BACTERIOBILITY

MICRIOBIOLOGY SUPPLEMENT
BY
ARHAM NASIR SZMC’24

DO REMEMBER IN PRAYERS

PNEUMONIA
↳ Acute inflammation

( RESPIRATORY SYSTEM )
PNEUMONIA IS AN INFECTION THAT INFLAMES AIR SACS IN ONE OR BOTH LUNGS.

PATHOGENS FOR TYPICAL AND ATYPICAL PNEUMONIA ARE:

TYPICAL PNEUMONIA ATYPICAL PNEUMONIA

STREPTOCOCCUS PNEUMONIAE MYCOPLASMA PNEUMONIAE

HAEMOPHILUS INFLUENZA CHLAMYDIAE PNEUMOPHILA

STAPH AUREUS LEGIONELLA PNEUMOPHILA

KLEBSIELLA PNEUMONIAE CHLAMYDIA PSITTACI ( ZOONOTIC )

MORAXELLIA COXELLIA Q FEVER ( ZOONOTIC )

RSV, CMV , INFLUENZA AND ADENO VIRUS ALSO CAUSE ATYPICAL PNEUMONIAE. FUNGI LIKE COCCIODES
AND HISTOPLASMOSIS ALSO CAUSE PNEUMONIA. PNEUMOCYSTIS J IS ALSO INVOLVED.

NOCARDIA ASTEROIDES AND PSEDUOMONAS AERUGINOSA CAUSE PNUEMONIA LIKE SYMPTOMS. THEY
PRODUCE GREENISH SPUTUM. P AERUGINOSA IS PROMINENT IN PATIENTS WITH HX OF CYSTIC FIBROSIS,
BURNS AND ICU. NOCARDIA OCCURS MOST OFTEN IN IMMUNOCOMPROMISED INDIVIDUALS (G+

s BRANCHING ROD FILAMENTS AND WEAK ACID FAST). BACCILUS ANTHRACIS PNEUMONIAE PATIENTS
PRESENT WITH HX OF WOOLSORTER DISEASE
Hx of CGD / ventilator
↓
DIFFERENCES BETWEEN TYPICAL AND ATYPICAL PNEUMONIAE ARE:
chronic
granulomatous
disease

TYPICAL PNEUMONIA ATYPICAL PNEUMONIAE

( LOBAR OR BRONCHO PNEUMONIA ) ( INTERSTITIAL PNEUMONIA )

HIGH GRADE FEVER LOW GRADE FEVER

PRODUCTIVE COUGH DRY COUGH

purulent sputum scanty non purulent sputum
X RAY CHANGES LOCALIZED X RAY CHANGES DIFFUSED

ONSET RAPID ONSET GRADUAL

LOBAR CONSOLIDATION ON XRAY PATCHY INFILTRATE OR ATYPICAL BILATERAL

MULTIPLE OPACITIES ON XRAY

NOT SO PROMINENT EXTRAPULMONARY

No entrapulmonary manifestations MANIFESTATIONS IE SJ IN MYCOPLASMA

Bordetella pertussis causes

whopping cough
↳ bronchitis not pneumonia
SOME KEY DIFFERENTIALS ARE:
of pneumococcus produce greenis
f) Some species
sputum as well so lobar pneumonia
a

STREP PNEUMONIAE: PLEURITIC PAIN, RUSTY COLORED SPUTUM, MOST IMPORTANT CA key word

PNEUMONIA. KEY: LOBAR PNEUMONIA

HAEMPHILUS INFLUENZA: FACTOR X AND V, MODIFIED CHOCOLATE AGAR, GREENISH SPUTUM. KEY:
BRONCHO PNEUMONIA AND HX OF COPD
STAPH AUREUS: AFTER INFLUENZA VIRUS INFECTION, AFTER NUERO SURGERY, YELLOW SPUTUM
KLEBSELLIA PNEUMONIAE: IN ALCOHOLISM. RED CURRANT JELLY SPUTUM / Hx of Diabetes
TYPICAL CANDIDATE OF LEGIONELLA IS OLD MAN WHO SMOKES ALOT AND CONSUMES
SUBSTANTIAL AMOUNT OF ALCOHOL commonly
military recruits
MYCOPLASMA PNEUMONIAE: MOST COMMON IN YOUNG ADULTS. WHITISH SPUTUM
LEGIONELLA PNEUMOPHILA: HX OF WATER AEROSOLS. UNILATERAL LOBAR PNEUMONIA BUT NOT
TYPICAL
CHLAMYDIA PNEUMOPHILA: IN INFANTS LESS THAN 3 YEARS ( BETWEEN 4TH AND 11WEEKS )
CHLAMMYDIA PSSITACI: HX OF BIRD EXPOSURE
risk
COXIELLA: HX OF SHEEP EXPOSURE Poor malnourished unvaccinated child with Measles
is at high
of getting giant cell pneumonia
PNEUMOCYSTIS PNEUMONIA VS CMV PNEUMONIA

