University of Pennsylvania Medical
Center Clinical Microbiology Laboratory Information and Non-UPHS Guidelines for Antimicrobial Therapy
The official UPHS Antimicrobial Therapy Guidelines have been moved to a new site. This site now contains UPHS Clinical Microbiology information, guidelines of national and international societies and other information useful to clinical microbiologists and infectious diseases specialists. |
Click on Our Bug for HUP/UPPMC Antimicrobial Susceptibility Data
TABLE OF CONTENTS
New Postings
Updated IDSA guidelines for:
(all © by the Infectious Diseases Society of America)
Updated CDC/NIH guidelines for:
Clinical Microbiology Laboratory
Antimicrobial Susceptibilities at UPHS
HUP Antimicrobial
Susceptibility Profiles for 2011 Jan-June
Presbyterian
Medical Center Susceptibility Profiles for 2011 Jan-June
Antimicrobial Susceptibility Testing and Interpretation & Drug Resistance
Antimicrobial Susceptibility of Rapidly Growing Mycobacteria
How
to Interpret Susceptibility Results - What "S", "I", and "R" Means
and How Testing is Performed
Eucast Expert Rules for Antimicrobial Susceptibility Test Interpretation (offsite pdf, 214 kb, 4/08)
Eucast Clinical Breakpoints (offsite link)
Drug Resistance Mechanisms and Prevalence
Problem bacteria at HUP (UPHS only) Gram Stains - Method, Interpretation, and Atlas
All
About Gram Stains and Gram Staining - Includes a Gram Stain Atlas
New
Gram Stain Atlas Specimen Collection
Alphabetical guide to laboratory specimen collection for all types of laboratory tests at UPHS (UPHS only)
Guide to Specimen Collection for Biowarfare Agents(UPHS only)
Mumps testing guidelines from CDC (4/10)
Influenza Testing and Results Information (10/10)
Blood culture collection (2/11)
Problem Sets
Teaching lectures (UPHS only)
Problem sets (Registered Blackboard users only)
HIV Testing
HIV antibody testing methods used at HUP
Bacterial Taxonomy
Professor
Euzeéby
Deutsche
Sammlung von Mikroorganismen und Zellkulturen
Bioterrorism Agents
ASM Sentinel Laboratory Guidelines (offsite link)
CDC Infectious Diseases Testing
CDC infectious diseases laboratory test directory (offsite link) (2/13)
CDC specimen submission instructions and electronic submission form (offsite link) (2/13)
Respiratory Virus Statistics Influenza for the Current Season
Winter 2012-Spring 2013
Winter 2011-Spring 2012
Winter 2010-Spring 2011
UPHS Guidelines for Infection Control
Infection
Control Policies (UPHS Intranet only)
Heros Wash Hands (42 mb movie)
Stop the Flu (24 mb movie)
UPHS Guidelines for Antimicrobial Prophylaxis
Guidelines
for Peri-procedure Prophylaxis
Antimicrobial
Prophylaxis for Prevention of Bacterial Endocarditis(Link to the 2007 AHA
Guidelines)
Guidelines and
Information
Endocarditis and Endovascular Infections
Endocarditis Diagnosis and Management
AHA Diagnosis
and Management of Infectious Endocarditis -1998 (link to
AHA
web page or link to
offsite pdf file 168kb)
AHA Infective Endocarditis (2005, offsite link)
BSAC Endocarditis Diagnosis and Treatment Guidelines -2012 (PubMed abstract) or off site pdf (
581 kb)
ESCMID, ISC Guidelines on the Prevention, Diagnosis and Treatment of Infective Endocarditis (2009, offsite 17 mb pdf)
Clinical Practice Guidelines by the Infectious Diseases Society of America for the Treatment of Methicillin-Resistant Staphylococcus Aureus Infections in Adults and Children (2010,pdf 370 kb) ©2011 by the Infectious Diseases Society
of America
Endocarditis Prophylaxis
AHA Endocarditis Prophylaxis Guidelines - April 2007 (pdf, 602 kb, off site link)
BSAC Endocarditis Prophylaxis Guidelines - 2006 off site pdf (103 kb)
Modified
