Definitions of Terms Used in the AMASS Reports and Publications about AMASS

Plain-language, citable definitions of the terms used in the AMASS reports and in the peer-reviewed publications about AMASS. Where a paper defines a term, we quote it word-for-word and give the source; where a term is used but not formally defined, we mark our own editorial definition; terms that belong to the AMASS report rather than the papers are marked as tool definitions.

AutoMated tool for Antimicrobial resistance Surveillance System 8 source publications (2020–2026) Built for people & AI retrieval

Maintained by the AMASS team, Mahidol Oxford Tropical Medicine Research Unit (MORU). Questions? Email AMASS@tropmedres.ac.

How to read this glossary

Quoted The definition is quoted verbatim from a publication; the citation follows in the grey line. Quotation marks and the source are shown so the wording can be reused with attribution.

Editorial The term is used in the publications but not given a formal definition there; the wording here is ours, written to match how the papers use it.

Tool The term belongs to the AMASS application/report (e.g. an Annex) rather than to these research papers; the definition is drawn from the AMASS tool and manual and is not from the publications above.

AMASS report The definition is quoted from the AMASS AMR Surveillance Report itself (the example output generated for Example_dataset_5, AMASS version 4.0). When a term has more than one definition, the AMASS-report version is shown first as the primary definition; other published variants follow underneath as secondary, each with its citation.

1The AMASS application & its reports

What the tool is, and the structure of the report it produces.

QuotedAMASS

Stands for: AutoMated tool for Antimicrobial resistance Surveillance System.

“An offline application to generate standardized AMR surveillance reports from routinely available microbiology and hospital data files was written in the R programming language (R Project for Statistical Computing).”

Lim C, et al. J Med Internet Res. 2020;22(10):e19762. PMC7568216

The application is offline and open-access, requires no internet to run, and produces the report in 1–3 minutes. By version: written in the R programming language in version 1; in R and Python in versions 2 and 3; and in Python in version 4. Input files: the microbiology data file, the hospital admission data file, and the drug (antimicrobial) dispensing data file (added in version 4).

QuotedAMR surveillance report — the six sections

Also: AMR_surveillance_report.pdf

“… report on AMR surveillance contains the following six sections (Figure 3): (1) data overview; (2) an isolate-based report; (3) an isolate-based report with stratification by origin of infection; (4) a sample-based report; (5) a sample-based report without stratification by infection; and (6) mortality involving AMR and antimicrobial-susceptible infections.”

Lim C, et al. J Med Internet Res. 2020;22(10):e19762. PMC7568216

AMASS reportTier-based approach

“AMASS uses a tier-based approach. In cases when only the microbiology data file with the results of culture-negative specimens is not available, only section one, two, and three would be generated for users. Section three would be generated only when data on admission date are available. This is because these data are required for the stratification by origin of infection. Section four would be generated only when data of specimens with culture negative (no microbial growth) are available in the microbiology data. This is because these data are required for calculating the AMR frequency. Section five would be generated only when both data of specimens with culture negative and admission date are available. Section six would be generated only when mortality data are available.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Methods.

Editorial In short, AMASS generates as much of the report as your data allow: microbiology data alone → Sections 1–2; + admission dates → Section 3 (stratification by origin); + culture-negative results → Section 4 (AMR frequency); + both → Section 5; + mortality/outcome data → Section 6. The annexes likewise appear only when their required inputs are present (e.g. the drug file for Annex D).

QuotedIsolate-based (or sample-based) report

“… (2) an isolate-based report; (3) an isolate-based report with stratification by origin of infection …”

Lim C, et al. J Med Internet Res. 2020;22(10):e19762. PMC7568216 (report Sections 2–3)

Editorial The unit of analysis is the isolate (isolate-based) or the specimen/sample (sample-based). AMR is expressed as the proportion of tested isolates that are resistant — the classic antibiogram. WHO GLASS historically collected AMR data mainly as sample-based surveillance (based on patient specimens such as blood or urine from designated laboratories). In AMASS this is the AMR proportion report (Sections 2–3), with isolates deduplicated to the first per patient.

Concept per WHO GLASS (sample-based surveillance) & ACORN. WHO GLASS report; ACORN (PMC7134533).

QuotedCase-based (or patient-based) report

In the AMASS report / publications: called the “sample-based report” (Sections 4–5).

