- A Complex Virus, A Coordinated Response: Public Health Laboratories Battle Zika
- Lessons from a Virus: Public Health Laboratories Respond to the H1N1 Pandemic
- Investigation of Acute Hepatitis in US Pediatric Population
- Adeno-associated virus type 2 in US children with acute severe hepatitis
- Acute Hepatitis and Adenovirus Infection Among Children — Alabama, October 2021–February 2022
- Considerations for SARS-CoV-2 Genomic Surveillance: A Joint Consensus Recommendation of the Association for Molecular Pathology and Association of Public Health Laboratories
- Strengthening the US Public Health Lab System: Summary of Coronavirus Disease (COVID-19) After Action Review Workshop
Infectious Diseases Resources and Trainings
APHL supports the infectious diseases work of public health laboratories with technical publications, resources, trainings, communities of practice and more.
Contact the Infectious Diseases team: [email protected]
Resources and Reports
Technical Publications (Current)
APHL produces a host of technical publications to inform or guide laboratory work, including reports, guidance, survey data, meeting summaries, fact sheets and more. Search within the repository or browse the curated list below.
General Resources
Below are publications that provide helpful context, either as a baseline overview of a topic or documentation of a public health event.
Historical Resources and Reports
Below are documents that provide helpful historical context or documentation of previous survey results.
RESOURCES
SURVEY REPORTS
- Viral Hepatitis Testing: 2009 APHL Survey Report
- HIV Diagnostics Survey: 2012 APHL Survey Report
- HIV Diagnostics Survey: 2014 APHL Survey Report (Includes HCV)
- HIV and HCV Diagnostics Survey: 2017 APHL Survey Report
- 2019-2020 HIV and HCV Diagnostics Survey Report
RESOURCES
- The Role of Public Health Laboratories in STD Testing, 2011 and 2017
- Consultation on Laboratory Diagnosis of Syphilis Meeting Summary Report, 2017
SURVEY REPORTS
- Chlamydia and Gonorrhea Testing Practices in 2013 and 2015
- Sexually Transmitted Diseases Testing Practices in Public Health Laboratories, 2016
- Sexually Transmitted Infections: 2021 APHL Survey Report
RESOURCES
- Core TB Laboratory Services for Public Health Laboratories
- The Future of TB Laboratory Services: A Framework for Integration, Collaboration and Leadership
- National Plan for Reliable Tuberculosis Laboratory Services Using a Systems Approach
- Clinical Laboratory Testing for Mycobacterium chimaera, 2017
REPORTS
- National TB Services Survey Report-APHL 2012
- National TB Laboratory Services Survey Report: Biosafety, 2015
- Public Health Laboratory Expansion of Nucleic Acid Amplification Testing for Mycobacterium tuberculosis Complex, 2015
Training Resources
Infectious Diseases Training Resources
APHL has developed many trainings including on-demand courses, videos and webinars for infectious diseases topics. Most of this material can be accessed through through the APHL Learning Center. You can also visit the Training Hub for many training resources and find upcoming webinars via the Event Calendar. The resources showcased on this page are available here without any continuing education credits and may not include completion certifications. Courses that are available for CEU in the ALC are noted.
MicrobeNET Training Videos
MicrobeNet is a CDC hosted, free database that provides detailed information on rare and unusual pathogens including bacteria and fungi. The information is curated by experts and is updated frequently. Clinical and public health laboratorians can access this information to improve their reference diagnostics and species identification capabilities. Visit the MicrobeNet homepage to sign in or request an account. Contact the team at [email protected] with questions.
Topics include:
- Mass Spectromy: Identifying Pathogens from MALDI-TOF Data
- Sequencing Analysis: Identifying Pathogens from 16S Sequencing
- Phenotypic Testing: Identifying Pathogens from Phenotypic Testing
View MicrobeNet Training Videos
Introductory Video
Training Resources
The following are online learning activities, training materials and other tools developed for public health laboratories outside of the US. APHL is not able to offer any continuing education credits for these activities. If you are based in the US and looking for courses offered by APHL please proceed to the APHL Learning Center.
Cross-Cutting
This learning activity consists of three modules that focus on the pre-analytical phase of the specimen handling lifecycle. Approximate time to complete course is 1 hour (~20 minutes per module); certificate of completion provided. Click the links below to view the on-demand videos.
ENGLISH
- Module 1:Proper Specimen Labeling & Packaging for Clinical Diagnosis
- Module 2: Proper Clinical Specimen Receiving & Accessioning
- Module 3: Understanding Laboratory Data Management
FRANÇAIS
Recordings from a training held September 2024. The videos include lectures on laboratory data management, accessioning, data privacy, confidentiality and security as well as topics on Microsoft Excel including data cleaning, formulas and functions and tables and graphs.