Duke Criteria for Endocarditis Nonvalvular Device Infections and Prophylaxis
AHA Nonvalvular Cardiovascular Device-Related
Infections -2010 (link to offsite
AHA pdf file or online version)
Guidelines
for the Management of Intravascular
Catheter–Related Infections (685 kb, pdf) 2009 by the Infectious Diseases Society of
America
Guidelines For The Prevention Of Intravascular
Catheter-Related Infections (August 2002; CDC, IDSA, SHEA, et
al) (pdf
file 340 kb) or link to CDC
html file
Fungal Infections
Introduction
to Antifungal Drugs (pdf, 33 kb), ©2000 by the Infectious Diseases Society of
America
Guidelines
for Treatment of Fungal Infections (pdf, 57 kb), ©2000 by
the Infectious Diseases Society of America
ATS 2011 Treatment of Fungal Infections in Adult Pulmonary and Critical Care Patients (offsite pdf, 367kb, requires subscription until posted on ATS Website)
Treatment of Aspergillosis (pdf, 483 kb), ©2008
by the Infectious Diseases Society of America
Management
of Patients with Blastomycosis (pdf, 265 kb), ©2008 by
the Infectious Diseases Society of America
Treatment
of Candidiasis (pdf, 480 kb), ©2009 by the Infectious Diseases Society of
America
Treatment
of Coccidioidomycosis (pdf, 98 kb), ©2005 by the Infectious Diseases Society of
America
Management
of Cryptococcal Disease (pdf, 461 kb), ©2010 by
the Infectious Diseases Society of America
Management
of Patients with Histoplasmosis (pdf, 172 kb), ©2007 by
the Infectious Diseases Society of America
Management
of Patients with Sporotrichosis (pdf, 120 kb), ©2007 by
the Infectious Diseases Society of America
Dr. Fungus-
A website with extensive information on fungi
Gastrointestinal Tract Infections
Diagnosis and Management of Foodborne Illnesses - CDC RR-4,
Apr 2004 (offsite
html or onsite pdf
368kb)
Practice
Guidelines for the Management of Infectious Diarrhea -IDSA Jan
2001 (pdf
284 kb), 2001 by the Infectious Diseases Society of America
Treatment Guideance for Clostridium difficile Infections (ESCMID, 2009, offsite pdf)
Clinical Practice Guidelines for Clostridium difficile Infections in Adults - 2010 Update (IDSA-SHEA, offsite pdf)
Cholera Management for Haitian Outbreak (CDC Dec 2010 pdf 144kb, offsite html)
Intraabdominal Infections
Diagnosis and Management of Complicated
Intra-abdominal Infection in Adults and Children, Surgical Infection Society, IDSA 2010 (
pdf, 732 kb) ©2010 by
the Infectious Diseases Society of America
Surgical Infection Society Link to Guidelines
2005 Guidelines from the International Society of Peritoneal Dialysis for the Diagnosis and Management of Peritoneal Dialysis-Associated Peritonitis
Updated (2010) ISPD Guidelines for Peritoneal Dialysis Related Infections (3/2011)
Chronic Hepatitis B Antiviral Treatment Guidelines Amer Assoc Study Liver Dis Guidelines 2009 (offsite pdf, 500 kb)
Chronic Hepatitis C type 1 treatment- Amer Assoc Study Liver Dis Guidelines 2011 (offsite pdf, 420 kb)
Urinary Tract Infections
Diagnosis and treatment of asymptomatic bacteriuria in adults - IDSA, ASN, AGA, March 2005 ©2005 by the Infectious Diseases Society of America pdf 133 kb
2010 International Practice Guidelines for Antimicrobial Treatment of Acute Uncomplicated Cystitis and Pyelonephritis in Women (pdf, 240 kb), ©2011 by the Infectious Diseases Society of America
Diagnosis, Prevention, and Treatment of Catheter-
Associated Urinary Tract Infection in Adults, 2009, IDSA pdf, (469 kb), ©2010 by the Infectious Diseases Society of America
Sexually Transmitted Diseases
CDC December 2010 Guidelines for the Treatment of Sexually Transmitted Diseases (pdf 1.1mb)
See also Hepatitis and HIV sections
