The Role of the Microbiology Laboratory

Chapter 7
The Role of the Microbiology
Laboratory
Smilja Kalenic

Key Points

 Microbes are infectious agents that are not visible to the naked eye; they are widespread in nature.
Some cause human diseases. They are divided into bacteria, fungi, viruses, prions, and protozoa.
Macroscopic parasites are also included.
 Diagnosis of infection by the microbiology laboratory has two important functions: clinical and epi-
demiological.
 An important innovation in microbiological diagnostics is development of point-of-care tests. This
can help overcome the issue of scarce microbiology laboratories in developing countries.
 The microbiology laboratory is an essential part of effective infection prevention and control (IPC).
The microbiology laboratory should be able to determine the most frequent microbes causing
healthcare-associated infections, and perform at least some basic typing of microorganisms for epi-
demiologic evaluations.
 The microbiology laboratory should produce routine reports for IPC personnel to develop incidence
graphs for specific pathogens, antibiotic resistance, wards, and groups of patients.
 Microbiologists, understanding the role of normal colonising flora of humans, the pathogenesis of infec-
tions, and the characteristics of specific pathogens, can interpret microbiological findings for IPC per-
sonnel.

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Basics of microbiology

Microbes are living organisms that are not visible to the naked eye. They are divided into bacteria, fungi,
viruses, prions, and protozoa. Macroscopic parasites are also included in the group. Microbes are ubiqui-
tous in nature, living as free organisms in the environment or on/in plants, animals, and humans, either
as normal flora (not causing harming) or as pathogenic microbes (causing diseases). While some microbes
are confined to only one host, most microbes can live on/in a wide array of hosts in nature. Plant mi-
crobes do not cause disease in humans, however some animal microbes can cause disease in humans (so
called zoonotic diseases).

When a microbe encounters a new host and begins to multiply, this phenomenon is usually called coloni-
sation. The microbe can remain in balance with the host and no disease will develop. However, if the mi-
crobe causes harm and disease, the disease is called an infectious disease (infection). Microbes that usu-
ally cause disease in a susceptible host are called primary pathogenic microbes. Microbes that live as nor-
mal flora of humans or live in the environment and do not cause disease in an otherwise healthy host are
called opportunistic pathogens (can cause disease in an immunocompromised host). When we encounter
unusual microbes on skin or non-living surfaces/items, it is called contamination.

Infection can be asymptomatic or symptomatic. During asymptomatic infections, as well as during the
incubation period in symptomatic infections, microbes can be shed from an infected host; the host is in-
fectious but may not realise it. After an infection, microbes can be present for some time in the host and
can be further released, although the person is clinically completely healthy. This state is referred to as a
“carrier state” and such persons are called “carriers”.

If infection is caused by microbes that are part of normal flora, we call it endogenous infection; exoge-
nous infection is an infection caused by microbes that are not part of the normal flora of that person.
Microbes are transmitted from one host to another by a number of pathways: through air, water, food,
live vectors, such as mosquitos, indirect contact with contaminated items or surfaces, or direct contact of
different hosts, including hands of healthcare workers (HCW).

To cause an infectious disease, a microbe first must enter the human body (portal of entry), either
through respiratory, gastrointestinal, or genitourinary tracts, or through damaged or even intact skin.
The microbe usually multiplies at the site of entry, then enters through mucous membranes to tissue and
sometimes to blood. When in the bloodstream, the microbe can spread throughout the body and enter
any susceptible organ. After multiplication, microbes usually leave the body (portal of exit) either through
respiratory, gastrointestinal, or genitourinary discharges and seeks a new host. Some microbes are trans-
mitted with the help of insect vectors that feed on human blood. Knowing the path of disease develop-
ment is essential for a clinical diagnosis. It is also important for timing and ordering the right specimen for
microbiological diagnosis, as well as for using the correct measures to prevent spread of microbes. Recog-
nition of who might get sick from a certain microbe (susceptible host) also helps with the prevention of
disease transmission.

Bacteria
Bacteria are the smallest unicellular organisms with all functions of a living organism. They multiply by
simple division from one mother cell to two daughter cells. When multiplying on a nutritious solid surface
in the laboratory, after some time, they form so called “colonies” that are visible to the naked eye, repre-
senting offspring of the same bacteria.

The genetic material (deoxyribonucleic acid or DNA) is situated in one circular chromosome and several

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independent units called plasmids. The chromosome is haploid (only one DNA chain) so every variation
can be easily expressed phenotypically. Genetic material is transferred vertically and horizontally be-
tween different bacteria. This has important consequences, especially when antibiotic resistance genes
are transferred.

Most bacteria are very easily adaptable to any kind of environment. All pathogenic and most opportunis-
tic bacteria have many virulence factors that are important in the development of infectious diseases.
Some bacteria can sporulate ‘form spores’ – the most resistant form of life we know – if the conditions
for the vegetative form is detrimental. When conditions are again favourable, the vegetative forms devel-
op from the spore.

Table 7.1 outlines the main groups of pathogenic and opportunistic bacteria that can cause healthcare
associated infections (HAI) with their usual habitat, survival in the environment, mode of transmission,
infections they cause, and main HAI prevention methods.

Fungi
Fungi are unicellular (yeasts) or multicellular (moulds) microorganisms that are widespread in nature.
Their cell is so-called “eucaryotic”, meaning they have DNA packed in the nucleus, as any other biological
cell in plants and animals. Their chromosome is diploid, so the variations in genome will not be as easily
expressed phenotypically as in bacteria. Some species of yeast are part of the normal flora in humans,
while moulds are usually living free in nature. Yeasts multiply by budding a new cell from the mother cell
(blastoconidia), while moulds multiply asexually (conidia) and sexually (spores).

It is important to remember that fungal spores are not as resistant as bacterial spores. Growth on a solid
surface will lead to the formation of a colony as for bacteria. Some pathogenic fungi can live as yeast (in
the host) and as a mould form (in the environment) so they are called dimorphic fungi.

Table 7.2 outlines the main groups of fungi that can cause HAI with their usual habitat, survival in the
environment, mode of transmission, infections they cause, and main HAI prevention methods.