English Videos
- Laboratory Data Management
- Data Organization and Cleaning in Excel
- Formulas and Functions in Excel
- Accessioning
- Tables and Graphs in Excel
- Data Privacy, Protection and Security
- Excel Exercises​
Vidéos en Français
This learning activity is offered in two formats: an online version and a version to deliver your own in-person workshop. Each format covers the same topics: overview of the scientific writing process; manuscript preparation and manuscript revision. A desktop computer or laptop is recommended for taking the online course. Specific modules and topics can be accessed from the directory once the course is launched.
ONLINE MODULES
The approximate time to complete the entire online course is 4 hours. A certificate of completion is provided for each module.
- English: Scientific Writing: The Basics - Online Course
- Français​: Rédaction Scientifique: Les Fondamentaux​ - Formation en Ligne​
- Español: Redacción CientÃfica: Conceptos Básicos - Capacitación en LÃnea​
IN-PERSON WORKSHOP MATERIALS
The in-person workshop is intended to be delivered over the course of two-three days. The workshop materials consist of a Facilitator's Guide, PowerPoint slides and a Participant Workbook.
Pathogen Specific
Regional Laboratory Quality Training for Bacterial Meningitis Surveillance
These recordings are of a live training given over the course of six days in September 2021. The videos include didactic lectures designed to introduce quality management systems and inform laboratorians of best practices to assure quality in laboratory processes.
English Videos
- Day 1: Introduction to Quality Management Systems and the 12 Quality System Essentials
- Day 2: Assuring Quality Through the Pre-analytic Phase-Samples and Reagents
- Day 3: Assuring Quality through the Analytical Phase-Test and Equipment
- Day 4: Assuring Quality Through the Post-analytical Phase-Documents and Records; Information Management
- Day 5: Assessing Competency of Personnel and Conducting Assessments
- Day 6: Learning from your Nonconforming Events and the Continual Improvement Process
Vidéos en Français
- Journée 1 : Introduction au système de gestion de la qualité et ses 12 points essentiels
- Journée 2 : Assurer la qualité en laboratoire grâce à la phase pré-analytique – Echantillons et réactifs
- Journée 3 : Assurer la qualité en laboratoire grâce à la phase analytique – Tests et équipement
- Journée 4 : Assurer la qualité au laboratoire grâce à la phase post-analytique – Documents et registres ; Gestion de l'information​
- Journée 5 : Evaluer les compétences du personnel et mettre en place des évaluations
- Journée 6 : Tirer des enseignements des évènements non conformes (ENC) et de l'amélioration continue des procédés
Preliminary Identification of Bacterial Meningitis Pathogens
This course focuses on the preliminary identification of bacterial meningitis pathogens. Approximate time to complete course is 30 minutes (~7 minutes per module).
English Videos
- 1-Biosafety and Good Laboratory Practices
- 2-Transporting and Handling Specimens
- 3.1-Examining Specimens-Cytology
- 3.2-Examining Specimens-Gram Stain
Vidéos en Français
- 1-Biosécurité et bonnes pratiques de laboratoire
- 2-Transport et manipulation des échantillons
- 3.1-Examen d'échantillons-cytologie
- 3.2-Examen d'échantillons coloration de Gram
Resources
This manual contains standard operating procedures
for the identification and characterization of bacterial meningitis pathogens
from cerebrospinal fluid by culture.
Standard Operating Procedure: Identification and Characterization of Neisseria meningitidis, Streptococcuspneumoniae and Haemophilus influenzae
Procédures Opérationnelles Standardisées Identification et Caractérisation de Neisseria meningitidis, Streptococcus pneumoniae et Haemophilus influenzae
These training materials were designed to facilitate a multi-sectoral discussion when there is detection of influenza virus of pandemic potential in poultry and human populations. The training was developed for an international audience but much of the material could be helpful for domestic preparedness as well. The materials consist of didactic lectures, group exercises and a case study-they can also be used in a modular manner for specific epidemiology, veterinary, laboratory or medical audiences. 
