microbiology and infectious diseases

Harvard referencing method Intext citation

Microbiology and Infectious
Diseases
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Contents
1. Infectious diseases and classification of the organism which causes each of them to their
correct domain, species and genus...............................................................................................3
2. Major issues for infection control in dealing with prion disease? What kinds of strategies are
possibly to reduce the risk of iatrogenic transmission?...............................................................4
3. Viral and bacterial infection that are significant within hospital setting and their preferred
habitats, means of survival and testing method and microbiological sampling required for
diagnosis......................................................................................................................................4
4. Implications of this knowledge about survival of bacteria on environmental surface and the
way organic matter presence prolong survival time for practice of infection control and
examples of protocols that could be influenced by it..................................................................5
5. Optimum method of collection and the way each specimen must be stored if there is delay
in transport and how long it takes to get a result for Viral swab, Urine, Blood culture and
Respiratory swab.........................................................................................................................6
6. Major components of each step of 'chain of infection' of S. aureus and rotavirus start with
the reservoir and proceeding in a clockwise direction and the intervention that will break this
chain.............................................................................................................................................7
7. A surgical patient, who has undergone an abdominal hysterectomy a few days before, has a
collection of pus just under the suture line, which is draining through the incision. A swab of
this exudate reveals +++ neutrophils (polymorphs) and +++ E. coli, +++ Bacteroides fragilis
and ++ Anaerobic streptococci. Is this infection endogenous or exogenous in origin? Give
reasons for your answer. How might this infection have been prevented?.................................8
8. Explain how the following organisms are transmitted, their incubation and infectious
periods and the infection control measures needed to prevent transmission...............................8
9. Recommendations and policies for AMS and AMR. What resources are available for
Infection Control practitioners?.................................................................................................11
REFERENCES..............................................................................................................................12
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1. Infectious diseases and classification of the organism which causes each of them to their
correct domain, species and genus
Name of the
infectious
disease
Organism which causes it Domain Genus Species
Pneumonia Streptococcus pneumoniae Bacteria Streptococcus S. pneumoniae
HIV/AIDS Human immunodeficiency
virus
Virus Lentivirus Human
Immunodeficiancy
Virus (HIV-1,
HIV-2)
Tuberculosis Mycobacterium tuberculosis Bacteria Mycobacterium M. tuberculosis
Malaria Plasmodium parasite Eukaryota Plasmodia P. falciparum
P. malariae
P. ovale
P. vivax
P. knowlesi
Diphtheria Corynebacterium
diphtheriae
Bacteria Corynebacteriaceae C. diphtheriae
Viral
hepatitis
Hepatitis A virus (HAV),
Hepatitis B virus (HBV),
Hepatitis C virus (HCV),
Hepatitis D virus (HDV)
and Hepatitis E virus (HEV)
Virus Hepatovirus (HAV)
Orthohepadnavirus
(HBV)
Hepatovirus A
Hepatitis B virus
Rubella
(German
measles)
Rubella virus Virus Rubivirus Rubella virus
Measles Measles morbillivirus Virus Morbillivirus Measles
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morbillivirus
Giardiasis Giardia Eukaryota Giardia Giardia lamblia
Chickenpox varicella-zoster virus Virus Varicellovirus Human
alphaherpesvirus
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2. Major issues for infection control in dealing with prion disease? What kinds of strategies are
possibly to reduce the risk of iatrogenic transmission?
In dealing with prion disease, the major issues for infection control includes its
transmission. The disease is not transmitted through droplet, direct contact and airborne spread.
The iatrogenic transmission of prion disease from individual to individual has resulted from
direct transplantation, inoculation or implantation of infectious materials either peripherally or
intracerebrally. It can be transmitted through samples acquired from people to non-human
primates. The peripheral routes of inoculation can be the way of transmission of disease, but
these routes need large doses than intracerebral inoculation. The abnormal prion protein
transmission through surgical instruments at the time of operations increases the risk. The issues
in infection control are related to blood products (Tsuji, and et. al., 2019). The exposure of
healthcare workers to high infectivity tissue by needle stick injuries with inoculation is the issue.
