Pan American Health Organization · 2021
Regional protocol for standardized AMR surveillance using isolate-level data from blood cultures, aligned with GLASS
- Issuer
- Pan American Health Organization
- Edition
- 2021
- Audience
- National coordinating centres, national reference laboratories, hospital laboratories, infectious disease specialists, clinical microbiologists, epidemiologists
- Evidence
- Expert consensus based on ReLAVRA network experience (1996–2020), GLASS methodology, CLSI standards, and CAESAR manual
- Reviewed
- 19 Oct 2026 · GMJ
What this guideline says
GMJ summary
This protocol establishes a standardized approach for enhanced antimicrobial resistance (AMR) surveillance across Latin America and the Caribbean, focusing initially on bloodstream infections. It transitions national systems from aggregate data reporting to isolate-level surveillance, integrating laboratory, clinical, and epidemiological data for nine priority pathogens: Acinetobacter baumannii, Escherichia coli, Enterococcus spp., Klebsiella pneumoniae, other Enterobacteriaceae, Pseudomonas aeruginosa, Salmonella spp., Staphylococcus spp., and Streptococcus pneumoniae.
The protocol defines three core components: a national coordinating centre (NCC), a national reference laboratory (NRL), and local surveillance sites (hospitals/laboratories). Data collection includes 24 standardized fields covering patient demographics, specimen details, hospital information, and antimicrobial susceptibility test results following CLSI standards. All data undergo quality checks, deduplication (first isolate per microorganism per person per year), and anonymization before quarterly submission to PAHO through the PLISA platform, using WHONET software as the recommended tool.
The methodology enables distinction between health care-associated infections (patients admitted >2 calendar days) and community-acquired infections (≤2 calendar days), calculation of multidrug resistance (MDR), extensively drug-resistant (XDR), and pandrug-resistant (PDR) patterns, and alignment with the Global Antimicrobial Resistance Surveillance System (GLASS). Data are analysed regionally and published annually, with interactive dashboards displaying resistance trends across participating countries.
Key points
For clinicians — doses and thresholds as stated in the guideline
- Nine priority pathogens under surveillance: <em>Acinetobacter baumannii</em>, <em>E. coli</em>, <em>Enterococcus</em> spp., <em>K. pneumoniae</em>, other Enterobacteriaceae, <em>P. aeruginosa</em>, <em>Salmonella</em> spp., <em>Staphylococcus</em> spp., and <em>S. pneumoniae</em>
- Health care-associated bloodstream infection defined as specimen obtained >2 calendar days after hospital admission; community-acquired if ≤2 calendar days
- 24 mandatory and required data fields must be collected, including patient ID, sex, age, date of admission, specimen date, specimen type (blood), organism, antibiotic tested, and susceptibility interpretation (S/I/R)
- Only first isolate per microorganism per person per year is included in regional analysis to minimize bias from repeated cultures
- CLSI standards recommended for antimicrobial susceptibility testing with harmonized breakpoints; uniform test panel required for all pathogen-antibiotic combinations listed in protocol
- Quarterly data submission recommended from local sites to NCC; annual data call from PAHO between 1 May and 30 June, with feedback by 31 August and final confirmation by 15 October
- Resistant phenotypes requiring NRL confirmation include: carbapenemase-positive Enterobacteriaceae, colistin-resistant <em>A. baumannii</em> and <em>P. aeruginosa</em>, vancomycin-resistant <em>Enterococcus</em>, VRSA (vancomycin MIC ≥16 mg/L) and VISA (vancomycin MIC 4–8 mg/L)
- External quality assessment (EQA) mandatory for all participating laboratories, coordinated by NRL and regional reference laboratory (Malbrán Institute, Argentina)
Mandatory and required data fields for isolate-level surveillance
Table extracted from the guideline
| Field | Type | Status | Description |
|---|---|---|---|
| Country | Text | Mandatory | Country name |
| Laboratory ID | Text | Mandatory | Unique hospital code |
| Patient ID | Text | Mandatory | Patient identification/code |
| Sex | Text | Required | m: male, f: female, o: other, u: unknown |
| Age | Text | Required | Years, months, days, or weeks |
| Date of admission | Date | Optional | Date of hospital admission (MON-DD-YYYY) |
| Department | Text | Mandatory | Ward where patient admitted (med/sur/icu/ped/neo/etc.) |
| Type of infection | Text | Required | ho: hospital origin, co: community origin, unk: unknown |
| Specimen date | Date | Mandatory | Date of sample collection (MON-DD-YYYY) |
| Specimen type | Text | Mandatory | bl: Blood |
| Organism | Text | Mandatory | Pathogen species and genus |
| Antibiotic | Text | Mandatory | Antimicrobial agent code |
| Interpretation | Categorical | Mandatory | S: susceptible, I: intermediate, R: resistant, NS: nonsusceptible |
Source: Pan American Health Organization, Protocol for Enhanced Isolate-Level Antimicrobial Resistance Surveillance in the Americas. Primary Phase: Bloodstream Infections. Reproduced in summary form.