Viruses
Viruses are the smallest particles – not cells – capable of reproducing themselves in living cells, either
bacterial, plant, or animal cells. Outside a living cell viruses can survive, however they cannot multiply.
They consist of one kind of nucleic acid (NA), either DNA or ribonucleic acid (RNA), and a protein coat
that protects the NA. Some viruses also have a lipid envelope outside the protein coat, referred to as
enveloped viruses; others do not have a lipid envelope (non-enveloped viruses).

A virus enters the host cell and the viral NA then takes over the host cell to synthesise viral proteins and
NA. It assembles these into a new virus and exits the host cell to enter other host cells. During this pro-
cess, host cells are damaged or even destroyed and signs and symptoms of infectious disease appear;
infection can be asymptomatic in a portion of the infected population. Some viruses can incorporate
their DNA into the host DNA, or can live in some host cells causing no harm – these are called latent in-
fections that can become overt in some circumstances, depending on the virus.

Table 7.3 outlines the main groups of viruses that can cause HAI with their usual habitat, survival in the
environment, mode of transmission, infections they cause, and main HAI prevention methods.

Prions
Prions are protein particles that do not contain any NA (neither DNA nor RNA). They are known to be
connected with some neurological diseases (Creutzfeldt-Jakob disease – familial spongiform encephalo-
pathy; variant Creutzfeldt-Jakob disease – bovine spongiform encephalopathy, and some other diseases).

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Prions are highly resistant to the usual methods of disinfection and even sterilisation. There is a possibil-
ity of iatrogenic transmission of these diseases through transplantation or contamination of instruments
with brain tissue, dura mater, cerebrospinal fluid, or blood of a diseased person. Prion diseases are not
transmitted from diseased to healthy persons by contact; transmission to a HCW has never been de-
scribed.

Parasites
Parasites are either 1) microscopic protozoa, i.e., unicellular microorganisms with eucaryotic diploid nu-
cleus that can live free in nature and/or live in some animal host including humans, some of them causing
infections or 2) they are macroscopic organisms, such as helminths (worms) (endo-parasites) or lice (exo-
parasites) that can cause infections – known also as infestations.

Although many parasites are widespread in the world and cause some of the most important community-
acquired infections (malaria, ascariasis, etc), not many parasites cause HAIs. Table 7.4 outlines the main
groups of parasites that can cause HAI with their usual habitat, survival in the environment, mode of
transmission, infections they cause, and main HAI prevention methods.

Arthropods
Arthropods are a large and very diverse group of animals. They comprise insects, ticks, mites, and some
other groups. Arthropods are very important as vectors of microbes (viruses, bacteria, protozoa, and hel-
minths) both between humans and between animals and humans. Some of them can also cause a disease
in humans called ectoparasitoses, as they only cause skin disease; these arthropods include Sarcoptes
scabiei (scab-mite) causing scabies and human lice causing pediculosis.

Scabies is a highly contagious skin disease that can be spread rapidly in a health care institution unless
very vigorous containment measures are instituted. The habitat of the scab-mite is only human skin;
however it can survive in clothing and bedding for several days. The primary method of transmission in
health care settings is by direct contact with the skin of an infested person; however transmission
through clothing and bedding can also occur. The primary preventive measure is use of Contact Precau-
tions (isolation/cohorting) in addition to simultaneous specific treatment of all cases and exposed per-
sons in a ward. Environmental cleaning and disinfection and processing of clothing and bedding as infec-
tious items are also necessary.

Another arthropod that can be transmitted in a health care institution is the louse. There are three types
of human lice: head, pubic, and body. Head and pubic lice live on hair and body lice live on clothing (only
contacting the body during feeding). Human lice survive a short time in the environment (<3 days for a
body louse). Lice are transmitted from person to person by close contact, therefore preventive measures
include Contact Precautions, bathing of patients, processing clothing and bedding as infectious items, and
specific treatment for head and pubic pediculosis. Generally only head lice are important in health care
institutions, specifically in paediatric wards.

Many arthropods can bite humans and provoke an allergic reaction to the bite. In the past decades one of
them, the bed bug (Cimex lectularius), has resurged in the developed world, including healthcare facili-
ties. Bed bugs do not live on humans, they live in the environment. However, it feeds on human blood;
this leads to an allergic reaction on the skin. As bed bugs do not live on humans, the primary prevention
method is good hygiene and pest control, including vacuuming, heat or cold treatment of the environ-
ment, trapping devices, and pesticides.

The role of the microbiology laboratory

The isolation and characterisation of microorganisms causing infections performed by the microbiology
laboratory has two important functions. The first is clinical - everyday management of infections. The
second is epidemiological - knowledge of an infective microbe in a patient can lead to finding its source

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and route of transmission. This allows staff to stop infections from spreading. Furthermore, the microbi-
ology laboratory interprets microbiology data for clinicians and for IPC professionals, thus participating in
HCW education. The microbiology laboratory also participates in the development of an institution’s anti-
biotic policy.

Clinical role
Some infections must be quickly diagnosed clinically and treated empirically without knowledge of the
causative microorganism or determination of antibiotic susceptibility (e.g., acute meningitis, sepsis, or
severe pneumonia). However, if there is a clinical suspicion of infection, laboratory tests may confirm the
diagnosis. Most HAIs are caused by bacteria and fungi that can be more antibiotic resistant than commu-
nity-acquired pathogens or their susceptibility to antibiotics is less predictable. Etiological diagnosis of
HAIs is therefore exceptionally important for targeted antimicrobial chemotherapy.

The microbiology laboratory is becoming more important in clinical medicine and in the prevention of
HAIs, especially as new or antibiotic-resistant pathogens emerge and new diagnostic technologies are
developed. The microbiology laboratory should be able to diagnose the most common infectious agents,
especially those causing HAIs. The laboratory should also be able to determine susceptibility to antibiotics
for bacteria and fungi (See Tables 7.1.-7.4.). Targeted antimicrobial therapy will lead to better patient
outcomes, and as eradication of a pathogen is achieved earlier, the danger of transmission to other pa-
tients will be decreased.

The right specimens from appropriate sites must be taken using proper techniques (See Tables 7.1.-7.4.).
The microbiology laboratory staff can assist in ensuring good specimens by educating other staff in proper
collection techniques. Identification of the microorganism and its antibiotic susceptibility should be as
precise as possible (identification to the species level).