“… (4) a sample-based report; (5) a sample-based report without stratification by infection …”

Lim C, et al. J Med Internet Res. 2020;22(10):e19762. PMC7568216 (report Sections 4–5)

Editorial The unit of analysis is the patient/case: results are deduplicated to one isolate per patient and can be linked to clinical and epidemiological data (infection origin, outcome). WHO GLASS describes case-based surveillance as combining microbiological data with clinical/epidemiological data (e.g. demographics, community- vs hospital-acquired infection). In AMASS this is the AMR frequency report (Sections 4–5, per 100,000 tested patients) and mortality (Section 6). Note: the AMASS report and Lim 2020 label Sections 4–5 the “sample-based report”, but because the denominators are patients, these are patient/case-based in the GLASS sense (see tested population).

Concept per WHO GLASS (case-based surveillance) & ACORN. ACORN case-based surveillance (PMC7134533); ACORN II protocol (PMC10579854).

EditorialWHO GLASS

Stands for: World Health Organization Global Antimicrobial Resistance (and Use) Surveillance System.

Editorial The WHO’s standard framework for collecting, analysing and sharing AMR surveillance data. AMASS follows GLASS recommendations for deduplication, stratification by origin of infection, and the choice of denominators. The papers describe it as the “World Health Organization Global Antimicrobial Resistance and Use Surveillance System (WHO GLASS)”.

Used in: Lim 2020, Sinto 2022, Lim 2024, Tuamsuwan 2024.

2Surveillance methodology

How AMASS cleans data and assigns each infection to a patient, an origin, and a denominator.

AMASS reportDeduplication

“AMASS application de-duplicated the data by including only the first isolate per patient per specimen type per evaluation period.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Section 2.

“When more than one blood culture was collected during patient management, duplicated findings of the same patient were excluded (de-duplicated). Only one result was reported for each patient per sample type (blood) and surveyed organisms. For example, if two blood cultures from the same patient had E. coli, only the first would be included in the report. If there was growth of E. coli in one blood culture and of K. pneumoniae in the other blood culture, then both results would be reported.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Methods (De-duplication) — i.e. only the first isolate per patient, per specimen type, per pathogen, per evaluation period.

Other wording in the publications (secondary)

“The application deduplicates the data by including only the first isolate per sample type per pathogen per survey period for each patient.”

Lim C, et al. J Med Internet Res. 2020. PMC7568216; also Srisuphan 2023 (PMC10349292).

EditorialBloodstream infection (BSI)

Editorial An infection identified by a blood specimen (blood culture) positive for a pathogen. In the AMASS papers, a patient with BSI is counted once per pathogen per reporting period after deduplication.

QuotedOrigin of infection

“The origin of infection is defined by using specimen collection date, location type (inpatient or outpatient setting), and hospital admission date for inpatient isolates as a proxy to define where the infection was likely contracted (community or hospital).”

Lim C, et al. J Med Internet Res. 2020;22(10):e19762. PMC7568216

AMASS reportCommunity-origin BSI

Also: community-origin infection

“The definitions of infection origin proposed by the WHO GLASS was used. In brief, community-origin bloodstream infection (BSI) was defined for patients in the hospital within the first two calendar days of admission when the first blood culture positive specimens were taken.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Methods (Definitions).

Other wording in the publications (secondary)

“Community-origin BSI was defined for patients with first positive blood specimens in the hospital taken within the first two calendar days of admission with calendar day one equal to the day of admission.”

Lim C, et al. PLoS One. 2024. PMC11104583; consistent in Sinto 2022 (PMC9117993) and Srisuphan 2023 (PMC10349292).

AMASS reportHospital-origin BSI

“Hospital-origin BSI was defined for patients in the hospital longer than the first two calendar days of admission when the first blood culture positive specimens were taken.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Methods (Definitions). If the user supplies an infection_origin variable (e.g. from the infection-control team or referral data), AMASS uses that instead of the 2-day rule.

Other wording in the publications (secondary)

“Patients with first positive blood specimens taken after the first two calendar days were categorized as cases of hospital-origin BSI.” … “The classification of community-origin and hospital-origin BSI was performed within AMASS and based on specimen dates and hospital admission dates …”

Lim C, et al. PLoS One. 2024. PMC11104583

AMASS reportBSI of unknown origin

Editorial A bloodstream infection that AMASS could not assign to either community-origin or hospital-origin. Origin is determined from the specimen collection date relative to the hospital admission date; when that comparison cannot be made, the record is reported separately as “unknown origin”. In other words, any record that is not classified as community-origin (CO) or hospital-origin (HO) is counted as unknown origin.