From the guideline
Verbatim
“Only the first isolate per microorganism per person per year is included in analyses at the regional and global levels.”
Editor’s perspective
Why this matters for Georgia and the region
Prof. Giorgi Pkhakadze, MD, MPH, PhD
Editor-in-Chief, Georgian Medical Journal · Chair, Public Health Institute of Georgia · WHO consultant, health and migration
As Chair of Georgia's Public Health Institute and having supported our GLASS enrolment, I recognize this PAHO protocol offers the South Caucasus a tested roadmap for the isolate-level surveillance GLASS requires but many countries struggle to implement. The protocol's most valuable element for Georgian clinicians is the standardized definition distinguishing health care-associated bloodstream infections (specimen >2 calendar days after admission) from community-acquired infections—this single criterion enables evidence-based empirical therapy decisions and infection prevention targeting that our tertiary centres urgently need as carbapenem resistance in <em>K. pneumoniae</em> exceeds 50% in some Tbilisi ICUs. The realistic challenge will be linking our hospital information systems to laboratory databases to automate this 2-day admission calculation, as most Georgian laboratories currently lack this interoperability and will require investment in either WHONET implementation or BACKLINK middleware to bridge legacy systems. Georgia's existing participation in WHO Europe's CAESAR network since 2012 and our National Reference Laboratory's CLSI proficiency testing since 2015 provide the quality foundation, but expanding beyond our five current sentinel hospitals to achieve national representativeness will require addressing the rural-urban laboratory capacity gap through the regional EQA programme this protocol describes.
ORCID 0000-0001-7609-4515 · Perspective written for the GMJ Guidelines Library, 19 Oct 2026
Applicability
Georgia and the South Caucasus
Georgia, as a WHO GLASS-enrolled country since the system’s launch, can use this protocol to strengthen isolate-level AMR surveillance within its existing laboratory network. The protocol’s stepwise implementation starting with bloodstream infections aligns with capacity-building needs in the South Caucasus, where tertiary centres in Tbilisi possess CLSI-standard antimicrobial susceptibility testing capability but regional laboratories may require external quality assessment support. National programmes should assess whether existing hospital information systems can link admission dates to laboratory data to enable automated classification of health care-associated versus community-acquired infections, or whether parallel data collection through specimen referral forms will be necessary. The quarterly reporting cycle and WHONET-based data management can integrate with Georgia’s existing public health surveillance infrastructure coordinated by the National Center for Disease Control and Public Health.
Questions this guideline answers
Quick answers
What is the minimum number of surveillance sites needed to start?
The protocol does not specify a minimum number. Countries at early implementation stages may start with a few sites that have the greatest laboratory diagnostic capacity and interest, then gradually expand. Sites should represent different geographical areas, hospital types (public/private, tertiary/general/paediatric), and both urban and rural settings to achieve national representativeness.
How are health care-associated and community-acquired bloodstream infections distinguished?
Hospital-origin (health care-associated): specimen obtained when patient admitted >2 calendar days, or admitted <2 calendar days but transferred from another facility where admitted ≥2 calendar days. Community-origin: patient in hospital ≤2 calendar days when specimen taken. If date of admission is unavailable, infection origin can be recorded directly from specimen referral form provided by medical staff.
Which resistant phenotypes must be sent to the national reference laboratory for confirmation?