Microbiological diagnostic methods can be divided into two types:

1. Direct methods (smear from specimens, isolation of infectious agents on culture media, or
proof of microbial antigens or nucleic acids in the specimen).
2. Indirect methods – proof of immune response to the infectious agents (serology).

Indirect methods are usually used for diagnosis of difficult to isolate bacteria and most viruses. It has to
be recognised that serologic testing is the confirmation of a diagnosis, not the diagnosis itself. For many
microorganisms antibodies take several days to develop, in many cases at least 10-14 days. Serology is
mostly considered an epidemiological method, with the clear exception of some viral diseases where it is
possible to make a diagnosis of an acute infection based on immunoglobulin class M (IgM), or avidity of
class G (IgG), or a combination of antibodies to different viral antigens.

An important new technology in microbiology is molecular diagnostics. Diagnosis can be rapid as it is not
dependent on waiting for microbial growth in cultures. These tests are sensitive, as they are based on
detection of only a few microorganisms; and they are specific, detecting microbe-specific genes.

Infection control role

The microbiology laboratory is an essential part of an effective IPC program and has many roles in the
control of HAIs: outbreak management, performing additional tests for epidemiologic studies, bacterial
and fungal typing, HAI surveillance, and reports about new alert microbes or unusual resistance. All these
functions enable the microbiological laboratory to educate not only clinical but also IPC personnel about
microorganisms and their role in infection and specifically in HAI. Furthermore, daily communication be-
tween laboratory staff and the Infection Control Team (ICT) is vital, allowing for timely and rapid infor-
mation sharing about causative agents of HAIs. The clinical microbiologist should ideally be a member of
the Infection Control and Antibiotic Stewardship Committees and a member of the ICT.

Additional tests during outbreak investigation

Sometimes the ICT requires additional data to clarify endemic or epidemic situations. Microbiological

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tests of blood products, environmental surfaces, disinfectants and antiseptics, air, water, hands of per-
sonnel, anterior nares of personnel, etc., may be required. During an outbreak or in endemic situations
when the causative agent is known, the microbiology laboratory may be able to use selective media for
the agent in question to minimise expense and increase the sensitivity of the cultures.

To determine the cause of a single-source outbreak, the causative microorganism must be defined. A mi-
crobial species may contain subspecies and variants that differ in particular characteristics. For example,
individual bacteria from the same species can differ as much as 30% in their genomes. Genetic differences
are often phenotypically expressed; however this is not a rule.

Typing of bacteria and fungi

Microorganism typing determines whether two epidemiologically connected strains are really related or
whether they differ from strains that are not epidemiologically connected. If strains are unrelated, the
patients do not belong to the same outbreak. If strains are related, it is impossible to state that the pa-
tients are involved in an outbreak without epidemiological analysis. Therefore, epidemiology and typing
are complementary. Typing methods differ in several important points:
1. Typability, i.e., the method can type most or even all strains of the same species;
2. Discriminatory power, i.e., the method can differentiate well between different types;
3. Inter-laboratory and intra-laboratory reproducibility, i.e., the method can provide the same
typing results in repeated testing by different sites or in different times;
4. The method should be simple, unambiguous to interpret, and inexpensive.

There are two groups of typing methods: phenotyping and genotyping.

Phenotyping
Using phenotyping methods we can determine physical characteristics that can distinguish different
strains of the same species. These methods may be based on antigenic structure (serotyping), physiologic
properties/metabolic reactions (biotyping), susceptibility to antimicrobial agents (sensitivity testing), and
colicines (colicino-typing) or bacteriophages (phage typing).

Phenotyping methods are well standardised with high reproducibility. Discriminatory power is not always
high if only a few types exist; however it can be very high if many types exist. These tests are simple and
unambiguous to interpret. Many are inexpensive enough to be performed in every microbiology labora-
tory.

The main objection to phenotyping of bacteria is that bacterial genes are not always expressed. Two phe-
notypically different strains can actually have the same genetic background or two phenotypically identi-
cal strains can actually differ genetically. Sometimes the emergence of a particular phenotype is specific
enough to explain an outbreak. However, if a phenotype is widespread and frequent, genotyping will be
required for outbreak management.

Genotyping
Molecular techniques have revolutionised the potential of the microbiology laboratory because they have
very high typability and discriminatory power. Genotyping can demonstrate definitively the relatedness
or difference between two isolates of the same species. However, genotyping methods require sophisti-
cated and expensive equipment and materials with trained staff. Furthermore, some techniques have a
low reproducibility, especially in inter-laboratory comparisons. Result interpretation is not always simple
or unambiguous.

Role in the surveillance of HAIs

The microbiology laboratory should produce routine periodic reports of isolates to allow the ICT to devel-
op incidence graphs for specific pathogens, wards, and groups of patients. These data can be made avail-
able immediately if the laboratory is computerised. A ‘baseline incidence’ can be established and any new
isolates can then be compared with this incidence. Graphs enable the ICT to discover the beginning of an

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outbreak earlier than it can be discovered clinically. Periodic reports are also important because they
demonstrate trends of specific pathogens and can be very useful in planning preventive measures.

Alert organism reports

The early isolation of a new or unusual microorganism, without any further typing, enables the ICT to
take appropriate measures to stop it from spreading. The ICT should identify, together with laboratory
personnel, possible ‘alert’ microorganisms, such as multi-resistant or highly pathogenic microorganisms
(e.g., methicillin resistant Staphylococcus aureus (MRSA), vancomycin intermediate Staphylococcus aure-
us (VISA), vancomycin resistant enterococci (VRE), multidrug resistant (MDR) P.aeruginosa, MDR
A.baumannii, MDR M.tuberculosis, C.difficile, extended spectrum beta-lactamase (ESBL) Enterobacteria,
carbapenem-resistant Enterobacteria (CRE), E.coli 0127, Legionella spp, penicillin resistant (PR) Strepto-
coccus pneumoniae, etc.). Any new isolates should be reported immediately to the wards and the ICT.
Alert organism surveillance may be all that can be performed if the facility is understaffed. In addition,
laboratory staff may report clustering of infections (two related isolates in different patients in the same
time frame).

