InstituteInstitute forfor Microbiology, Faculty ofMicrobiology, Faculty of Medicine,Medicine, Masaryk UniversityMasaryk University and St. Anna Faculty Hospitaland St. Anna Faculty Hospital, Brno, Brno Vladana WoznicováVladana Woznicová Miroslav VotavaMiroslav Votava Ondřej ZahradníčekOndřej Zahradníček Clinical MicrobiologyClinical Microbiology Lectures - dentistry studies 2016Lectures - dentistry studies 2016 InstituteInstitute forfor Microbiology, Faculty ofMicrobiology, Faculty of Medicine,Medicine, Masaryk UniversityMasaryk University and St. Anna Faculty Hospitaland St. Anna Faculty Hospital, Brno, Brno Agents of respiratory diseasesAgents of respiratory diseases Part OnePart One Importance of respiratoryImportance of respiratory infectionsinfections • The most important/frequent infectionsThe most important/frequent infections in GP‘s officein GP‘s office (respiratory tract = an ideal incubator)(respiratory tract = an ideal incubator) • BigBig economiceconomic impactimpact on the economics in general andon the economics in general and on the health care in particularon the health care in particular • Often produceOften produce outbreaks and epidemicsoutbreaks and epidemics • 75 %75 % (and even more in children) are caused by(and even more in children) are caused by virusesviruses WhereWhere is RTI localized?is RTI localized? • clinical symptomatology + specific agentsclinical symptomatology + specific agents • It is necessary to distinguish:It is necessary to distinguish: – upper respiratory tract (URT) infectionsupper respiratory tract (URT) infections (+ adjacent organs infections)(+ adjacent organs infections) – lower respiratory tract (LRT) infectionslower respiratory tract (LRT) infections (infections of lower respiratory ways + pneumonias)(infections of lower respiratory ways + pneumonias) URT infections and infections ofURT infections and infections of adjacent organsadjacent organs – infections ofinfections of nose a nasopharynxnose a nasopharynx – infections ofinfections of oropharynxoropharynx incl.incl. tonsillaetonsillae – infections ofinfections of paranasal sinusesparanasal sinuses – otitis mediaotitis media – conjunctivitisconjunctivitis LRT infections and lung infectionsLRT infections and lung infections Infections ofInfections of LRTLRT – infection ofinfection of epiglottisepiglottis – infection ofinfection of larynxlarynx andand tracheatrachea – infection ofinfection of bronchibronchi – infection ofinfection of bronchiolibronchioli • infections ofinfections of lungslungs Common flora in respiratory waysCommon flora in respiratory ways • i.e. bacteria typically found in respiratory tracti.e. bacteria typically found in respiratory tract of a healthy personof a healthy person • Nasal cavity:Nasal cavity: usually Staph. epidermidisStaph. epidermidis, less often sterile, coryneform rods, Staph. aureusStaph. aureus, pneumococcipneumococci • Pharynx:Pharynx: always neisseriae and streptococcineisseriae and streptococci (viridans group)(viridans group), usually haemophili, rarely pneumococci, meningococci, enterobacteriae, yeasts • LRW:LRW: sterilesterile, clinical materials from these sites are often contaminated by URW flora Rhinitis/nasopharyngitis - ETIOLOGYRhinitis/nasopharyngitis - ETIOLOGY • VirusesViruses – the most common -– the most common - „common cold“„common cold“:: – more than 50 % rhinovirusesmore than 50 % rhinoviruses – coronavirusescoronaviruses – other respiratory viruses (NOT flu!)other respiratory viruses (NOT flu!) • BacteriaBacteria:: – AcuteAcute infections: usually secondaryinfections: usually secondary • Staph. aureus, Haem. influenzae, Strep.Staph. aureus, Haem. influenzae, Strep. pneumoniae, Moraxella catarrhalispneumoniae, Moraxella catarrhalis – ChronicChronic infections:infections: • Klebsiella ozaenae, Kl. rhinoscleromatisKlebsiella ozaenae, Kl. rhinoscleromatis Rhinitis/nasopharyngitis - TREATMENTRhinitis/nasopharyngitis - TREATMENT • Viral etiology -Viral etiology - does NOT need antibioticdoes NOT need antibiotic treatmenttreatment andand bacteriological examinationbacteriological examination • If necessaryIf