Institute for Microbiology, Medical
Faculty of Masaryk University
and St. Anna Faculty Hospital in Brno
Agents of respiratory infections – I + II
Ondřej Zahradníček (with use of prof. Votava's
slideshows from 2011)
Lecture for 3rd-year students
21st of September, 2012
Significance of respiratory
diseases
The most significant infections in general
practitioner‘s office (respiratory tract = an
ideal incubator)
 Big economic effect on the economics
(people stay home, including mothers of ill
children)
 They tend to be seen in collectives and
often produce outbreaks and epidemics
 ¾ of respiratory infections (and even more in
children) are caused by viruses

Localization of infection in the
respiratory tract

The localization of infection in the
respiratory tract
– influences the clinical symptomatology
– enables us to suspect specific agents

Therefore, we have to distinguish
– upper respiratory tract (URT) infections (and
infections of adjacent organs )
– lower respiratory tract (LRT) infections (infections of
lower respiratory ways and of lungs) (lungs are not
a „way“, therefore they are often taken apart)
Of course, it is also possible, that a disease
influences more than one part together
Respiratory infections – Classification:
URT infections and
LRT infections and lung
infections of adjacent
infections
organs
 infection of epiglottis
 infections of nose a
 infection of larynx and
nasopharynx
trachea
 infections of oropharynx
 infection of bronchi
incl. tonsillae
 infection of bronchioli
 infections of paranasal
 infections of lungs
sinuses
 otitis media*
For practical reasons they use to be
taken here, as the sites of infection are
 conjunctivitis*
related anatomically with the URT
„Flu“ and influenza

Commonly, acute respiratory infections are rhinitis,
pharyngitis or mixed rhinopharyngitis (inflammations of
nasal and pharyngeal cavities). Epidemiologists use
an abbreviation „ARI“ – acute respiratory illness
Many people describe this as a „flu“, but it is not a true
influenza.
 True influenza rather attacks lower respiratory tract, it
contains dry cough and whole-body symptomatology
(fever, muscle pain). Nevertheless, similar
symptomatology can be also seen in case of
parainfluenzas and other diseases. Epidemiologists
use abbreviation „ILI“ (influenza-like illness).
.
Common flora in respiratory ways
Nasal cavity has no its specific flora, but it is
usually colonized by skin bacteria (=
staphylococci, coryneforms, especially the
anterior part) or pharynx (the posterior part)
 The pharynx (similarly as oral cavity) contains
neisseriae and streptococci (viridans group),
usually haemophili, sometimes small amounts
of pneumococci, meningococci etc.
 Lungs and LRT is usually microbes-free, but
the specimens coming from here use to be
contaminated by URT flora

Rhinitis, rhinopharyngitis (or
nasopharyngitis) acuta
It is almost caused by viruses („common cold“).
More than 50 % are caused by rhinoviruses, 2nd place
have coronaviruses, other viruses may be also
present (but NOT influenzavirus)
 Bacteria* may multiply secondarily; they are often
patient‘s own bacteria from skin or pharynx. They
disappear without treatment, antibiotic treatment is
useless and usually also ineffective.

*Staphylococcus aureus, Haemophilus influenzae, Streptococcus
pneumoniae, Moraxella catarrhalis; in rather chronical cases:
Klebsiella ozaenae, Klebsiella rhinoscleromatis
In differential diagnostics, we
should think about allergic and
vasomotoric rhinitis
http://www.drgreene.org/body.cfm?xyzpdqabc=0&id=21&action=detail&ref=1285
http://www.bupa.co.uk/health_information/a
sp/direct_news/general_health/rhinitis_240
706.asp
Examination and treatment for rhinitis