The risk of iatrogenic transmission can be reduced by adopting the strategies like disinfection
and sterilization along with quarantine procedures, taking standard precautions while caring for
patients, use of personal protective equipment like masks, gloves, gown etc. Apart from this,
sterilization guidelines must be followed by the healthcare practitioners and professionals.
3. Viral and bacterial infection that are significant within hospital setting and their preferred
habitats, means of survival and testing method and microbiological sampling required for
diagnosis
Bacterial infection: Tuberculosis
The infection is caused by mycobacterium tuberculosis bacteria which is the leading
cause of mortality worldwide. This disease is not very common in healthcare settings however,
can be spread by air from proximal contact to the person who is infected. The organisms of
tuberculosis are becoming resistant to antibiotics and antimicrobials. It is highly contagious
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disease which causes lung infection. The bacteria usually found in lungs and infects mononuclear
phagocytes. Human is the only known reservoir of bacteria and it survive within macrophages
for around 48 hours. The microbiological sampling in testing method needed for diagnosis
includes The microbiological sampling and testing method needed for diagnosis involves Culture
for AFB, Identification of AFB and Antimicrobial Susceptibility Testing tuberculin skin test
(TST) and IFN-γ release assays (de Cueto, and et. al., 2017).
Viral infection: Hepatitis B
It can cause chronic liver infections or acute infections. An acute infection exhibits
vomiting, jaundice and liver inflammation and some can turn in to chronic hepatitis B. This
causes lifelong infection, liver cancer, cirrhosis, liver failure and death. The virus spread through
the fluids of body of an infected individual being transmitted into non infected one. In healthcare
settings, the infection spread often through contaminated syringes, needles, surgical blades and
other sharps. The virus can survive for at least 7 days outside the body. Its incubation period is
75 days, but can be vary from 30 days to 180 days (Morel, and et. al., 2015). The microbiological
sampling in testing method needed for diagnosis includes HBsAg, HBsAg – confirmation test,
anti-HBs, anti-HBc, anti-HBc IgM, anti-HBe and HBeAg.
4. Implications of this knowledge about survival of bacteria on environmental surface and the
way organic matter presence prolong survival time for practice of infection control and
examples of protocols that could be influenced by it
The implications of knowledge about survival of bacteria on environmental surfaces and
the way the presence of organic matter can prolong survival time for practice of infection control
helps healthcare professionals in in controlling the infections effectively. This will help in
providing the patients with proper treatment and medications which will reduce or eliminate the
risk of infections. This will also help in controlling the risk of transmitting infections by
implementing appropriate interventions along with transmission based precautions and standard
precautions. The knowledge about bacteria survival will also help Health Care professionals in
taking decisions about antibiotic treatment by keeping in mind the microbiology results (Török,
Moran, and Cooke, 2016). For example: the previous versions of protocol replace by new
protocol and more emphasis is given on speedy containment, new annexes are developed on non-
pharmaceutical interventions, laboratory preparedness, ethical issues and communications. More
preference is given over hand hygiene, use of mask and gowns, use of standardized equipment
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and disinfectants etc. Some of the protocols are related to investigation and management of
outbreak of infectious diseases, exposure of emergency service workforce to infectious diseases,
Public Health on call system, reporting of infectious diseases. The protocol includes food safety
protocol 2018, operational approaches for food safety guidelines 2018 and infectious diseases
protocol 2018.
5. Optimum method of collection and the way each specimen must be stored if there is delay in
transport and how long it takes to get a result for Viral swab, Urine, Blood culture and
Respiratory swab
Blood culture: The specimen of blood is collected into heparin tube which is preservative
free for peripheral blood leukocytes. For serological test, the sample is collected into dry storage
container. If there is delay in transportation of a specimen, then the container of specimen is
refrigerating at 4 degrees centigrade or in melting ice. Generally, the freezing of sample is
avoided but if delay occurs then it is frozen at -70 degrees Celsius. In the blood culture, it takes
two to three days to see the bacteria, but sometimes it takes 10 days or more to show up (Persing,
and et. al., 2020).