PNEUMOCYSTIS PNEUMONIAE CMV PNEUMONIA

↳ Plasma cell pneumonia

GROUND GLASS OPACITIES ON X RAY SAME, WITH DENSE AREAS OF

CONSOLIDATION

HX OF HIV/AIDS HX OF IMMUNOSUPPRESSION
PARTICULARLY STEM CELL/RENAL CELL
TRANSPLANT
 CD4 < 200 CD4 < 100

HONEYCOMB EXUDATE EOSINOPHILIC INCLUSIONS IN EXUDATE

Q FEVER AFFECT THE LUNGS. HEPATITIS IS FREQEUNT ENOUGH THAT COMBINATION OF PNEUMONIAE
CA pneumonia AND HEPATITIS IS SUGGESTIVE OF Q FEVER
1- Cause)
1- pneumococcus ( no -

Bacterial Fungal viral

a- Hemophilus meningitis meningitis meningitis .

Pneumonia caused by Ascari's is termed

3- staph
as toffler's Pneumonia /
4. Klebsiella toffler syndrome turbid CSF
↓ CSF glucose
clearest
normal/
dearest
normal

MENINGITIS
HCA pneumonia is usually caused 440mg /dl low
by enteric rods lymphoma
Neutrophil ia lymphocytosis
↑ proteins mild ↑
causing meningitis
normal
virus
↑ ICP normal ICP

( CENTRAL NERVOUS SYSTEM

Rapid )
↑ ICP
-
Mumps onset I -7 days 7 > days
Polio " " 4h "
-

1- Brudzinskisign
-
Coxsackie 2 signs for meningitis 2- hernia sign
-
echovirus MENINGITIS IS INFLAMMATION OF MENINGES OF BRAIN.
HSV 'd
SHORT MNEMONIC FOR BACTERIAL PATHOGENS CAUSING MENINGITIS OTHER THAN NEISSERIA: SHE
-

Parasite causing
CAUSES HEADACHE. ( S PNEUMONIA, H INFLUENZA, E COLI )
meningitis / class testmca ) tuberculous meningitis -7
1- Angiostrongylus complication of -113,10W CSF glucose with lymphocytosis
BACTERIAL PATHOGENS ( BY AGE GROUPS ) ( < 40mg /dl)
2- baylisascan's

3- Gnatnostoma a bacterial infection in

which
TB is
S PNEUMONIA: MOST COMMON OVERALL CAUSE lymphocytosis occurs
S. AGALACTIE: MOST COMMON CAUSE OF NEONATAL M. FOLLOWED BY E COLI AND LISTERIA
N MENIGITIS: COMMON IN TEENAGERS AND ADULTS. ( ALSO S PNEUMONIA )
LISTERIA MONOCYTOGENES: IN VERY YOUNG, VERY OLD OR IMMUNOCOMPROMISED OR PREGNANT
PATIENTS.
H INFLUENZA: IN YOUNG CHILDREN 6 MONTHS-6 YEARS ( MENIGTIDIS AND STREP P ALSO INVOLVED
). IF CHILD IS UNVACCINATED, H INFLUEZA BECOMES NUMBER 1 CAUSE. H INFLUEZA MENINGITIS IS
CLINICALLY INDISTINGUISHABLE FROM OTHER PATHOGENS BUT HAS MARKED RAPID ONSET

OTHER PATHOGENS ( BY HISTORY )