Examination is useless. Even mucopurulent
secretion does not necessarily mean bacteriological
examination, except long time durating secretion.
 The treatment is symptomactical (nasal drops for
decongestion of the mucous membrane, tea etc.;
even antipyretics are not very useful, as elevated
temperature is helpful against viruses.
 Antibiotic treatment is not recommended. In
borderline cases it is possible to use local
antibiotic treatment (e. g. bacitracin + neomycin)
 Only for infection durating 10–14 days it is
recommended to examinate nasal swab (to avoid
skin contamination!) and to perform targeted
antibiotic treatment
Carriership of MRSA strains
Nasal carriership of Methicilin-resistant
Staphylococcus aureus strains (MRSA) is
relatively common.
 It uses to be asymptomatic
 Treatment is not routinely recommended.
Eradication of MRSA strains is quite difficult
and often only temporary
 Nevertheless, sometimes we try to get rid of
MRSA in nasal cavity, especially prior to
surgery. Mupirocin is mostly used for this.

Sinusitis acuta (inflamation of
paranasal sinuses)
Transient finding in sinuses is normal during
common cold and it is not a reason for
treatment (even if found in X-rays)
 Treatment is recommended in case of painful
sinusitis with pain of teeth, head, fever,
headache and durates at least a week,
eventually nervus trigeminus is involved
 Although viral infection may be primary, the
important causative agents are bacteria,
almost Streptococcus pneumoniae and
Haemophilus influenzae

Sinusitis acuta
http://www.drgreene.org/body.cfm?xyzpdqabc=0&id=21&action=detail&ref=1285
Examination and treatment of
sinusitis

Treatment should be started immediatelly, even
without examination
 Drug of 1st choice is amoxicilin (e. g. AMOCLEN), an
alternative is e. g. doxycycline (DOXYBENE), in
children co-trimoxazol (BISEPTOL)
 Examination of nasal of pharyngeal swab is useless
 In case that we wish to perform targeted treatment,
the only way is properly performed punction or
sinus washing (usually on oto-rhinolarangological department of a hospital), of course,
it should be washed by saline, not disinfectant!
Middle ear inflammation – otitis media
Middle ear is anatomically related to respiratory tract
Common in children (short horizontal tuba auditiva)
Agents: Streptococcus pneumoniae, Haemophilus
influenzae, Moraxella catarrhalis, less commonly
anaerobic bacteria
In chronical inflamations also G– rods etc.
It is necessary to differenciate – otitis media × otitis
externa: In case of otitis externa, the causative agents
are the same as for skin infections – almost
Staphylococcus aureus. The treatment is local.
Otitis media
http://www.medem.com/MedLB/articl
e_detaillb.cfm?article_ID=ZZZPMV6
D1AC&sub_cat=544
Examination and treatment
of otitis media

Treatment has a sense, if it is a really proven
inflammation (pain, redness, fever) and it is not
suppressed by anti-inflammatory treatment
 Drug of choice is again amoxicilin (e. g. AMOCLEN),
an alternative co-trimoxazol
 Examination of external ear swab is a logical
nonsense, except in case of perforated tympanon
(spontaneously or artificially at paracentesis)
 Of course, in case of having pyogene liquid taken
during paracentesis, it is recommended to examinate
it microbiologically
Etiology of conjunctivitis




Conjunctivitis is usually of viral origin
It usually accompanies acute URT infections
In adenoviral infections typically: follicular conjunctivitis,
pharyngoconjunctival fever (adenoviruses 3, 7), epidemic
keratoconjunctivitis (adenoviruses 8, 19)
Viral conjunctivitis of other origin:
– hemorrhagic conjunctivitis (enterovirus 70)
– herpetic keratoconjunctivitis (HSV)


Treatment is usually only local
Bacterial conjunctivitis
– Acute suppurative conjunctivitis: S. pneumoniae, S. aureus, in
children also other bacteria
– Inclusion conjunctivitis: C. trachomatis D – K
– Chronical bacterial conjunctivitis: S. aureus, C. trachomatis A – C
(trachoma)
– Allergic, mechanic (alien body)
Acute tonsillitis and pharyngitis
majority (70–85 %) viral (rhinoviruses,
coronaviruses, adenoviruses, but also EB virus
= infection mononucleosis)
 The most significant of bacterial ones (more
than 95 % cases): accute tonsilitis caused
Streptococcus pyogenes (group A haemolytical
streptococcus). More bacteia: arcanobacteria,
possibly also haemolytical streptococci of other
groups, pneumococci etc.
 Rare, but important: diphtheria, gonorrhoea

