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IDSA antimicrobial resistant gram negative guidance 2024 Coxiella burnetii CDC treatment Burkholderia melioidosis CDC

antimicrobial therapy AND bacteria

site:cdc.gov Coxiella burnetii treatment doxycycline melioidosis treatment ceftazidime trimethoprim sulfamethoxazole treatment

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CDC Clinical Guidance for Q fever doxycycline 2025 treatment site:cdc.gov/q-fever and CDC tularemia brucellosis treatment

mkdir -p "/tmp/workspace/antimicrobial-reference/src" "/tmp/workspace/antimicrobial-reference/output" && python - <<'PY' from pathlib import Path p=Path('/tmp/workspace/antimicrobial-reference/src/create_reference.py') p.write_text(r'''from reportlab.lib import colors from reportlab.lib.enums import TA_CENTER, TA_LEFT from reportlab.lib.pagesizes import A4 from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle from reportlab.lib.units import mm from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle, PageBreak, KeepTogether from reportlab.pdfbase.ttfonts import TTFont from reportlab.pdfbase import pdfmetrics from reportlab.lib.colors import HexColor from reportlab.pdfbase.pdfmetrics import stringWidth from reportlab.lib import utils from pathlib import Path OUT='/tmp/workspace/antimicrobial-reference/output/Printable_Antimicrobial_Reference.pdf' NAVY=HexColor('#123047'); TEAL=HexColor('#176D73'); PALE=HexColor('#E9F2F3'); GREY=HexColor('#F4F6F7'); RED=HexColor('#9C2E2E') styles=getSampleStyleSheet() styles.add(ParagraphStyle(name='CoverTitle', parent=styles['Title'], fontName='Helvetica-Bold', fontSize=25, leading=30, textColor=NAVY, alignment=TA_CENTER, spaceAfter=10)) styles.add(ParagraphStyle(name='CoverSub', parent=styles['BodyText'], fontSize=11, leading=15, alignment=TA_CENTER, textColor=HexColor('#40515b'))) styles.add(ParagraphStyle(name='H1x', parent=styles['Heading1'], fontName='Helvetica-Bold', fontSize=16, leading=20, textColor=NAVY, spaceBefore=4, spaceAfter=8)) styles.add(ParagraphStyle(name='H2x', parent=styles['Heading2'], fontName='Helvetica-Bold', fontSize=11, leading=14, textColor=TEAL, spaceBefore=9, spaceAfter=4)) styles.add(ParagraphStyle(name='Bodyx', parent=styles['BodyText'], fontSize=8.2, leading=10.5, spaceAfter=4)) styles.add(ParagraphStyle(name='Small', parent=styles['BodyText'], fontSize=6.8, leading=8.2)) styles.add(ParagraphStyle(name='Tiny', parent=styles['BodyText'], fontSize=5.9, leading=7.1)) styles.add(ParagraphStyle(name='Callout', parent=styles['BodyText'], fontSize=8, leading=10, leftIndent=5, rightIndent=5, textColor=NAVY)) def P(x,style='Small'): return Paragraph(str(x),styles[style]) def footer(canvas,doc): canvas.saveState(); w,h=A4 canvas.setStrokeColor(TEAL); canvas.setLineWidth(.5); canvas.line(15*mm,12*mm,w-15*mm,12*mm) canvas.setFont('Helvetica',7); canvas.setFillColor(HexColor('#52616A')) canvas.drawString(15*mm,7.5*mm,'Printable Antimicrobial Reference | Targeted therapy summary | September 2026') canvas.drawRightString(w-15*mm,7.5*mm,f'Page {doc.page}') canvas.restoreState() def table(rows, widths=(38*mm,52*mm,55*mm,40*mm)): data=[[P(x,'Small') for x in r] for r in rows] t=Table(data,colWidths=widths,repeatRows=1,hAlign='LEFT') t.setStyle(TableStyle([('BACKGROUND',(0,0),(-1,0),NAVY),('TEXTCOLOR',(0,0),(-1,0),colors.white),('FONTNAME',(0,0),(-1,0),'Helvetica-Bold'),('VALIGN',(0,0),(-1,-1),'TOP'),('GRID',(0,0),(-1,-1),.25,HexColor('#BDCCCF')),('ROWBACKGROUNDS',(0,1),(-1,-1),[colors.white,GREY]),('LEFTPADDING',(0,0),(-1,-1),3),('RIGHTPADDING',(0,0),(-1,-1),3),('TOPPADDING',(0,0),(-1,-1),3),('BOTTOMPADDING',(0,0),(-1,-1),3)])) return t def section(story,title,intro, rows): story += [Paragraph(title,styles['H1x']), Paragraph(intro,styles['Bodyx']), table([['Organism / context','Usual targeted first choice','Alternatives / escalation','Key cautions / exceptions']]+rows), Spacer(1,6)] story=[] story += [Spacer(1,28*mm),Paragraph('ANTIMICROBIAL<br/>REFERENCE',styles['CoverTitle']),Paragraph('Organism-centered targeted therapy for common, resistant, atypical, zoonotic, and selected fungal, parasitic, and viral pathogens',styles['CoverSub']),Spacer(1,12*mm)] cover=[['PURPOSE','A printable educational quick-reference. Adult regimens are named, not dosed. It is not an empiric-therapy guide and does not replace local susceptibility testing, national guidance, or infectious-diseases consultation.'],['HOW TO READ','“First choice” means usual definitive treatment when the organism is susceptible and the clinical syndrome is typical. Infection site, source control, MIC, allergy, pregnancy, renal/hepatic function, immune status, and local resistance can change the choice.'],['URGENT FLAGS','Meningitis, endocarditis, bacteremia, necrotizing infection, septic shock, pregnancy, neonatal disease, prosthetic material, immunocompromise, and biothreat/select-agent pathogens require specialist input.']] ct=Table([[P(a,'Small'),P(b,'Small')] for a,b in cover],colWidths=[35*mm,150*mm]) ct.setStyle(TableStyle([('BACKGROUND',(0,0),(0,-1),PALE),('BOX',(0,0),(-1,-1),.6,TEAL),('INNERGRID',(0,0),(-1,-1),.25,HexColor('#BDCCCF')),('VALIGN',(0,0),(-1,-1),'TOP'),('LEFTPADDING',(0,0),(-1,-1),6),('RIGHTPADDING',(0,0),(-1,-1),6),('TOPPADDING',(0,0),(-1,-1),5),('BOTTOMPADDING',(0,0),(-1,-1),5)])) story += [ct,Spacer(1,13*mm),Paragraph('Scope: bacteria, mycobacteria, fungi, parasites and viruses most often requested in clinical and examination settings. Exact dosages and durations are intentionally omitted because they depend on syndrome and patient factors.',styles['Callout']),PageBreak()] story += [Paragraph('Use and stewardship',styles['H1x']),Paragraph('<b>Before selecting treatment:</b> identify infection rather than colonization; obtain cultures where possible; assess severity and source; begin syndrome-appropriate empiric therapy only when indicated; then narrow to the least broad effective agent. In vitro “susceptible” does not necessarily mean clinically preferred.',styles['Bodyx']),Paragraph('Intrinsic resistance, inducible resistance, and inadequate tissue penetration are common causes of failure. For bloodstream infection, endocarditis, CNS infection, deep abscess, osteomyelitis, prosthetic-device infection, and biofilm-associated infection, consult site-specific guidance.',styles['Bodyx']),Paragraph('Quick cautions',styles['H2x'])] cautions=[['Scenario','Do not oversimplify'],['MSSA','Use an anti-staphylococcal beta-lactam when possible. Vancomycin is generally inferior for definitive MSSA bacteremia.'],['Enterococcus','Species and susceptibility to ampicillin and vancomycin matter. Serious endovascular infection may require combination therapy.'],['ESBL Enterobacterales','For infection outside uncomplicated cystitis, carbapenem therapy is often preferred when susceptible.'],['AmpC-risk Enterobacterales','Avoid relying on ceftriaxone for invasive infection