Guidelines for Infection Control and Immunization
Infection Control Guidelines
CDC Guidelines for the Prevention of Nosocomial
Pneumonia (2003 published Mar04 offsite
html link or onsite pdf file
(811kb)
Guidelines for Preventing Infectious Complications
among Hematopoietic Cell Transplantation Recipients:
A Global Perspective (ASBMT, IDSA, 2009)
pdf
file 1.4 mb
HICPAC Guidelines for the Prevention of Intravascular Catheter-Related Infections, 2011, pdf 1.0 mb
Guidelines for the Prevention of Perinatal Group B Streptococcal Disease (Nov 2010; CDC) pdf file 1.6 MB
CDC-HICPA Guidelines for Environmental Infection Control in Health-Care Facilities (June 2003) link to pdf file (1 MB) or html document
HICPAC Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Healthcare Settings, 2007 (6/07, 1.3 mb pdf)
CDC- Prevention of TB Transmission in Health Care Facilities, Dec 2005 (pdf 1.2 mb)
Guideline for Hand Hygiene in Healthcare Settings (October 2002; CDC) pdf file 506kb or link to CDC html file
Updated Norovirus Outbreak Management and Disease Prevention Guidelines (CDC, 3/11) pdf 850kb
Post-exposure Prophylaxis
CDC
guidelines for postexposure prophylaxis for occupational HIV, HBV, and HCV
(August 2001,
pdf, 343kb)
CDC guidelines for occupational HIV postexposure prophylaxis (Sept 2005, pdf )
CDC guidelines for postexposure prophylaxis for sexual, injection drug and other nonoccupational HIV exposure (Jan 2005, pdf 112kb)
CDC ACIP guidelines for postexposure hepatitis A prophylaxis (Oct 2007, offsite link)
CDC guidelines for postexposure non-occupational hepatitis B prophylaxis (2006, offsite link)
CDC guidelines for HBV, HCV, HIV, Tetanus Postexposure prophylaxis after bombing or other mass-casualty event (August 2008, pdf 263kb)
Immunization
Adult and Pediatric Immunization Guidelines (2002; IDSA) pdf file 670 kb or link to IDSA html file 2002 by the Infectious Diseases Society of America
Adult Immunization Schedule 2013, ACIP pdf file 347kb
Pertussis Treatment and Postexposure Prophylaxis, CDC, Dec 2005, pdf file 210kb
Smallpox vaccination and adverse Reactions (Jan 2003; CDC) link to pdf file (13MB) or html document ACIP-HICPAC Use of Tdap (Tetanus, reduced diphtheria toxoid, acellular pertussis) Vaccine in Adults, Dec 2006 (pdf 412 kb)
ACIP Immunization Schedule for Persons 0-18 Years of Age, Jan 2011, (pdf 160 kb)
ACIP Immunization of Health Care Personnel, Nov 2011, (pdf 722 kb)
Surgical Prophylaxis
Antimicrobial Prophylaxis for Surgery IDSA/ASHP/SIS/SHEA Feb 2013 (offsite link pdf 1 mb)
Prevention of Infections Associated with Combat Injuries SIS, IDSA August 2011 (offsite pdf link 860 kb)
Communicable Disease Reporting
Reporting communicable diseases
in Philadelphia (external link to Philadelphia Dept. of Public Health Division of Disease Control)
Infectious Diseases Society of America
and British Society for Antimicrobial Chemotherapy Guidelines
IDSA Guidelines in iPhone and iPad format
2010
Guidelines for the Use of Antimicrobial Agents in Neutropenic
Patients with Cancer (pdf, 518 kb) or
link to IDSA guidelines ©2011 by the Infectious Diseases Society
of America
Guidelines for evaluation of new fever in critically ill adult
patients: 2008 Amer. Coll. Crit. Care
Med. & IDSA(offsite pdf, 198 kb)
Fungal Infections
The Clinical Assessment, Treatment, and Prevention
of Lyme Disease, Human Granulocytic Anaplasmosis,
and Babesiosis - IDSA Oct 2006, pdf 2.8 mb Excellent update of guidelines ©2006 by the Infectious Diseases Society of America
Practice
Guidelines for Outpatient Parenteral Antimicrobial Therapy
(pdf 189 kb, June 2004), ©2004
by the Infectious Diseases Society of America
Diagnosis