S PNUEMONIAE: HX OF CSF LEAK, SPEELECTOMY OR SICKLE CELL ANEMIA

with
in infant
STAPH EPIDERMIDIS: HX OF PERITONEAL SHUNTS → nosocomial meningitis weight
low birth
CRYPTOCOCCUS NEOFORMANS: HX OF HIV/AIDS 1 renal transplant)
NEGLERIA FOWLERI: HX OF SWIMMING AND DIVING IN FRESH WATER
→ syphilitic Aseptic meningitis
TREPONEMA PALLIDUM ( SECONDARY SYPHILIS ): ASEPTIC MENINGITIS AS IT IS NOT GROWN ON
↳ untreated syphilis
CULTURE. LUMBAR PUNCTURE FINDINGS: CSF CLEAR, GLUCOSE CONTENT NORMAL, AND
ELEVATED PROTEINS tertiary syphilis presents with neuro syphilis ( neuropathy tubes , paresis) >

MYCOBACTERIA TUBERCULOSIS ( IN EXTRAPULMONARY TUBERCULOSIS ) LYMPHADENITIS IS MOST

COMMON EXTRA PULMONARY MANIFESTATION. virus causing aseptic meningitis
1- Mumps 5- echovirus
2- Polio
ASEPTIC MENINGITIS →
3- Coxsackie
4- HSV2
UMBRELLA TERM FOR ALL MENINGITIS WITH NEGATIVE CSF BACTERIAL CULTURE. OVERALL VIRAL
INFECTION IS MOST COMMON FORM OF ASPECTIC MENINGITIS, AND ENTEROVIRUSES ARE MOST
COMMON CAUSE ( ALPHA VIRUSES _ TOGA VIRUS FAMILY CAUSE ENCEPHALITIS )
18
child than 2 months 21018 years of more than
childless than 2 months greater
age I Years of AGE
1-
streptagalactiae i
street pneumoniae
meningitidis
-
.

µ .
↓
2- E. coli IV. meningitidis
2-
Haemophilus pneumococcus
3- Listeria in unvaccinated child
becomes no -1 cause
 GENITAL PATHOGENS
( GENITAL SYSTEM )
DDX OF INVOLVED PATHOGENS ARE:

C ALBCANS: VAGINAL CANDIDIASIS, COTTAGE CHEESE EXUDATE

T VAGINALIS: TRICHOMONIASIS. MALODROUS GREEN EXUDATE. COMPARE: MALODOROUS WHTE
GREEN
EXUDATE OF GARDERELLA VAGINALIS ↳ itchy burning foul smelling
vaginal discharge
T PALLIDUM: HX OF SYPHILIS
whiff test is positive
HSV 2: GENITAL HERPES, ULCERS WITH ERYTHMATOUS BASE in both gardnerella
CHLAMYDIA: LYPMHOGRANULOMA VENERUM 4 trichomonas

LACTOBACCILUS: NORMAL FLORA, CLEAR MUCOID EXUDATE infection

N GONNORHEA: CERVITIS. ALSO CAUSE FITZ HUGH CURTIS SYNDROME
G. vaginalis : malodorous WHITE / GREY coloured vaginal discharge with
Fishy smell
CLOSTRIDIUM PERFRINGENS ENDOMETRIOSIS: FOUL SMELLING BLOODY VAGINAL DISCHARGE

BRAIN ABSCESS
( CENTRAL NERVOUS SYSTEM )
DDX OF BACTERIAL PATHOGENS INVOLVED ARE:

STREPTOCOCCUS ( IN MIXED INFECTIONS ) IE PEPTOSTREPTOCOCCI MIXED INFECTION AFTER

DENTAL SURGERY
NOCARDIA ASTEROIDES ( FILAMENTOUS RODS )
STAPH AUREUS ( IN INFECTIVE ENDOCARDITIS, NUEROSURGERY )

DDX OF FUNGAL PATHOGENS INVOLVED ARE:

brain lesion
ring enhancing
ASPERGILLUS ( IN NUETROPENIA )
MUCOR AND RHIZOPUS ( IN NEUTROPENIA )

