University of Pennsylvania Medical Center Clinical Microbiology Laboratory Information and Non-UPHS Guidelines for Antimicrobial Therapy



New Postings

Clinical Microbiology Laboratory

SARS-CoV-2 and COVID-19

Endocarditis and Endovascular Infections

Fungal Infections

Gastrointestinal Tract Infections

Intraabdominal Infections


Urinary Tract Infections

Sexually Transmitted Infections

Infection Control and Immunization

Pneumonia and Uppper Respiratory Tract Infections


WHO and IUATLD Guidelines

Parasitic, Tick Borne, Travel-Related Infections



New Postings

Updated Susceptibility Data UPHS for Candida spp., S. pneumoniae and Rapidly Growing Mycobacteria (10/2020)

Updated IDSA guidelines for:

Updated CDC/NIH guidelines for:

Clinical Microbiology Laboratory

Antimicrobial Susceptibilities at UPHS

UPHS antimicrobial susceptibility data for commonly isolated Gram-negative and Gram-positive isolates is only available on the UPHS intranet, with the exception of data for pneumococcus, rapidly growing mycobacteria, anaerobes and Candidia spp, which are publicly available (see below). UPHS antimicrobial treatment guidelines are publicly available.

Antimicrobial Susceptibility of Pneumococci 2020 onsite link

Antimicrobial Susceptibility of Rapidly Growing Mycobacteria 2020 onsite link

Fluconazole Susceptibility of Candida spp.2020 onsite link

Antimicrobial Susceptibility of Anaerobes 2019 onsite link

How to Interpret Susceptibility Results - What "S", "I", and "R" Means and How Testing is Performed onsite link

Older susceptibility data for HUP and PPMC are available publicly, including some organism specific (Stenotrophomonas, detailed data on Candida, etc.) data not available on the frequently updated site. Archived data for the last decade are available on request.

What's an ECV, and How is it Determined? onsite link

CLSI M100-S30 2020, free online viewing, offsite link - click on "Click here to use guest access", in upper right

Eucast Expert Rules for Antimicrobial Susceptibility Test Interpretation offsite link

Eucast Clinical Breakpoints offsite link


University of Adelaide Descriptions of Medical Fungi 2017 ed - color atlas and morphologic descriptions offsite link

International Society for Human and Animal Mycology ISHAM offsite link

ISHAM Resources for Antifungal Guidelines offsite, books offsite and mycologic resources offsite

Mycology Online Univ of Adelaide offsite link

Aspergillus and Aspergillosis offsite link

Doctor Fungus US Mycoses Study Group - antifungals, descriptions of fungi - all things fungal offsite link


M. tuberculosis time to detection from culture 2013 onsite link

Molecular detection of macrolide resistance in rapidly growing mycobacteria 2016 onsite link

M. abscessus complex taxonomy 2017 onsite link

Specimen Collection

Alphabetical guide to laboratory specimen collection for all types of laboratory tests at UPHS UPHS only

CDC Mumps testing guidelines 2010 offsite link

Blood culture collection 2013 onsite link

CDC Hepatitis serology training videos 2021 offsite link

Bacterial Taxonomy

LPSN - List of Prokaryotic names with Standing in Nomenclature

Bioterrorism Agents

ASM Sentinel Laboratory Guidelines offsite link

CDC Infectious Diseases Testing

CDC infectious diseases laboratory test directory offsite link

CDC specimen submission instructions and electronic submission form offsite link

CDC Viral Hemorrhagic fevers Lassa, Ebola, etc. offsite link

Ebola Virus Status, Procedures and Guidelines

CDC Ebola Virus Information offsite link

UK Ebola Virus Triage, Clinical Management, Testing Guidelines offsite link

UK Viral Hemorrhagic Fever Risk Assessment, Patient Managment offsite link

Australian Guidance - Laboratory Precautions for Patient Samples Suspected VHF offsite link

WHO Ebola Virus Information offsite link

Respiratory Virus Statistics Influenza for the Current Season UPHS, Pennsylvania, US and World

