Pathogen agents

Diagnostic & treatment

Anca Streinu-Cercel MD PhD

May 2019
 Germs classification

• Bacteria
• Viruses
• Fungus
• Prions
• protozoans
 CLASSIFICATION OF INFECTIOUS
AGENTS

• Bacteria – survive on appropriate media, stain

gram-positive or -negative
• Viruses – obbligate intracellular parasites which
only replicate intracellularly (DNA, RNA)
• Fungus – non-motile filamentous, branching
strands of connected cells
• Metazoar – multicellular animals (e.g.parasites)
with complicated life cycles often involving
several hosts
 CLASSIFICATION OF INFECTIOUS
AGENTS

• Protozoar – single cell organisms with a well-

defined nucleus
• Rickettsia – very small bacteria spread by ticks
• Prions – unique proteins lacking genetic
molecules
• Chlamydia – bacteria lacking cell walls
Size Comparison of Microbes
Differences between GRAM positive and
GRAM negative organisms
 Simply say

Self transmissible plasmid (F plasmid)

has a gene that encodes enzymes and
proteins that form that sex pilus
Clinical microbiology made ridiculously simple, Mark Gladwin, Bill Trattler
 Bacteria
4 major shapes:
•Cocci
•Bacilli:rods
•Spiral forms
•Pleomorphic: lacking a distinct shape

•G+ 6 germs
•2 are cocci: -Streptococcus….strips
• - Staphylococcus…clusters
• other 4 are rods shapes (bacilli)
• - Bacilus
• - Clostridium
• - Corynebacterium
• - Listeria
•G- all other
•One group of cocci: Neisseria
•Spiral shape: Spirochetes:Treponema pallidum
•The rest are rods or pleomorphic
Microbiological Classification of
Infectious Diseases
Morphological differences among the bacteria

Clinical microbiology made ridiculously simple, Mark Gladwin, Bill Trattler

Clinical microbiology made ridiculously simple, Mark Gladwin, Bill Trattler
 Bacteria
Coccus Gram positive aerobe Coccus Gram negative
• Staphylococcus spp aerobe
– Staphylococci auriu (coagulase – Branhamella (Moraxella)
positive) catarrhalis ?
– Stafilococ alb (epidermidis, – Neisseria meningitidis
saprophyticus…)(coagulase negative) – Neiserria gonorrhoeae
• Streptococcus spp
– S.pyogenes (group A beta hemolytic)
– S.agalactiae (group B)
– Streptococi “orali” salivarius, mutans,
sanguis (viridans)
– S. pneumoniae
– S.bovis (grup D)
• Enterococcus spp (faecalis, faecium,
durans, avium)
Coccus Gram positive Coci Gram positive
anaerobe anaerobe
– Peptococcus – Veionella parvum
– Peptostreptococcus
 Bacteria
Bacilli Gram positive aerobe
• Bacillus anthracis
• Bacillus cereus
• Corynebacterium diphteriae
• Erysipelothrix rhusiopathiae
• Listeria monocytogenes
• Nocardia
Bacilli Gram positive anaerobe
• Actinomyces israelii
• Clostridium perfringens
• Clostridium tetani
• Clostridium botulinum
• Clostridium difficile
• Lactobacillus
• Propionibacterium acnes
 Bacteria
Bacilli Gram negative aerobe
Fermentative
• Escherichia coli
• Proteus mirabilis
• Salmonella spp (typhi, paratyphi)
• Shigella (dysenteriae, flexneri, boydii, sonnei)
• Klebsiella
• Enterobacter sp
• Citrobacter sp
• Serratia sp
• Providencia, Morganella morganii
• Yersinia
• Aeromonas sp
• Vibrio sp (cholerae parahemolyticus)
 Bacteria
Bacilli Gram negative aerobe
Nefermentativi
• Pseudomonas aeruginosa (piocianic)
• Burkolderia cepacia
• Stenotrophomonas maltophila
• Acinetobacter
• Moraxella
Other BGN
Brucella, Pasteurella,Bordetella pertussis, Legionella,
Campylobacter, Helicobacter, Gardnerella vaginalis
Fermentativi dificulty growth
Haemophilus, Actinobacillus, Cardiobacterium, Capnocytophaga,
Eikenella, Kingella (HACEK)
Bacilli Gram negative anaerobe
• Bacteroides
• Prevotella
• Fusobacterium
 Bacteria
Other bacteria
• Mycoplasmataceae
– M.pneumoniae, hominis, Ureaplasma urealyticum
• Chlamydiaceae
– C.trachomatis, psittaci, pneumoniae
• Rickettsiaceae
– R.conorii, typhi, prowazekii…Coxiella burnetii, Ehrlichia,
Bartonella henselae, quintana
• Spirochaetaceae
– Treponema, Borrelia, Leptospira
• Mycobacteriaceae
– Complexul tuberculosis (BK, bovis, africanum)
– M.leprae
– Micobacterii atipice (M.avium intracellulare, kansasii,
marinum, xenopi)
 Bacteria frequently involved in community
acquired infections