ASPERGILLUS MUCOR AND RHIZOPUS

DICHOTOMOUS V SHAPED FUNGI HYPAHAE BRANCH AT 90 DEGREE

SEPTATE HYPHAE ASEPTATE HYPHAE

REGULAR WALLS IRREGULAR WALLS

RADIATING CONIDIA CONIDIA IN SPORANGIUM

TOXOPLASMA ( PROTOZOA ) ALSO CAUSE BRAIN ABSCESS

Inclusion bodies viruses

bodies Rabies
Negri
Guarnieri bodies pox virus

intranuclear bodies
with owl 's
eye
appearance
CMV
ERYTHEMA
Herpes > Measles
intranuclear ( Condry )
viruses Forming synctitium
VZV MMR HIV Respiratory
( SKIN INFECTION )
Herpes > > > ,

synctia virus
ERYTHEMA MULTIFORME ( STEVENS JOHNSON SYDROME )

HSV 1: ALSO ENCEPHALITIS WITH FOCAL TEMPORAL LESIONS, KERATOCONJUCTIVITS AND GO

HSV 2: GENITAL HERPES, NEONATAL HERPES AND COLD SORES
MYCOPLASMA PNEUMONIAE ( EXTRAPULMONARY MANIFESTATION, EATONS AGAR )

RULE OF THUMB IS HSV 1 CAUSES DISEASES ABOVE THE WAIST AND HSV 2 BELOW THE WAIST

ERYTHEMA NODUSUM ( ON TIBIA )

MYCOBACTERIUM TUBERCULOSIS
MYCOBACTERIUM LEPRAE ( ERYTHEMA NODUSUM LEPROSUM )
COCCIDIOMYCOSIS
HISTOPLASMOSIS

ERYHTHEMA CHRONICUM MIGRANS IS DISTINCTIVE OF LYME DISEASE ( STAGE 1 ). ERYTHEMA

INFECTIOSUM IS DISTINCTIVE OF PARVO ( B19 ) VIRUS _ SLAPPED CHEEK FEVER. ERYTHEMA
MARGINATUM IN ACUTE RHEUMATIC FEVER

EXANTHEMS ARE WIDESPREAD RASHES THAT ARE ACCOMPANIED BY SYSTEMIC SYSTOMS. CLASSICAL
CHILDHOOD EXANTHEMS ARE:

1. VZV, HERPES FAMILY CAUSES CHICKEN POX

2. MEASLES, PARAMYXO FAMILY CAUSES RUBEOLA
3. HHV 6, HERPES FAMILY CAUSES ROSEALA ( EXANTHEM SUBITUM OR ROSEOLA INFANTUM )
4. RUBELLA, TOGA FAMILY CAUSES GERMAN MEASLES
5. B19 , PARVO FAMILY CAUSE ERYTHEMA INFECTIOSUM OR 5TH DISEASE

CHICKEN POX SHOULD BE DIFFERENTIATED FROM SMALL POX AS:

CHICKEN POX ( VZV VIRUS ) SMALL POX ( POX VIRUS )

ASYNCHROUS RASH SYNCHROUS RASH

RAPID DEVELOPMENT SLOW DEVELOPMENT

MORE POCKS ON BODY MORE POCKS ON ARMS AND LEGS

USUALLY ABSENT ON PALMS AND SOLES PRESENT

 MEASLES VS GERMAN MEASLES

MEASLES BEGIN BELOW THE EAR, AROUND THE NECK AND THEN SPREAD DOWNWARDS. GERMAN
MEASLES BEGINS ON THE FACE AND PROGRESSES TO TORSE. PATIENT IS MORE SICK IN MEASLES ( 7
DAYS ) AS COMPARED TO GERMAN MEASELS ( 3 DAYS ). THERE IS PROMINENT LYMPHADENOPATHY IN
RUBELLA

CONJUCTIVITIS
( EYE INFECTIONS )
S AURUES IS LEADING CAUSE OF CONJUCTIVITIS IN ADULTS ( PRESENTED WITH BILATERAL PURULENT
DISCHARGE AS COMPARED TO CONJUCTIVITIS IS KAWASAKI DISEASE THAT PRESENTS WITH UNILATERAL
NON PURULENT DISCHARGE ). HEAMOPHILUS INFLUNZA AND STREP PNEUMONIA ARE LEADING CAUSES
OF CONJUCTIVITIS IN CHILDREN. NEISSERIA GONORRHEA ( OPTHALMIC NEONATORUM ) AND
CHLAMYDIA ARE LEADING CAUSES IN INFANTS.

NEISSERIA GONORRHEA CONJUCTIVITIS APPEARS IN FIRST 5 DAYS AFTER BIRTH. CHLAMMYDIA

CONJUCTIVITIS APPERS IN BETWEEN 7 TO 12 DAYS AFTER BIRTH.