and Treatment of Diabetic Foot Infections (pdf 455 kb, May 2012) ©2012 by
the Infectious Diseases Society of America
Practice
Guidelines for the Management of Bacterial Meningitis (pdf
319kb, Nov 2004) ©2004
by the Infectious Diseases Society of America
Practice Guidelines for the Diagnosis and Management of Skin and Soft Tissue Infections (pdf 313 kb, Nov 2005)
©2005 by the Infectious Diseases Society of America
Guidelines for the prophylaxis and treatment of methicillin-resistant Staphylococcus aureus ( MRSA) infections in the UK- BSAC Working Party offsite link (230 kb, pdf) (2/06)
Clinical Practice Guidelines by the Infectious Diseases Society of America for the Treatment of Methicillin-Resistant Staphylococcus Aureus Infections in Adults and Children (2010,pdf 370 kb) ©2011 by the Infectious Diseases Society of America
Use of antibiotics in penetrating craniocerebral injuries -BSAC Working Party (2000), offsite link
The management of neurosurgical patients with postoperative bacterial or aseptic meningitis or external ventricular drain-associated ventriculitis- BSAC Working Party (2000), offsite link
Guideline for the management of the hot swollen joint in adults -BSR, BSAC, et al. (2006) offsite link
Diagnosis and Management of Prosthetic Joint Infection - IDSA (2013) pdf 500 kb ©2013 by the Infectious Diseases Society of America
Surviving Sepsis Campaign: International
Guidelines for Management of Severe Sepsis
and Septic Shock: 2012 by multiple organizations (offsite link pdf 2.9 mb)
Vancomycin monitoring and dosing (1/09)
Evaluation of fever and infection in long term care facilities ©2009 by the Infectious Diseases Society of America
Guidelines for Preventing Infectious Complications
among Hematopoietic Cell Transplantation Recipients:
A Global Perspective Amer Soc Blood Marrow Transplantation/IDSA, 2009
Pneumonia & Upper Respiratory Tract
Community Acquired Pneumonia
Hospital and Healthcare-Associated Pneumonia
CDC Guidelines for the Prevention of Nosocomial Pneumonia (2003
published Mar04) offsite html link or onsite pdf file (811kb)
ATS/IDSA Guidelines for the Management of Adults with Hospital-Acquired, Ventilator-associated, and Healthcare-associated pneumonia (2004, published 2005)-Offsite ATS link (360Kb, pdf)
British Society for Antimicrobial Chemotherapy Guidelines for the Management of Hospital-Acquired Pneumonia in the UK (July 2008) offsite link (342 kb, pdf)
Influenza
Upper Respiratory Tract Infections
Tuberculosis
General Primers and Definitions
CDC
Core Clinical Curriculum on Tuberculosis - includes information
on prophylaxis, diagnosis, antituberculous drugs, epidemiology,
and therapy (offsite link, updated periodically)
CDC Self-Study Modules on Tuberculosis (offsite link)
American Thoracic Society /CDC/IDSA Statement on Diagnostic Standards and Classification of Tuberculosis in Adults and Children -1999 (published April 2000, pdf 474 kb)
IUATLD Management of Tuberculosis (Orange Guide) (2010)-offsite link pdf 1 mb
NICE - TB Clinical Diagnosis and Management (UK National Institute for Health and Clinical Excellence (March 2011) - excellent, offsite link
Treatment Guidelines
American Thoracic Society/CDC/IDSA Statement on the Treatment of Tuberculosis (Oct 2002, pdf 525 kb)
Practice Guidelines for the Treatment of Tuberculosis -IDSA Oct 2000, pdf 70kb; ©2000 by the Infectious Diseases Society of America
WHO Treatment of MDR Tuberculosis - Field Guide, 2010, offsite pdf, 980 kb
Also see the above NICE guidelines
HIV Specific Treatment and Prevention Guidelines
Prevention and Treatment of Tuberculosis Among Patients Infected
with Human Immunodeficiency Virus: Principles of Therapy and