• Respiratory tract inf.

Streptococcus pyogenes, Streptococcus pneumoniae,
Haemophilus influenza, Moraxella catarrhalis,
Mycoplasma pneumoniae
• Urinary: E.coli
• SSTI: Streptococcus pyogenes, Staphylococcus
aureus
• Genital: N. gonorrhoeae, Chlamydia trachomatis
• Intestinal: Salmonella, Shigella
 Bacteria involved in nosocomial
infections

Stafilococ-MR

• More frequent nosocomial inf = higher gravity

• Outcome = worse
• Treatment options (antibiotics) - low (antibiogram is
essential)
• Treatment costs – higher

Every “hospital” Staphylococci

Is consider a priori MR
If not proven otherwase
 Germs involved in nosocomial
infections

Enterococcus

• enterococii – second or third place

nosocomial infections in USA
• Normal intestinal flora humans, (almost all
infectious are endogenus?)
• The majority of inf developed by hospitalised
patients, (peritoneal dialisis, hemodialisis, and the
microorganisms surse exogen)
 Germs involved in nosocomial
infections
Enterococ

• Low rate respiratory inf

• Can determine endocarditis,
urinary/renal infections
• frecvent involved in pelvic inf and intra-
abdominal
 Germs involved in nosocomial
infections

Bacilli Gram negative

• Enterobacterii (E.coli, Klebsiella,

Enterobacter, Serratia, Proteus, Citrobacter,
less frequent Salmonella si Yersinia

• Other BGN: Acinetobacter, Pseudomonas

• Most frequent cause of NI, mortality 10-15%

 Germs classification

• Bacteria √
• Viruses
• Fungus
• Prions
• protozoans
 Microbiological Classification of
Infectious Diseases
• Viruses are acellular, obligate intracellular
organisms.
• The complete infectious virus is termed a virion.
• The virion consists of the specific nucleic acid
(DNA or RNA) surrounded by a protein coat
(capsid).
– Some viruses are enveloped which means that they
possess a lipoprotein coat that surrounds the capsid
and is acquired from infected host cell membrane.
– Viruses that lack an envelope are “naked.”
 Microbiological Classification of
Infectious Diseases
• Viruses are typically classified by:
– Genetic material (DNA vs. RNA)
– Strandedness (single vs. double)
– Size and shape of the capsid and whether its
enveloped or non-enveloped
– Method of replication
 Viruses
ARN ADN
Family Virus Family Virus
Picornaviridae Poliovirus, Coxsackie, Hepatnaviridae v.hepatitei B
Echovirus, v.hepatitei A,
rinovirus Parvoviridae Parvovirus B19
Astroviridae Astrovirus Polyomaviridae v.JC
Caliciviridae v.Norwalk Papovaviridae papiloma
Togaviridae v.rubeolic Adenoviridae Adenovirus
Flaviviridae v.febrei galbene Herpesviridae HHS1,2, EBV, CMV
v.hepatitei C, G VZV, HHV6,7,8
Coronaviridae coronavirus Poxviridae v.vaccinal,
v.variolei,
Rhabdoviridae v. rabiei poxvirusuri (molluscum)
Paramyxoviridae v.rujeolei, v.urlian,
VRS, v.paragripal
Filoviridae v. febrelor Ebola,
Marburg
Arenaviridae v.coriomeningitei
limfocitare
Orthomyxoviridae v. gripei
Reoviridae rotavirus
Retroviridae HIV, HTLV
viruses
 Germs classification