necessary (pus full of polymorphonuclears,(pus full of polymorphonuclears, high CRP levelshigh CRP levels  markers of bacterialmarkers of bacterial infection) treatment based on theinfection) treatment based on the result ofresult of bacteriological examinationbacteriological examination • Topical treatment -Topical treatment - carriers of epidemiologicallycarriers of epidemiologically important pathogensimportant pathogens - e.g. MRSA – mupirocin- e.g. MRSA – mupirocin (Bactroban)(Bactroban) Infectious rhinitis VS. allergic/vasomotoric rhihitis http://www.bupa.co.uk/health_inf ormation/asp/direct_news/gener al_health/rhinitis_240706.asp http://www.drgreene.org/body.cfm?xyzpdqabc=0&id=21&action=detail&ref=1285 Sinusitis/otitis media – ETIOLOGY ISinusitis/otitis media – ETIOLOGY I • AcuteAcute sinusitis and otitissinusitis and otitis usually started byusually started by respiratory virusesrespiratory viruses,, M. pneumoniaeM. pneumoniae (myringitis)(myringitis) • SecondarySecondary pyogenic inflammationspyogenic inflammations:: S.S. pneumoniaepneumoniae,, H. influenzaeH. influenzae type btype b, Moraxella, Moraxella catarrhalis, Staph. aureus,catarrhalis, Staph. aureus, Str. groupStr. group A, ORA, OR eveneven anaerobesanaerobes (genus(genus BacteroidesBacteroides,, PrevotellaPrevotella,, Porphyromonas...Porphyromonas...)) ComplicationsComplications: mastoiditis, purulent meningitis: mastoiditis, purulent meningitis Sinusitis/otitis media – ETIOLOGY IISinusitis/otitis media – ETIOLOGY II • SinusitisSinusitis maxillarismaxillaris chronicachronica, sinusitis, sinusitis frontalis chronica:frontalis chronica: Staph. aureusStaph. aureus,, genusgenus PeptostreptococcusPeptostreptococcus • OtitisOtitis mediamedia chronicachronica:: PseudomonasPseudomonas aeruginosa, Proteus mirabilisaeruginosa, Proteus mirabilis Sinusitis/otitis media -Sinusitis/otitis media EXAMINATION + TREATMENTEXAMINATION + TREATMENT • Relevant specimenRelevant specimen – only a– only a punctatepunctate from the middle earfrom the middle ear or paranasal sinus; NOT nasal, ear swabs (contaminants)or paranasal sinus; NOT nasal, ear swabs (contaminants) • SinusitisSinusitis ATB treatment ONLYATB treatment ONLY inin painful sinusitispainful sinusitis, with, with teathacheteathache, headache, fever, lasting at least a weak,, headache, fever, lasting at least a weak, eventually neuralgia of N. Trigeminuseventually neuralgia of N. Trigeminus • Otitis mediaOtitis media ATB when inflammation (pain, red colour,ATB when inflammation (pain, red colour, fever) and anti-inflammatory treatment not sufficientfever) and anti-inflammatory treatment not sufficient • e.g. Aminopenicillin or 1st gen. cephalosporine.g. Aminopenicillin or 1st gen. cephalosporin Sinusitis http://www.drgreene.org/body.cfm?xyzpdqabc=0&id=21&action=detail&ref=1285 Otitis media http://www.medem.com/Me dLB/article_detaillb.cfm? article_ID=ZZZPMV6D1AC &sub_cat=544 http://www.otol.uic.edu/rese arch/microto/Microtoscopy/ acute1.htm • Causative agents • as in sinusitis Conjunctivitis - ETIOLOGYConjunctivitis - ETIOLOGY • UsuallyUsually viral,viral, accompanies acute URT infections/accompanies acute URT infections/ adenovirus, enterovirusadenovirus, enterovirus - hemorrhagic conjunctivitis,- hemorrhagic conjunctivitis, HSVHSV -- herpetic keratoconjunctivitisherpetic keratoconjunctivitis • BacterialBacterial a.a. Acute:Acute: suppurative conjunctivitis:suppurative conjunctivitis: S. pneumoniae, S. aureusS. pneumoniae, S. aureus inclusion conjunct.:inclusion conjunct.: C. trachomatisC. trachomatis D – KD – K b.b. Chronic:Chronic: S. aureusS. aureus,, C. trachomatisC. trachomatis A – C (trachoma)A – C (trachoma) • Allergic, mechanicAllergic, mechanic (allien body)(allien body) • UsuallyUsually topicaltopical treatmenttreatment Oropharyngeal infections - ETIOLOGYOropharyngeal infections - ETIOLOGY • Acute tonsillitis and pharyngitis:Acute tonsillitis and pharyngitis: usuallyusually viralviral (rhinoviruses, coronaviruses,(rhinoviruses, coronaviruses, adenoviruses, EBV – inf. mononucleosis,adenoviruses, EBV – inf. mononucleosis, coxsackieviruses – herpangina)coxsackieviruses – herpangina) Most important bacterialMost important bacterial:: S. pyogenesS. pyogenes (=(= ββ-- haemol. streptococcushaemol. streptococcus group Agroup A)) • Other bacterialOther bacterial: streptococci group C, F, G,: streptococci group C, F, G, pneumococci,pneumococci, H. influenzaeH. influenzae?,?, N. meningitidisN. meningitidis?,?, • Rare, butRare, but importantimportant:: Corynebacterium diphtheriae,Corynebacterium diphtheriae, Neisseria gonorrhoeaeNeisseria gonorrhoeae Oropharyngeal infections -TREATMENTOropharyngeal infections -TREATMENT • Throat swab recommended in all casesThroat swab recommended in all cases, incl., incl. „typical tonsilitis“„typical tonsilitis“ • Streptococcus pyogenesStreptococcus pyogenes -- penicillinpenicillin stillstill the best!the best! • Macrolides, e.g. clarithromycin in allergic patientsMacrolides, e.g. clarithromycin in allergic patients only (resistance, worse effect)only (resistance, worse effect) • determinationdetermination of CRP levelof CRP level (marker of a bacterial(marker of a bacterial infection)infection) Tonsilopharyngitis http://medicine.ucsd.edu/Clinicalimg/He ad-Pharyngitis.htm http://www.newagebd.com/2005/sep/12 /img2.html Viral tonsilopharyngitis http://upload.wikimedia.org/wikipedia/commons/thumb/b/b1/Pharyngitis.jpg/250px- Pharyngitis.jpg Purulent bacterial tonsilitis http://www.meddean.luc.edu/lumen/MedEd/medicine/PULMONAR/diseases/pul43b.htm Epiglottitis http://health.allrefer.com/health/epiglottitis-throat- anatomy.html de.wikipedia.org/wiki/E piglottitis George Washington died of epiglottitis www.fathom.com/course/10701018/session4.html EpiglottitisEpiglottitis • Serious disease – medical emergencySerious disease – medical emergency The child could suffocate!The child could suffocate! • Haemophilus influenzaeHaemophilus influenzae type b („Hib“)type b („Hib“) - vaccination- vaccination Laryngitis and tracheitisLaryngitis and tracheitis • RespiratoryRespiratory virusesviruses (other(other than in nasopharyngitis):than in nasopharyngitis): parainfluenza/influenzaparainfluenza/influenza AA virusesviruses && RSVRSV Treatment symptomatic -Treatment symptomatic - antibiotics NOT recommendedantibiotics NOT recommended • Bacterial:Bacterial: Chlamydophila pneumoniaeChlamydophila pneumoniae,, MycoplasmaMycoplasma pneumoniaepneumoniae, secondary:, secondary: S. aureusS. aureus andand HaemophilusHaemophilus influenzae,influenzae, laryngotracheitis pseudomembranosalaryngotracheitis pseudomembranosa (croup):(croup): Corynebacterium diphtheriaeCorynebacterium diphtheriae • Throat swab is useless, except for chronical situations.Throat swab is useless, except for chronical situations. Lagyngitis acuta http://www.emedicine.com/asp/image_search.a sp?query=Acute%20Laryngitis www.cartoonstock.com/directory/l/laryngitis.asp Bronchitis - ETIOLOGYBronchitis - ETIOLOGY • Acute bronchitis:Acute bronchitis: influenzainfluenza, parainfluenza, adenoviruses, RSV, parainfluenza, adenoviruses, RSV Bacterial -Bacterial - secondary: pneumococci, haemofili,secondary: pneumococci, haemofili, stafylococci, moraxellaestafylococci, moraxellae Bacterial -Bacterial - primary:primary: MycoplasmaMycoplasma pneumoniae,pneumoniae, Chlamydophila pneumoniae,Chlamydophila pneumoniae, BordetellaBordetella pertussispertussis • Chronic bronchitisChronic bronchitis (cystic fibrosis):(cystic fibrosis): Pseudomonas aeruginosa, Burholderia cepaciaPseudomonas aeruginosa, Burholderia cepacia Bronchitis acutaBronchitis acuta http://www.yourlungheal th.org/lung_disease/cop d/nutshell/index.cfm http://www.lhsc.on.ca/resptherapy/students/ patho/brnchit5.htm BronchiolitisBronchiolitis • Isolated bronchiolitisIsolated bronchiolitis in newborns andin newborns and infantsinfants only:only: PneumovirusPneumovirus (=(= RSVRSV)) MetapneumovirusMetapneumovirus https://www.nlm.nih.gov PneumoniaPneumonia www.medicin enet.com/pn eumonia/arti cle.htm Types of pneumoniaeTypes of pneumoniae • Acute – community-acquired pneumoniae CAPAcute – community-acquired pneumoniae CAP – in originally healthy • adults • children – in debilitated persons – after a