DIARRHEA
(GASTROINTESTINAL INFECTION)

WATERY DIARRHEA BLOODY DIARRHEA

E COLI ( AFEBRILE, VOMITING PRODROME ) E COLI VERO TOXIN ( AFEBRILE ) ( LACTOSE F )

VIRO CHOLERAE ( AFEBRILE, TCBS AGAR ) SHIGELLA ( NON LACTOSE FERMENTER, NO H2S )

S AUREUES ( INCUBATION PERIOD 8HRS, SALMONELLA ( NON LACTOSE FERMENTER, H2S

CLOSTRIDIUM PERFRINGEN 8-16 1HRS AND E WIDAL TEST + : STOOL CULTURE IS TAKEN )
COLI +3 DAYS )

LISTERIA MONOCYTOGENS CAMPYLOBACTER ( CVA/SKIRROW MEDIUM )

NORVO AND ROTA VIRUS _ YOU CAN WALK, YOU CLOSTRIDIUM DIFFICILE _ MOST COMMON
HAVE NORWALK NOCOSOMIAL DIARRHEA
 GIARDIA ( AFEBRILE, ABDOMINAL PAIN, FATTY YERSINIA ( INVASINS AND COAGULASE + )
DIARRHEA, STRING TEST

CRYPTOSPORIDIUM ( ABDOMINAL PAIN, ENTAMOEBA ( ABDOMINAL PAIN )

KINYUON ACID FAST STAIN )

SHIGELLA CAUSES BACILLARY DYSENTRY WHILE ENTAMOEBA CAUSES AMOEBIC DYSENTRY.

ACID FAST PATHOGENS ARE: MYCOBACTERIUM TUBERCULOSIS, NOCARDIA ASTEROIDES,

CRYPTOSPORIDIUM AND ISOSPORA
All DNA viruses replicate
in cytoplasm except in
Influenza that replicates
nucleus

OTHER DISEASES All RNA viruses replicate

in nucleus except pox
in
( MISCELLANOUS )
virus that replicates
cytoplasm

STREPTOCOCCUS PNUEMONIAE IS LEADING CAUSE OF SINUSITIS AND PHARYNGITS. ( MNEMONIC MOPS:

MENINGITIS, OTITIS MEDIA, PNEUMONIA AND SINUSITIS ). S PNEUMONIA IS LEADING CAUSE OF ALL
THESE. HEAMOPHILUS INFLEUZA ALSO CAUSE OTITIS MEDIA AND SINUSITIS. IMPORTANT PATHOGENS OF
PHARYNGITIS ARE: pathogens
sinusitis /Acute otitis media
:
-

pneumococcus
1. GROUP A STREPTOCOCCI ( GAS )
i -

2. NEISSERIA GONORHHEA
2-
Herophilus
3- Mora ✗ ella
3. INFLUENZA VIRUS
4- Rhinovirus
4. PARA INFLUEZA VIRUS
5- RSV

PATHOGENS CAUSING REACTIVE ARTHRITIS ( STYC GROUP IN CONTRAST TO STEC GROUP ):

otitis externa pathogens
: -

1. SHIGELLA Aureus
1-
staph
2. SALMONELLA ( TYPHOID ) 2- Candida
3. YERSINIA 3- Proteus
otitis
4. CAMPYLOBACTER 9- Pseudomonas → malignant
externa
5. CHLAMYDIA ( ACCOMPANIED BY CONJUCTIVITS AND URETHRITIS = REITERS SYNDROME ).
CHLAMYDIA CAUSE REACTIVE ARTHRITIS IN DISSEMINATED GONOCOCCAL INFECTIONS

COCXSAKIE B VIRUS IS INVOLVED IN MYOCARDITIS. BORRELIA BURGODFERI MYOCARDITIS IS

ACCOMPANIED BY VARIOUS FORMS OF HEART BLOCK, NEUROPATHIES. BILATERAL FACIAL NERVE PALSY
IS HIGHLY SUGGESTIVE OF BORRELIA

STREPTOCOCCUS PYOGENS CAUSE CARDITIS IN ACUTE RHEUMATIC FEVER THAT DAMAGES THE MITRAL
AND AORTIC VALVES

PATHOGENS CAUSING PERICARDITIS ARE ( PATCH GROUP ):