Revised Recommendations - CDC Recommendation October 1998 (pdf 750 kb) OR offsite link
Appendix to above HIV /TB treatment html document (link to CDC web)
Managing drug interactions in the treatment of HIV-related tuberculosis -CDC recommendations Dec 2007
pdf 228 kb OR offsite link
Diagnosis and Treatment of Latent TB
American Thoracic Society/CDC/IDSA/AAP Statement on Targeted Tuberculin Testing and Treatment of Latent Tuberculosis Infection -1999 (published April 2000, pdf 699 kb) -Also view the warnings on use of rifampin/pza together (Aug 2002, html)
CDC - Treatment of latent TB with INH+rifapentine (published 12/2011, with erratum 2/2012) pdf 485 kb
TB Drug Side-effect and Interactions
ATS-Hepatotoxicity of anti-Tb drugs (offsite pdf, 1.2 mb, 2006)
Managing drug interactions in the treatment of HIV-related tuberculosis -CDC recommendations Dec 2007 pdf 228 kb OR offsite link Non-Tuberculous Mycobacterial Infections
ATS-IDSA guidelines for the diagnosis and treatment of non-tuberculous mycobacterial infections (offsite link, pdf 930 kb, 2/07)
WHO, IUATLD Tuberculosis Guidelines, Especially for Low Income Countries
Laboratory Diagnosis and Management
IUATLD Direct Microscopy Guide for the Diagnosis of TB (5th ed, 2000) pdf 707kb
IUATLD Guide for Nat. TB Ref. Labs and National Laboratory Networks (1998) pdf 1.1 mb
Res. Inst. of TB/IUATLD AFB Microscopy Training (2005)-complete document pdf 11.4 mb
Research Inst. of TB/IUATLD AFB Microscopy Training (2005)Part 1 pdf 4mb
Research Inst. of TB/IUATLD AFB Microscopy Training (2005) Part 2 pdf 6mb
Research Inst. of TB/IUATLD AFB Microscopy Training (2005) Part 3 pdf 1.5 mb
Priorities for tuberculosis bacteriology services in low income countries. IUATLD (2007) Offsite link (pdf 5.4 mb)
Clinical Manuals
WHO TB and HIV Clinical Manual (2nd ed, 2004) pdf 726 kb
WHO Treatment of Tuberculosis (4th ed, 2010), pdf 908kb
WHO/IAUTLD TB Manual for Medical Students (1999) pdf 1.1 mb
WHO Diagnosis and Treatment of Smear Negative Pulmonary and Extrapulmonary TB in HIV prevalent, resource-constrained regions (2007) pdf 460 kb
IAUTLD Diagnostic Atlas of Intrathoracic TB in Children (2003) pdf 6.2 mb
IUATLD Management of Tuberculosis (Orange Guide) (2010)-offsite link pdf 1 mb
IUATLD - Diagnosis and Treatment of TB in Children (2010) pdf 860 kb
IUATLD - 2nd line drugs for MDR TB treatment: availability and price (2nd ed, 2012) pdf 1.4 mb
IUATLD - Guidelines for the management of MDR TB (2013) offsite pdf 1.4 mb
Links
WHO (World Health Organization)
IUATLD (International Union Against Tuberculosis and Lung Diseases, has other useful manuals for the management of lung diseases)
Parasitic, Tick-Borne Diseases, Travel Medicine
HUP Malaria Treatment Guidelines
CDC
Malaria Treatment and Diagnosis (2012) (off site link)
CDC Malaria Treatment Guidelines
Only (Sept 2011 pdf, 38 kb)
WHO Guidelines for the Treatment of Malaria, 2nd edition (2010, pdf 1.3 mb)
Tick borne North American rickettsial diseases - excellent review of epidemiology, treatment and diagnosis
- CDC March 2006 (pdf 790 kb)
The Clinical Assessment, Treatment, and Prevention
of Lyme Disease, Human Granulocytic Anaplasmosis,
and Babesiosis - IDSA Oct 2006, pdf 2.8 mb Excellent update of guidelines ©2006 by the Infectious Diseases Society of America
Treatment of Nervous System Lyme Disease - American Academy of Neurology, May 2007 (offsite link, 190 kb pdf)
Guidelines for the Diagnosis of Tickborne Bacterial Infections in Europe (ESCMID, 2004, offsite link)
IDSA Guidelines for the Practice of Travel Medicine (Jan 07, 3.8 Mb, pdf). A very good travel medicine primer.
