microbiology

1. Rosemary Mwifi
Given Sishekano

2.  Introduction
 Epidemiology
 Risk factors
 Microbiology of commonly implicated organisms
 Infection prevention and control measures
 Reducing Antimicrobial resistance
 Quiz
 References

3.  Hospital acquired infections (HAI) are also known as nosocomial infections.
• The word is derived from the Greek word nosokomeon meaning
hospital.
• Nosos = disease and
• komeo=to take care of.
 They are infections acquired by:
 patients in the hospital while they are receiving treatment for other
conditions
 or health workers in the health setting as they perform their duties.
 HAI appear 48 hours or more after hospital admission, in a previously
uninfected patient. Time is however relative depending on the infection.

4.  A prevalence study conducted under WHO in 55hospitals of 14 countries
in Europe, Eastern Mediterranean, South-east Asia and Western pacific
showed an average of 8.7% hospital patients had nosocomial infections.
 In South Africa, studies reflect an infection rate of nosocomial of 15% and
an associated attributable mortality rate of 5%.
 Nosocomial infections occur about 25% more in hospital patients in
developing countries than in developed countries.
 Developed countries are less likely to have more surgical wound/trauma
due to less invasive surgical practices. They however experience more
UTI’s.

5.  Some patients present with risk factors upon arrival.
 Patients are at risk when they are at extremes of age due to poor
immune defenses (very young or very old).
 Patients with underlying chronic conditions that compromise their
immune system; such as HIV, cancer, diabetes and renal failure.
 Patients with trauma, or from road accidents may have cuts or burns are
more susceptible as a result of skin breach.
 Medication such as immunosuppressive, cytotoxic agents as well as
steroids are known to put patients at risk of more infections.

6.  While in hospital, more risk factors can arise.
 Skin may be breached after surgery or subsequent wound care .
 The use of indwelling devices such as urinary catheters, endotracheal
tubes and other monitoring devices may be a route for entry of bacteria.
 Certain drug therapy may increase the risks. E.g. broad spectrum
antimicrobial agents, or unnecessary use of antibiotics in addition to fighting
infections also reduce normal flora and leave the patient exposed to other
infections.
 Blood transfusions or parenteral therapy.
 Hospital staff infected with transmissible illnesses.
 The use of sharps such as needles, and IV devices.

7.  The hands of health care workers are the highest risk factor especially in the
absence of gloves when carrying out patient care duties.
 White coats and other uniform. Student lab coats especially using the same coat
for dissection, lab work and hospital.
 The use of sharps, such as needles and IV needles.

8. SOURCES AND TRANSMISSION OF HAI
 Can be endogenous or exogenous.
 Contact; Colonisation or infection with multi-resistant organisms MRSA, Methicillin
Resistant Staphylococcus Aureus), etc
 Enteric diseases eg Human Rotavirus, Hepatitis A, Clostridium difficile
 Respiratory diseases, eg SARS, Bronchiolitis/RSV (also refer to Droplet Precautions)
 Skin infections
 Direct contact from the hands/body of health care staff. This is from caring from various
patients, and coming into contact with bodily fluids, catheters, administering medication or
manipulating IV sites. (especially the moist, warm area under the watch strap).
 Indirect contact from an object such as linen, doors,ward telephones or trolley handles.
 Improper use of gloves where health workers wear gloves continuously, offer cross
infection.
 Needles not disposed off properly are hazardous and may transmit blood borne viruses
such as HIV and Hepatitis.

9. SOURCES AND TRANSMISSION OF HAI
 Skin (both direct and indirect contact)
 Individuals may shed a lot of skin. Those with eczema or psoriasis are
particularly more prone to shed while their skins are heavily colonised
with Staphylococci.
 Vehicles of transmission
 Food-borne transmission of gastrointestinal pathogens is rare unless
kitchen hygiene is compromised.
 Waterborne transmission occurs more as a result of birthing pools,
hydrotherapy pools, air conditions, endoscopy washers disinfectants.
These may be associated with environmental mycobacteria,
environmental Gram negative bacilli as well as Legionella species.

10. SOURCES AND TRANSMISSION OF HAI
 Iatrogenic
 Contaminated drugs for administration
 Blood for transfusion
 Environmental
 Overcrowding
 Cleaning practices that are not adequate, appropriate, regular or not
using appropriate chemicals.
 Sterilization of objects that is inadequate.

11. SOURCES AND TRANSMISSION OF HAI
 Droplets
 Large droplets are larger than 5micrometers in size and fall onto surfaces
within a 1-metre radius. Generated by coughing, sneezing, talking or from
procedures such as bronchoscopy or suctioning. They are propelled into
the air and may land on nasal mucosa or conjuctival mucosa.
 Nasal secretions may contaminate health workers hands if they are ill,
contaminating everything they touch from then on.
 These include Bronchiolitis, Meningococcal infections
 Viral infections including influenza, mumps and rubella
 Small droplets are less than 5micrometers in diameter and are responsible
for airborne transmission. These pathogens such as chicken pox virus,
respiratory virus and Mycobacterium tuberculosis remain suspended in the
air for long periods of time.