Urine: The urine sample for culture is collected in the morning. A sterile, leak proof, dry
and wide necked screw capped container is provided to the patient to collect the specimen. The
sample is labelled and generally send to laboratory within 2 hours. But, if delay occurs the
specimen is refrigerating until dispatch or is keep on ice in insulated flask. In case, the delay is
longer, then 0.5 gram of borax is added in 20 ml of urine. It takes only few minutes to do urine
test or the results usually get in 1 to 3 days.
Respiratory swab and Viral swab: The specimen of respiratory swab is collected through
nose in which a sterile fine bore catheter is pass into the nostril of patient and then to upper
pharynx. After this, an intermittent suction is applied by placing thumb over the free arm end of
Y suction catheter. The intermittent suction is applied continuously while withdrawing the
catheter slowly and mucus is collected. Then the specimen is dispensed into sterile container and
deliver to laboratory (Sheitoyan-Pesant, and et. al., 2016). If there is delay in the transportation,
then the specimen is kept into minus 70 degree centigrade. The test may take about 24 hours.
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6. Major components of each step of 'chain of infection' of S. aureus and rotavirus start with the
reservoir and proceeding in a clockwise direction and the intervention that will break this
chain
S. aureus:
Steps of chain of infection Major components
The reservoir Environment, human nares and person to person
contact. It is found in nose, perineal area (males),
groin, axillae, mucous membranes, hair, mammary
glands, the mouth, and the intestinal, upper
respiratory and genitourinary tracts (Goldman, and
Green, 2015).
The portal of exit from the reservoir It spread into bloodstream and dispersed by
circulatory flow and infects surrounding tissues
The mode of transmission having direct contact with an infected person, by
utilizing a contaminated object, or through inhaling
infected droplets dispersed by coughing or sneezing.
The portal of entry into the ‘host’ respiratory tract, hair follicle, surgical wound
The susceptible host people with chronic conditions like vascular disease,
eczema, diabetes, lung disease, cancer and people
who inject drugs.
Infectious agent bacterium which is a member of Firmicutes
Intervention: antimicrobial treatments
Rotavirus:
Steps of chain of infection Major components
The reservoir Stool of infected humans and gastrointestinal tract
Portal of exit from reservoir Unwashed hands which are contaminated with poop
into mouth (Cowan, 2018).
The mode of transmission fecal–oral route
The portal of entry into ‘host’ It is often spread through fecal-oral route but, can
also be caused through drinking or eating
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contaminated water or food. It may live on surfaces
like toys, doorknobs and other hard objects for longer
time.
The susceptible host Children of age between 6 and 24 months
Infectious agent Double-stranded, non-enveloped RNA viruses which
are belonging to the family Reoviridae.
Intervention: Rotavirus vaccines
7. A surgical patient, who has undergone an abdominal hysterectomy a few days before, has a
collection of pus just under the suture line, which is draining through the incision. A swab
of this exudate reveals +++ neutrophils (polymorphs) and +++ E. coli, +++ Bacteroides
fragilis and ++ Anaerobic streptococci. Is this infection endogenous or exogenous in
origin? Give reasons for your answer. How might this infection have been prevented?
This infection is endogenous in origin as the exudate microorganisms within the organ
space or tissue hinder the postoperative curative procedures, and can lead to wound dehiscence,
superficial incisional infections and anastomotic leaks. This infection has been prevented through
Antimicrobial therapy and supportive care (Cox, 2020).
8. Explain how the following organisms are transmitted, their incubation and infectious periods
and the infection control measures needed to prevent transmission
Organisms Transmitted
through
Portal of
entry
Portal of
exit
Incubation
and
infectious
periods
Infection
control
measures
needed to
prevent
transmission
Staphylococcus
aureus
direct
contact with an
infected
person, infect
distant organs
and
respiratory
tract, hair
follicle,
surgical
wound
bloodstream
and dispersed
by
circulatory
flow and
infects
2 and 4
hours
Some
measures to
prevent this
infection
includes
Keeping
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bloodstream surrounding
tissues
hands clean
through
washing
them
thoroughly
with water
and soap,
avoid contact
with
bandages or
wounds of
other people
and not
sharing
personal
items like
clothing,
cosmetics or
towels.
