Section A

Provide a reasoned definition of each of the 4 hazard groups outlined by the Advisory Committee on Dangerous Pathogens. (50%) For each group provide an example microorganism and reasons for its allocation into this group. (50%)

According to The Advisory Committee on Dangerous Pathogens (ACDP), there are 4 hazard groups that classify different microbiological agents into these groups. This classification depends on the ability of the organism to infect an individual. Classification of these organisms relies on four basic questions which are: Is it pathogenic for humans? Is it a hazard to employees? Is it transmissible to the community? And is there an effective treatment available for these microbes?. These criteria, produced by the World Health Organization, only applied to healthy individuals who are not seeking medical attention, nor the young, pregnant, or breastfeeding women [1].

There are different explanations for the different hazard groups. For Hazard group 1, it applies to organisms that are unlikely to infect a healthy person and cause disease but can cause diseases to vulnerable individuals. This group contains non-pathogenic organisms such as yeast and E.coli K-12. E.coli K-12 is in hazard group 1 because it cannot survive in the human digestive system and does not produce toxins [2] As for Hazard group 2, applies to organisms that can cause diseases and may be a hazard to employees but it is unlikely to spread to the community and usually, there is an effective treatment to it. Examples of Hazard group 2 are Escherichia coli, Mumps, and Measles. Measles is in Hazard Group 2 because it is a highly contagious virus that can spread through coughing and sneezing [3]. Hazard group 3 contains organisms that can cause severe human disease and can be a hazard to employees. These organisms can spread to the community but there’s usually a treatment available. Examples of Hazard group 3 are Escherichia coli 0157 and blood-borne viruses Hepatitis B, C. D and E. Escherichia coli 0157 is highly transmitted to humans through contaminated food and its categorized as a toxin-producing E.coli [4]. Lastly, Hazard group 4 consists of organisms that can cause severe diseases to humans and are a serious hazard to employees. They are likely to spread to the community and there is usually no effective treatment available for them. Examples of Hazard group 4 are viruses, Congo hemorrhagic fever and Kyasanur forest disease, Russian spring-summer encephalitis. The Russian spring-summer encephalitis is considered in the Hazard 4 group since it an endemic is marshy forested localities of some eastern provinces of Russia (Jervis, Higgins (1953) [1,5]).

References:

1- Biological Hazard Groups. (n.d.). Retrieved January 08, 2021, from https://www.sgul.ac.uk/about/our-professional-services/safety-health-and-environment/workplace-health-safety-and-welfare/workplace-health-and-safety-lab-research/biological-hazard-groups

2- (n.d.). Retrieved January 08, 2021, from https://2014.igem.org/Safety/Risk_Group_Guide

3-Transmission of Measles. (2020, November 05). Retrieved January 08, 2021, from https://www.cdc.gov/measles/transmission.html

4-E. coli O157:H7 Infection (Escherichia coli) and Hemolytic Uremic Syndrome (HUS) – Minnesota Dept. of Health. (n.d.). Retrieved January 08, 2021, from https://www.health.state.mn.us/diseases/ecoli/index.html

5- Jervis, G. A., & Higgins, G. H. (1953). Russian Spring-Summer Encephalitis: Clinico-Pathologic Report of a Case in the Human. Journal of Neuropathology & Experimental Neurology, 12(1), 1-10.

2. Evaluate the laboratory tests you would perform to identify fungal infections in clinical specimens and highlight any limitations of each diagnostic approach?

I would use two different methods to identify fungal infections. These two methods are Culture, Direct Microscopy, And Histopathology, in addition to Serology. Culture, Direct Microscopy, And Histopathology have been for several decades to diagnose fungal infections. By this method, several fungal-specific strains such as C. neoformans, P. jirovecci, Candida spp. and Aspergillus spp. Has played important role in diagnosing several infections. Of course, there is a limitation to this method, since these agents are specific to each fungal infection, it can be a limitation in diagnosing the infection. In addition, the source and the quality of the specimen are crucial in the diagnostic test. Finally, a diagnosis by direct microscopy and histopathology requires biopsies of deep tissues which can be sometimes hard to get and can cause a risk to the patients who are susceptible to invasive viruses and infections [1]. Apart from this method, culture from a fungal sample results in high quality in diagnosing fungal infections. There are many advantages to this method such as high yielding of the specific agent that causes the infection and allows for susceptibility testing. However, this method has significant limitations, such as delays in having results with different filamentous fungi. In addition to that, blood culture has more than 50% error in detecting the etiological agent in patients with fungal infections (Fraser et al. 1992; Ostrosky-Zeichner and Pappas 2006; Ostrosky-Zeichner (2012),[1,2,3,4]).