• Bacteria √
• Viruses √
• Fungus
• Prions
• protozoans
• Fungus are eucaryotic cells, which lack
chlorophyll, so can not generate energy by
photosynthesis,
• They do require an aerobic environment
 Categories
 Yeast :  Hyphae: Molds
 unicelular - ocazional  multicelular
produc pseudohyphae sau
chiar hyphae  Threadlike, branching,
 round – size of WBC filamentoas,
 Can be fagociteted
 Can not be fagociteted
 normal – comensale
 colonizarea suprafeţelor  Never comensale
corpului – deobicei precede
invazia sitemică
 IFI
 Reproduce at a slower rate
then bacteria  Rapid growth
Fungus
 Germs classification

• Bacteria √
• Viruses √
• Fungus √
• Prions…..CJD
• Protozoans…
 Microbiological Classification of
Infectious Diseases
• Types of Parasites:
– Protozoa: Single-celled, microscopic organisms that
can perform all necessary functions of metabolism
and reproduction. Some protozoa are free-living,
while others parasitize other organisms for their
nutrients and life cycle.
• The morphology of protozoa varies widely and includes oval,
spherical and elongated cells that can range in size from 5-
10 to 1-2 mm.
• Structurally, the protozoa resemble other eukaryotic cells and
possess a cytoplasmic membrane that encloses cytoplasm
containing membrane-bound nuclei, mitochondria, 80s
ribosomes and a variety of organelles.
 Microbiological Classification of
Infectious Diseases
• Types of Parasites:
– Helminths: A large, multicellular organism (worm) that
is generally visible to the naked eye in its adult
stages.
– Helminths can be free-living or parasitic.
• Nematodes: Roundworms
• Trematodes: Flukes
• Cestodes: Tapeworms
 Microbiological Classification of
Infectious Diseases

• Prions are abnormal, transmissible agents that

are able to induce abnormal folding of normal
cellular prion proteins in the brain, leading to
brain damage and the characteristics signs and
symptoms of the disease.
•
• Prion diseases are usually rapidly progressive
and always fatal.
Prion:
normal protein NP
and abnormal prion
protein PP
 ID diagnostic