Influenza droplets made
when
individuals
with influenza
cough, sneeze
or talk.
nose by
droplets from
an infected
individual
who sneezes
or coughs
respiratory
tract through
sneezing or
coughing by
infected
person
3 - 4 days The
measures to
prevent
influenza
includes
good hygiene
habits and
personal
health. The
hygiene
habits
include not
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touching
nose, eyes or
mouth,
covering
sneezing and
coughing,
frequent
hand wash
with alcohol
based hand
rub, water
and soap,
avoiding
close contact
with people
who are sick
and wearing
masks.
Measles coughing and
sneezing
mouth, nose,
or eyes
splatter of
body fluids
involving
coughing,
sneezing, and
saliva
10 – 12 days For
preventing
measles, an
individual
needs to
avoid work
for at least 4
to 5 days
when
initially
developed
measles rash
and avoid
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contact with
individuals
vulnerable to
infection like
pregnant
women and
young
children
when a
person is ill.
9. Recommendations and policies for AMS and AMR. What resources are available for Infection
Control practitioners?
AMS Policies: The AMS policies includes open, full and timely access to data; licences
about reuse of AMS journal content; data policy and guidelines for achieving and citing data
sets; AMS copyright policy; and open access for BAMS authors and AMS journals. It is
recommended to AMS that all the ethical guidelines and standards must be followed.
AMR (Antimicrobial resistance): The AMR policy is developed to direct the review of
national policies in order to better understand existing policies which address antimicrobial
resistance as well as revealed the gaps in policy. This policy state the objectives which a
government seeks to accomplish and sustain a decision made by organisations, government or
individuals which are oriented towards addressing the issue (Simner, Miller and Carroll, 2018).
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REFERENCES
Books and Journals
Tsuji, B.T., and et. al., 2019. International Consensus Guidelines for the Optimal Use of the
Polymyxins: Endorsed by the American College of Clinical Pharmacy (ACCP), European
Society of Clinical Microbiology and Infectious Diseases (ESCMID), Infectious Diseases
Society of America (IDSA), International Society for Anti‐infective Pharmacology
(ISAP), Society of Critical Care Medicine (SCCM), and Society of Infectious Diseases
Pharmacists (SIDP). Pharmacotherapy: The Journal of Human Pharmacology and Drug
Therapy, 39(1), pp.10-39.
de Cueto, M., and et. al., 2017. Executive summary of the diagnosis and treatment of urinary
tract infection: Guidelines of the Spanish Society of Clinical Microbiology and Infectious
Diseases (SEIMC). Enfermedades infecciosas y microbiologia clinica, 35(5), pp.314-320.
Morel, A.S., and et. al., 2015. Complementarity between targeted real-time specific PCR and
conventional broad-range 16S rDNA PCR in the syndrome-driven diagnosis of infectious
diseases. European Journal of Clinical Microbiology & Infectious Diseases, 34(3),
pp.561-570.
Török, E., Moran, E. and Cooke, F., 2016. Oxford handbook of infectious diseases and
microbiology. Oxford University Press.
Persing, D.H., and et. al., 2020. Molecular microbiology: diagnostic principles and practice.
John Wiley & Sons.
Sheitoyan-Pesant, C., and et. al., 2016. Clinical and healthcare burden of multiple recurrences of
Clostridium difficile infection. Clinical Infectious Diseases, 62(5), pp.574-580.
Goldman, E. and Green, L.H. eds., 2015. Practical handbook of microbiology. CRC press.
Cowan, M.K., 2018. Microbiology: a systems approach. McGraw-Hill.
Cox, R.A., 2020. Immunology of the fungal diseases. CRC Press.
Simner, P.J., Miller, S. and Carroll, K.C., 2018. Understanding the promises and hurdles of
metagenomic next-generation sequencing as a diagnostic tool for infectious
diseases. Clinical Infectious Diseases, 66(5), pp.778-788.
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