12. Contact precautions
• Contact Precautions are
undertaken to reduce the
risk of transmission of
pathogenic micro-
organisms by direct or
indirect contact. Contact
transmission can occur
from:
• Skin to skin contact
• A contaminated piece of
equipment
• The client’s environment
• Examples of pathogens
transmitted by this mode
include:
• Deleted this by accident,
please re-add these
organisms here?
Airborne precautions
• Airborne Precautions are
taken to reduce the risk of
transmission of pathogenic
micro-organisms through
airborne particles. Airborne
particles are smaller than
droplet (less than 5 um)
and remain suspended in
the air for long periods of
time. They are transmitted
when susceptible people
inhale contaminated air.
• Examples of conditions
transmitted by airborne
particles include:
• Pulmonary Tuberculosis
• Measles
• Varicella
• Severe Acute Respiratory
Syndrome (SARS).
Droplet infections
• Unlike air borne particles
that remain suspended in
the air for extended
periods, droplets are larger
than 5um in size and fall
onto surfaces within a 1-
metre radius.
• Examples of conditions
transmitted through
droplets include:
• Bronchiolitis
• Meningococcal infections
• Viral infections including
influenza, mumps and
rubella.

13. Skin precautions
• As per Contact
Precautions scabies can
be transmitted from skin
to skin or from
contaminated client
environment or equipment
to susceptible people.
Due to the copious
amounts of skin shedding
and large number of mites
present on the client and
their surrounding
environment extra
precautions are required.
• This category of
precautions is exclusive
to:
• Crusted (formally called
Norwegian Scabies)
scabies.

14.  Urinary tract Infections (80%)
 Esterichia coli
 Ventilator associated Pneumonia (3%)
 Acetinobacter, Kleibsella, Staphylococcus
 Surgical site infections (0.5 to 15%)
 Pseudomonas,
 Coagulase negative Staphylococci
 Bloodstream infections; Staphylococcus
 Gastroenteritis; Clostridium defficile
 Rotavirus

15.  Methicillin Resistant Staphylococcus aureus
 Vancomycin resistant Enterococci
 ESBL producing organisms
 Legionella
 Viruses
 Fungi: Candida albicans, Aspergillus

16.  Methicillin Resistant S.
aureus(MRSA)
 One of the most important Nosocomial
pathogens worldwide.
 It is resistant to methicillin and other
members of the penicillinase-resistant
penicillins
 This is because it possesses a penicillin-
binding protein 2a that has reduced
affinity for binding to beta-lactam agents.
 This protein is encoded by the mec A
gene, which is carried by a large mobile
element referred to as staphylococcal
chromosome cassette(SCC) mec.
 These are occasionally sensitive only to
Vancomycin and Teicoplan
 Vancomycin Intermediate
Resistant S. aureus(VISA)
 Resistance may occur due to prolonged
exposure to vancomycin, renal failure
requiring dialysis, invasive intravascular
devices, and prior infection with MRSA.
 Resistance mechanism has yet to be
clarified. Cell wall thickening has however
been identified as a common feature of
VISA. Experiments have shown that
resistance may be caused by clogging of
the thickened cell wall with vancomycin.
 VISA remain susceptible to tetracyclines,
Linezolid, Tigecycline and TMP/SMX

17.  They are gram positive cocci, they mediate virulence by producing
slime or glycocalyx to form a biofilm on intravascular catheters and
prostheses.
 Bacteria embedded in biofilm can cause serious systemic infections
and are difficult to treat as most antibiotics are unable to penetrate or
eradicate biofilms.
 Multi-drug resistant strains are fast becoming major hospital pathogens.
 Common resistance to quinolones, cephalosporins and vancomycin.

18.  Enterococci are gram positive cocci, seen in pairs of short chains.
 Forms part of the normal flora of the human intestines and female
genital tract and are often found.
 May cause infections, particularly in hospitalized and debilitated
individuals.
 Enterococci are intrinsically resistant to many antibiotics.
 In treatment, combinations of a cell wall active agent and an
aminoglycoside is necessary for effective treatment.
 Vancomycin or Teicoplanin is a glycopeptide that is often used to treat
infections caused by enterococci.

19.  VREs are resistant to vancomycin, infections with VREs occur most
commonly in hospitals.
 This resistance is transferable, through mobile genetic elements
carrying the van A(high level resistance) or van B(low level resistance)
genes.
 The potential mergence of vancomycin resistance in methicillin
resistant staphylococcus or S. epidermis is a great threat.