Clinical dates

Epidemiological Date Lab date

 Lab Diagnostic in ID
• General Exams (orientative)
– CBC
– Acute inflamation Markers
– Citochimic examen of biological fluids
(CSF, ascita, pleural efusion )
– Imgistic (Rx, CT, echo, MRI)
• Specific Exams
– Direct ( germ identification, Ag, ADN
fragment)
– Indirect ( serologic tests)
 Tips
ANEMIA : Hb < 12 g dl/14g/dl
• Periferic – hemolitic:
• sepsis due to Clostridium
perfringens,
• pneumonia due to
Mycoplasma pneumoniae
(aglutinine la rece),
• malarie
• Central (inflamator / toxic)
direct action of the pathogen
agentul (Parvovirus B 19,
HIV, TBC)
NEUTROFILIA > 7.000
neutrofile/mmc
• Bacterial inf extracelular:
local/general
• Not present for intracelular
inf
NEUTROPENIA < 1.000
neutrofile/mmc
• Virale inf
• Severe bacterial inf (BGN)
 Tips
AGRANULOCITOZA < 500 /mm3
• Inf: extracelulare bacteria
comensale / fungus
• pneumonia / celulite / angine
ulceronecrotice
EOZINOFILIA: > 500 eozinofile /
mmc
• Parasites (helmintiaze –
trichineloză ...)
• alergies, inflamator diseases
& disimunitare, hemopatii
and cancer
LIMFOCITOZA: > 4.000
limfocite / mmc
virale inf
rar: bacterial inf : whooping
cough
LIMFOPENIE: < 1.000 limfocite
/ mmc
HIV, Legionella pneumophila
MONOCITOSIS : > 1.000
monocyte / mmc
virale inf, listeriosis, TBC,
toxoplasmosis
 Tips
TROMBOCITOSIS: > TROMBOPENIE: <
500.000/mmc 150.000/mmc
(infectious biological • Medular hipofunction:
inflammatory sindrom) virale inf
TB • Ab antiplatlets: virale
inf
• DICS: severe bacterial
inf : BGN sepsis,
pneumococ,
meningococ, (purpura
fulminans), paludism
 Ethiologic Diagnostic -direct (1)
• Microbiologic exam direct (microscopie)
Fast and easy minutes
Practic important: gives the clinician the suposed ethiology and
orients treatmet till the culture resoults comes
”Preparat proaspăt „= direct smear (lamă – lamelă) :
Trichomonas vaginalis, Treponema palidum, Entamoeba
histolitica
Smers colored:
Gram (Meningite!), Giemsa (Plasmodium), Ziehl (BK)
Direct immunofluorescence:
• Chlamydia trachomatis ( genital swabs)
• Pneumocystis carinii (BAL)
• Legionella pneumophila (sputum, pleural fluid)
• Bordetella pertussis (sputum)
• respiratori virusis (secretions rinofarigiene): influenta,
parainfluenza , respiratory syncytial
 Ethiologic Diagnostic -direct (2)
• Culture
– Usual culture medium acelulare (bacterii uzuale)
– Anaerobi culture medium
– Lowenstein (BK)
– Sabouraud (fungi)
– selective (Loffler – difterie)
– celular (virusis, chlamydia)
Reading the result:
• Idetifiing a pathogen agent =hight dianostic value:
– Salmonella typhi
– gonococ
– plasmodium
• Idetifing an oprtunistic agent (staf. alb, candida) = interpret acording to:

– Site of isolation: pleura / CSF / ascites

– Clinical simptoms/ clinical context (Staf alb: proteze, catetere)
– Host imunitar state (Staf alb: imunodepresie)
– Complementare ethiologic exams (serology, anapat)
 Ethiologic Diagnostic -direct (3)
• Highlighting the soluble antigens
– blood, urine, CSF, biopsy tissue
– dg. etiol. meningite bacteriene decapitate cu AB:
pneumococ, meningococ, H.influenzae
– dg. etiol. infecţii cu: Legionella pneumophila /
Cryptococcus
• Identifying bacterial genom
- by PCR
– Variate biological products
– CSF: rapidcdg. / modern for viraleCNS inf
– quantitative techniques(viral load): HIV, VHB, VHC
 Ethiologic Diagnostic - indirect (1)
Serum Identification of specific Ab for the pathogen agent
suspected
NOT a rapid diag: RI develop 7 -14 days after clinical debut, no
clinical relevance for extracelulat bacterial inf
Kinetics of antibodies in infection:
– after 7-10 days AB specific IgM :
– Acute inf = recent
– Vanish after a few months to 1 year
– AB IgG, life long persistance-> imunity
For serological diagnosis:
– 2 blood drowns , 2 weeks interval
– Same lab same procedure
– Ab titer dynamics IgG between the 2 samples
ELISA (Enzyme Linked Immuno Sorbent Assay): modernă
 Ethiologic Diagnostic - indirect (2)

A positive serological result NOT a certain diag of

acute infection
Interpretation of serological tests:
• evidence of seroconversion: primo infection = acute infection
= = diagnose value
• highlighting specific IgM = current acute infection, = diagnose
value
• highlighting increased 4-fold titer between the two
determinations specific Ac = recent acute infection, diagnose
value
• All serological results must be interpreted
according to the sensitivity and specificity
There is serological cross-reactions due to antigenic
similarities between some infectious agents:
ID Treatment
 ID Treatment (1)
Prophylactic: treatment as prevention!!!
– Primary prevention - measures to avoid infection
(source of infection, routes of transmission,
responsiveness *) * administration of serums and
vaccines

– secondary-prevention measures to avoid

complications, relapse (eg, identifying the
infection early / asymptomatic in the treatment
and eradication in STDs, TB latency)

– Tertiary Prevention: Applicable for HIV

(inf.oportuniste prevention, tertiary prevention is
the primary and secondary reference to HIV
infection
 Active immunization programs
• In children: BCG, diphtheria, tetanus, polio, whooping
cough, measles, rubella, mumps, hepatitis B, hepatitis A,
H.influenzae b

• For travel: typhoid fever, yellow fever, meningococcal,

Japanese encephalitis, tick encephalitis ...