Interpreting Microbiology Data

Microbiologists are required to interpret microbiological data (e.g., results of isolation, identification, sus-
ceptibility tests, serology, and typing). To interpret microbiological data for infection in an individual pa-
tient, one should first determine if the specimen was correct. The next step is to take into account if the
isolated or otherwise proven microorganism is a primary or an opportunistic pathogen. Another factor is
the clinical suspicion or working diagnosis. Lastly, understand the actual immune status of the patient at
the time of specimen collection.

It is relatively easy to interpret the results of so-called primary sterile specimens (e.g., blood, cerebral
spinal fluid, or biopsy materials). It is more difficult to interpret results of non-sterile samples (e.g., differ-
ent swabs, respiratory specimens, or wound exudates) or specimens that are easy to contaminate (urine).
The microbiology laboratory result often is known after antibiotic treatment has already begun, and the
patient has improved or not improved in response to the antibiotic. Therefore the concordance of the
microbiological result with the patient’s course is another important factor in interpretation of the micro-
biological result if dealing with opportunistic microorganisms. It is also important to look for concordance
with other laboratory and/or imaging results of the patient.

To interpret microbiological data for IPC purposes, the first issue is always to determine if the specimen
was correct, either from a patient, healthy contacts, or the environment. Then the microbiologist who
understands normal colonising flora of humans, the pathogenesis of infections (incubation period, inocu-
lum size, and kind of vehicle), and the characteristics of specific pathogens (natural habitat, resistance to
drying or disinfectants, and antibiotics) – can interpret the laboratory data for the ICT. In more complicat-
ed outbreaks or an endemic situation, in addition to good microbiology (especially typing) there is a need
to include epidemiologic considerations for the correct interpretation of microbiological data. The micro-
biologist should be a clinical scientist with appropriate training; the professional background varies from
country to country.

Antibiotic policy role

Determining antibiotic susceptibility patterns for microorganisms causing HAIs is vital for individual pa-
tient care. It can also help in planning antibiotic policy and designing the local antibiotic formulary. The
microbiology laboratory should work closely with physicians and pharmacists to determine appropriate
antibiotics to be included in susceptibility testing panels. Then the microbiology laboratory should pro-
vide restricted antibiotics reports to the wards, according to the formulary. The microbiology laboratory
should produce periodic resistance reports for specific wards and for the entire hospital, stratified by
pathogen species and infection site. These reports should be available for every physician who prescribes
antibiotics; they are very important for the design of local empirical therapy.

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IPC in the laboratory

In every clinical laboratory in which biological samples are investigated, the first IPC concern is usually
exposure to viruses that are spread through blood and bodily fluids (human immunodeficiency virus [HIV]
and hepatitis B and C viruses [HBV, HCV]). It is very important that laboratory workers take all necessary
preventive measures against those viruses (see Chapter “Prevention of blood-borne virus infections in
patients and personnel”).

A clinical microbiology laboratory is usually classified as a biosafety level 2 laboratory. This means that it
diagnoses well-characterised agents that do not cause severe or untreatable diseases in healthy adult
humans and poses only a moderate potential hazard to personnel and the environment. The laboratory
must have limited access. Laboratory workers must have specific training to work with microbes and take
all standard precautions with all biological specimens and microbial cultures (hand hygiene, disinfection
of the environment, specific precautions with sharps, working in biological safety cabinets if aerosols may
be created, proper disposal of waste, and sterilisation of culture material once testing is complete).

In some clinical microbiology laboratories, pathogens such as Mycobacterium tuberculosis or Legionella

pneumophila are diagnosed. These diagnostics are to be performed in a biosafety level 3 laboratory
(agents which may cause serious or potentially lethal disease in healthy adult humans after inhalation,
but for which vaccine or other treatment exists). Sometimes it is not possible to have a level 3 facility;
therefore these microbes may be diagnosed in a level 2 laboratory. In that case, laboratory workers must
be properly educated and wear appropriate personal protective equipment (PPE), the filtered exhaust air
from the laboratory room is to be discharged to the outdoors, the room has negative air pressure, and all
recommended practices for biosafety level 3 are rigorously followed.

Point of care microbiological tests

The main problem of microbiological diagnostics in low resource countries is the lack of nearby microbiol-
ogy laboratories; these are typically not sited outside of major urban areas. Therefore, it is very important
to develop point of care (POC) microbiological tests that are sensitive and specific enough, rapid, easy to
perform for HCWs that have no specific education in laboratory procedures, do not require special equip-
ment, unambiguous to interpret, and affordable. Several such tests are already in use (for the diagnosis of
malaria, HIV, HCV, syphilis, measles, respiratory viruses, and tuberculosis), however much more has to be
done in this field. Especially important tests from the point of view of HAI prevention and control are
tests for diagnosing pathogens causing HAIs, as well as antibiotic sensitivity to identify multidrug resistant
strains to rapidly stop their spread. Staff performing the POC tests must also be provided education on
PPE, hazards of specimens, and good methods to dispose of specimens and tests once the testing is com-
pleted.

Minimal Requirements for Microbiology Laboratories in the Control of HAIs

1. Should be sited inside the hospital; if this is not possible, then negotiate a contract for diag-
nostic microbiology with the nearest laboratory.
2. Should be available every day, including Sundays and holidays, ideally on a 24-hour basis.
3. Should be able to examine blood, cerebrospinal fluid, urine, stool, wound exudates or swab,
and respiratory secretions, and perform serological tests (at least HIV, HBV, HCV).
4. Should be able to identify common bacteria and fungi that can cause HAIs to the species
level (Staphylococcus aureus, Escherichia coli, Salmonella, Shigella, Pseudomonas aerugino-
sa, Klebsiella pneumoniae, Streptococcus pyogenes (Group A streptococci), Streptococcus
agalactiae (Group B streptococci), enterococci, Campylobacter jejuni/coli, Enterobacteri-
aceae, Neisseria meningitidis, Candida albicans, Aspergillus spp, etc.), besides other com-
mon microorganisms that cause severe community-acquired infections (Streptococcus pneu-
moniae, Neisseria gonorrhoeae, Vibrio cholerae, Corynebacterium diphtheriae).
5. Should be able to perform susceptibility testing for relevant antibiotics using disc-diffusion

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methodology.
6. Should be able to perform basic typing - serotyping (for salmonellae, shigellae, N. meningiti-
dis) and biotyping (e.g., for S. typhi).
7. Should have quality assurance procedures (both internal quality control and external quality
control [national or international]).
8. Should have a clinical microbiologist who is able to communicate well with clinical and ICT
staff.
9. May have the ability to perform simpler genotyping methods or access to genotyping meth-
ods centrally at state or regional laboratories. The central laboratory can then assist with
epidemiological investigations of HAIs.