Viral tonsilopharyngitis
http://upload.wikimedia.org/wikipedia/commons/thumb/b/b1/Pharyngitis.jpg/250px-Pharyngitis.jpg
Tonsilopharyngitis
http://medicine.ucsd.edu/Clinicalimg/Head-Pharyngitis.htm
http://www.newagebd.com/2005/sep/12/img2.html
Purulent (= pyogenic, puscontaining) bacterial tonsilitis
http://www.meddean.luc.edu/lumen/MedEd/medicine/PULMONAR/diseases/pul43b.htm
Pharyngitis: Examination and treatment

A throat swab (tonsils swab) should be always
performed to find the causative agens. (The fact that
many GPs do not do it does not mean that this is
the good way how to do it.)
 As it is usually not possible to wait for results of
culture, in the same time CRP is examined (elevated
in bacterial infections), the result is available soon
 Treatment should be targeted. In tonsillitis caused
by Streptococcus pyogenes (huge majority of bacterial
ones) the drug of choice is V-penicillin. Macrolids
(RULID, KLACID, SUMAMED, AZITROX) should be
used in allergic patients only
 Eventually serology of EB virus and cytomegalovirus
might be examined in unclear subacute cases
Dangers

Many doctors think that they are able to distinguish
clinically bacterial tonsillitis against the viral one.
The research shows that it is not true in many cases.
So, at least CRP examination ought to be done.
 Another common mistake is use of macrolids
(KLACID, SUMAMED, RULID), although the patient is
not allergic. It is not good: macrolids are bakteriostatic
antibiotics only, the effectiveness of treatment is only
80–90 % (against 100 % for penicillin – in the Czechia,
no strain resistant to penicillin was found until now!)
Even use of ampicillinu or amoxicillin instead of
penicillin is a mistake, especially when the
examination was not performed. Aminopenicillins may
cause hard damage in case of infection
mononucleosis!
Etiology of epiglottitis
disease – medical emergency
 The child may suffocate!
 Serious
One only really important causative agent:
Haemophilus influenzae type b
 Treatment: transport to emergency unit, first
aid, among antibiotics: 3rd generation
cephalosporins
 Examination if often not performed (it might
lead to a new disease attack), eventually blood
culture is performed
 It is very rare now (vaccination)
Epiglottitis
de.wikipedia.org/wiki/Epiglottitis
http://health.allrefer.com/health/epiglottitis-throat-anatomy.html
Even George Washington died
because of this disease
www.fathom.com/course/10701018/session4.html
Etiology of laryngitis and tracheitis

Again respiratory viruses, but other than agents of
nasopharyngitis: parainfluenza and influenza A viruses
+ respiratiory syncitial (RS) virus
 Bacteria are rather rare here: Chlamydia
pneumoniae, possibly Mycoplasma pneumoniae
 Secondarily sometimes: Staphylococcus aureus and
Haemophilus influenzae
 Laryngotracheitis pseudomembranosa (croup):
Corynebacterium diphtheriae
Lagyngitis acuta
http://www.emedicine.com/asp/image_search.asp?query=Acute%20Laryngitis
Examination and treatment
of laryngitis and tracheitis
No examination is needed, even possible.
Throat swab is a nonsense, as the microflora in
pharynx is different from larynx and trachea. In
subacute or chronical states it is possible to
examinate serum for antibodies againts
respiratory viruses (and simillar agents)
 Treatment is almost symptomatical. Unlike
very rare cases, antibiotics are not indicated

www.cartoonstock.com/directory/l/laryngitis.asp
www.cartoonstock.com/directory/l/laryngitis.asp
www.cartoonstock.com/directory/l/laryngitis.asp
Acute bronchitis and
tracheobronchitis