“Unknown origin could be because admission date data are not available or the patient was not hospitalised.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Section 3.

In the publications

“These specimens were categorized as BSI of unknown origin in the summary reports generated by the AMASS.”

Tuamsuwan K, et al. J Infect. 2024;89(4):106249. PMC11409609 — for specimens that could not be linked to hospital admission dates.

EditorialTested patients (patients tested for BSI)

Editorial In AMASS, “tested patients” (or “patients tested for BSI”) means the patients who had a blood culture taken during the reporting period — i.e. the patients who were tested for a bloodstream infection. This count is the denominator for the sample-based / case-based reports (frequency per 100,000 tested patients).

“The AMASS calculates the total numbers of tested populations and uses them as denominators in section four and section five of the output report based on the WHO GLASS recommendations …”

Lim C, et al. J Med Internet Res. 2020. PMC7568216. See also patients tested for community-origin BSI and patients tested for hospital-origin BSI.

QuotedPatient tested for community-origin BSI

“Patients tested for community-origin BSI were defined as patients with the first blood culture performed within the first two calendar days of admissions during the reporting period.”

Sinto R, et al. Antimicrob Resist Infect Control. 2022;11(1):73. PMC9117993 — the denominator for community-origin frequency (per 100,000 tested patients).

QuotedPatient tested for hospital-origin BSI

“Patients tested for hospital-origin BSI were defined as patients with the first blood culture performed after the first two calendar days of admissions during the reporting period.”

Sinto R, et al. Antimicrob Resist Infect Control. 2022;11(1):73. PMC9117993 — the denominator for hospital-origin frequency (per 100,000 tested patients).

EditorialReporting period (survey period)

Editorial The time window of data analysed in one AMASS run (for example one calendar year). Deduplication is performed per survey period, so the same patient can contribute one isolate per pathogen in each reporting period. The papers use “reporting period” and “survey period” interchangeably.

EditorialPatient-days

Editorial The total number of inpatient days, counted by calendar days. The admission day is counted as one day, so for a single admission patient-days = (discharge date − admission date) + 1. Summed across admissions, patient-days is the denominator for population rates such as incidence per 100,000 patient-days.

EditorialPatient-days at risk

Editorial The total number of inpatient days contributed by patients while they are at risk of a hospital-origin infection (i.e. after the first two calendar days of admission). It is the denominator for hospital-origin frequency/incidence expressed “per 100,000 patient-days at risk”.

Used in: Sinto 2022, Lim 2024, Tuamsuwan 2024.

3Infection & resistance parameters

The core numbers the reports produce, quoted as the papers calculate them.

AMASS reportAMR BSI

Also: antimicrobial-resistant bloodstream infection

In the AMASS report, an AMR BSI is a (deduplicated) patient whose blood culture is positive for one of the organisms under surveillance and whose isolate is resistant (R) to the relevant antibiotic — i.e. the numerator of the Proportion of R. The report does not use a single combined “AMR BSI” label; it reports each resistant organism–antibiotic combination separately.

Basis: AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Section 2 (Proportion of R) and Methods (organisms).

Operational definition in the publications (secondary)

“AMR BSI is defined as a case of infection in patients with blood culture positive for CRAB, CRPA, 3GCREC, 3GCRKP, CREC, CRKP or MRSA.”

Lim C, et al. PLoS One. 2024. PMC11104583 (see acronyms).

AMASS reportAMR pathogens in the AMASS report

What AMASS reports: nine bacterial species, from blood specimens, deduplicated to the first isolate per patient.

“Organisms included for the AMR Surveillance Report: Staphylococcus aureus, Enterococcus faecalis, Enterococcus faecium, Streptococcus pneumoniae, Salmonella spp., Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Methods & Section 2.