caused by E. cloacae complex, K. aerogenes, or C. freundii; cefepime is often used if susceptible.'],['Pseudomonas / Acinetobacter','Use a susceptible antipseudomonal or CRAB-directed regimen, guided by local and IDSA AMR guidance.'],['Anaerobes','Drainage/debridement is often as important as antibiotics.']] story += [table(cautions),PageBreak()] section(story,'1. Gram-positive cocci and rods','“Targeted” assumes a clinically significant isolate. Listed agents are usual choices, not universal empiric regimens.',[ ['MSSA','Cefazolin or nafcillin/oxacillin','Flucloxacillin where used; vancomycin only for severe beta-lactam allergy','For bacteremia/endocarditis, beta-lactam preferred; remove infected devices.'], ['MRSA','Vancomycin for invasive disease','Daptomycin for bacteremia/right-sided endocarditis; linezolid for pneumonia; TMP-SMX/doxycycline for selected uncomplicated SSTI','Do not use daptomycin for pneumonia. Source control essential.'], ['Coagulase-negative staphylococci','Vancomycin if methicillin-resistant or susceptibility unknown','Cefazolin/nafcillin if methicillin-susceptible','Often contaminant; assess prosthetic material and multiple positive cultures.'], ['Group A Streptococcus (S. pyogenes)','Penicillin or amoxicillin','Cephalexin; macrolide only if susceptible','In necrotizing fasciitis or streptococcal toxic shock: penicillin + clindamycin plus urgent surgery.'], ['Group B Streptococcus (S. agalactiae)','Penicillin G or ampicillin','Cefazolin','Clindamycin only if documented susceptible. Neonatal disease needs syndrome-specific treatment.'], ['S. pneumoniae','Penicillin/amoxicillin if susceptible, non-CNS','Ceftriaxone/cefotaxime; respiratory fluoroquinolone selected settings','For meningitis, use ceftriaxone/cefotaxime + vancomycin empirically then tailor to MIC.'], ['Viridans streptococci','Penicillin G or ceftriaxone','Vancomycin for serious beta-lactam allergy','Endocarditis regimen depends on penicillin MIC and valve type.'], ['Enterococcus faecalis','Ampicillin if susceptible','Vancomycin; ampicillin + ceftriaxone for many endocarditis cases','Cephalosporins lack reliable activity. Check high-level aminoglycoside resistance.'], ['Enterococcus faecium / VRE','Linezolid or high-dose daptomycin when susceptible','Tigecycline for non-bacteremic selected sites','Often ampicillin- and vancomycin-resistant; specialist input for bacteremia/endocarditis.'], ['Listeria monocytogenes','Ampicillin','Penicillin G; TMP-SMX for allergy','Cephalosporins are ineffective. Consider gentamicin synergy only case-specifically.'], ['Corynebacterium diphtheriae','Erythromycin or penicillin plus antitoxin','Azithromycin','Antitoxin and isolation matter; confirm eradication culture.'], ['Bacillus anthracis','Ciprofloxacin or doxycycline','Levofloxacin; severe systemic disease requires combination treatment + antitoxin consideration','Notify public health. Inhalational/meningeal disease requires specialist protocol.'], ['Erysipelothrix rhusiopathiae','Penicillin','Ceftriaxone','Intrinsic resistance to vancomycin. Endocarditis needs prolonged therapy.']]) section(story,'2. Anaerobes and toxin-mediated bacteria','Therapy must cover the whole polymicrobial syndrome when applicable.',[ ['Bacteroides fragilis group','Metronidazole; beta-lactam/beta-lactamase inhibitor; carbapenem','Ceftriaxone + metronidazole','Drain intra-abdominal/pelvic collections. Clindamycin resistance is common.'], ['Fusobacterium necrophorum','Ampicillin-sulbactam or piperacillin-tazobactam','Ceftriaxone + metronidazole; carbapenem','Lemierre syndrome: assess thrombosis and metastatic infection.'], ['Clostridium perfringens myonecrosis','Urgent surgery + penicillin G + clindamycin','Broad regimen until cultures define pathogen','Surgical debridement is life-saving; do not delay.'], ['Clostridioides difficile','Fidaxomicin','Oral vancomycin','Stop unnecessary antibiotics. Fulminant disease needs urgent specialist/surgical assessment.'], ['Actinomyces spp.','Penicillin G then oral amoxicillin','Doxycycline; clindamycin','Requires prolonged therapy and drainage when abscessed.'], ['Cutibacterium acnes','Penicillin G or ceftriaxone','Clindamycin if susceptible','Consider true infection with prosthetic joint/shunt, not simple skin contamination.']]) section(story,'3. Enterobacterales and common urinary/GI gram-negative bacilli','For urinary isolates, choose agents that achieve urinary concentrations. For invasive disease, culture-directed IV therapy and source control are needed.',[ ['E. coli, non-ESBL','Ceftriaxone for invasive infection; nitrofurantoin or TMP-SMX for uncomplicated cystitis if susceptible','Amoxicillin-clavulanate selected cases; fluoroquinolone only when benefit outweighs risk','Avoid nitrofurantoin for pyelonephritis/bacteremia.'], ['Klebsiella pneumoniae, non-ESBL','Ceftriaxone if susceptible','Cefepime or piperacillin-tazobactam per syndrome/susceptibility','Beware ESBL and carbapenemase production.'], ['Proteus mirabilis','Ceftriaxone or TMP-SMX if susceptible','Amoxicillin-clavulanate','Intrinsic resistance to nitrofurantoin; consider stone with recurrent infection.'], ['Morganella, Providencia, Serratia','Cefepime if invasive and susceptible','Carbapenem when ESBL or resistance pattern warrants','Variable inducible AmpC patterns. Avoid simplistic ceftriaxone use in serious infection.'], ['Enterobacter cloacae complex, K. aerogenes, C. freundii','Cefepime if susceptible','Carbapenem for ESBL/co-resistance or severe infection','Moderate risk of clinically relevant AmpC induction.'], ['ESBL-producing Enterobacterales','Carbapenem for invasive disease','TMP-SMX or fluoroquinolone only if susceptible and appropriate site; uncomplicated cystitis has specific options','Avoid extrapolating UTI options to bacteremia/CNS infection.'], ['Carbapenem-resistant Enterobacterales','Mechanism-guided newer beta-lactam/beta-lactamase inhibitor regimen','Ceftazidime-avibactam + aztreonam for MBL producers; cefiderocol selected cases','Require carbapenemase testing and ID/AMR guidance.'], ['Salmonella Typhi/Paratyphi','Ceftriaxone or azithromycin guided by regional resistance','Meropenem for XDR/severe disease','Fluoroquinolone susceptibility is geographically variable.'], ['Nontyphoidal Salmonella','Supportive care if uncomplicated; ceftriaxone for invasive disease','Azithromycin or ciprofloxacin if susceptible','Antibiotics not routine for uncomplicated gastroenteritis.'], ['Shigella spp.','Azithromycin, ciprofloxacin, or ceftriaxone only if treatment indicated and susceptible','TMP-SMX if susceptible','Resistance is evolving; obtain susceptibility especially in severe illness.'], ['Yersinia enterocolitica','Supportive care usually','TMP-SMX, ciprofloxacin, or ceftriaxone for severe/invasive disease','Antibiotics reserved for severe, systemic, or high-risk disease.']]) section(story,'4. Non-fermenters and resistant