Pennsylvania Dept Health Influenza Activity offsite link

Biofire US Syndromic Trends offsite link

CDC Influenza Activity offsite link

WHO Influenza Activity offsite link

UPHS Respiratory Virus Archived Results 2010-2020 onsite link

Guidelines and Other Information

SARS-CoV-2 and COVID-19

IDSA Covid-19 Treatment and Management offsite link

CDC Covid-19 offsite link

NIH Covid-19 Management offsite link

ACIP Covid-19 Vaccines offsite link

NLM LitCovid offsite link

Hopkins Coronavirus COVID-19 Cases Worldwide offsite link

COVID-19 test results in Philadelphia offsite link

Montgomery County PA- COVID-19 offsite link

COVID-19: Data - NYC Health offsite link

Coronavirus disease 2019 WHO offsite link

National COVID-19 surveillance reports - GOV.UK offsite link

Coronavirus (COVID-19) in the UK offsite link

Commercial Laboratory Seroprevalence Surveys COVID-19 CDC offsite link

How many tests for COVID-19 are being performed around the world? - Our World in Data offsite link

Coronavirus Update (Live): Cases and Deaths from COVID-19 Virus Pandemic - Worldometer offsite link

Norweigan Institute of Public Health Systematic Evidence on COVID-19 offsite link

Endocarditis and Endovascular Infections

Endocarditis Diagnosis and Management

AHA Infective Endocarditis 2015, offsite link

BSAC Endocarditis Diagnosis and Treatment Guidelines -2012 off site link

European Soc of Cardiology Guidelines on the Prevention, Diagnosis and Treatment of Infective Endocarditis 2015,offsite link

Clinical Practice Guidelines by the Infectious Diseases Society of America for the Treatment of Methicillin-Resistant Staphylococcus Aureus Infections in Adults and Children* 2010,offsite link


Endocarditis Prophylaxis

AHA Endocarditis Prophylaxis Guidelines - 2007 off site link

BSAC Endocarditis Prophylaxis Guidelines - 2006 offsite link

Modified Duke Criteria for Endocarditis onsite link

Nonvalvular Device Infections and Prophylaxis

AHA Nonvalvular Cardiovascular Device-Related Infections -2010 offsite link

EHRA Prevention, Diagnosis and Treatment of Cardiac Implantable Electronic Devices - 2019 offsite link

IDSA Guidelines for the Management of Intravascular Catheter–Related Infections 2009* offsite link

CDC Guidelines For The Prevention Of Intravascular Catheter-Related Infections 2011 offsite link

HRS Expert Consensus Statement on Cardiovascular Implantable Electronic Device Lead Management and Extraction 2017offsite link

(*, marked as archived as IDSA and may need update)

Fungal Infections

ATS Treatment of Fungal Infections in Adult Pulmonary and Critical Care Patients 2011 offsite link

IDSA Diagnosis and Management of Aspergillosis - 2016 offsite link 

Diagnosis and Management of Aspergillosis in Neonates and Children - ESCMID-ECMM 2019 offsite link

Diagnosis and Management of Aspergillus Disease ESCMID-ECMM-ERS 2018 offsite link

IDSA Management of Patients with Blastomycosis- 2008* offsite link

IDSA Management of Candidiasis - 2015 offsite link 

IDSA Treatment of Coccidioidomycosis - 2016 offsite link

IDSA Management of Cryptococcal Disease -2010* offsite link

IDSA Management of Patients with Histoplasmosis -2007* offsite link,

IDSA Management of Patients with Sporotrichosis - 2007* offsite link

Antifungal Drugs Pharmacology and Drug-Drug Interactions offsite link, 2018. Also has smartphone app

(*, marked as archived as IDSA and may need update)

Gastrointestinal Tract Infections

IDSA Practice Guidelines for the Diagnosis and Management of Infectious Diarrhea - 2017 offsite link

IDSA-SHEA Clinical Practice Guidelines for Clostridium difficile Infections in Adults - 2017 offsite link

Intraabdominal Infections

Surgical Infection Society Guidelines offsite link

The Surgical Infection Society Revised Guidelines on the Management of Intra-Abdominal Infection 2017 offsite link

ISPD Peritoneal Dialysis Catheter Infections Guidlines 2017 offsite link

ISPD Peritoneal Dialysis Peritonitis Guidelines 2016 offsite link


AASLD Chronic Hepatitis B Prevention, Diagnosis and Treatment Guidelines - 2018 offsite link

Diagnosis, Management and Treatment of Hepatitis C Infections AASLD & IDSA Website - updated frequently offsite link