Another method such are serologic tests has been useful for non-culture based diagnosis of fungal infections, technologies such as immunodiffusion (ID), complement fixation (CF), an enzyme immunoassay (EIA) has been associated with this method. Moreover, the ID test detects the precipitation that happens to antibodies Histoplasma H and M antigens. Serological tests help in diagnosing coccidioidomycosis, an infection caused by fungus Coccidioides [5], especially in patients who are not able to produce a sputum sample. The detection of antibodies, in this case, coccidioidal IgM, is useful to diagnose coccidioidomycosis where the sensitivity of the test is above 80%. There are of course advantages and disadvantages to this method. Advantages of serological tests are having positive results when the culture tests show negative or difficult to get. In addition, serological tests can reduce the need for a culture that uses several fungal-specific strains which some of which are hazardous, such as Coccidioides spp. However, there are limitations to this method such as a low level of sensitivity and specificity. In addition, some serological tests can be time-consuming and require trained individuals [1].

References:

1- Kozel, T. R., & Wickes, B. (2014). Fungal diagnostics. Cold Spring Harbor perspectives in medicine, 4(4), a019299.

2- Fraser VJ, Jones M, Dunkel J, Storfer S, Medoff G, Dunagan WC 1992. Candidemia in a tertiary care hospital: Epidemiology, risk factors, and predictors of mortality. Clin Infect Dis 15: 414–421

3- Ostrosky-Zeichner L 2012. Invasive mycoses: Diagnostic challenges. Am J Med 125: S14–S24

4-Ostrosky-Zeichner L, Pappas PG 2006. Invasive candidiasis in the intensive care unit. Crit Care Med 34: 857–863

5-Valley Fever (Coccidioidomycosis). (2020, October 28). Retrieved January 08, 2021, from https://www.cdc.gov/fungal/diseases/coccidioidomycosis/index.html

Section B

What is antibiotic stewardship and why it is it of increasing importance in public health.

Antibiotic or antimicrobial stewardship is a program that assists the appropriate use of antimicrobials including antibiotics, also, it improves patients outcomes, reduces microbial resistance, and decreases the infection spread by using multi-drug-resistant organisms. This program was initiated to solve one of the most important public health problems, the misuse and the overuse of antimicrobials. Organisms adapt to the antimicrobials and antibiotics that are designed to eliminate them, they gain resistance to the drug, hence, making the drug ineffective in killing them. This problem causes longer hospitalization periods, more expensive to the patient, and may cause death eventually because of the infection [1]. Unfortunately, there are patients every day who die from infections due to antibiotic-resistant organisms that cannot be treated with the available antibiotics. Almost 23,000 people die each year as a result of infections that occur due to antibiotic-resistant organisms [3]. One huge factor that plays a role here is the appropriate use of antibiotics. According to File, Srinivasan, and Bartlett (2014), there is a huge percentage of antibiotic use in both inpatient and outpatient settings is either unnecessary or incorrectly prescribed” [2,3].

The stewardship program has proven to be highly successful in improving the use of antibiotics. Studies and research shows that the stewardship program helped in improving the patient outcome, reduce readmission rates to the hospital, and also, most importantly reduces antibiotic resistance [4]. This led to an increase in the implementation of the program in more hospitals. Other than the focus on antibiotic resistance, the stewardship program also focuses on other patient safety issues. One of the major threats in hospitals is Clostridium difficile, this has led to the emergence of BI/NAP1 epidemic strain of C. difficile that caused increases in morbidity and mortality. Moreover, there are 250,000 C.difficile cases that resulted in 14,000 deaths each year in the United States. The antimicrobial stewardship program has shown to be highly effective against C. difficile in hospitals. Many institutes have shown that there is a significant reduction in C. difficile after implementing the program in different hospitals. Finally, one of the most important patients safety crises is the proper treatment of infections. Studies show that the infections that were kept under control with the help of a stewardship program resulted in a 70% increase in curing the infection and an 80% decrease in treatment failure [2]. Thus, we can see that antimicrobial stewardship programs are successful in improving antibiotic use and increase antibiotic-resistance infection cures [2].

References:

1- Antimicrobial stewardship. (n.d.). Retrieved January 08, 2021, from https://apic.org/professional-practice/practice-resources/antimicrobial-stewardship/

2-File, T. M., Jr, Srinivasan, A., & Bartlett, J. G. (2014). Antimicrobial stewardship: importance for patient and public health. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 59 Suppl 3(Suppl 3), S93–S96. https://doi.org/10.1093/cid/ciu543

3-Centers for Disease Control and Prevention. Antibiotic resistance threats in the US, 2013. Available at: www.cdc.gov/AntibioticResistanceThreats/index.html. Accessed 17 June 2014.