References and Further Reading

1. Baron EJ, Miller M, Weinstein MP, et al. A guide to utilization of the microbiology laboratory for diag-
nosis of infectious disease: 2013 recommendations by the Infectious Diseases Society of America
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2. Brooks K, Ready Reference to microbes, 3rd ed., Association for Professionals in Infection Control and
Epidemiology, Inc., Washington, DC, 2012.
3. Brown M. Microbiology basics. In: APIC Text of Infection Control and Epidemiology, 4th Edition, Clini-
cal Editor Grota P. Washington, DC, Association for Professionals in Infection Control and Epidemiolo-
gy, Inc., 2014: Chapter 24.
4. Chosewood LC, Wilson DE (editors) (2009). Biosafety in Microbiological and Biomedical Laboratories
(5th ed.). http://www.cdc.gov/biosafety/publications/bmbl5/BMBL.pdf [Accessed 1 September
2015]
5. Damani N. Manual of infection prevention and control, 3rd Ed., Oxford University Press, Oxford, UK,
2012.
6. Diekema DJ, Pfaller MA. Prevention of health care-associated infections. In Manual of Clinical Micro-
biology, 11th Ed., Jorgensen JH and Pfaller MA, Editors in Chief, ASM Press, Washington, DC, 2015:106
-119.
7. Diekema DJ, Saubolle MA. Clinical microbiology and infection prevention. J Clin Microbiol 2011;
49:S57-S60.
8. Gastmeier P, Schwab F, Baerwolff S, Rueden H, Grundmann H. Correlation between the genetic diver-
sity of nosocomial pathogens and their survival time in intensive care units. J Hosp Infect 2006;
62:181-186.
9. Gerner-Schmidt P, Hyytia-TreesE, Rota PA. Molecular Epidemiology. In Manual of Clinical Microbiolo-
gy, 10th Ed., Versalovic J, Editor in Chief, ASM Press, Washington, DC, 2011:100-123.
10. Guidance for Control of Carbapenem-resistant Enterobacteriaceae (CRE) 2012 CRE Toolkit, Centers
for Disease Control and Prevention, Atlanta, GA, USA. http://www.cdc.gov/hai/organisms/cre/cre-
toolkit/ [Accessed 27 August 2015]
11. Iram S, Zeenat A, Yusuf NW, Aslam M. Rapid diagnosis of tuberculosis using Xpert MTB/RIF assay–
Report from a developing country. Pak J Med Sci 2015; 31:105-110.
12. Kalenic S, Budimir A. The role of microbiology laboratory in healthcare-associated infection preven-
tion. Int J Infect Control 2009; 5(2).
13. Kramer A, Schwebke I, Kampf G. How long do nosocomial pathogens persist on inanimate surfaces? A
systematic review. BMC Infect Dis 2006; 6:130. http://www.biomedcentral.com/1471-2334/6/130
[Accessed 1 September 2015]
14. Kulich PA, Taylor DL. The Infection Preventionist’s Guide to the Lab. Washington DC, Association for
Professionals in Infection Control and Epidemiology, Inc., 2012.
15. Memish ZA, Al-Tawfiq JA, Alhakeem RF, et al. Middle East respiratory syndrome coronavirus (MERS-
CoV): A cluster analysis with implications for global management of suspected cases. Travel Med In-
fect Dis 2015; pii:S1477.
16. Moore C. Point-of-care tests for infection control: should rapid tests be in the laboratory or at the
front line? J Hosp Infect 2013; 85(1):1-7.
17. Murray PR. The clinician and the Microbiology Laboratory. In: Mandell, Douglas and Bennett’s Princi-

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ples and Practice of Infectious Diseases, 8th Ed., Bennett JE, Dolin R, Blaser MJ, Editors, Elsevier Saun-
ders, Philadelphia, 2015:191-223.
18. Peeling RW, Mabey D. Point-of-care tests for diagnosing infections in the developing world. Clin Mi-
crobiol Infect 2010; 16:1062-1069.
19. Pereira-Neves A, Benchimol M.Trichomonas vaginalis: in vitro survival in swimming pool water sam-
ples. Exp Parasitol 2008; 118:438-41.
20. Peterson LR, Hamilton JD, Baron EJ, et al. Role of clinical microbiology laboratory in the management
and control of infectious diseases and the delivery of health care. Clin Infect Dis 2001; 32:605-611.
21. Robertson LJ, Campbell AT, Smith HV. Survival of Cryptosporidium parvum oocysts under various en-
vironmental pressures. Appl Environ Microbiol 1992; 58:3494-3500.
22. Shonhai A, Warrener L, Mangwanya D, et al. Investigation of a measles outbreak in Zimbabwe, 2010:
potential of a point of care test to replace laboratory confirmation of suspected cases. Epidemiol In-
fect 2015; 13:1-9.
23. Smyer J. Laboratory testing and diagnostic. In: APIC Text of Infection Control and Epidemiology, 4th
Edition, Clinical Editor, Grota P. Washington DC, Association for Professionals in Infection Control and
Epidemiology, Inc., 2014: Chapter 25.
24. Soun VV, Eidson M, Wallace BJ, et al. Antemortem diagnosis of New York human rabies case and re-
view of U.S. cases. Intl J Biomed Sci 2006; 2: 434-45.
25. Stratton CW IV, Greene JN. Role of the Microbiology Laboratory and Molecular Epidemiology in
Healthcare Epidemiology and Infection Control. In: Hospital Epidemiology and Infection Control, 4rd
Ed., Mayhall CG, Editor, Lippincott, Williams & Wilkins, Philadelphia, 2012:1418-1431.
26. Studdiford JS, Conniff KM, Trayes KP, Tully AS. Bedbug infestation. Am Fam Physician 2012; 86:653-
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27. Williams J. Bed bugs in hospitals: more than just a nuisance. CMAJ 2013; 185:E524.