environmental gram-negative bacilli','Susceptibility testing is central. Colonization, especially in cystic fibrosis and chronic wounds, must be distinguished from infection.',[ ['Pseudomonas aeruginosa','A susceptible antipseudomonal beta-lactam: cefepime, piperacillin-tazobactam, ceftazidime, or meropenem','Newer agents based on phenotype: ceftolozane-tazobactam, ceftazidime-avibactam, imipenem-relebactam, cefiderocol','Do not treat colonization. DTR strains need IDSA AMR-guided selection.'], ['Acinetobacter baumannii, susceptible','Ampicillin-sulbactam if susceptible','Carbapenem if susceptible','For CRAB, sulbactam-durlobactam plus imipenem-cilastatin is preferred where available; specialist input.'], ['Stenotrophomonas maltophilia','TMP-SMX when active','Minocycline, levofloxacin, or cefiderocol depending on syndrome and susceptibility','Frequently colonizes respiratory tract; intrinsic resistance limits beta-lactams. Severe infection may need combination strategy.'], ['Burkholderia cepacia complex','TMP-SMX if susceptible','Ceftazidime, meropenem, minocycline guided by susceptibility','Intrinsically resistant to polymyxins and aminoglycosides. CF specialist input.'], ['Burkholderia pseudomallei (melioidosis)','Initial: ceftazidime or meropenem; eradication: TMP-SMX','Amoxicillin-clavulanate when TMP-SMX cannot be used','Two phases are essential. Resistant to aminoglycosides and many early cephalosporins.'], ['Burkholderia mallei (glanders)','Ceftazidime or meropenem initial, then TMP-SMX eradication','Amoxicillin-clavulanate','Rare/select-agent infection: public health and specialist management.'], ['Achromobacter xylosoxidans','TMP-SMX, piperacillin-tazobactam, or meropenem if susceptible','Ceftazidime','Variable multidrug resistance; do not assume Pseudomonas regimen applies.'], ['Elizabethkingia anophelis','Minocycline or fluoroquinolone based on susceptibility','TMP-SMX; rifampin combinations selected cases','Often resistant to carbapenems and many beta-lactams; seek expert advice.']]) section(story,'5. Respiratory, fastidious, water-associated, and bite-related bacteria','Treat clinical infection, not an isolated colonization result. Water-exposure and animal-bite history can change empiric coverage.',[ ['Neisseria meningitidis','Ceftriaxone or cefotaxime','Penicillin G if susceptible','Droplet precautions and contact chemoprophylaxis.'], ['Neisseria gonorrhoeae','Ceftriaxone','None routinely preferred; obtain culture for suspected failure','Add chlamydia therapy if not excluded. Follow current national guidance.'], ['Haemophilus influenzae','Amoxicillin if beta-lactamase negative; ceftriaxone for invasive disease','Amoxicillin-clavulanate','Ampicillin resistance via beta-lactamase is common.'], ['Moraxella catarrhalis','Amoxicillin-clavulanate','Doxycycline or macrolide where appropriate','Most produce beta-lactamase.'], ['Legionella pneumophila','Azithromycin or levofloxacin','Doxycycline','Use urinary antigen/PCR as appropriate; beta-lactams do not treat intracellular infection.'], ['Mycoplasma pneumoniae','Azithromycin','Doxycycline; respiratory fluoroquinolone for adults','No cell wall: beta-lactams ineffective. Macrolide resistance varies.'], ['Chlamydia trachomatis','Doxycycline','Azithromycin, especially selected pregnancy/adherence contexts','Use syndrome-specific STI guidance; treat partners and test for co-infection.'], ['Bordetella pertussis','Azithromycin','Clarithromycin or TMP-SMX','Early treatment limits transmission more than it alters late cough.'], ['Vibrio vulnificus','Doxycycline + third-generation cephalosporin','Fluoroquinolone-based regimen','Necrotizing wound infection requires emergency debridement.'], ['Vibrio cholerae','Rehydration is primary; doxycycline/azithromycin for severe disease','Ciprofloxacin if susceptible','Antibiotic choice reflects local resistance.'], ['Aeromonas spp.','Ciprofloxacin or cefepime if susceptible','TMP-SMX','Water-associated severe SSTI requires surgery when indicated; resistance patterns variable.'], ['Campylobacter jejuni','Supportive care; azithromycin if severe/high risk','None routinely','Fluoroquinolone resistance common.'], ['Helicobacter pylori','Bismuth quadruple therapy, 14 days','Susceptibility-guided regimens','Not a simple single-drug infection. Avoid empiric clarithromycin triple therapy unless proven appropriate.'], ['Pasteurella multocida','Amoxicillin-clavulanate','Ampicillin-sulbactam; doxycycline selected allergy contexts','Animal bites commonly polymicrobial.'], ['Capnocytophaga canimorsus','Amoxicillin-clavulanate or ampicillin-sulbactam','Piperacillin-tazobactam','Sepsis risk is high after dog exposure in asplenia/alcohol use.'], ['Eikenella corrodens','Amoxicillin-clavulanate or ampicillin-sulbactam','Ceftriaxone','Human-bite flora; intrinsically resistant to clindamycin and metronidazole.']]) section(story,'6. Zoonotic, intracellular, and rare bacteria','Many of these organisms require special diagnostic testing, prolonged therapy, or public-health notification. Routine laboratory culture may be hazardous or unhelpful.',[ ['Coxiella burnetii, acute Q fever','Doxycycline','TMP-SMX in pregnancy in consultation','Do not await early serology if clinical suspicion is high.'], ['Coxiella burnetii, endocarditis/vascular infection','Doxycycline + hydroxychloroquine','Specialist-directed alternatives','Prolonged therapy, serology monitoring, and ophthalmic monitoring are required.'], ['Brucella spp.','Doxycycline + rifampin','Doxycycline + aminoglycoside for selected focal/severe disease','Combination and prolonged treatment; assess focal osteoarticular/endocardial disease.'], ['Francisella tularensis','Ciprofloxacin, doxycycline, or gentamicin','Levofloxacin','Severe disease often uses aminoglycoside; current CDC 2025 guidance supports several first-line choices.'], ['Bartonella henselae, uncomplicated cat-scratch','Usually supportive; azithromycin may shorten lymphadenopathy','Doxycycline + rifampin for complicated disease','Bacillary angiomatosis/endocarditis needs specialist regimens.'], ['Bartonella endocarditis','Doxycycline + gentamicin, specialist-directed','Doxycycline + rifampin in selected cases','Culture-negative endocarditis work-up required.'], ['Rickettsia rickettsii / typhus group','Doxycycline','None preferred','Treat immediately on suspicion. Do not defer for test confirmation.'], ['Ehrlichia / Anaplasma','Doxycycline','Rifampin only selected alternatives','Doxycycline is appropriate for severe disease in children when indicated.'], ['Orientia tsutsugamushi','Doxycycline','Azithromycin','Pregnancy and regional resistance influence choice.'], ['Leptospira spp.','Doxycycline or penicillin/ceftriaxone for severe disease','Amoxicillin','Severity determines route; manage organ failure.'], ['Borrelia burgdorferi','Doxycycline','Amoxicillin or cefuroxime; ceftriaxone for selected neurologic/cardiac