contact with animals (e.g. Pasteurella multocida, Coxiella burnetii - Q-fever, Chlamydophila psittaci - psittacosis) • Acute – nosocomialAcute – nosocomial pneumoniaepneumoniae - ventilator-associated a) early b) late - others • Subacute and chronic pneumoniaeSubacute and chronic pneumoniae Pneumoniae – ETIOLOGY IPneumoniae – ETIOLOGY I Acute,Acute, community-acquiredcommunity-acquired, in healthy, in healthy adultsadults • bronchopneumoniabronchopneumonia and lobar pneumonia:and lobar pneumonia: – Streptococcus pneumoniaeStreptococcus pneumoniae – Staph. aureusStaph. aureus – Haemophilus influenzaeHaemophilus influenzae type btype b • atypical pneumonia:atypical pneumonia: – Mycoplasma pneumoniaeMycoplasma pneumoniae – Chlamydophila pneumoniaeChlamydophila pneumoniae – Influenza A virusInfluenza A virus Pneumoniae – ETIOLOGY IIPneumoniae – ETIOLOGY II • Acute,Acute, community-acquiredcommunity-acquired, in, in debilitateddebilitated individuals:individuals: – pneumococci, staphylococci, haemofilipneumococci, staphylococci, haemofili – KlebsiellaKlebsiella pneumoniaepneumoniae (alcoholics)(alcoholics) – LegionellaLegionella pneumophilapneumophila • InIn more serious immunodeficiencymore serious immunodeficiency:: – Pneumocystis jiroveciiPneumocystis jirovecii – CMVCMV – atypical mycobacteriaatypical mycobacteria – Nocardia asteroidesNocardia asteroides – aspergilli, candidaeaspergilli, candidae Pneumoniae – ETIOLOGY IIIPneumoniae – ETIOLOGY III Acute,Acute, nosocomial:nosocomial: • Ventilator-associated pneumoniaVentilator-associated pneumonia - VAP:- VAP: – earlyearly (up to the 4th day of hospitalization):(up to the 4th day of hospitalization): sensitivesensitive communitycommunity strainsstrains – latelate (from the 5th day):(from the 5th day): resistantresistant hospital strainshospital strains • OthersOthers – viruses (RSV, CMV)viruses (RSV, CMV) – LegionellaLegionella Pneumoniae – ETIOLOGY IVPneumoniae – ETIOLOGY IV • Subacute and chronic:Subacute and chronic: – aspirationaspiration pneumonia and lung abscessespneumonia and lung abscesses • PrevotellaPrevotella melaninogenicamelaninogenica • BacteroidesBacteroides fragilisfragilis • peptococci andpeptococci and peptostreptococcipeptostreptococci – lung tuberculosis andlung tuberculosis and mycobacteriosesmycobacterioses • Mycobacterium tuberculosisMycobacterium tuberculosis • Mycobacterium bovisMycobacterium bovis • atypical mycobacteriaatypical mycobacteria PneumoniaPneumonia http://www.uspharmacist.com/in dex.asp? page=ce/105057/default.htm BronchopneumoniaBronchopneumonia www.szote.u-szeged.hu/radio/mellk1/amelk4a.htm See the inhomogenous shadow in the lower and middle lobes of the right lung Lobar and lobular pneumonia www.supplementnews.org/ pneumonia Lung infections - EXAMINATIONLung infections - EXAMINATION • Clinical examination and chest X-ray,Clinical examination and chest X-ray, differentiation classical × atypical pneumoniadifferentiation classical × atypical pneumonia • Classical pneumoniae -Classical pneumoniae - sputumsputum is useful, bloodis useful, blood forfor blood culture, S. pneumoniae Ag in urineblood culture, S. pneumoniae Ag in urine • Atypical pneumoniae -Atypical pneumoniae - serologyserology - mycoplasma- mycoplasma and chlamydophila (+ „viral screen“).and chlamydophila (+ „viral screen“). • Hospital pneumoniae alsoHospital pneumoniae also LegionellaLegionella examinationexamination – Ag in urine– Ag in urine Bronchitis and pneumonia -Bronchitis and pneumonia - TREATMENTTREATMENT • CAPCAP amoxicilinamoxicilin, (eventually according to a, (eventually according to a causative agent and antibiotic susceptibility)causative agent and antibiotic susceptibility) • Atypical pneumoniaeAtypical pneumoniae tetracyclinstetracyclins or (esp. inor (esp. in children < 8)children < 8) macrolidesmacrolides.. • Combination therapyCombination therapy • HospitalHospital infections -infections - susceptibility testsusceptibility test -- resistances!resistances! • In TB usually combination of drugsIn TB usually combination of drugs Gerrit Dou (1613 - 1675)Gerrit Dou (1613 - 1675) The PhysicianThe Physician