20.  Acinebacter and pseudomonas are gram negative rods, commonly found in
soil and water.
 Acinebacter can also be found on skin of healthy people, especially
healthcare personnel.
 A. baumannii accounts for about 80% of all reported Acinebacter infections.
 Infection with Pseudomonas and Acinebacter rarely occurs outside of
healthcare settings.
 Outbreaks typically occur in intensive care units and units that care for
seriously ill and debilitated individuals.
 These two are resistant to most commonly prescribed antibiotics.
 Decision on treatment should be made on a case-to-case basis after culture
and susceptibility results are available.

21.  Extended-spectrum beta-lactamases (ESBL) are enzymes that confer
resistance to most beta-lactam antibiotics, including penicillins,
cephalosporins, and the monobactam aztreonam. Infections with ESBL-
producing organisms have been associated with poor outcomes.
 Multi-drug resistant extended spectrum beta-lactamases are emerging
as important nosocomial pathogens.
 Klebsiella spp and more recently E. coli are the most commonly
implicated organisms harbouring a variety of ESBL genotypes.
 Several outbreaks of ESBL producing organisms has been reported
worldwide.
 Organisms producing ESBLs are able to hydrolyse the third generation
cephalosporins

22.  Through the production of different enzymes(TEM or SHV) coded for by
different gene types.
 More recently, CTX-M type ESBLs have been detected which
preferentially hydrolises cefotaxime, although mutation can confer
ceftazidime resistance activity.(these enzymes are sometimes referred
to as cefotaximases.
 The range of drugs used to treat ESBL producing organisms is
restricted to the carbapenems.

23.  It is a gram positive, rod shaped, sporeforming opportunistic pathogen.
 Does not normally cause infection unless the normal intestinal flora is
altered.
 These alterations, most commonly due to antibiotic therapy, decrease
the number of other colonising intestinal flora.
 Most commonly associated antibiotics include; amoxicillin,
cephalosporins, and clindamycin, though virtualy any antibiotic can be
associated with C. defficile infection.
 The severe diarrhoea and the lesions seen are due to and enterotoxin.
 This enterotoxin has two components, toxin A which causes
accumulation of fluid in the bowel lumen, toxin B which is cytotoxic and
is thought to be primarily responsible for ulceration of the bowel wall.

24.  Legionnaires' disease (LD) can be nosocomial, community acquired or travel related.
 The source of Legionella infection is potable water systems that become colonized by
the microorganism (water heaters etc.).
 Prevention studies involved mainly hospital water systems.
 Different strategies have been suggested but none are fully successful: engineering
modifications, heating of water to temperatures above 59°C, heating and flushing the
plumbing with hot water (80°C), water chlorination, silver-copper ionization of the
water, UV-light disinfection of water, instant heating in order to avoid hot-water tanks
and others.
 It can cause two different forms of disease in humans:
 Legionnaire’s Disease, (incubation period: 2-10 days, multisystem illness that involves the
lungs, causing pneumonia, and can cause neurological symptoms, diarrhea and has a high
mortality rate (up to 50%), and
 Pontiac fever, with a shorter incubation period of 1-2 days, which is an acute, self-limited,
influenza-like disease that does not cause pneumonia.

25.  Viruses have a long incubation period.
 Disease may not easily be linked to hospitalisation, unless if
surveillance is conducted using epidemiological methods.
 Viruses may cause both respiratory and GI disease including SARS
and diarrhoea(commonly caused by Rotavirus in children)
 Other diseases include measles, chicken pox etc. theses may require
isolation of patients to avoid transmission to other patients.
 Viruses such as Hep B and C, respiratory syncytial virus, CMG, HIV,
HSV, VZV may be transmitted

26.  Aspergillus spp.
 Invasive aspergillosis has become a devastating opportunistic fungal
infection among the immunocompromised hosts.
 Commonly caused by Aspergillus fumigatus
 Can infect the lungs and other organs.
 Building dust is common source, hospital wards close to building sites
should ensure the air is passed through special air handling units
before admitting vulnerable patients.
 Invasive aspergillosis commonly manifests as a lung infection and is
almost always fatal

27.  Candida albicans is an opportunistic fungal pathogen that is responsible for
candidiasis in human hosts.
 C. albicans grow in several different morphological forms, ranging from unicellular
budding yeast to true hyphae
 Typically, C. albicans live as harmless commensals in the gastrointestinal and
genitourinary tract and are found in over 70% of the population.
 Overgrowth of these organisms, however, will lead to disease, and it usually occurs in
immunocompromised individuals, such as HIV-infected victims, transplant recipients,
chemotherapy patients, and low birth-weight babies.

28.  Measures practiced by health care personnel to prevent spread,
transmission and acquisition of infection between clients, from health
care providers to clients and from clients to health care providers.
 Infection control measures are based on how an infectious agent is
transmitted, they include:
 The standard and
 Additional precautions.