disease','Regimen depends on syndrome and pregnancy.'], ['Treponema pallidum','Benzathine penicillin G for uncomplicated syphilis','Doxycycline for nonpregnant penicillin-allergic patients','Neurosyphilis/ocular/otic disease requires IV penicillin; pregnancy requires penicillin desensitization.'], ['Tropheryma whipplei','Ceftriaxone or meropenem induction then prolonged TMP-SMX or doxycycline-hydroxychloroquine','Specialist-directed','CNS involvement and relapse require careful follow-up.'], ['Nocardia spp.','TMP-SMX','Linezolid, imipenem, amikacin depending on species/severity','Speciate and test susceptibility. Brain imaging is often indicated in disseminated disease.']]) section(story,'7. Mycobacteria','Never treat mycobacterial infection from a single generic susceptibility rule. Species identification and standardized susceptibility methods are necessary.',[ ['Drug-susceptible M. tuberculosis','Rifampin + isoniazid + pyrazinamide + ethambutol, then continuation phase','Use national TB program regimen','Always obtain susceptibility, assess interactions, and use public-health/DOT systems.'], ['Drug-resistant TB','All-oral, susceptibility-guided multidrug regimen','National TB expert program','Do not improvise. Bedaquiline-containing regimens often central under current guidance.'], ['M. leprae','Multidrug therapy: rifampin + dapsone + clofazimine','National program protocol','Classify paucibacillary/multibacillary per local program.'], ['M. avium complex','Macrolide + ethambutol + rifamycin for pulmonary disease','Add parenteral amikacin for severe/cavitary disease','Avoid macrolide monotherapy due to resistance.'], ['M. kansasii','Rifampin + ethambutol + isoniazid or macrolide','Susceptibility-guided','Rifampin susceptibility strongly predicts outcome.'], ['M. marinum','Doxycycline or clarithromycin','Rifampin + ethambutol for deeper disease','Fish-tank exposure; consider surgery for tenosynovitis.'], ['M. abscessus complex','Macrolide-based multidrug regimen with IV agents guided by subspecies/susceptibility','Amikacin, imipenem, cefoxitin, tigecycline selected combinations','Inducible macrolide resistance via erm gene is pivotal. Specialist care required.']]) section(story,'8. Selected fungi, parasites, and viruses','These are included because “antimicrobial” extends beyond antibacterial agents. Site and host immune status fundamentally change therapy.',[ ['Candida albicans invasive infection','Echinocandin','Fluconazole step-down if stable, susceptible, and bloodstream cleared','Remove/replace implicated catheter where feasible; obtain eye evaluation per guidance.'], ['Candida glabrata / auris','Echinocandin','Susceptibility-guided azole or amphotericin B','C. auris requires infection-control actions and expert advice.'], ['Aspergillus invasive disease','Voriconazole','Isavuconazole; liposomal amphotericin B','Therapeutic drug monitoring for voriconazole; reduce immunosuppression if possible.'], ['Mucormycosis','Liposomal amphotericin B + urgent debridement','Isavuconazole or posaconazole','Emergency condition. Reverse ketoacidosis/immunosuppression where possible.'], ['Cryptococcal meningitis','Liposomal amphotericin B + flucytosine induction','Fluconazole consolidation/maintenance','Control raised intracranial pressure; regimen differs by host setting.'], ['Pneumocystis jirovecii pneumonia','TMP-SMX','Atovaquone, pentamidine, clindamycin-primaquine','Add corticosteroids for hypoxemic disease; check G6PD where relevant.'], ['Malaria, uncomplicated P. falciparum','Artemisinin-based combination therapy','Atovaquone-proguanil, per regional guidance','Species, location of acquisition, pregnancy, and severity determine regimen.'], ['Severe malaria','IV artesunate','None equivalent','Medical emergency; follow national malaria protocol.'], ['Toxoplasma encephalitis','Pyrimethamine + sulfadiazine + leucovorin','TMP-SMX','Treat empirically in compatible HIV presentation while confirming.'], ['HSV encephalitis','IV acyclovir','None preferred','Start immediately when suspected; renal adjustment required.'], ['Influenza','Oseltamivir','Zanamivir, peramivir, baloxavir selected cases','Treat hospitalized/severe cases promptly regardless of timing.'], ['COVID-19 outpatient high-risk','Nirmatrelvir-ritonavir if eligible','Remdesivir; molnupiravir when options unsuitable','Screen major drug interactions and renal/hepatic eligibility.'], ['HIV','Combination antiretroviral therapy','Individualized regimen','Use current national guideline and resistance/genotype testing.']]) story += [PageBreak(),Paragraph('Reference sources and update note',styles['H1x']),Paragraph('This compact reference synthesizes standard textbook microbiology and pharmacology principles with current public-health and specialty guidance. It intentionally avoids fixed doses and treatment durations. Users should check their local antimicrobial formulary and antibiogram before prescribing.',styles['Bodyx']),Paragraph('<b>Key sources consulted</b>',styles['H2x']),Paragraph('• Jawetz, Melnick & Adelberg’s Medical Microbiology, 28th ed.<br/>• Medical Microbiology, 9th ed.<br/>• Sherris & Ryan’s Medical Microbiology, 8th ed.<br/>• Harrison’s Principles of Internal Medicine, 22nd ed.<br/>• Goodman & Gilman’s The Pharmacological Basis of Therapeutics.<br/>• CDC Clinical Guidance for Q Fever: doxycycline is first-line for most adults with acute Q fever; chronic endocarditis/vascular infection requires doxycycline plus hydroxychloroquine and prolonged monitoring.<br/>• CDC Tularemia Recommendations, 2025: ciprofloxacin, levofloxacin, gentamicin, or doxycycline are first-line options depending on patient and illness factors.<br/>• CDC Melioidosis Clinical Overview and consensus references: initial ceftazidime or meropenem, followed by prolonged TMP-SMX eradication therapy when appropriate.<br/>• IDSA Guidance on Treatment of Antimicrobial-Resistant Gram-Negative Infections, 2024, for ESBL-E, AmpC-E, CRE, DTR P. aeruginosa, CRAB, and S. maltophilia.',styles['Bodyx']),Spacer(1,8),Paragraph('<b>Important update warning:</b> AMR recommendations, particularly for ESBL/CRE, carbapenem-resistant A. baumannii, DTR Pseudomonas, and S. maltophilia, change rapidly. The 2024 IDSA AMR guidance (PMID 39108079) should be checked against newer local or national updates. Recent systematic reviews identified continuing global resistance pressure (PMIDs 38800756, 40234749), but they do not replace pathogen- and site-specific guidance.',styles['Callout'])] doc=SimpleDocTemplate(OUT,pagesize=A4,rightMargin=12*mm,leftMargin=12*mm,topMargin=14*mm,bottomMargin=17*mm,title='Printable Antimicrobial Reference',author='Orris') doc.build(story,onFirstPage=footer,onLaterPages=footer) print(OUT) ''') PY python "/tmp/workspace/antimicrobial-reference/src/create_reference.py" && ls -lh "/tmp/workspace/antimicrobial-reference/output/Printable_Antimicrobial_Reference.pdf"