Acute bronchitis:
– Caused almost only by viruses, influenza is a
typical example.
– Outbreaks in scholar childrend and young aduls
may be caused by Mycoplasma pneumoniae.
– Other bacterial species, like Streptococcus
pneumoniae and Haemophilus influenzae, are not
important here. When isolated from sputum
specimen, their origin is probably in URT.
Bronchitis acuta
http://www.yourlunghealth.
org/lung_disease/copd/nut
shell/index.cfm
http://www.lhsc.on.ca/resptherapy/st
udents/patho/brnchit5.htm
Chronical bronchitis
Bronchiolitis

Chronical bronchitidy (cystic fibrosis,
diseased people):
– Pseudomonas aeruginosa, Burkholderia cepacia,
Staphylococcus aureus
Bronchiolitis attacts small babies and seniors.
Causative agents are mostly viruses
(Pneumovirus/respiratory syncytial virus,
Metapneumovirus), sometimes hospitalisation
is needed. Targeted treatment is not possible.
Whooping cough is an exceptional case. Here
antibiotics are always needed.

Bronchitis and bronchiolitis –
examination and treatment

The basis is clinical examination and eventually Xrays, showing development of cough without finding
on lung tissue
 Laboratory examination is almost useless. When
sputum is expectorated, it is possible to send it to the
laboratory, as in such case a secondary bacterial
infection is likely. Here, CRP may be also examined. It
is also possible to perform serological examination
(mycoplasmas, chlamydia)
 Antibiotic treatment is almost useless, in
mycoplasms and chlamydia macrolids or tetracyclins
are used
Particular situation: accute
exacerbation of chronical bronchitis
(EACB)

Characterized by
– Worsening ot the cough
– Elevated expectoration and change of character of sputum
and its colour
– Often also worsened breathing

Less than 40 % of these are caused by viruses
 Among bacteria, causative agents are H. influenzae,
Streptococcus pneumoniae and Moraxella catarrhalis.
 Routine antibiotic treatment is not recommended, it
should be individual
Different types of pneumoniae
Acute – community-acquired pneumonia (outpatients)
in originally healthy (subdivision: adults × children)
in disabled persons
after a contact with animals
Acute – nosocomial pneumonia
VAP = ventilator-associated
 early (before 4. day)
 late
other
Subaccute and chronical
Pneumonia
www.medicinenet.c
om/pneumonia/artic
le.htm
Acute, community-acquired, in
healthy persons
Streptococcus pneumoniae: the most
frequent (almost in seniors > 65 years)
 Haemophilus influenzae: less common
 Moraxella catarrhalis: rare
 Legionella pneumophila: rare
 Staphylococcus aureus: very rare (influenza
epidemic only)
 In newborns also Streptococcus agalactiae

Atypical pneumoniae (small clinical
finding, but X-rays show it)
In adults almost atypical bacteria (it is not
possible to find them in sputum specimen,
antibody examination is needed):
 Mycoplasma pneumoniae
 Chlamydia pneumoniae
In small children respiratory viruses are
important (RSV, influenza A, adenoviruses)
In newborns also Chlamydia trachomatis,
serotypes D–K (perinatal infection)
Pneumonia
http://www.uspharmacist.com/index.asp?page=c
e/105057/default.htm
People with diseased immunity
Not serious dammage of immunity
 pneumococci, stafylococci, hemophili
 Klebsiella pneumoniae (alcohol abusers)
 Legionella pneumophila
Rather serious dammage:
 Pneumocystis jiroveci (a strange fungus)
 cytomegalovirus
 atypic mycobacteria (related to TB)
 Filamentous bacterium Nocardia asteroides
 fungi (Aspergillus, Candida)
Particular situation:
contact with animals
Bronchopneumoniae
 Pasteurella multocida (contact with dogs
and cats)
 Francisella tularensis (tularemia – contact
with hares or agricultural stuff contaminated
by hares)
Atypic pneumoniae
 Chlamydia psittaci (psitacosis, ornithosis)
 Coxiella burnetii (Q-fever)
Pneumonia
http://www.uspharmacist.com/index
.asp?page=ce/105057/default.htm
Acute, nosocomial:
VAP (ventilator)
soon (sooner than 4th day):
susceptible „normal“ strains of common
causative agents (like in community acquired
pneumoniae)
 late: resistant hospital strains (Klebsiella
pneumoniae and others)