While the advice and information in this chapter is believed to be true and accurate, neither the authors
nor the International Federation of Infection Control can accept any legal responsibility or liability for any
loss or damage arising from actions or decisions based on this chapter.

Published by the International Federation Of Infection Control

47 Wentworth Green
Portadown, BT62 3WG, N Ireland, UK
www.theific.org

©International Federation of Infection Control, 2016. All rights reserved.

10
 Table 7.1. Characteristics of main groups of bacteria potentially causing HAI

Bacteria Multidrug Habitat Survival in Transmission in Healthcare Specimens for Main preventive
resistant the environ- healthcare associated diagnosis of measures**
strains (MDR) ment (dry infections infection/
surfaces)13* colonisation
Acinetobacter MDR strains Humans: moist 3 days – 5 Air; indirect*** Urinary tract Urine, blood, Contact precautions
baumannii parts of skin, months and direct contact infection (UTI), cerebral spinal
gastrointesti- sepsis, fluid (CSF),
nal (GI) tract meningitis, sputum, aspirates
pneumonia
Bordetella Humans: naso- 3-5 days Droplets Pertussis Nasopharyngeal Droplet precautions
pertussis pharyngeal (NP) swab
mucosa
(patients)
Campylobac- Humans, Up to 6 days Faecal-oral, water, Diarrhoea Stool Contact precautions

©International Federation of Infection Control

ter jejuni, animals: GI food Safe food and water
C.coli tract
Clostridium Humans: GI Highly Faecal-oral; indirect Clostridium Stool Contact precautions
difficile tract resistant and direct contact difficile infec- Use of soap and water for
(spores – 5 tions (CDI) hand hygiene rather than
months) alcohol-based sanitizer
Clean hands of patients
Prudent use of antibiotics
Clostridium Environment: Highly Entering umbilical Tetanus Sterilisation of instruments for
tetani earth, dust resistant cord wound (on umbilical cord
(spores) dirty instruments)
Coagulase Methicillin Humans: skin, ND Contact (direct, Different Different Standard precautions
negative resistant CNS mucous indirect) infections in specimens
staphylococci (MRSE) membranes endogenous immunocom- depending on
promised host infection
Corynebacte- Humans: NP 7 days – 6 Droplets, contact NP swab; throat Droplet precautions; single
rium mucosa months (direct, indirect) swab room/cohorting
(patients, Contact precautions
diphtheriae carriers) (healthcare worker [HCW]
vaccination)

11
The Role of the Microbiology Laboratory
 Table 7.1. Characteristics of main groups of bacteria potentially causing HAI

Bacteria Multidrug re- Habitat Survival in Transmission in Healthcare Specimens for Main preventive
sistant strains the environ- healthcare associated diagnosis of measures**
(MDR) ment (dry infections infection/
surfaces)13*
colonisation
Enterococcus Glycopeptide Humans: GI 5 days – 4 Indirect and direct UTI, sepsis Urine, blood, Contact precautions
species resistant enter- tract, months contact; stool
ococci (GRE) genitourinary endogenous
tract
Enterobacter Extended Environment, ND Contact, food UTI, sepsis, Urine, blood, Contact precautions
species spectrum β human GI tract wound wound exudate, Prudent use of antibiotics
lactamase infection stool (avoiding the use of 3rd
strains (ESBL), generation cefalosporins)
multidrug
resistant (MDR)
Escherichia coli ESBL strains Humans: GI and 1.5 hours – Faecal-oral, indirect UTI, sepsis, Urine, blood, Contact precautions
IFIC Basic Concepts of Infection Control, 3rd edition, 2016

Carbapenem genitourinary 16 months and direct contact, pneumonia, sputum, Safe food and water

©International Federation of Infection Control

resistant tract food, water, peritonitis, aspirates, CSF, Prudent use of antibiotics
enterobacteria endogenous neonatal wound (avoiding the use of 3rd
(CRE) meningitis exudate, stool generation cefalosporins
and carbapenems)
Helicobacter Gastric Less than 90 Contaminated GI Acute and Biopsy material; Properly disinfected GI
pylori mucosa of minutes endoscopes chronic urea breath endoscopes
humans gastritis test; stool for
antigen
detection
Klebsiella ESBL strains Humans: GI 2 hours – Indirect and direct UTI, sepsis Urine, blood, Contact precautions
CRE tract; humid more than 30 contact, (neonatal sputum, Prudent use of antibiotics
pneumoniae
environment months endogenous units), aspirates, stool (avoiding the use of 3rd
pneumonia generation cefalosporins
and carbapenems)
Legionella Water (natural NA Aerosols from Legionnaire’s Sputum, blood Hyperchlorination of water
waters, tap environmental disease for serology; or heating to at least 55°C
pneumophila
water, water sources urine No patient isolation needed
shower heads, (usually warm
cooling towers, water in hospitals);
hot water tanks, no person-to-
humidifiers res- person transmission
piratory therapy
equipment)

12
 Table 7.1. Characteristics of main groups of bacteria potentially causing HAI

Bacteria Multidrug Habitat Survival in Transmission in Healthcare Specimens for Main preventive
resistant the environ- healthcare associated diagnosis of measures**
strains (MDR) ment (dry infections infection/
surfaces)13* colonisation
Listeria Soil, 1 day - Contaminated food; Meningitis, Blood, CSF Safe food
monocytogenes vegetables, months perinatal bacteraemia Standard precautions in
human GI transmission; contact nurseries
tract (rarely); with contaminated
human birth equipment in
canal nurseries
Mycobacterium MDR strains Respiratory 1 day – 4 Airborne, droplets Tuberculosis sputum Airborne precautions (if not
tuberculosis Extremely DR tract of months possible, then droplet isola-
strains (XDR) patients tion) (HCW vaccination)
Neisseria NP mucosa of ND Droplets Acute CSF Droplet precautions
meningitidis humans meningitis Chemoprophylaxis