4-Fridkin SK, Srinivasan A. Implementing a strategy for monitoring inpatient antimicrobial use among hospitals in the United States. Clin Infect Dis 2014; 58:401–6

Section B

Outline the current status and strategies for development of a malaria vaccine.

It remains a priority to develop a highly effective vaccine against human malaria parasites such as Plasmodium falciparum and P. vivax [1]. There is steady progress is being made over the years, especially after the discovery and understanding of new cellular and molecular mechanisms. According to Moorthy (2013), “The revised Malaria Vaccine Technology Roadmap to 2030 now calls for a next-generation vaccine to achieve 75% efficacy over 2 years against P. falciparum and/or P. vivax” (Moorthy, 2013, [2]). A Malaria vaccine candidate in clinical development showed that the vaccine can inhibit the merozoite invasion, prevent the IRBC-mediated pathology, inhibit the sexual-stage development, killing of infected hepatocytes, and inhibits the sporozoite infection. This will inhibit the malaria parasite to take action in the human body [3]. The most tested vaccine candidate for P. falciparum malaria prevention is RTS,S/AS01 which increases the immune response against the major circumsporozoite protein (PfCSP) covering the surface of the infecting sporozoite [1]. RTS,S/AS01 Is the only vaccine that provided protective efficacy against clinical malaria [4]. However, this protection doesn’t last, it wanes over time and it is also age-dependent where protection was lower in infants than in young children. In addition, a study showed that there is a rebound in malaria incidences after 5 years post-vaccination [5]. Therefore, extending the period of protection is the most important and crucial thing to be considered in future improvements of the RTS,S/AS01 vaccine. This will require more understanding of the cellular and molecular mechanisms of malaria parasites. Thus, there is another approach to handling malaria parasites at this time which is modifying the dose and the schedule of vaccination. Another approach is the use of structure-based vaccines. This is done by isolating monoclonal antibodies (mAb) from humans that are exposed to malaria, by doing this, a structure of an epitope that is bound by the mAb is determined at atomic resolution. These results are used to design immunogens/antibodies that have a functional activity [6]. Another method is targeting the sexual stage of the parasite that can impact its life cycle in the mosquito aiming to block transmission to humans. Transmission-blocking vaccine (TBV) will not protect an individual directly but rather arresting onward transmission of malaria and thus providing the necessary protection to the community [1].

References:

1- Draper, S. J., Sack, B. K., King, C. R., Nielsen, C. M., Rayner, J. C., Higgins, M. K., Long, C. A., & Seder, R. A. (2018). Malaria Vaccines: Recent Advances and New Horizons. Cell host & microbe, 24(1), 43–56. https://doi.org/10.1016/j.chom.2018.06.008

2- Moorthy V.S., Newman R.D., Okwo-Bele J.M. Malaria vaccine technology roadmap. Lancet. 2013;382:1700–1701.

3-Nilsson S.K., Childs L.M., Buckee C., Marti M. Targeting human transmission biology for malaria elimination. PLoS Pathog. 2015;11:e1004871

4-RTS,S Clinical Trials Partnership Efficacy and safety of RTS,S/AS01 malaria vaccine with or without a booster dose in infants and children in Africa: final results of a phase 3, individually randomised, controlled trial. Lancet. 2015;386:31–45.

5-Olotu A., Fegan G., Wambua J., Nyangweso G., Leach A., Lievens M., Kaslow D.C., Njuguna P., Marsh K., Bejon P. Seven-year efficacy of RTS,S/AS01 malaria vaccine among young African children. N. Engl. J. Med. 2016;374:2519–2529

6-Kwong P.D. What are the most powerful immunogen design vaccine strategies? A structural biologist’s perspective. Cold Spring Harb. Perspect. Biol. 2017;9:a029470.

Section C

Evaluate the contribution of the medical microbiology laboratory in the diagnosis of syphilis and as part of your answer explain how serological tests for syphilis are interpreted.

Bacterial infections, such as syphilis, usually spread by sexual intercourse between individuals. The infection symptoms are painless sore in the genitals, rectum, or mouth. In addition, it causes rashes in the genitals, swollen glands and an individual can have mild flu-like symptoms [1]. After the initial infection, syphilis becomes dormant in the human body and remains inactive for a long time before it gets activated again. However, early diagnostics of the infection can make treatments easier and more effective. One method of treating early syphilis infection is by taking injections of penicillin. In addition, syphilis can cause severe damages to the organs such as the heart, brain, and other organs. Syphilis is also passed down to unborn infants from their mothers who have syphilis infection [2]. Many unsuspected cases of syphilis are discovered by medical laboratory testings. Treponema pallidum is an invasive bacterium that causes syphilis infections [3], however, this bacteria cannot be cultured, and therefore, there is not an alternative test for it. One of the frequently used methods for laboratory diagnosis of syphilis is serological tests. In this essay, I will discuss the multiple serological and alternative tests that are used to diagnose syphilis infections, in addition to the limitations of these laboratory tests [4].