Category 1 phenotypes (rare or not previously reported) include: carbapenemase-positive Enterobacteriaceae, colistin/polymyxin-resistant Enterobacteriaceae, ceftazidime/avibactam-nonsusceptible wild-type Enterobacteriaceae (non-MBL producers), cephalosporin III intermediate/resistant <em>Salmonella</em> or <em>Shigella</em>, colistin-resistant <em>Acinetobacter baumannii</em>, polymyxin intermediate/resistant <em>Pseudomonas aeruginosa</em>, vancomycin-resistant or linezolid/tedizolid-nonsusceptible <em>Enterococcus</em>, VRSA (vancomycin MIC ≥16), VISA (vancomycin MIC 4–8), and linezolid-resistant <em>Staphylococcus aureus</em>. All pandrug-resistant isolates require confirmation.
What data quality checks are performed before regional submission?
NCC/NRL must: assess 100% completeness of mandatory and required variables; evaluate microbiological results for consistency and plausibility; ensure pathogen and resistance pattern confirmation; verify adherence to CLSI or EUCAST standards; confirm appropriate S/I/R breakpoints; perform deduplication to include only first isolate per microorganism per person per year; and anonymize patient identifiers. PAHO provides automated validation including technical details on records accepted/rejected, unusual resistance phenotypes, isolate counts per pathogen and laboratory, and demographic distributions.
Related on GMJ
Interconnected resources
Dictionary of Public Health
Drugs A–Z
GMJ News coverage
- Candida auris endocarditis emerges as life-threatening infection in hospitalised patientsOct 2026
- Sepsis AI Algorithms Fail When Trained on Future Data, Study Reveals Critical FlawsJul 2026
- Hospital-Acquired Infections Rising in UK: Latest Surveillance Data Shows Increases in Dangerous PathogensAug 2026
- Overuse of 'Just in Case' Antibiotics Accelerates Antimicrobial Resistance Crisis, Researchers WarnSep 2026
- WHO Adopts New Decade-Long Strategy to Combat Antimicrobial Resistance Through 2036Aug 2026
Quality & accreditation
- ASF Laboratory — Standard 1 — Governance & Document Control
- ASF Laboratory — Standard 6 — Pre-Examination: Specimen Pathway
- ASF Laboratory — Standard 7 — Examination: Process & Safety
- ASF Laboratory — Standard 8 — Post-Examination: Reporting & Critical Values
- ASF Hospital — Standard 5 — Safety & Emergency Preparedness
- ASF Hospital — Standard 11 — Critical Care
- ASF Medical Transport — Standard 6 — Emergency Response During Transport
Other guidelines on this topic
- Guide for the preparation of a risk communication strategy for COVID-19 vaccines
- Guidelines for Prophylaxis and Management of Patients with Mild and Moderate COVID-19 in Latin America and the Caribbean
- Developing national meningitis plans: an operational manual
- Regional Framework for the Monitoring and Re-Verification of Measles, Rubella and Congenital Rubella Syndrome Elimination in the Americas
- Influenza and Other Respiratory Viruses: Surveillance in the Americas 2021
- Issuer
- Pan American Health Organization
- Type
- Procedures, manuals, guidelines
- Edition
- 2021
- Status
- Current
- Published
- 2021-01-01
- Languages
- English, Spanish
- Scope
- Bloodstream infections caused by nine priority bacterial pathogens in Latin America and the Caribbean
- Audience
- National coordinating centres, national reference laboratories, hospital laboratories, infectious disease specialists, clinical microbiologists, epidemiologists
- Licence
- CC BY-NC-SA 3.0 IGO
- ISBN
- 978-92-75-12268-6
- Evidence
- Expert consensus based on ReLAVRA network experience (1996–2020), GLASS methodology, CLSI standards, and CAESAR manual
- Record history
- Created 19 Oct 2026 · updated 19 Oct 2026 · next check Apr 2027
Pan American Health Organization. Protocol for Enhanced Isolate-Level Antimicrobial Resistance Surveillance in the Americas. Primary Phase: Bloodstream Infections. Washington, D.C.: PAHO; 2021. ISBN: 978-92-75-12268-6.GMJ Guidelines Library records are original summaries written by the GMJ editorial team from the issuer’s published document and reviewed by a physician. They do not replace the full guideline. The document is the copyright of its issuer and is linked, not hosted. Spotted an error or a newer edition? Tell the Guidelines Desk.
Was this article helpful?