CDC Guidelines for Hepatitis C Laboratory Testing 2013 link

CDC Viral Hepatitis Serology Training Videos offsite link 2021

CDC Educational Resources for Viral Hepatitis offsite link 2021

Urinary Tract Infections

IDSA Management of asymptomatic bacteriuria - 2019 offsite link

IDSA and Others 2010 International Practice Guidelines for Antimicrobial Treatment of Acute Uncomplicated Cystitis and Pyelonephritis in Women* offsite link

IDSA Diagnosis, Prevention, and Treatment of Catheter- Associated Urinary Tract Infection in Adults - 2009* offsite link

(*, marked as archived as IDSA and may need update)

Sexually Transmitted Diseases

CDC Sexually Transmitted Diseases guidelines, data, etc. offsite link

See also Hepatitis and HIV sections

Guidelines for Infection Control and Immunization

Infection Control Guidelines

UPHS Infection Control Policies - UPHS Intranet only

CDC Infection Control Guidelines 2020 offsite link

CDC Guidelines for the Prevention of Nosocomial Pneumonia - 2003 offsite link

SHEA/IDSA Strategies to Prevent Ventilator‐Associated Pneumonia in Acute Care Hospitals 2008 offsite link

ASBMT, IDSA Guidelines for Preventing Infectious Complications among Hematopoietic Cell Transplantation Recipients - 2009* offsite link

HICPAC Guidelines for the Prevention of Intravascular Catheter-Related Infections offsite link

ACOG Prevention of Perinatal Group B Streptococcal Disease - 2020 offsite link

CDC Compendium of Group B Streptococcal Neonatl Disease Prevention & Treatment Guidelines 2020 offsite link

CDC-HICPA Guidelines for Environmental Infection Control in Health-Care Facilities - 2003 offsite link

HICPAC Guideline for Isolation Precautions: Preventing Transmission of Infectious Agents in Healthcare Settings - 2007 offsite link

CDC- Prevention of TB Transmission in Health Care Facilities - 2005 offsite link additional guidance

CDC- Guideline for Hand Hygiene in Healthcare Settings -2002 offsite link

CDC Norovirus Outbreak Management and Disease Prevention - 2011 offsite link

Post-exposure Prophylaxis

CDC guidelines for occupational HIV postexposure prophylaxis 2013 with 2018 update, offsite link

AETC non-occupational HIV post-exposure prophylaxis - 2019 offsite link

CDC ACIP guidelines for postexposure hepatitis A prophylaxis - 2007 offsite link

CDC guidelines for postexposure hepatitis B prophylaxis - offsite link

CDC guidelines for hepatitis C postexposure treatment and diagnosis offsite link

CDC guidelines for HCV-exposed health care personnel - 2020 offsite link

CDC Guidance for Evaluating Hepatitis B Virus-infected Health-Care Personnel - 2012 offsite link

CDC guidelines for HBV, HCV, HIV, Tetanus Postexposure prophylaxis after bombing or other mass-casualty event - 2008 offsite link

CDC Tetanus guidelines, including passive and active immunization after injury - 2020 pink book offsite link


ACIP guidelines updated automatically via CDC server


Adults by Medical Condition


Children by Medical Condition

CDC vaccines guidelines offsite link

ACIP offsite link

ACIP COVID-19 vaccines 2021 offsite link

ACIP Seasonal Influenza Vaccination Guidelines 2020-2021 season offsite link

ACIP Haemophilus influenzae Vaccination Guidelines - 2019 offsite link

ACIP Human Papillomavirus Vaccination Guidelines - 2019 offsite link

IDSA Guidelines for the Vaccination of Immunocompromised Hosts -2013* offsite link