©2007 by the Infectious Diseases Society of America
US Military Medical Textbooks - great chapters on parasitic and non-parasitic infectious diseases (offsite link)
Global Disease Alert Map - Alerts of current worldwide infectious diseases outbreaks based on public health, news and Promed alerts (July 08, offsite link)
HIV-Related Information
HIV testing methods used at HUP - Nov 2012, onsite html
Antiretroviral treatment of adults with HIV infection, 2012 USA recomendations- Intnl Antiviral Society July 2012, offsite pdf 200kb
Guidelines for the Use of Antiretroviral
Agents in HIV-Infected Adults and Adolescents - Feb 2013 USPHS pdf 1.4mb OR
go
to the offsite html link
. These are frequently updated, so check the offsite version if possible.
Link to AIDSinfo US Dept
HHS Website
Prevention and Treatment of Opportunistic Infections in HIV-Infected Adults and Adolescents -2009, CDC, NIH, IDSA. (pdf, 2 mb)
Recommendations for Use of Antiretroviral Drugs in Pregnant HIV-1-Infected Women for Maternal Health and Interventions to Reduce Perinatal HIV Transmission in the United States -2012, NIH (pdf, 4.7 mb), offsite link. These are frequently updated, so check the offsite version if possible
Guidelines for the Use of Antiretroviral
Agents in Pediatric HIV Infection -2012, NIH (pdf 7 mb, offsite link)
Prevention and Treatment of Opportunistic Infections in HIV-Exposed and HIV-Infected Children (2009), CDC, NIH, IDSA, PedIDS, AAP (pdf, 1.8 mb)
Managing drug interactions in the treatment of HIV-related tuberculosis -CDC recommendations Dec 2007 pdf 228 kb OR offsite link
CDC guidelines for postexposure prophylaxis for sexual, injection drug and other nonoccupational HIV exposure (Jan 2005, pdf 112kb)
Management of Occupational HIV exposure - CDC Sept 2005
Guidelines
for the evaluation and management of dyslidipemia in HIV-infected
adults - IDSA Aug 2003 ©2003 by the Infectious
Diseases Society of America
National HIV/AIDS Clinician's
Consultation Center
Primary
Care Guidelines for the Management of Persons Infected with Human
Immunodeficiency Virus IDSA (pdf 4622kb, Sept 2009) ©2009 by the Infectious
Diseases Society of America
HIV Testing in Health Care Settings- Revised Recommendations - CDC Sept 2006 (pdf 214 kb)
Bioterrorism
CDC Bioterrorism
Webpages (link)
Classical
Clinical Description of Inhalation Anthrax (Dec 1960 Am J. Med.
paper by Plotkin and colleagues)
Consensus
Statements on Bioterrorism Agents, published in JAMA (links)
ASM Sentinel Laboratory Agent Summaries and Guidelines (offsite link)
Public health response to biological and chemical weapons: WHO guidance (2004) (offsite link)
UPMC Center for Biosecurity (offsite link)
U.S. Army Medical Dept. Textbooks of Military Medicine (offsite link)
U.S. Army Medical Department Medical Aspects of Biological Warfare( 2007, offsite link)
Powerpoint
slides of
cutaneous anthrax - much better quality than the CDC ones - from
PHLS website (see below) ppt, 98kb.
UK HPA
Training Slides on Clinical Aspects of Deliberate Release of Biological Agents - an excellent site with information on several biological agents (2009, offsite link)
IDSA Biodefense Information and Resources
(offsite link)
European
Guidelines on Bioterrorism ("Bichat" Guidelines)-
(offsite link) excellent brief summaries by agent, January 2005 |