It is important to diagnose syphilis correctly with the appropriate laboratory tests with the reference to the patient’s history and his/her physical examinations. Since syphilis progresses through different stages, primary, secondary latent, and tertiary stages, it is best to diagnose it in primary and initial stages so it can be treated easily. However, there are problems that laboratorians face when diagnosing syphilis. These include asymptotic syphilis in early stages, neurosyphilis, HIV, and individuals who are co-infected with serologically cross-reacting agents [4]. One simple way to diagnose syphilis infections directly is to detect T pallidum using microscopic examination of fluids, wounds, ulcers, and histological examinations of tissues. Moreover, the indirect way includes the serological tests which fall into two classifications: nontreponemal tests for screening and treponemal tests for confirmation [4]. In the nontreponemal test, the immunoglobulins G and IgM (antiphospholipid antibodies) that are formed by the individual immune system in response to the release of lipoidal materials of the host cells because of syphilis infection are measured and tested [4]. In addition, this test also measures the lipids from the treponeme cell surface. Moreover, the treponemal test includes the use of T pallidum as an antigen. Moreover, serological tests check for the presence of treponemal antibodies, however, it does not tell us how severe the syphilis infection is or what the stage of the infection is. In addition, the late stages of syphilis can only be measured using serological tests [4].

Nontreponemal Serological tests include Centers for Disease Control and Prevention (CDC)-approved standard tests which are the VDRL slide test, the rapid plasma reagin (RPR) card test, the unheated serum reagin (USR) test, and the toluidine red unheated serum test (TRUST) [5]. In a VDRL test, a blood sample is taken from the patient, heated, and combined with a Non-treponemal antigen on a test slide to check if a reaction would occur under the microscope. If it is positive then, the immune system formed antibodies in-response to antigens produced by the host cell that was damaged by T pallidum [6]. However, a disadvantage of the VDRL test, is that antigens must be made fresh daily [4]. The USR test uses the same principles as the VDRL test, however, EDTA and choline chloride are added to eliminate the daily preparation of antigens and heat to enhance the reactivity of the antigens [7]. These tests are quantitative tests that allow for the evaluation of syphilis infection and response to the treatment period [4]. On the other side, treponemal serological tests are mainly used to confirm the reactivity in nontreponemal tests, it can also be used with patients that have nonreactive nontreponemal tests but have signs of syphilis infection in late stages [4]. These tests are more expensive and more difficult to perform. The most commonly used treponemal tests Fluorescent treponemal antibody absorption test. In this test, the blood sample is treated with absorbents to remove non-specific antibodies and uses antibodies that are specific to Treponema pallidum proteins. These tests are highly specific and sensitive but may produce different results due to different equipment and reagents [4].

To conclude, the use of nontreponemal and treponemal tests in combination to screen for syphilis has provided excellent results and accurate screening for all stages of syphilis. The only exception is in the very early infection stage that the treponemal test may not be positive yet.

References:

1- Parenthood, P. (n.d.). What Are the Symptoms & Signs of Syphilis? Retrieved January 09, 2021, from https://www.plannedparenthood.org/learn/stds-hiv-safer-sex/syphilis/what-are-the-symptoms-of-syphilis

2- Syphilis. (2019, September 19). Retrieved January 09, 2021, from https://www.mayoclinic.org/diseases-conditions/syphilis/symptoms-causes/syc-20351756

3- Radolf JD. Treponema. In: Baron S, editor. Medical Microbiology. 4th edition. Galveston (TX): University of Texas Medical Branch at Galveston; 1996. Chapter 36. Available from: https://www.ncbi.nlm.nih.gov/books/NBK7716/

4- Ratnam S. (2005). The laboratory diagnosis of syphilis. The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale, 16(1), 45–51. https://doi.org/10.1155/2005/597580

5-Larsen SA, Pope V, Johnson RE, Kennedy EJ Jr. A Manual of Tests for Syphilis. Washington DC: American Public Health Association, 1998.

6-Holm, G. (2018, September 29). VDRL Test: Purpose, Procedure, and Results. Retrieved January 09, 2021, from https://www.healthline.com/health/vdrl-test

7-Pettit, D. E., Larsen, S. A., Pope, V., Perryman, M. W., & Adams, M. R. (1982). Unheated serum reagin test as a quantitative test for syphilis. Journal of Clinical Microbiology, 15(2), 238-242.