Hepatitis B, ACIP offsite link 2018

ACIP Meningococcal vaccine 2020 offsite link

Measles, mumps and rubella, ACIP 2018,offsite link

ACIP Measles, mumps, rubella, varicella vaccine offsite link

MMMR and MMRV vaccines - general information CDC offsite link

Pneumococcal vaccine guidelines older adults, CDC, 2019, offsite link

Pertussis Postexposure Prophylaxis, CDC,2019, offsite link

Tetanus, diphtheria, pertussis vaccine, CDC 2019 offsite link

ACIP Typhoid Vaccine Guidelines 2015 offsite link

ACIP Smallpox vaccination offsite link

ACIP Shingles Vaccine 2018 offsite link

Vaccine Information Statements, CDC offsite link


Air Travel Infection Control Guidelines

European CDC Air Travel Infectious Diseases on Aircraft offsite link

WHO Tb and Air Travel Guidelines 3rd edition 2008 offsite link


Surgical and other Prophylaxis

Antimicrobial Prophylaxis for Adults with Cancer 2018 ASCO/IDSA offsite link

Antimicrobial Prophylaxis for Surgery IDSA/ASHP/SIS/SHEA 2013 offsite link

Guideline for Prevention of Surgical Site Infection CDC 2017 offsite link


Communicable Disease Reporting

Reporting communicable diseases in Philadelphia external link to Philadelphia Dept. of Public Health Division of Disease Control

(*, marked as archived as IDSA and may need update)


Infectious Diseases Society of America, British Society for Antimicrobial Chemotherapy, and Other Society Guidelines


IDSA Practice Guidelines website

Practice Guidelines for Outpatient Parenteral Antimicrobial Therapy 2018 offsite link

Practice Guidelines for Healthcare Associated Ventriculitis and Meningitis 2017 offsite link

Practice Guidelines for the Diagnosis and Management of Skin and Soft Tissue Infections 2014 offsite link

Diagnosis and Management of Periprosthetic Joint Infections AAOS 2019 endorsed by IDSA offsite link

Diagnosis and Treatment of Native Vertebral Osteomyelitis in Adults -IDSA 2015 offsite link

Implementing an Antibiotic Stewardship Program - IDSA and SHEA 2016 offsite link

Outpatient management of fever and neutropenia in patients treated for malignancy -ASCO/IDSA, 2018 offsite link


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

Antimicrobial stewardship e-book and MOOC - Univ Dundee online course on antimicrobial stewardship

Treatment of methicillin-resistant S. aureus infections - updated guidelines 2021 offsite link

Miscellaneous organizations

Antimicrobial Stewardship Guidance - NICE 2016 offsite link

Surviving Sepsis Campaign: International Guidelines for Management of Severe Sepsis and Septic Shock: 2016 by multiple organizations offsite link

Sepsis and Septic Shock Definitions - Society for Critical Care Medicine 2016 offsite link

Pneumonia & Upper Respiratory Tract

Community Acquired Pneumonia

British Thoracic Society Guidelines for the Management of Adults with Community-Acquired Pneumonia 2009 offsite link

British Thoracic Socieity Guidelines for the Management of Adults with Community-Acquired Pneumonia - 2015 update to show harmonization with 2014 NICE guidelines 2015, offsite link

NICE Guidance on Community and Hospital Acquired Pneumonia in Adults 2014, offsite link

ATS/IDSA Diagnosis and Management of Community-acquired Pneumonia 2019, offsite link

European Respiratory Society/ESCMID Adult Lower Respiratory Tract Infections 2011, offsite link

Community Acquired Pneumonia Severity Calculator offsite link

British Thoracic Society Pneumonia Severity Scoring System (CURB-65, CRB-65) onsite link

Hospital-Associated Pneumonia

CDC Guidelines for the Prevention of Nosocomial Pneumonia 2003 published Mar04 offsite link

ATS/IDSA Guidelines for the Management of Adults with Hospital-Acquired and Ventilator-associated Pneumonia 2016 offsite link

British Society for Antimicrobial Chemotherapy Guidelines for the Management of Hospital-Acquired Pneumonia in the UK 2008 offsite link

ERS/ESICM/ESCMID/ALAT Guidelines on hospital-acquired and ventilator-acquired pneumonia in adults 2017 offsite link


Influenza Treatment and Prophylaxis, CDC 2021 offsite link

ACIP Seasonal Influenza Vaccination 2020 Guidelines offsite link

CDC Influenza Website offsite link

WHO Influenza Website offsite link

IDSA Seasonal Influenza in Adults and Children—Diagnosis, Treatment, Chemoprophylaxis, and Institutional Outbreak Management 2018 offsite link

WHO Pandemic Influenza H1N1pdm offsite link

Upper Respiratory Tract Infections

AHA 2009 Guidelines for the Prevention of Rheumatic Fever and Diagnosis and Treatment of Acute Streptococcal Pharyngitis 2009 offsite link