Priority antibiotic-resistant “AMR pathogens” flagged in the frequency, incidence and mortality reports (Sections 4–6):

MRSA (methicillin-resistant S. aureus)
Vancomycin-resistant Enterococcus spp. (E. faecalis, E. faecium) — i.e. VRE
Penicillin-resistant S. pneumoniae
Fluoroquinolone-resistant Salmonella spp.
Third-generation-cephalosporin-resistant (3GC-R) and carbapenem-resistant E. coli
3GC-resistant and carbapenem-resistant K. pneumoniae
Carbapenem-resistant P. aeruginosa
Carbapenem-resistant A. baumannii

Resistance is reported using the standard S/I/R interpretation (see S/I/R); from AMASS version 4.0 the main report presents the proportion resistant (R).

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Sections 2–6.

QuotedNon-AMR BSI

Also: antimicrobial-susceptible BSI

“Non-AMR BSI is defined as cases of infection in patients who had blood culture positive for carbapenem-susceptible A. baumannii (CSAB), carbapenem-susceptible P. aeruginosa (CSPA), third-generation cephalosporin-susceptible E. coli (3GCSEC) or K. pneumoniae (3GCSKP), or methicillin-susceptible S. aureus (MSSA).”

Lim C, et al. PLoS One. 2024;19(5):e0303132. PMC11104583

Editorial “Non-AMR BSI” is not a term used in the AMASS reports; it is used in some AMASS-related publications (e.g. Lim 2024) to denote the antimicrobial-susceptible counterparts of the AMR pathogens.

AMASS reportProportion of AMR (“Proportion of R”)

“Proportion of R represents the number of patients with blood culture positive for resistant isolates (numerator) over the total number of patients with blood culture positive for the organism and the organism was tested for susceptibility against the antibiotic (denominator). AMASS application de-duplicated the data by including only the first isolate per patient per specimen type per evaluation period.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Section 2 (AMR proportion report).

Other wording in the publications (secondary)

“The proportion of AMR (%) was calculated as the percentage of patients with new AMR BSI over all patients with new BSIs for each pathogen of interest during the reporting period.”

Lim C, et al. PLoS One. 2024 (PMC11104583); same in Tuamsuwan 2024 & Srisuphan 2023. Sinto 2022 uses “proportion of resistance” (PMC9117993).

AMASS reportFrequency of AMR BSI

“For each pathogen and antibiotic under surveillance, the frequencies of patients with new AMR BSI are calculated per 100,000 tested patients. … Frequency of AMR BSI per 100,000 tested patients represents the number of patients with blood culture positive for a pathogen (numerator) over the total number of tested patients (denominator).”

Adapted from the AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Section 4 (the report’s own wording uses “new infections” / “Frequency of infection”) — the denominator the report uses in Sections 4–5 (see per 100,000 patients tested).

Extended definition in the publications (secondary) — additional denominators

“AMR frequency was calculated as the number of patients with a new BSI caused by the AMR pathogen during the reporting period per 100,000 (a) admissions, (b) patient-days, (c) patient-days at risk for hospital-acquired BSI, (d) patients tested for BSI, and (e) patients tested for hospital-acquired BSI.”

Werayingyong P, et al. Int J Infect Dis. 2026. doi:10.1016/j.ijid.2026.108830 · PMID 42202898 — the most complete statement of the denominators; a subset appears in Lim 2024 (PMC11104583) and Tuamsuwan 2024 (PMC11409609).

The numerator is always the number of deduplicated patients with a new AMR BSI during the reporting period. The entries below differ only in the denominator — what that count is divided by — which changes what the rate means and which infection origin it suits.

Quoted… per 100,000 admissions

(Patients with a new AMR BSI ÷ total hospital admissions) × 100,000. Used mainly to represent the burden of frequency per total number of hospital admissions.

Denominator (a) in Werayingyong 2026 (PMID 42202898); “per 100,000 admissions (for community-origin BSI)” — Lim 2024 (PMC11104583).

Quoted… per 100,000 patient-days (bed-days)

(Patients with a new AMR BSI ÷ total inpatient days) × 100,000. “Patient-days” and “bed-days” are used interchangeably in the papers; this denominator accounts for how long patients stay in hospital.

Denominator (b) in Werayingyong P, et al. Int J Infect Dis. 2026 (PMID 42202898).

Quoted… per 100,000 patient-days (bed-days) at risk of hospital-acquired infection

“The incidence rate of hospital-origin AMR BSI is defined as the ratio of the number of patients with hospital-origin AMR BSI for each pathogen and antibiotic per 100,000 bed-days at risk of hospital-acquired infection.”