©International Federation of Infection Control

Proteus species ESBL GI flora of 1-2 days Endogenous, contact UTI, sepsis Urine, blood, Contact precautions
humans (direct and indirect) stool
Pseudomonas MDR and pan Humans: GI 6 hours to 16 Direct and indirect Different usually Different Standard precautions
aeruginosa -drug tract, humid months contact (humid severe specimens de- MDR/PDR strains: contact
resistant skin regions; items: poorly infections in pending on precautions
(PDR) strains ubiquitous in disinfected items, hospitalised, infection Prudent use of antibiotics
humid ventilator circuits) especially
environment, immunocom-
(water, soil, promised
plants) patients
Salmonella spp GI tract of NA Faecal-oral, water, Diarrhoea, Stool, blood Safe food and water
humans and food sepsis Standard precautions
animals
Salmonella GI tract of 6 hours – 4 Faecal-oral, water, Typhoid fever Stool, blood Safe food and water
typhi humans weeks food Standard precautions
Salmonella GI tract of 10 months – Faecal-oral, water, Diarrhoea, Stool, blood Safe food and water
typhimurium humans and 4.2 years food sepsis Standard precautions
animals

13
The Role of the Microbiology Laboratory
 Table 7.1. Characteristics of main groups of bacteria potentially causing HAI

Bacteria Multidrug Habitat Survival in Transmission in Healthcare asso- Specimens for Main preventive
resistant the environ- healthcare ciated infections diagnosis of measures**
strains ment (dry infection/
(MDR) surfaces)13* colonisation
Serratia Humans: GI tract; 3 days – 2 Indirect and direct Sepsis, wound Blood, wound Standard precautions
marcescens humid environ- months; on contact, infection exudate
ment dry floors 5 contaminated
weeks intravenous fluids
(especially heparin
solutions)
Shigella species GI tract of humans 2 days – 5 Faecal-oral, water, Diarrhoea stool Safe food and water
months food Contact precautions
Staphylococcus Methicillin Humans: skin, 7 days - 7 Droplets, direct and Skin infections, Swabs, sputum, Contact precautions
aureus resistant S. mucous mem- months indirect contact, pneumonia, nares, blood, Prudent use of
aureus branes medical equipment; sepsis, osteomye- aspirates, biopsy, antibiotics (avoid
(MRSA) endogenous litis wound exudate, ciprofloxacin)

©International Federation of Infection Control

perianal swab,
stool
IFIC Basic Concepts of Infection Control, 3rd edition, 2016

Streptococcus Humans: birth ND Intrapartal; direct Sepsis and Blood, CSF, vaginal Antibiotic prophylaxis
agalactiae canal and indirect contact meningitis of swab during delivery when
Group B in delivery room newborn indicated
and nurseries Standard precautions
streptococcus
(GBS)
Streptococcus Humans: oropha- 3 days-6.5 Droplets, contact, Pharyngitis Oropharyngeal Staff with GAS infections
pyogenes ryngeal mucosa months endogenous (“strep throat”), swab, wound or carriers of GAS should
Group A surgical wound exudate not work in the
infection operating theatre
streptococcus
(GAS)
Vibrio cholerae GI tract of humans; 1 – 7 days Faecal-oral, water, Cholera stool Safe water and food
water raw seafood Standard precautions
Yersinia GI flora of many ND Blood transfusion in Bacteraemia con- Blood, stool Safe blood products
enterocolitica animals, causes hospitals; faecal- nected to blood Standard precautions
diarrhoea in young oral in the transfusion;
animals; rarely community diarrhoea in the
humans as carriers community

* Survival is better if conditions are humid for most microorganisms (exception being Staphylococcus aureus), and
if microorganism is in biological material (blood, faeces, wound exudate), if the temperature is lower and if bacte-

14
ria are in higher numbers
** See “Isolation precautions”
*** whenever indirect contact is involved, it is most frequently by hands of healthcare workers
ND = not done; NA = not applicable
 Table 7.2. Characteristics of main groups of fungi potentially causing HAI

Fungi Habitat Survival in the Transmission Healthcare associated Specimens for diagno- Main preventive measures**
environment in healthcare infections sis of infection/
(dry surfaces)13* colonisation
Candida albi- Soil, animals, 1-120 days Direct and Different opportunistic Different specimens Standard precautions
cans (yeast) humans, indirect*** infections depending on infection
inanimate contact,
objects endogenous
Candida gla- Soil, animals, 102-150 days Direct and Different opportunistic Different specimens Standard precautions
brata (yeast) humans, indirect contact, infections depending on infection
inanimate endogenous
objects
Candida para- Soil, animals, 14 days Direct and Different opportunistic Different specimens Standard precautions
psilosis (yeast) humans, indirect contact, infections depending on infection
inanimate endogenous
objects
Aspergillus Ubiquitous in Conidia and Inhalation, Pneumonia, disseminat- Sputum, different other Protective isolation of suscepti-

©International Federation of Infection Control

species (mould) soil, water, spores are (contact) ed infections in severely specimens depending on ble patients
food, decaying resistant forms immunocompromised infection Containment of areas where
material, patients construction/ renovation is in
outdoor and process to reduce exposure****
indoor air Safe tap water, food and drinks
Mucor (mould) Soil, plants, Conidia and Inhalation Different opportunistic Different specimens Protective isolation of suscepti-
fruits, animal spores are infections in depending on infection ble patients
excreta, food resistant forms immunocompromised Containment of areas where
patients (zygomycosis) construction/ renovation is in
process to reduce exposure****
Safe food and drinks
Rhizopus Soil, plants, Conidia and Inhalation Different opportunistic Different specimens Protective isolation of suscepti-
(mould) fruits, animal spores are infections in depending on infection ble patient
excreta, food resistant forms immunocompromised Containment of areas where
patients (zygomycosis) construction/ renovation is in
process to reduce exposure****
Safe food and drinks

*Survival is better in low temperature, high humidity and presence of serum or albumin;
** See “Isolation precautions”
*** Whenever indirect contact is involved, it is most frequently by hands of healthcare workers
**** See “Health care facility design, construction and renovation”

15
The Role of the Microbiology Laboratory
 Table 7.3. Characteristics of main groups of viruses potentially causing HAI

Virus Habitat Survival in the Transmission in Healthcare Specimens for Main preventive
environment healthcare associated diagnosis of measures***
(dry surfaces)13* infections infection**
Adenovirus Humans, water, 7 days – 3 months Direct and indirect**** Eye infections, Conjunctival swab Standard precautions
Several types fomites (e.g., contact respiratory NP swab Separate eye drops for every
ophthalmological infections patient
equipment and
solutions),
environment
Coronavirus Humans 3 hours Droplets Respiratory Serum sample Droplet precautions
Direct and indirect infections Respiratory sample
contact Diarrhoea Stool sample
Contact precautions