~/antimicrobial-reference/src/create_reference.py

python "/tmp/workspace/antimicrobial-reference/src/create_reference.py" && python - <<'PY' from pypdf import PdfReader p='/tmp/workspace/antimicrobial-reference/output/Printable_Antimicrobial_Reference.pdf' r=PdfReader(p) print('pages',len(r.pages),'size',__import__('os').path.getsize(p)) for i in [0,1,len(r.pages)-1]: t=r.pages[i].extract_text() or '' print(i+1, len(t), t[:120].replace('\n',' | ')) PY ls -lh "/tmp/workspace/antimicrobial-reference/output/Printable_Antimicrobial_Reference.pdf"

infective endocarditis AND treatment

2023 ESC guidelines infective endocarditis antibiotic treatment rare culture negative endocarditis Coxiella Bartonella Brucella

https://api.iscpcardio.org/storage/guidelines/___23_ESC_Endo…

infective endocarditis AND guideline

https://pmc.ncbi.nlm.nih.gov/articles/PMC12779890

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2023 ESC Guidelines endocarditis Table antibiotic treatment blood culture negative infective endocarditis dosing PDF

infective endocarditis AND treatment

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mkdir -p "/tmp/workspace/ie-treatment-reference/src" "/tmp/workspace/ie-treatment-reference/output" && python - <<'PY' from pathlib import Path Path('/tmp/workspace/ie-treatment-reference/src/create_ie_pdf.py').write_text(r'''from reportlab.lib import colors from reportlab.lib.pagesizes import A4 from reportlab.lib.styles import getSampleStyleSheet, ParagraphStyle from reportlab.lib.units import mm from reportlab.lib.enums import TA_CENTER from reportlab.lib.colors import HexColor from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, Table, TableStyle, PageBreak from pypdf import PdfReader OUT='/tmp/workspace/ie-treatment-reference/output/Infective_Endocarditis_Treatment_Adult_Dosing_Reference.pdf' NAVY=HexColor('#123047'); TEAL=HexColor('#126B70'); PALE=HexColor('#E9F3F3'); GREY=HexColor('#F5F7F7'); AMBER=HexColor('#FFF4D6'); RED=HexColor('#8E2525') S=getSampleStyleSheet() S.add(ParagraphStyle(name='CT',parent=S['Title'],fontName='Helvetica-Bold',fontSize=23,leading=27,textColor=NAVY,alignment=TA_CENTER)) S.add(ParagraphStyle(name='CS',parent=S['BodyText'],fontSize=10.5,leading=14,alignment=TA_CENTER,textColor=HexColor('#47565F'))) S.add(ParagraphStyle(name='H1x',parent=S['Heading1'],fontName='Helvetica-Bold',fontSize=15,leading=18,textColor=NAVY,spaceBefore=2,spaceAfter=6)) S.add(ParagraphStyle(name='H2x',parent=S['Heading2'],fontName='Helvetica-Bold',fontSize=10,leading=12,textColor=TEAL,spaceBefore=7,spaceAfter=3)) S.add(ParagraphStyle(name='B',parent=S['BodyText'],fontSize=7.3,leading=9.2,spaceAfter=3)) S.add(ParagraphStyle(name='T',parent=S['BodyText'],fontSize=6.25,leading=7.45)) S.add(ParagraphStyle(name='N',parent=S['BodyText'],fontSize=6.75,leading=8.3,textColor=NAVY)) def p(x,sty='T'): return Paragraph(str(x),S[sty]) def foot(c,d): c.saveState(); w,h=A4; c.setStrokeColor(TEAL); c.setLineWidth(.5); c.line(12*mm,11*mm,w-12*mm,11*mm); c.setFillColor(HexColor('#53616A')); c.setFont('Helvetica',6.5); c.drawString(12*mm,7*mm,'Infective Endocarditis - Adult Dosing Reference | Educational use only | 20 Sep 2026'); c.drawRightString(w-12*mm,7*mm,f'Page {d.page}'); c.restoreState() def tbl(rows,widths=(37*mm,63*mm,29*mm,53*mm)): data=[[p(x) for x in r] for r in rows] t=Table(data,colWidths=widths,repeatRows=1,hAlign='LEFT') t.setStyle(TableStyle([('BACKGROUND',(0,0),(-1,0),NAVY),('TEXTCOLOR',(0,0),(-1,0),colors.white),('FONTNAME',(0,0),(-1,0),'Helvetica-Bold'),('VALIGN',(0,0),(-1,-1),'TOP'),('GRID',(0,0),(-1,-1),.24,HexColor('#BDCBCE')),('ROWBACKGROUNDS',(0,1),(-1,-1),[colors.white,GREY]),('LEFTPADDING',(0,0),(-1,-1),2.7),('RIGHTPADDING',(0,0),(-1,-1),2.7),('TOPPADDING',(0,0),(-1,-1),2.8),('BOTTOMPADDING',(0,0),(-1,-1),2.8)])) return t def section(story,title,desc,rows): story += [Paragraph(title,S['H1x']),Paragraph(desc,S['B']),tbl([['Pathogen / situation','Preferred adult regimen','Usual duration','Key constraints / alternatives']]+rows),Spacer(1,5)] story=[] story += [Spacer(1,25*mm),Paragraph('INFECTIVE ENDOCARDITIS<br/>TREATMENT',S['CT']),Paragraph('Adult organism-specific dosing tables: native valve, prosthetic valve, culture-negative and rare pathogens',S['CS']),Spacer(1,10*mm)] intro=[['Intended use','A compact adult reference for targeted therapy after cultures, susceptibility and valve/device status are known. Doses are typical adult doses with normal renal function. It is not a substitute for an Endocarditis Team, local protocol, infectious-diseases pharmacy review, or formal guideline.'],['Scope','Native-valve IE (NVE), prosthetic-valve IE (PVE), cardiac-device infection, common bacteria, HACEK, non-HACEK gram-negative bacilli, and rare blood-culture-negative IE. Pediatric, pregnancy, dialysis and severe hepatic disease require separate regimens.'],['Non-negotiable steps','Before antibiotics whenever possible obtain 3 blood-culture sets. Perform TTE and usually TOE/TEE. Repeat cultures until clear. Identify/remove infected device material; drain abscesses. Assess early surgery for heart failure, uncontrolled infection, abscess, persistent bacteremia, large embolic-risk vegetations, fungal IE, and resistant pathogens.']] t=Table([[p(a,'N'),p(b,'N')] for a,b in intro],colWidths=[34*mm,148*mm]) t.setStyle(TableStyle([('BACKGROUND',(0,0),(0,-1),PALE),('BOX',(0,0),(-1,-1),.6,TEAL),('INNERGRID',(0,0),(-1,-1),.25,HexColor('#BDCBCE')),('VALIGN',(0,0),(-1,-1),'TOP'),('LEFTPADDING',(0,0),(-1,-1),5),('RIGHTPADDING',(0,0),(-1,-1),5),('TOPPADDING',(0,0),(-1,-1),5),('BOTTOMPADDING',(0,0),(-1,-1),5)])) story += [t,Spacer(1,8*mm),Paragraph('<b>Important:</b> “Duration” is a usual minimum and is measured from the first day of effective therapy, generally the first negative blood culture. PVE generally requires ≥6 weeks. Dose-adjust all renally cleared drugs. Do not use these tables to select empiric treatment in unstable patients.',S['B']),PageBreak()] story += [Paragraph('Core dosing and monitoring',S['H1x']),Paragraph('Use therapeutic drug monitoring and specialist oversight. Aminoglycosides and vancomycin require individualized pharmacokinetic targets; the simple doses below do not replace local TDM protocols.',S['B'])] monitor=[['Drug','Common adult IE dose shown in tables','High-yield monitoring / caution'],['Vancomycin','15-20 mg/kg IV every 8-12 h, individualized','AUC-guided monitoring preferred; renal function; avoid unnecessary concomitant nephrotoxins.'],['Gentamicin, synergy','1 mg/kg IV every 8 h or local extended-interval protocol','TDM and renal function at least weekly. Ototoxicity/nephrotoxicity. Avoid routine use in staphylococcal NVE.'],['Daptomycin','10 mg/kg IV every 24 h','Creatine kinase weekly or more often with statins; not for pneumonia.'],['Rifampin','300 mg PO/IV every 8 h or 600 mg every 12 