IDSA Diagnosis and Management of Group A Streptococcal Pharyngitis 2012* offsite link

IDSA Clinical Practice Guideline for Acute Bacterial Rhinosinusitis in Children and Adults 2012* offsite link

(*, marked as archived as IDSA and may need update)


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

IUATLD Management of Tuberculosis Orange Guide 2019-offsite link

NICE - TB Clinical Diagnosis and Management UK National Institute for Health and Clinical Excellence 2019 offsite link

Canadian TB Standards, 7th edition 2014 - superb source for everything about clinical and diagnostic aspects of TB offsite link

ATS/IDSA/CDC Diagnosis of TB in Adults and Children, including supplemental information-2017 offsite link

CDC Compendium of TB Testing and Diagnostic Guidelines offsite link

Treatment Guidelines

American Thoracic Society/CDC/IDSA Statement on the Treatment of Drug-Susceptible Tuberculosis-2016 offsite link

ATS/ERS/CDC/IDSA Treatment of Drug-Resistant Tuberculosis 2019 offsite link

WHO Treatment of Drug Resistant Tuberculosis Consolidated Guidelines -2020 offsite link

Also see the above NICE guidelines

European Union standards for TB care 2017, offsite link

International Union Against Tuberculosis and Lung Disease IUATLD TB and Other Guidelines offsite link

Diagnosis and Treatment of Tuberculous Infection without Disease (TBInd), née Latent TB

American Thoracic Society/CDC Statement on Targeted Tuberculin Testing and Treatment of Latent Tuberculosis Infection -1999 offsite link This was updated in 2003 to warn against the use of PZA/Rif prophylaxis - see updated CDC treatment guidelines below

ATS/IDSA/CDC Diagnosis of TB in Adults and Children, including supplemental information-2017 offsite link

CDC Latent TB Resources offline link

CDC Guidelines for the Treatment of Latent TB 2020 offsite link

WHO Consolidated Guidelines on TB: TB Preventive Treatment 2020 offisite link

TB Drug Side-effect and Interactions

ATS-Hepatotoxicity of anti-Tb drugs 2006 offsite link

MSF HIV Medication and TB Drug Interactions offsite link

Univ of Liverpool HIV Drug Interactions offsite link

Non-Tuberculous Mycobacterial Infections

ATS/ERS/ESCMID/IDSA guidelines for the treatment of non-tuberculous mycobacterial infections 2020 offsite link

BTS Management of non-tuberculous mycobacterial disease 2017 offsite link

WHO, IUATLD and Other Organization Guidelines

WHO TB guidelines offsite link

IUATLD guidelines offsite link

FIND TB offsite link

Stop TB Partnership offsite link


Parasitic, Tick-Borne Diseases

CDC Malaria Treatment and Diagnosis off site link

WHO Guidelines for the Treatment of Malaria, 3rd edition 2015 offsite link

CDC Tickborne Diseases of the United States, Reference Manual, 5th ed., 2018 offsite link

CDC Tick-borne Diseases offsite link

IDSA Babesiosis Guidelines 2020 offsite link

IDSA and ASTMH Neurocysticercosis Guidelines 2018 offsite link

IDSA AAN ACR Prevention, Diagnosis and Treatment of Lyme Disease 2020 offsite link; guideline summary

Global Disease Alert Map - Alerts of current worldwide infectious diseases outbreaks based on public health, news and Promed alerts offsite link

HIV-Related Information

AIDS info US Dept HHS Website  offsite link

UCSF National HIV/AIDS/Hepatitis C Clinician's Consultation Center offsite link

IDSA Primary Care Guidelines for Persons With HIV 2020 offsite link

IDSA Prevention and Treatment of Opportunistic Infections in Adults and Adolescents with HIV 2020 offsite link

CDC HIV Testing Guidelines offisite link


CDC Bioterrorism offsite link

Classical Clinical Description of Inhalation Anthrax offsite link

Consensus Statements on Bioterrorism Agents, published in JAMA links

CDC Anthrax offsite link

ASM Sentinel Laboratory Agent Summaries and Guidelines offsite link

WHO Public health response to biological and chemical weapons 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 2018 offsite link

PHE Chemical, Biological and Radiological Incidents offsite link

European Guidelines on Bioterrorism ("Bichat" Guidelines)-offsite link