• Occupationally exposed persons: anthrax, rabies

• Post exposure: hepatitis B, measles, pertussis, rabies, in

association with the Ig
 Vaccines prophlaxy
• Attenuated bacteria:
• BCG (id)
• typhoid (oral)
• Attenuated virus:
• polio (oral)
• measles (sc)
• rubella (sc)
• Mumps (sc)
• varicella (sc)
• Amaril / yellow fever (im / sc)
• Rotavirus (oral)
• intranasal influenza
 Vaccins
Bacterian inactivat (bacteria complete):
• pertussis (IM)
• typhoid (sc)
• cholera (im, sc)
• fever (IM)
• leptospirosis
Inactivated viral
• inactivated polio (im / sc)
• Influenza (IM)
• rabies (IM)
• Hepatitis A (IM),
• Japanese encephalitis (SC) *
• tick encephalitis *
 Vaccines
Inactivated bacteria: bacterial fractions
• toxoids: tetanus, diphtheria (IM)
• acellular pertussis, Anthrax
• polysaccharides:
– unconjugated: meningo AC (SC), air 23 (im /
sc), typhoid Vi (im / sc)
– conjugate: air conjugate Hib (conjugate),
meningo
Inactivated virus: split vaccine
• Hepatitis B (IM)
• HPV
 Immunotherapy prophylaxis
(seroterapy)
• Heterologous serum
– Prevention: tetanus, rabies
– Treatment: tetanus, diphtheria, botulism
Desensitization, "immunological tolerance" method Besredka
Disadvantages: local reactions, immediate allergic reactions (anaphylactic
shock), delayed (serum sickness)
• Specific hyperimmune human immunoglobulin
prophylaxis, tetanus, rabies, hepatitis B, measles, rubella, mumps,
antizoster
• 10-16% nonspecific human immunoglobulin
– nonspecific anti-infective activity (primitive or secondary immune
deficiency CLL, MM)
– ITP, Kawasaki disease, prevention measles, hepatitis A
 ID Treatment (2)
Treatment:
– hygienic-dietary (environmental measures, diet)
– symptomatic (pain, cough, hyperthermia,
agitation)
– pathogenic:
• inflammatory
• anticonvulsant, depletion in HTIC
• HE rebalancing and AB
• cardiotonic, respiratory support, treatment of renal failure
– Etiology:
– antibacterial, antiviral, antifungal, antiparasitic
 Non-specific treatment of infections
• Purpose: To facilitate the action AB, increase the
body's defense capacity, avoiding the effects of
infections delete

• Means:
• surgery: drainage of abscesses and infections, "the
obstacle" to withdraw foreign material (prosthesis,
catheter, etc.)
• immunoglobulin serum (toxic pathogenic diseases)
• interferon (chronic hepatitis, Kaposi's sarcoma,
anogenital warts)
• hematopoiesis stimulating factors (G-CSF, GM-CSF)
• glucocorticoids
 Indications for treatment with
corticosteroids in infectious diseases
Recommended for:
– acute sinusitis
– acute laryngitis
– COPD with obstructive component
– Convulsive-severe cough
– MNI severe (forms dysphagia, neurologic, cardiac, hematologic severe)
– Acute bacterial meningitis
– Typhoid fever with severe neurological and cardiac
– Tuberculosis: pleurisy, pericarditis, meningitis
– Treatment of severe side-Herxheimer Jarish (syphilis, Lyme disease,
leptospirosis)
Facilitating the diffusion of microbial infection multiplication

Bacterial infections in which treatment is not suitable AB

Skin and subcutaneous (and NSAIDs are CI)

!! Digestive intolerance, bleeding

Treatment with corticosteroids should be short
Clinical microbiology made ridiculously simple, Mark Gladwin, Bill Trattler