1. S PNEUMONIA
 DNA virus causing tumor
Bacteria tumor
causing HPV Genital warts > cervical CA
A. pylori → Gastric adenocarcinoma nasopharyngeal
EBV Burkitt 's lymphoma
2. S AUREUS ↳ MALT lymphoma CA
A
HBV Hepatocellular
3. TUBERCULOSIS parasite causing tumor KSHV / Hav-8 Kaposi sarcoma
donor chis → cholangiocarcinoma Merkel cell virus Merkel cell CA
4. COCXSACKIE hematobium → squamous cell CA of bladder
5.
RNA viruses causing tumor
5. HISTOPLASMOSIS ( TUBERCULOUS PERICARDITIS )
HTLV 1- -

→ T-cell leukemia
Hcv → Hepatocellular AA
PATHOGENS CAUSING ENDOCARDITIS ARE DIVIDED INTO 2 GROUPS:

NATURAL VALVES ENDOCARDITIS PROSTHETIC VALVES ENDOCARDITIS

S AUREUS ( RIGHT SIDED ENDOCARDITIS ) CULTURE + PATHOGENS ARE S EPIDERMIDIS AND

ONSET IS VERY RAPID VIRIDIANDS STREPTOCOCCI

CANDIDA ALBICANS AND PSEUDOMONAS WITH CULTURE - PATHOGENS ARE BARTONELLA,

HX OF IV CATHETERS BRUCELLA AND COXIELLA

reactive arthritis Parvovirus 1319

viruses
causing →

Hepatitis B
Rubella virus
STAPH AURUES IS LEADING CAUSE OF INFECTIVE ARTHRITIS AND OSTEOMYLITIS. GONORRHEA
ARTHRITS HAS HX OF SEXUALLY ACTIVE PERSON. VERTERBRAL OSTEOMYLITIS ( POTTS DISEASE ) IS
CAUSED BY M TUBERCULOSIS Two
segmented viruses

Rotavirus ( dsDNA )

REYE SYNDROME IS ASSOSIATED WITH INFLUENZA AND VZV. Influenza virus ( ssRNA)

DECREASED OXIDATION REDUCTION POTENTIAL IS IMPORTANT FACTOR FOR ANAEROBES TO SURVIVE IE

IN PERIDONTAL POCKET ( ACTINOMYCETES, FILAMENTOUS ROD WITH COMPACT SULFUR GRANULED
THAT ARE ALSO PRESENT IN MYCETOMA/MADURA FOOT ), TRAUMA, AND COLON ( BACTERIODES )

TREPONEMA PALLIDUM CAUSE 8TH NERVE DEAFNESS ( VIRAL CAUSE IS CMV ). CONGENITAL RUBELLA
SYNDROME CAUSE DEAFNESS, CATARACTS AND PDA
catalase
Encapsulated pathogens pigment producing bacteria + ve
organisms
Pseudomonas Actinomycesisraellii yellow pigments
:
staph Aureus
pneumococcus P pseudomonas
Golden Pigment
:

Staph Aureus
iv. meningitidis
A. influenzae type
]→Hyper-
B
capnic
bacteria
Pseudomonas
blue-green pigment
A
C :
:
Aspergillus
Candida
Serratia red Pigment E E. coli
E. coli
:

Salmonella L : listeria
Klebsiella
Biofilm producing bacteria
H : A. pylori
5. epidermidis
streptagalactiae B : Bordetella
Cryptococcus stgeptvigidans Nocardid
N
pseudomonas :

Urease pathogens H.in/-1uenzaelunencapsU1ated) ( SPACE

+ re LHBN
)
Proteus with vertical transmission
organism coagulase tire bacteria
Cryptococcus Bacteria
listeria Yersinia pestis
It -

pylori treponema +
staph Aureus
urea plasma Parasite
Nocardia toxoplasma organisms producing granulomas
Klebsiella Virus
5- epidermidis CMV
Bacteria Fungi
Rubella Francisca Bartonella Histoplasma
saprophytic
,
5.
Agra listeria coccidioides
1319 Mycobacterium Blastomyces
coxasackie B
Treponema Aspergillus
Polio Brucella parasite
Hiv
Actinomycetes Schistosoma Entamoeba
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