29.  Specific precautions designed to prevent harmful bacteria and viruses
from infecting people who are providing first aid or health care.
 They are a set of practices designed to prevent the transmission of HIV,
Hepatitis B and other blood borne pathogens (bacteria and viruses).
 Under SP, blood and other body fluids of all patients are considered
potentially infectious.

30.  Hand hygiene
 Personal protective equipment(PPE)
 Immunization
 Environmental sanitation
 Waste management
 Sharps management
 Decontamination

31. Hand hygiene
• The most important
of the infection
prevention and
control strategies
• Cost-effective and
practical measure to
reduce the
incidence of
healthcare-
associated infection
and the spread of
antimicrobial
resistance across all
settings. However,
PPEs
• Specialized clothing
or equipment worn
by an employee for
protection against
infectious materials
• These include:
• Gloves
• Aprons
• Whitecoats
• Gowns
• Protective eyewear
• Face shields
• Masks
Immunization
• Immunization of
health care workers
against infections
like Hep B virus is
one of the most
importatant way
infections are
prevented from
patients to Health
care workers.

32. Waste + Sharps
management
• Proper handling and
disposal of needles.
• Taking precautions to
prevent injury from
scalpels, needles, and
other sharp instruments.
• Place waste in a bag and
tie it.
• Place in second bag and
tie again (double bag
technique)
• Place all sharps (used
needles) in sharps
container.
• Wash hands after
removing gloves.
Decontamination
• Reprocessing of
reusable medical
equipment and
instruments
• Keeping aseptic
non-touch
technique asceptic.
Environmental
sanitation
• Routine
environmental
cleaning

33.  Additional Precautions refer to IPAC interventions (e.g., PPE,
accommodation, additional environmental cleaning) to be used in
addition to Routine Practices to protect staff and patients/residents by
interrupting transmission of suspected or identified infectious agents.
they are based on the mode of transmission (e.g., direct or indirect
contact, airborne or droplet). There are three categories of Additional
Precautions:
 Contact Precautions
 Droplet Precautions
 Airborne Precautions

34.  Two methods arused:
 1. Disc diffusion method(Kirby-baur test)
 Commonly used agar: Mueller Hinton agar
2. Broth dilution method

35. Antimicrobial
Stewardship team
1. Leadership
commitment:
Dedicate
necessary human,
financial, and IT
resources
2. Accountability:
Appoint a single
leader responsible
for program
outcomes.
3. Drug expertise:
Appoint a single
pharmacist leader
to support
improved
prescribing.
4. Action: Take at
least one
prescribing
improvement
action
5. Tracking:
Monitor prescribing
and antibiotic
resistance
patterns.

36.  Nosocomial infections are widespread.
 They are important contributors to morbidity and mortality
 They are becoming even more important as a public health problem
with increasing economic and human impact because of:
 Increasing numbers and overcrowding of people
 New microorganisms Increasing bacterial resistance to antibiotics
 Prevention is better than control
 Antimicrobial resistance raises a new threat against humanity.
 Proper measures need to be put in place in order to win the war against
anti microbial resistance.

37.  1. _________ and _________ are the most common causes of infection in hospitals
A. Bacterial and fungal
B. Staphylococci and E.coli
C. Staphylococci and P.aeruginosa
D. E.coli and P.aeroginosa
 2. ______________ is the most commonly acquired hospital infection.
A. Surgical wound infection
B. Urinary tract infection
C. Respiratory tract infection
D. Infectious diarrhea

38. 3. Standard precautions do not include:
A. Washing handas before and after patient contact
B. Appropriate handling of contaminated clinical waste
C. Use of asceptic technique
D. Use of gloves and gowns at all times
4. Which mode of transmission does not require the use of additional precautions
A. Airborne transmission
B. Bloodborne transmission
C. Droplet transmission
D. Contact transmission

39.  Shetty, N. Tang,J.W. Andrews, J. (2009). Infectious diseases. Oxford, UK: Blackwell
publishing.
 Duse, A. (2005). Infection control in developing countries with particular emphasis on
South Africa. The Southern African journal of epidemiology and infection, Volume
20(2), 37-41.
 Brink, A. Feldman, C. Duse, A. et al. (2006). Guideline for the management of
nosocomial infections in South Africa . The Southern African journal of epidemiology
and infection, Volume 21(4), 152-160.
 WHO(2002). Prevention of hospital-acquired infections, a practical guide(2nd edition)
 Yatin Mehta, Abhinav Gupta, Subhash Todi, SN Myatra, D. P. Samaddar, Vijaya Patil,
Pradip Kumar Bhattacharya, and Suresh Ramasubban(2014). Guidelines for
prevention of hospital acquired infections. Indian J Crit Care Med. 2014 Mar; 18(3):
149–163.