Sinto R, et al. Antimicrob Resist Infect Control. 2022. PMC9117993 — the same measure is denominator (c) “patient-days at risk for hospital-acquired BSI” in Werayingyong 2026 (PMID 42202898).

Editorial The denominator counts only the inpatient (bed) days during which a patient is at risk of a hospital-acquired infection — i.e. after the first two calendar days of admission (see patient-days at risk). It is the preferred denominator for hospital-origin BSI.

Quoted… per 100,000 patients tested

“… (d) patients tested for BSI, and (e) patients tested for hospital-acquired BSI.”

Denominators (d)–(e), Werayingyong 2026 (PMID 42202898). See tested patients for who counts as “tested”.

Editorial (Patients with a new AMR BSI ÷ number of patients who had a blood culture taken) × 100,000. This denominator adjusts for how much blood-culture testing a hospital does; the papers note that under-use of blood cultures inflates the per-tested frequency while lowering the per-admission frequency (Tuamsuwan 2024). AMASS uses it for the case-based (sample-based) report (Sections 4–5); Lim 2020 describes “the frequency of bloodstream infections per 100,000 tested patients (section four in the report).”

QuotedIncidence rate (of AMR BSI)

“The incidence rate of community-origin AMR BSI is defined as the ratio of the number of patients with community-origin AMR BSI per 1,000 admissions.” … “The incidence rate of hospital-origin AMR BSI is defined as the ratio of the number of patients with hospital-origin AMR BSI for each pathogen and antibiotic per 100,000 bed-days at risk of hospital-acquired infection.”

Sinto R, et al. Antimicrob Resist Infect Control. 2022;11(1):73. PMC9117993

Editorial ‘AMR frequency’ and ‘incidence rate’ can be used interchangeably when the frequency is expressed per a defined location (e.g. a hospital or ward) and per a defined period of time — i.e. a count of new cases over a population (or population–time) denominator during the reporting period.

AMASS reportIn-hospital mortality (all-cause)

“Mortality was calculated from the number of in-hospital deaths (numerator) over the total number of patients with blood culture positive for the organism (denominator). Please note that this is the all-cause mortality calculated using the outcome data in the data file, and may not necessarily represent the mortality directly due to the infections.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Methods / Section 6.

Other wording in the publications (secondary)

“In-hospital mortality (%) following AMR BSI for each pathogen of interest was calculated as the percentage of patients with new AMR BSI who died in the hospitals.” … “All-cause in-hospital mortality was defined using the discharge summary regularly completed by the attending physicians and reported to the MoPH.”

Lim C, et al. PLoS One. 2024 (PMC11104583); Srisuphan 2023 (PMC10349292); same approach in Jitpeera 2025 (PMC11936208).

AMASS reportAnnex E — epidemiology of bloodstream infection

“This supplementary report is generated to improve our understanding of the distribution and mortality associated with community-origin and hospital-origin bloodstream infection (BSI). … Because of the difficulty in determining the clinical significance of organisms commonly associated with contamination, these organisms are excluded from the analysis of the Annex E. These excluded organisms include coagulase-negative staphylococci, viridans group streptococci, Corynebacterium spp., Bacillus spp., Diptheroid spp., Micrococcus spp. and Propionibacterium spp.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex E.

4Pathogens & resistance phenotypes

The organisms and resistance labels the reports track.

EditorialWHO priority pathogen list (WHO Bacterial Priority Pathogens List, BPPL)

Also: WHO BPPL; global priority list of antibiotic-resistant bacteria.

Editorial WHO’s ranked list of antibiotic-resistant bacteria that most threaten human health, used to guide research, development and public-health action. The current edition is the 2024 WHO Bacterial Priority Pathogens List (BPPL), which updates the 2017 list and covers 24 pathogens across 15 families in three tiers:

Critical: carbapenem-resistant Acinetobacter baumannii; third-generation cephalosporin-resistant Enterobacterales; carbapenem-resistant Enterobacterales; rifampicin-resistant Mycobacterium tuberculosis.
High: fluoroquinolone-resistant Salmonella Typhi and non-typhoidal Salmonella; fluoroquinolone-resistant Shigella spp.; vancomycin-resistant Enterococcus faecium; carbapenem-resistant Pseudomonas aeruginosa; third-generation-cephalosporin- and/or fluoroquinolone-resistant Neisseria gonorrhoeae; methicillin-resistant Staphylococcus aureus (MRSA).
Medium: macrolide-resistant group A streptococci and Streptococcus pneumoniae; ampicillin-resistant Haemophilus influenzae; penicillin-resistant group B streptococci.