h','Major drug interactions; hepatotoxicity. Use only for foreign-material IE in standard staphylococcal regimens, generally after bacteremia is controlled.'],['Hydroxychloroquine','200 mg PO every 8 h','Baseline and serial eye exams for prolonged Coxiella regimen; QT and interaction review.']] story += [tbl(monitor),Spacer(1,6)] story += [Paragraph('Abbreviations: IV = intravenous; PO = oral; q24h/q12h/q8h/q6h/q4h = every 24/12/8/6/4 hours; MIC = minimum inhibitory concentration; HLAR = high-level aminoglycoside resistance; TDM = therapeutic drug monitoring.',S['B']),PageBreak()] section(story,'1. Staphylococcal infective endocarditis','Prefer an anti-staphylococcal beta-lactam for susceptible MSSA. Routine aminoglycoside addition is not recommended in staphylococcal NVE because toxicity exceeds benefit. Regimens must be tailored to surgical/device status and susceptibility.',[ ['MSSA, NVE','Nafcillin or oxacillin 2 g IV q4h <b>or</b> cefazolin 2 g IV q8h','6 weeks','Cefazolin is a common alternative for non-anaphylactic penicillin allergy. Consider allergy evaluation rather than default vancomycin.'], ['MRSA, NVE','Vancomycin, AUC-guided <b>or</b> daptomycin 10 mg/kg IV q24h','6 weeks','Use daptomycin at high dose. Obtain susceptibility; persistent bacteremia needs source-control and surgical review.'], ['Methicillin-susceptible CoNS, NVE','Nafcillin/oxacillin 2 g IV q4h or cefazolin 2 g IV q8h','6 weeks','Confirm true infection versus contaminant.'], ['Methicillin-resistant CoNS, NVE','Vancomycin, AUC-guided <b>or</b> daptomycin 10 mg/kg IV q24h','6 weeks','Device/prosthetic material changes management.'], ['MSSA PVE','Nafcillin/oxacillin 2 g IV q4h + rifampin 300 mg PO/IV q8h; add gentamicin 1 mg/kg IV q8h for first 2 weeks only if used by local protocol','≥6 weeks; gentamicin 2 weeks','Strongly consider surgery. Rifampin has major interactions; contemporary practice varies on adjunctive gentamicin/rifampin, so follow local specialist protocol.'], ['MRSA or methicillin-resistant CoNS PVE','Vancomycin, AUC-guided + rifampin 300 mg PO/IV q8h; add gentamicin for first 2 weeks only if local specialist protocol','≥6 weeks','High toxicity/interaction burden. Obtain ID and surgical input.'], ['CIED lead/device IE','Target organism-directed regimen + complete device extraction','Usually 4-6 weeks after extraction; individualized','Extraction is standard for definite device-related IE; do not retain infected hardware if feasible.']]) section(story,'2. Streptococci, Granulicatella and Abiotrophia','Use penicillin MIC to direct therapy. Avoid short-course regimens in PVE, complications, renal dysfunction, or high aminoglycoside risk.',[ ['Viridans streptococci or S. gallolyticus, penicillin MIC ≤0.12 mg/L, NVE','Penicillin G 12-18 million units/day IV continuously or q4h <b>or</b> ceftriaxone 2 g IV q24h','4 weeks','Vancomycin if true severe beta-lactam allergy. Investigate colon pathology for S. gallolyticus.'], ['Same, selected uncomplicated NVE only','Penicillin G 12-18 million units/day + gentamicin 3 mg/kg IV/IM q24h <b>or</b> ceftriaxone 2 g q24h + gentamicin','2 weeks','Only if normal renal function, uncomplicated NVE, highly susceptible isolate, and no extracardiac focus.'], ['Viridans / S. gallolyticus, relatively resistant penicillin MIC >0.12 to ≤0.5 mg/L, NVE','Penicillin G 24 million units/day IV + gentamicin 3 mg/kg q24h <b>or</b> ceftriaxone 2 g q24h + gentamicin','4 weeks beta-lactam + 2 weeks gentamicin','If MIC higher or allergy, seek specialist-directed regimen.'], ['Viridans / S. gallolyticus, PVE','Penicillin G 24 million units/day IV or ceftriaxone 2 g IV q24h','6 weeks','Add gentamicin only if resistance/MIC and renal risk permit.'], ['Beta-hemolytic streptococci (groups A, B, C, G)','Penicillin G 18-24 million units/day IV or ceftriaxone 2 g IV q24h','4-6 weeks','Group B often aggressive and may need surgical assessment. Gentamicin sometimes considered for initial 2 weeks in selected cases.'], ['Granulicatella / Abiotrophia (nutritionally variant streptococci)','Penicillin G 18-30 million units/day <b>or</b> ceftriaxone 2 g q24h + gentamicin 3 mg/kg q24h','6 weeks; gentamicin usually first 2 weeks','Higher relapse/complication risk. Treat like enterococcal IE when susceptibility uncertain; specialist care.']]) section(story,'3. Enterococcal infective endocarditis','Species, ampicillin susceptibility, HLAR and renal function determine therapy. Ampicillin plus ceftriaxone avoids aminoglycoside renal toxicity and is a standard choice for E. faecalis.',[ ['E. faecalis, ampicillin-susceptible, NVE or PVE','Ampicillin 2 g IV q4h + ceftriaxone 2 g IV q12h','6 weeks','Preferred when HLAR or renal impairment, and commonly used broadly.'], ['E. faecalis, susceptible and no HLAR, selected NVE','Ampicillin 2 g IV q4h + gentamicin 1 mg/kg IV q8h or local TDM protocol','4-6 weeks','Many programs limit gentamicin to 2 weeks due to nephrotoxicity. Use TDM.'], ['Enterococcus, beta-lactam allergy but vancomycin-susceptible','Vancomycin, AUC-guided + gentamicin 1 mg/kg IV q8h','6 weeks','High renal toxicity risk. Confirm genuine beta-lactam allergy.'], ['E. faecium or VRE, resistant to ampicillin and vancomycin','Linezolid 600 mg IV/PO q12h <b>or</b> daptomycin 10-12 mg/kg IV q24h, susceptibility-guided','≥6 weeks','Specialist-only regimen. Monitor CBC/neuropathy with linezolid and CK with daptomycin; surgery often considered.']]) section(story,'4. HACEK and gram-negative bacillary IE','HACEK organisms: Haemophilus, Aggregatibacter, Cardiobacterium, Eikenella, Kingella. Non-HACEK gram-negative IE is uncommon and severe, often requiring combination therapy and early surgical discussion.',[ ['HACEK, NVE','Ceftriaxone 2 g IV q24h','4 weeks','Alternatives: ampicillin 2 g IV q4h if beta-lactamase negative/susceptible, or ciprofloxacin 400 mg IV q12h.'], ['HACEK, PVE','Ceftriaxone 2 g IV q24h','6 weeks','As above.'], ['Pseudomonas aeruginosa IE','Two active anti-pseudomonal drugs, typically cefepime 2 g IV q8h <b>or</b> meropenem 2 g IV q8h <b>plus</b> ciprofloxacin 400 mg IV q8-12h or an aminoglycoside, susceptibility-guided','≥6 weeks','Endocarditis Team mandatory. Newer beta-lactams may be preferred for resistant isolates. Surgery commonly needed.'], ['Non-HACEK gram-negative bacilli, including Serratia','Two active agents based on susceptibility, often beta-lactam + fluoroquinolone or aminoglycoside','≥6 weeks','No universal regimen. ESBL/AmpC/carbapenemase phenotype and source control are central. Surgical assessment recommended.'], ['Cutibacterium acnes PVE','Penicillin G 18-24 million units/day IV or ceftriaxone 2 g IV q24h','≥6 weeks','Slow-growing. Prolonged culture incubation and valve/device surgery often needed.']]) section(story,'5. Blood-culture-negative and rare IE','Obtain exposure history and send targeted serology/PCR: Coxiella, Bartonella, Brucella, T. whipplei, fungi and mycobacteria. This table is specialist-directed by definition.',[ ['Coxiella burnetii IE (Q fever)','Doxycycline 100 mg PO q12h + hydroxychloroquine 200 mg PO q8h','≥18 months native valve; ≥24 months prosthetic valve','Monitor serology, hydroxychloroquine level where used, QT and retina. Valve/vascular surgery assessment is often required.'], ['Bartonella henselae or B. quintana IE, confirmed','Doxycycline 100 mg PO/IV q12h + gentamicin 1 mg/kg IV q8h','Doxycycline 6 weeks; gentamicin ≥14 days','If gentamicin contraindicated, doxycycline + rifampin 300 mg PO q12h is an alternative in expert care.'], ['Bartonella suspected BCNIE','Doxycycline 100 mg q12h + gentamicin 1 mg/kg q8h + ceftriaxone 2 g IV q24h','Initial regimen specialist-directed','Ceftriaxone covers more routine culture-negative bacterial causes pending diagnosis.'], ['Brucella IE','Doxycycline 100 mg PO q12h + rifampin 600-900 mg/day PO + gentamicin 5 mg/kg IV q24h','Usually ≥6 weeks; often ≥3 months for focal/complex disease','Many experts add ceftriaxone or a fluoroquinolone. Surgical valve replacement often needed.'], ['Tropheryma whipplei IE','Ceftriaxone 2 g IV q24h for 2-4 weeks then doxycycline 100 mg PO q12h + hydroxychloroquine 200 mg PO q8h','Maintenance ≥12 months','Alternative induction: penicillin G + streptomycin. Trimethoprim alone is not active. Add sulfadiazine if CNS involvement per specialist guidance.'], ['Legionella IE','Levofloxacin 750 mg IV/PO q24h or azithromycin 500 mg IV/PO q24h, often combination strategy','Specialist-directed, prolonged','Extremely rare. Verify molecular diagnosis and consider surgery.'], ['Mycoplasma IE','Doxycycline 100 mg PO/IV q12h or azithromycin 500 mg q24h, often combined/susceptibility-guided','Specialist-directed','Cell-wall agents are ineffective. Usually culture-negative and requires molecular diagnosis.'], ['Chlamydia psittaci IE','Doxycycline 100 mg PO/IV q12h','Usually ≥6 weeks','Rare. Exposure history and reference-lab confirmation.'], ['Mycobacterial IE, including M. chimaera','Species-specific multidrug regimen','Months; specialist-directed','Often related to cardiac surgery/heater-cooler exposure; surgery is usually required.']]) section(story,'6. Fungal IE and selected unusual pathogens','Fungal IE frequently requires early surgery plus prolonged induction and suppressive therapy. Do not use this table without ID and cardiac-surgical co-management.',[ ['Candida native/prosthetic valve IE','Liposomal amphotericin B 3-5 mg/kg IV q24h ± flucytosine 25 mg/kg PO q6h <b>or</b> high-dose echinocandin: micafungin 150 mg IV q24h, anidulafungin 200 mg IV q24h, or caspofungin 150 mg IV q24h','Induction until stable/cleared; then long-term azole step-down; chronic suppression often for PVE','Valve replacement preferred when feasible. Step-down fluconazole 400-800 mg/day only for susceptible isolate and clinical stability.'], ['Aspergillus IE','Voriconazole 6 mg/kg IV q12h x 2 doses then 4 mg/kg IV q12h, or weight-based PO; consider liposomal amphotericin B 3-5 mg/kg q24h','Prolonged, often lifelong suppressive therapy','Urgent surgery usually required. Perform TDM and interaction review. Blood cultures often negative.'], ['Fungal device IE','Organism-directed antifungal + complete device removal','Individualized','Culture valve/device tissue; obtain fungal markers and molecular studies where available.'], ['Staphylococcus lugdunensis IE','Treat as aggressive MSSA: nafcillin/oxacillin 2 g IV q4h or cefazolin 2 g IV q8h if susceptible','6 weeks','High destruction/embolism risk; low threshold for surgery.'], ['Coxiella / Bartonella / Brucella with valve dysfunction','As above + early surgical evaluation','As above','Antibiotics alone may not control structural complications.']]) story += [PageBreak(),Paragraph('Empiric therapy is not one-size-fits-all',S['H1x']),Paragraph('The preceding tables are for definitive therapy. If a patient is unstable, has acute sepsis, early PVE, health-care-associated IE, prior antibiotics, or an intracardiac device, empiric treatment requires local protocol and immediate Endocarditis Team review. Early PVE and health-care-associated IE must cover methicillin-resistant staphylococci, enterococci, and often gram-negative bacilli until cultures are known.',S['B']),Paragraph('Surgical / urgent review triggers',S['H2x']),tbl([['Trigger','Action'],['Heart failure from valve dysfunction, prosthetic dehiscence, fistula','Urgent cardiac-surgical assessment.'],['Perivalvular abscess, enlarging vegetation, conduction block, persistent bacteremia/fever despite active therapy','Assess for uncontrolled infection and surgery.'],['Fungal IE, multiresistant pathogen, Pseudomonas/non-HACEK GNB IE','Early multidisciplinary surgery discussion.'],['Definite CIED infection','Complete extraction without delay when feasible.'],['Embolic event or large/mobile vegetation','Risk-based surgical assessment and neurologic imaging.']],widths=(70*mm,112*mm)),Spacer(1,8),Paragraph('Primary sources',S['H1x']),Paragraph('• 2023 European Society of Cardiology Guidelines for management of endocarditis, Eur Heart J 2023;44:3948-4047. The guideline states that therapy should change to targeted treatment within 24-48 hours after organism identification; NVE is usually treated for 2-6 weeks and PVE for ≥6 weeks.<br/>• Harrison’s Principles of Internal Medicine, 22nd ed. Table: antibiotic treatment of IE caused by common organisms.<br/>• The Washington Manual of Medical Therapeutics. Endocarditis treatment tables.<br/>• CDC Q Fever clinical guidance for acute and chronic Q fever therapy.<br/>• Dosing and duration must be checked against the current local guideline, antibiogram, product label and renal/hepatic dosing system before prescribing.',S['B']),Paragraph('<b>Recent-evidence warning:</b> A broad recent systematic-review PubMed search did not identify a directly relevant IE treatment meta-analysis in the top results. Guidance, cohorts and organism-specific studies remain the practical evidence base. In particular, management of adjunctive rifampin/gentamicin in staphylococcal PVE and resistant gram-negative IE may vary by guideline and local practice.',S['N'])] doc=SimpleDocTemplate(OUT,pagesize=A4,leftMargin=12*mm,rightMargin=12*mm,topMargin=13*mm,bottomMargin=16*mm,title='Infective Endocarditis Treatment - Adult Dosing Reference',author='Orris') doc.build(story,onFirstPage=foot,onLaterPages=foot) r=PdfReader(OUT) print('CREATED',OUT,'PAGES',len(r.pages),'BYTES',Path(OUT).stat().st_size) for i in [0,len(r.pages)-1]: print('PAGE',i+1,(r.pages[i].extract_text() or '')[:120].replace('\n',' | ')) ''') PY python "/tmp/workspace/ie-treatment-reference/src/create_ie_pdf.py" && ls -lh "/tmp/workspace/ie-treatment-reference/output/Infective_Endocarditis_Treatment_Adult_Dosing_Reference.pdf"