Coronavirus: SARS Animals SARS virus: 72-96 Droplets Severe respira- Serum sample Airborne precautions (if not

©International Federation of Infection Control

(Severe Acute Humans hours Direct and indirect tory infections Respiratory sample possible then droplet
Respiratory contact precautions) plus contact
Faecal-oral ? precautions
Syndrome)-CoV
IFIC Basic Concepts of Infection Control, 3rd edition, 2016

Coronavirus: Animals ND Droplets Severe Respiratory sample Airborne precautions (if not
MERS (Middle East Humans Direct and indirect respiratory possible then droplet
Respiratory contact infections precautions) plus contact
precautions
Syndrome)-CoV
Coxackie B virus Humans >2 weeks Faecal-oral; direct and Generalized Serum sample Standard precautions
indirect contact disease of Blood
newborn CSF
Cytomegalovirus Humans 8 hours Blood products, tissue Huge range of Serum sample Safe blood products and
and organs for transplan- different dis- tissues/organs for
tation; mucosal contact eases transplantation
with secretions and ex-
cretions
Ebola (Marburg) Humans ND Direct contact Haemorrhagic Serum sample, blood Airborne precautions (if not
Animals Blood, secretions, fever possible then droplet
respiratory droplets, precautions) plus contact
semen, contaminated precautions
syringes and needles,

16
aerosols
 Table 7.3. Characteristics of main groups of viruses potentially causing HAI

Virus Habitat Survival in the Transmission in Healthcare Specimens for Main preventive
environment healthcare associated ‘diagnosis of measures***
(dry surfaces)13* infections infection**
Hepatitis A virus Humans 2 hours – 60 days Faecal-oral Hepatitis A Serum sample Safe food and water
Standard precautions
Hepatitis B virus Humans >1 week Blood, bodily fluids, tissue Hepatitis B Serum sample Safe blood products and
and organs for tissues/organs for
transplantation transplantation
Hepatitis C virus Humans NA Blood, bodily fluids, tissue Hepatitis C Serum sample Safe blood products and
and organs for tissues/organs for
transplantation transplantation
Herpes simplex Humans 4.5 hours – 8 Droplets, close contact Different mu- Lesion swab If infected, HCW should not
virus weeks cosal and skin CSF care for susceptible persons
infections (newborn,
immunocompromised)
HIV Humans >7 days Blood, bodily fluids, tissue AIDS Serum sample Safe blood products and

©International Federation of Infection Control

and organs for tissues/organs for
transplantation transplantation
Influenza virus Humans 1-2 days Droplets, directs and Influenza NP swab Droplet precautions
indirect contact, HCW as HCW vaccination
symptomatic or
asymptomatic diseased
persons
Norovirus Humans 8 hours – 7 days Faecal-oral, direct and Diarrhoea Stool Contact precautions
indirect contact, aerosols
from vomitus
Rabies virus Dogs (and other Inactivated soon Saliva and other body Rabies Corneal impression Droplet precautions and con-
animals); humans by drying24 fluids and secretions of Skin biopsy tact precautions
patient through contact Saliva Post-exposure prophylaxis in
with open wounds, skin CNS tissue at persons who were exposed
abrasions or mucous autopsy to saliva and other body
membranes fluids and secretions of
Human bite/scratch patient or were bitten/
Aerosol transmission? scratched by patient

17
The Role of the Microbiology Laboratory
 Table 7.3. Characteristics of main groups of viruses potentially causing HAI

Virus Habitat Survival in the Transmission in Healthcare Specimens for Main preventive
environment healthcare associated diagnosis of measures***
(dry surfaces)13* infections infection**
Respiratory Humans Up to 6 hours Droplets, direct and Acute NP exudate Droplet precautions
syncycial virus indirect contact respiratory
infections in
young children
Rotavirus Humans 6-60 days Faecal-oral, direct Diarrhoea Stool Contact precautions
and indirect
contact
Rubula virus Humans ND Droplets Mumps Serum sample Droplet precautions
(parotitis) HCW vaccination
Rubivirus Humans ND Droplets Rubella Serum sample Droplet precautions
(German HCW vaccination
measles)

©International Federation of Infection Control

Morbillivirus Humans ND Droplets Measles Serum sample Droplet precautions
HCW vaccination
Varicella-zoster Humans ND Droplets, close Varicella Serum sample Droplet/airborne precautions
virus contact HCW vaccination
IFIC Basic Concepts of Infection Control, 3rd edition, 2016

* Survival is better in low temperature, presence of biological material and if viruses are in higher numbers
** Diagnosis is performed using serology, if applicable and if laboratory can perform direct diagnostics, it will be mostly antigen detection or
nucleic acid detection in the sample from infectious site, rarely virus isolation
*** See “Isolation precautions”
**** whenever indirect contact is involved, it is most frequently by hands of healthcare workers
NA = not applicable; ND = not done; HCW = healthcare worker

18
 Table 7.4. Characteristics of main groups of parasites potentially causing HAI

Parasite Habitat Survival in the Transmission in Healthcare Specimens for Main prevention methods*
environment healthcare associated diagnosis of
infections infection
Cryptosporidium Humans 2 hours on dry Faecal-oral, water, Diarrhoea Stool Safe water and food
(protozoa) surface13 food Standard precautions
longevity in
water21
Plasmodium Liver, NA Mosquito-borne in Malaria Blood Safe blood products
species erythrocytes of the community;
(protozoa) diseased person infected blood
Trichomonas Vaginal mucosa Several hours Sexually Vaginal Vaginal discharge Disinfected/sterilised medical
vaginalis in humid transmitted in the infection in equipment in gynaecology
(protozoa) environment19 community; women
contaminated

©International Federation of Infection Control

medical equipment
in gynaecology
Enterobius Intestinal tract of Faecal-oral, Enterobiasis Perianal tape Standard precautions
vermicularis diseased person ingestion of para- Changing linen and patient
(helminth) site eggs that can clothes without creating
contaminate aerosols
environment;
airborne

* See “Isolation precautions”

19
The Role of the Microbiology Laboratory