WHO Bacterial Priority Pathogens List, 2024 (17 May 2024; ISBN 978-92-4-009346-1). who.int/publications/i/item/9789240093461. Prioritisation study: Lancet Infect Dis. 2025 (PMC12367593).

As used in AMASS

The AMASS report states its organisms and antibiotics were “selected based on the global priority list of antibiotic resistant bacteria and… GLASS of WHO” (citing the 2017 list). For the exact species and drug–bug combinations AMASS reports, see AMR pathogens in the AMASS report.

EditorialSusceptible / Intermediate / Resistant (S/I/R)

Editorial The three antimicrobial susceptibility testing (AST) categories reported for an organism–antibiotic pair. AMASS reads each result as S, I or R after mapping through the microbiology dictionary.

ToolNon-susceptible

Editorial Non-susceptible = Intermediate + Resistant (I+R), reported over the total tested (S+I+R). Usage note: “non-susceptible” was used in the WHO GLASS early implementation but is no longer used in the current WHO GLASS; likewise it was used in AMASS versions 1, 2 and 3, but is no longer used from AMASS version 4.0. From version 4.0 the main report presents “Resistance” (the proportion resistant, R), using the standard S/I/R interpretation (see S/I/R and Proportion of AMR).

QuotedResistance-phenotype acronyms

Expansions are taken verbatim from the papers (Lim 2024, Tuamsuwan 2024, Sinto 2022).

Resistant phenotypes:
MRSA — methicillin-resistant Staphylococcus aureus
3GCREC — third-generation cephalosporin-resistant Escherichia coli
3GCRKP — third-generation cephalosporin-resistant Klebsiella pneumoniae
CREC — carbapenem-resistant Escherichia coli
CRKP — carbapenem-resistant Klebsiella pneumoniae
CRPA — carbapenem-resistant Pseudomonas aeruginosa
CRAB — carbapenem-resistant Acinetobacter baumannii
CRACI — carbapenem-resistant Acinetobacter spp.
Susceptible counterparts (Non-AMR BSI):
MSSA — methicillin-susceptible S. aureus; CSAB — carbapenem-susceptible A. baumannii; CSPA — carbapenem-susceptible P. aeruginosa; 3GCSEC / 3GCSKP — third-generation cephalosporin-susceptible E. coli / K. pneumoniae.

Lim C, et al. PLoS One. 2024 (PMC11104583); Tuamsuwan K, et al. J Infect. 2024 (PMC11409609).

5Notifiable diseases (Annex A)

Terms from the notifiable-disease reports (Annex A) and national surveillance.

QuotedNotifiable bacterial disease (NBD)

“NBD cases were defined as having any clinical specimen (including blood, respiratory tract specimens, urine, stool, cerebrospinal fluid, genital swabs and other specimens) culture positive for a pathogen.”

Jitpeera C, et al. PLOS Glob Public Health. 2025;5(3):e0003995. PMC11936208

Notifiable bacteria under surveillance (AMASS Annex A): Bacillus anthracis, Burkholderia pseudomallei, Brucella spp., Corynebacterium diphtheriae, Neisseria gonorrhoeae, Neisseria meningitidis, non-typhoidal Salmonella spp., Salmonella Paratyphi, Salmonella Typhi, Shigella spp., Streptococcus suis, non-cholera Vibrio spp., and Vibrio cholerae. The list was compiled from common notifiable bacterial diseases in Thailand with the Department of Disease Control (MoPH) and can be expanded in future versions. So an NBD case is not just “a pathogen” — it is an inpatient culture-positive for one of these notifiable bacteria. Jitpeera 2025 evaluated NBDs caused by 11 of these pathogens, focusing on Burkholderia pseudomallei, Streptococcus suis, Salmonella spp., Shigella spp. and Vibrio spp.

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex A; Jitpeera 2025 (PMC11936208).

Original proof-of-concept (AMASSplus)

“The NBD cases were defined as having a clinical specimen culture positive for a pathogen.”