~/ie-treatment-reference/src/create_ie_pdf.py

python "/tmp/workspace/ie-treatment-reference/src/create_ie_pdf.py" && python - <<'PY' from pypdf import PdfReader from pathlib import Path p=Path('/tmp/workspace/ie-treatment-reference/output/Infective_Endocarditis_Treatment_Adult_Dosing_Reference.pdf') r=PdfReader(str(p)) print('pages:',len(r.pages),'bytes:',p.stat().st_size) for n in (0,1,len(r.pages)//2,len(r.pages)-1): text=r.pages[n].extract_text() or '' print(n+1, len(text), text[:145].replace('\n',' | ')) assert len(r.pages)>=6 assert 'Coxiella' in ''.join((x.extract_text() or '') for x in r.pages) PY ls -lh "/tmp/workspace/ie-treatment-reference/output/Infective_Endocarditis_Treatment_Adult_Dosing_Reference.pdf"

~/ie-treatment-reference/src/create_ie_pdf.py

python "/tmp/workspace/ie-treatment-reference/src/create_ie_pdf.py" && python - <<'PY' from pypdf import PdfReader from pathlib import Path p=Path('/tmp/workspace/ie-treatment-reference/output/Infective_Endocarditis_Treatment_Adult_Dosing_Reference.pdf') r=PdfReader(str(p)); alltext=''.join((x.extract_text() or '') for x in r.pages) print('pages:',len(r.pages),'bytes:',p.stat().st_size) for n in (0,1,len(r.pages)//2,len(r.pages)-1): text=r.pages[n].extract_text() or '' print(n+1, len(text), text[:145].replace('\n',' | ')) assert len(r.pages)>=6 and 'Coxiella' in alltext and 'Bartonella' in alltext and 'Vancomycin' in alltext PY ls -lh "/tmp/workspace/ie-treatment-reference/output/Infective_Endocarditis_Treatment_Adult_Dosing_Reference.pdf"

python - <<'PY' from pypdf import PdfReader from pathlib import Path p=Path('/tmp/workspace/ie-treatment-reference/output/Infective_Endocarditis_Treatment_Adult_Dosing_Reference.pdf') r=PdfReader(str(p)); alltext=''.join((x.extract_text() or '') for x in r.pages) print('pages:',len(r.pages),'bytes:',p.stat().st_size) for term in ['Coxiella','Bartonella','Vancomycin','Tropheryma','Candida']: print(term,term in alltext) print('first',alltext[:200].replace('\n',' | ')) print('last',alltext[-300:].replace('\n',' | ')) assert len(r.pages)>=5 assert all(term in alltext for term in ['Coxiella','Bartonella','Vancomycin','Tropheryma','Candida']) PY