forty percent of the laboratories have active personal pro-
Biosafety officer 21 (70) tective equipment (PPE) programs (eg, lab coats, gowns,
Biosecurity officer 1 (3.3) gloves, face masks) with clearly defined procedures; 53.3%
Laboratory manager 24 (80) have some procedures regarding PPE but lack oversight in
Scientific manager 4 (13.3) implementation; and 6.6% of laboratories have limited
Microbiologist 26 (86.7) resources for PPE. Proper use of PPE can be effective in
Pathologist 21 (70) limiting the incidents of LAIs if used and maintained
Laboratory workforce 3 (10)
properly.
Figure 4a.
377
LABORATORY-ACQUIRED INFECTIONS IN PAKISTAN
Yes No
Procedure No. % No. %
Pouring, splitting, or decanting liquid specimens 28 (93.3) 2 (6.7)
Removing caps or swabs from culture containers 26 (86.7) 4 (13.3)
Spilling infectious material 22 (73.3) 8 (26.7)
Preparing smears, performing heat fixing, staining slides 27 (90) 3 (10)
Performing serology, rapid antigen tests, wet preps, and slide agglutinations 26 (86.7) 4 (13.3)
Throwing contaminated items into biohazardous waste 25 (83.3) 5 (16.7)
Aspirating and transferring body fluids 21 (70) 9 (30)
Separating needles from syringe 23 (76.7) 7 (23.3)
Subculturing and streaking culture media 27 (90) 3 (10)
Mixing, blending, grinding, shaking, and vortexing specimens or cultures 29 (96.7) 1 (3.3)
Risk Assessment cut on mucous membrane (3.3%), and falls and burn in-
juries (3.3%). Subcutaneous needlestick injury was the
Seventy percent of facilities were not aware of the importance
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Figure 5. Presence and compliance with SOP for responding to a needlestick injury in various institutions
Incident Reporting
Data regarding activities that resulted in suspected LAIs
reveal that 5 of the individuals received an LAI by needle-
stick injury and 1 from subculturing in a microbiology lab.
Table 7. Transmission Routes and Potential Causes of LAIs
In 5 individuals it was proven that the infection was work-
related based on an investigation done in their respective Route Frequency, No. (%)
laboratories. In the case of 26.6% suspected LAIs, the in- Unknown 25 (83.3)
fection was not transmitted to another person, while for
Inhalation 4 (13.3)
73.3% it was not known whether it was transmitted to
another person or not. Percutaneous inoculation 4 (13.3)
Pathogenic strain was identified in only a few cases of Contact with mucous membranes 0
inhalation as Mycobacterium tuberculosis. Percutaneous in- Ingestion 0
fections were mainly hepatitis C; others were not identified, Potential causes of LAIs
because for LAIs there was no protocol in place for incident
Unknown 22 (73.3)
reporting and further investigation up to the level of or- No compliance to biosafety measure 7 (23.3)
ganism identification. This needs to be addressed properly Lack of knowledge regarding the biorisk 2 (6.7)
to ensure the safety of people working in laboratories and to related to activity
examine the risk group for that organism, which will help in Lack of appropriate containment device 0
developing proper preventive and treatment modalities for Failure of containment device 0
a functional and effective medical surveillance program. Not enough training 4 (13.3)
In 12.5% of the R&D laboratories, there is no policy for Lack of attention 2 (6.7)
incident reporting. However, 26.7% of clinical laborato- Lack of space 0
ries, 60% of the university hospital laboratories, and 25% Too much workload 2 (6.7)
Other 0
of the R&D laboratories have procedures for incident
reporting, but they are not strictly followed. In 73.3% of while 10% of the LAI cases caused a reported physical
the clinical laboratories, 40% of the university hospital disability or severe illness for more than 20 days. No fa-
laboratories, and 62.5% of the R&D laboratories, there is talities have been reported in relation to LAIs in any in-
a strict policy for incident reporting (Figure 6). stitute. In 10% of the facilities, exposure to LAIs has been
reported, while in 26.7% of the laboratories, infection was
reported postexposure, which may be due to inappropriate
Individual Vulnerability biosafety measures resulting in inadequate reporting of
The most vulnerable individuals identified in the laboratory incidents (Figure 7).
environment in this survey were pathologists, laboratory
technicians, researchers, and housekeepers (Table 8).
Medical Surveillance
Overall, 40% of the clinical laboratories, 60% of the uni-
Exposure versity hospital laboratories, and 12.5% of the R&D lab-
In 16.6% of the LAIs, there were no reported physical oratories have functional medical surveillance programs,
disabilities or severe illnesses in the infected individuals, while none of the animal facilities have any medical sur-
veillance program in place (Figure 8).
LAI in fungal infections.20 However, the LAIs reported in are following WHO or BMBL as guidelines. However,
our study are not from these enteric bacteria. The differ- commitment to laboratory biosecurity is extremely low in
ence could be the ineffective system for the determination most of the facilities, and they lack proper occupational
of LAIs as described. This study provides the pilot data to health and medical surveillance programs. There is a serious
identify the gaps for implementation of a biorisk man- gap in the risk assessment strategy that must be addressed
agement system to safeguard laboratory workers from LAIs before adopting any diagnostic/research processes in the
and highlights the critical need for reporting and investi- laboratories surveyed.
gating infections in lab professionals. We have also found serious gaps in effective SOPs to
determine and regulate LAIs. Inhalation and percutaneous
inoculation were found to be the major source of LAIs, and
Conclusion most of the LAIs were caused by HCV and Mycobacterium
tuberculosis, which is highly endemic in our country. Most
We believe that this was the first-ever study focused on LAIs of the clinical and university hospitals have BSL-2 labora-
in Karachi, Pakistan. This study has identified the gaps in tories. University hospital laboratories were found to be the
the biosafety and biosecurity practices in various laborato- most committed to biosafety management. The WHO
ries, including human, animal, and research, biomedical, biosafety manual was followed in most of the clinical lab-
and university hospital laboratories. These data will help oratories, while most of the university hospitals follow
us to focus on standard microbiological practices, special BMBL guidelines for biosafety. In light of our findings, we
practices, use of PPEs, primary barriers, and facility design would recommend the following:
in identifying the root causes of LAIs and why they have not
received enough attention in Pakistan. Develop and implement guidelines for labs to imple-
In this survey most of the laboratories were affiliated with ment a medical surveillance program for staff.
academic or university facilities and are dealing with bac- Use a data driven approach to making policy and
teriology. Most of the laboratories have started a commit- smart investments to lab biorisk management capacity
ment to the implementation of biosafety in the facility and and biosafety competence of lab professionals.
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