Introduction
Clinical
- C1: Novel Influenza A Clinical Case Presentation and Clinical Course
- C2: Assessment, diagnosis and management of patients with novel influenza A virus infections 
- C3: Post-exposure Management of Human Infection with Novel Influenza A Viruses: Use of Neuraminidase Inhibitors 
- C-Ex1: Clinical Case Scenario 1: Low Resource Settings - Participants
- C-Ex1: Clinical Case Scenario 1: Low Resource Settings - Facilitator
- C4: Use of Non-Pharmaceutical Interventions (NPIs) 
- C5: Infection Control in Healthcare Settings
- C6: Infection Prevention and Control Preparedness
Epidemiology
- E1: Role of Indicator and Event-based Surveillance in Pandemic Early Warning
- E2: Surveillance in Humans after a Poultry Event Detection
- E-Ex1: Short Exercise on Event-Based Surveillance - Facilitator
- E-Ex1: Short Exercise on Event-Based Surveillance - Participant
- E-Ex2: Case Investigation Scenario-Facilitator
- E-Ex2: Case Investigation Scenario-Participant
- E3: Forming a Rapid Response Team
- E4: Epidemiologic Case Investigation of Human Infections with HxNy
Veterinary
- V1: Value Chain as a Basis for Animal Disease Surveillance and Response
- V2: FAO Guidelines for Avian Influenza Surveillance in Asia
- V3: Avian Influenza Viruses and the OIE: An Overview
- V-Ex1: Prioritize and Implement LBM Surveillance Along the Value Chain 
- V4: Control Strategies for HPAI and LPAI in Poultry Populations
- V5: Laboratory Algorithms for Comprehensive Influenza A Surveillance in Poultry
- V6: Avian Influenza Virus Poultry Vaccines and Their Use
- V-Ex2: Veterinary Scenario 2 and Resource Materials
- V-Ex2: Veterinary Scenario 2 Handouts
Laboratory
- L1: Human Specimen Collection, Transport & Virus Sharing 
- L2: General Biorisk Management
- L-Ex1: Specimen Collection, Laboratory Diagnostics, and Biosafety Issues - Facilitator
- L-Ex1: Specimen Collection, Laboratory Diagnostics, and Biosafety Issues - Participant
- L3: Overview of Molecular and Serological Diagnostics for Influenza A(H7N9)
- L-Ex2: Class Exercise: Laboratory Detection, reporting and characterization of novel influenza virus infections - Participant
- L-Ex2: Class Exercise: Laboratory Detection, reporting and characterization of novel influenza virus infections - Facilitator
Case Study
Using the Yellow Fever MAC-HD Kit to Detect IgM to Yellow Fever Virus
These modules demonstrate how to use the Yellow Fever MAC-HD ELISA Test Kit to detect immunoglobulin M antibodies to yellow fever virus, including how to set up and conduct the ELISA, calculation demonstrations and results analysis. Video is available in mutliple languages.
Training Resources
The following are online training materials intended to assist a broad public health audience beyond the public health laboratory, including clinical and non-clinical testing staff, public health nurses, staff at health departments and at care facilities that may be engaged in activities with public health entities. If you are based in the US and looking for courses offered by APHL, please proceed to the APHL Learning Center where these courses are available with certificates of completion and/or continuing education credits.
Syphilis Diagnostics: Rapid Plasma Reagin (RPR) Manual Test Methods
- This on-demand course outlines the intended use of the manual Rapid Plasma Reagin procedure and then describes and demonstrates how to perform testing (both qualitative and semi-quantitative). The course also covers interpretation of results, reporting and additional testing considerations. This activity is intended for bench level laboratorians
Understanding Tuberculosis (TB) Laboratory Testing for Public Health Nurses
- This just-in-time resource provides education and on-demand access to understand the basics of laboratory testing for tuberculosis, from proper collection through test methods and results interpretation. With clear navigation, it is easy to watch from beginning to end or jump right to the information you need.
Brought to you by the Association of Public Health Laboratories and the Antimicrobial Resistance Laboratory Network (AR Lab Network) these learning resources were created to assist staff at health care facilities understand the role of colonization screening for carbapenemase-producing organisms (CPOs) and Candida auris.
​Continuing education credit is not available for these learning resources. If you are based in the US and need credit for course completion​ or are interested in courses offering CEU please proceed to the APHL Learning Center.
- Module 1: Overview and Importance of Screening for Multidrug-resistant Organisms (MDROs)
- Module 2: Carbapenemase-producing Organisms Colonization Screening
- Module 3: Candida auris Colonization Screening
- Module 4: Video-Packaging and Shipping for Colonization Screening​
For any questions, email [email protected].​
Find Your Community
APHL’s ColLABorate Online Communities provide an opportunity to connect with others working in the same field or with similar areas of interest. Learn more about joining one of our communities:
-
Microbiology Discussion Community
ColLABorate CommunityA forum for questions, solving problems and contributing to the overall advancement of the field of public health microbiology.
-
Pathogen Papers Community of Practice
ColLABorate Community and Monthly MeetingsPathogen Papers is an APHL hosted moderator-led virtual journal club that meets monthly to discuss the selected journal article(s) that will allow participants to have in-depth conversations. Pathogen Papers-the journal club and ColLABorate community is open to anyone interested in engaging in a collaborative space where public health laboratorians can participate in regular discussions, share insights, foster connections and learn more about new research. Topics include laboratory testing, methodology and applied research for infectious diseases.