Lim C, et al. Am J Trop Med Hyg. 2024;111(1):151–155. PMC11229635 — this study extended AMASS to generate NBD reports (called AMASSplus), which counts culture-confirmed NBD cases; the national notifiable-disease surveillance system (NNDSS) instead counts suspected, probable and confirmed cases, so the two are not directly comparable.

QuotedSuspected / probable / confirmed case (national surveillance)

“Suspected case is defined as a case with clinical criteria (at least one symptom) and a risk factor … Probable case is defined as a case with clinical criteria, plus an epidemiological history associated with confirmed case or animals or a positive result according to presumptive diagnosis of laboratory criteria … Confirmed case is defined as a case with clinical criteria plus a positive result according to specific diagnosis of laboratory criteria.”

Jitpeera C, et al. PLOS Glob Public Health. 2025 — S2 Text (national surveillance case definitions). PMC11936208

Editorial Shown for contrast: AMASS instead counts an NBD case purely as an inpatient with a culture-positive specimen, so an AMASS count and a national-surveillance count of the same disease are not directly equivalent.

ToolNotifiable antibiotic–pathogen combination

Editorial A data-quality indicator (AMASS Annex B): an antibiotic–organism result that should be reported/reviewed because the combination is clinically notifiable or biologically implausible. Introduced with the Annex A notifiable-disease and Annex B contamination reports in AMASS v2.0 (Lim 2024, PMC11104583). Definition drawn from the AMASS report rather than a formal definition in the papers.

6Data quality parameters (Annex B)

Terms from the data-quality indicators (Annex B).

QuotedBlood culture contamination

“Blood culture contamination was defined as the isolation of one or more common commensal organisms listed on National Healthcare Safety Network the Centers for Disease Control and Prevention list 2022 in only one set of blood culture or one of a series of two or more blood culture.”

Sinto R, et al. Antimicrob Resist Infect Control. 2022;11(1):73. PMC9117993

AMASS reportBlood culture contamination rate

“Blood culture contamination rate is defined as the number of raw contaminated cultures per number of blood cultures received by the laboratory per reporting period. Blood culture contamination rate will not be estimated in case that the data of negative culture (specified as ‘no growth’ in the dictionary file for microbiology data) is not available.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex B (data indicators).

Other wording in the publications (secondary)

“The blood culture contamination rate is defined as the ratio of the number of blood cultures with common commensal organisms over the total number of blood cultures.”

Lim C, et al. PLoS One. 2024 (PMC11104583); equivalent in Sinto 2022 (PMC9117993).

QuotedBlood culture utilization rate

“The blood culture utilization rate was defined as the ratio of the number of blood cultures per 1,000 patient-days.”

Sinto R, et al. Antimicrob Resist Infect Control. 2022;11(1):73. PMC9117993

EditorialCommon commensal organism

Editorial An organism from the normal skin/mucosal flora (e.g. coagulase-negative staphylococci) that, when grown from a single blood culture, is treated as a likely contaminant rather than a true pathogen. AMASS uses the National Healthcare Safety Network / US CDC common-commensal list to flag contamination.

7Drug parameters (Annex D)

Antimicrobial-use parameters, quoted from the AMASS AMR Surveillance Report (Annex D — “Definitions of key parameters”; example output for Example_dataset_5, AMASS version 4.0).

AMASS reportAntimicrobials (Annex D scope)

“Antimicrobials” in this supplementary report include antibiotics listed in the “The selection and use of essential medicines, 2025: WHO AWaRe (Access, Watch, Reserve) classification of antibiotics for evaluation and monitoring of use”, and antimycotics for systemic use (J02 and D01BA) listed on NIPH WHO CC for Drug Statistics Methodology website. [Annex D, “Definitions of key parameters”; URLs omitted]

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex D.

AMASS reportDays of Therapy (DOT)

“Days of Therapy (DOT)” is defined as the number of days that an in-patient receives an antimicrobial agent (regardless of dose) during hospital admission. The DOT for a given patient on multiple antibiotics will be the sum of DOT for each antibiotic that the patient is receiving. In theory, DOT will be close to DDD (Defined Daily Dose).

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex D.

AMASS reportLength of Therapy (LOT)

“Length of Therapy (LOT)” is defined as the number of days that an inpatient receives at least one antimicrobial agent (regardless of dose) during hospital admission. Therefore, LOT will be lower than DOT.