Other
Viruses (RS virus, cytomegalovirus)
 Legionella

Nosocomial pneumoniae
Subacute and chronic:
Aspiration pneumonia and lung abscesses
– Anaerobic bacteria (Prevotella
melaninogenica, Bacteroides fragilis,
peptococci and peptostreptococci)
Lung tuberculosis and mycobacterioses
 Mycobacterium tuberculosis
 Mycobacterium bovis
 atypical mycobacteria (e.g. the complex M.
avium–M. intracellulare)
Bronchopneumonie
www.szote.u-szeged.hu/radio/mellk1/amelk4a.htm
Lobar a lobular pneumonia
www.supplementnews.org/pneumonia
Microbiological examination in lung
infections

Classis community-aquired pneumoniae
– blood for blood culture (haemoculture)
– sputum – microscopical and basic cultivation
examination
– sputum – cultivation of Legionella pneumophila
– urine – detection of antigen of L. pneumophila

Atypic pneumoniae
–
–
–
–
blood – serological examination (antibodies)
Blood and sputum for bacteriology (just for sure)
search for viruses (serology, direct examination)
sputum – direct detection (ELISA, PCR)
Treatment of LRT/lung infections
Classical community-acquired pneumoniae:
amoxicillin, eventually targeted treatment
 Atypical pneumoniae: tetracyclins or
(especially in children < 8) macrolids.
 Hospital infections: targeted treatment
needed, high risk of resistant strains
 In TB combination of three of four drugs usually
needed

„Respiratory viruses“ and non-viral
agents tested by virological methods
Respiratory viruses are related to many
types of respiratory infections, therefore it is
useful to know them
 Virology laboratories examine patients sera
labeled „examination of antibodies
against respiratory viruses“ – usually, they
perform tests for the most common agents
 Such examinations often include non-viral
agents – atypical bacteria that cannot be
detected by bacteriological cultivation


Respiratory viruses often tested
serologically in the lab
The most important and most common:
–
–
–
–
influenzavirus A and B
adenoviruses
RSV and metapneumovirus
parainfluenzaviruses (type 1+3 = Respirovirus, type 2+4 =
Rubulavirus)
– rhinoviruses
– coronaviruses (incl. SARS agent)

Less common viral agents
–
–
–
–
–
HSV
coxsackieviruses
echoviruses
EBV
Ťahyňa virus
Bacterial agents causing atypical
pneumonia (but diagnosed in
virologic laboratories):
Mycoplasma pneumoniae – the most
common one
 Coxiella burnetii – agent of Q-fever
 Chlamydia (Chlamydophila) psittaci –
agent of ornithosis & psittacosis
 Chlamydia (Chlamydophila)
pneumoniae

Direct examination for influenza





For bacteria it is not recommended to send
pharyngeal swabs in LRT infections
For influenza it is different: pharyngeal swab is
useful here
It is necessary to use a swab with a special
transport medium for viruses
The specimen should be sent to the laboratory as
soon as possible
Such specimen may be processed by methods of
direct diagnostics (virus isolation on cell cultures,
especially the modern shell-vial technique)
Sputum
What to take Sterile container
 How to také it

– A doctor or nurse has to survey it
– The patient should wash the mouth
– Patient coughs now, trying to get out the secret
of lower respiratory ways.
– The amount should be at least 1ml.
It is possible to keep it < 24 h at refrigerator
temperature (but it is better to send it
immediately)
 Transport: < 2 h at room temperature

Other specimens from LRT and lungs
Trachal aspiration
 Bronchoalveolar lavage
 Endotrachal cannula (after extraction)
Some of these have special ways of
procession in the laboratory, even
semiquantitative, enabling to differentiate
between a contamination and a true
infection

Thank you for your
attendance
Foto: archiv MÚ