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex D.

AMASS reportAntimicrobial Use (AMU) prevalence

“Antimicrobial Use (AMU) prevalence” is calculated by dividing the total LOT by total number of patient-days. In theory, this AMU prevalence will be close to AMU prevalence estimated by PPS (point-prevalence survey) method.

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex D. In the example report, AMU prevalence of parenteral antibiotics = 43.6% (167,359 LOT / 383,668 patient-days).

AMASS reportDOT per 1,000 patient-days (bed-days)

Antibiotic use expressed as (DOT ÷ total patient-days) × 1,000. In the example report the denominator is the total number of patient-days after excluding day admissions (383,668), and only parenteral antimicrobials are counted (total 626.4 DOT/1,000 patient-days). “Patient-days” and “bed-days” are used interchangeably.

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex D1 (DOT/1,000 patient-days tables).

AMASS reportParenteral use

“For analyses IV, IM, IP and ITH routes are considered parenteral use. Other injection routes (e.g., intra-articular and intra-vitreal routes) are not included as parenteral use in this report.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex D1. The Annex D DOT/LOT/AMU-prevalence tables count parenteral antimicrobials only.

AMASS reportAWaRe classification (Access / Watch / Reserve; AMASS Low–Medium–High Watch)

For AWaRe classification in this report, “Watch” category is divided into 3 groups of “Low/Medium/High Watch”. “Low Watch” includes most third-generation cephalosporin (e.g., cefotaxime/ceftriaxone). “Medium Watch” includes antibiotics with partial anti-extended-spectrum beta-lactamase (ESBL) or pseudomonal activity (e.g., piperacillin-tazobactam/ceftazidime/fluoroquinolones) and all fourth-generation cephalosporins. “High Watch” includes carbapenems (e.g., meropenem) and glycopeptides (e.g., vancomycin).

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex D. Based on the WHO AWaRe (Access, Watch, Reserve) classification, with the Watch group subdivided by AMASS.

AMASS reportDay admission

“Day admission” is defined as an inpatient case where the admission and discharge dates are the same, and the final outcome is neither ‘death’ nor ‘discharge against advice’. This supplementary report exclude ‘day admission’ from the calculation of patient-days.

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex D.

AMASS reportPatient-days (for DOTs)

The total number of inpatient days in the evaluation period used for antimicrobial-use parameters (DOT and AMU prevalence), excluding day admissions. It is the denominator for AMU prevalence and DOT/1,000 patient-days. (This differs from the general Patient-days, which includes day admissions.)

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex D1.

8Fungi terms (Annex F)

Fungal-infection and antifungal-resistance terms from Annex F (AMASS-FUNGI).

AMASS reportFungemia

A bloodstream infection caused by a fungal organism — a blood specimen culture positive for a fungus (the fungal analogue of bacteraemia / BSI). Annex F1 (AMASS-FUNGI) reports the prevalence of fungemia, including all fungal isolates in the blood specimen records, deduplicated to the first isolate of a given fungal species per patient per evaluation period, regardless of hospital admission status.

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex F1.

AMASS reportFungal species under evaluation (Annex F)

Organisms under this survey (Annex F, AMASS-FUNGI):

Candida albicans
Candidozyma auris (Candida auris)
Pichia kudriavzevii (Candida krusei)
Nakaseomyces glabratus (Candida glabrata)
Candida parapsilosis
Candida tropicalis
Cryptococcus spp. (includes C. neoformans and other Cryptococcus species)
Histoplasma spp.
Fusarium spp.
Talaromyces marneffei (Penicillium marneffei)

“The organisms under this survey are selected from the critical and high priority groups of WHO fungal priority pathogens list to guide research, development and public health action.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex F. P. kudriavzevii and T. marneffei are WHO medium-priority; blood fungi outside this list are grouped as “other fungal organisms”. Antifungals tested: amphotericin B, caspofungin, fluconazole, flucytosine, micafungin, voriconazole (see AFR).

AMASS reportYeast / Mold / Fungus (unspecified species)

When a blood-culture record identifies only a broad fungal category rather than a species, AMASS-FUNGI groups it accordingly: records reported as “yeast”, “mold” or “fungus” (without a species name) are classified as Yeast, Mold and Fungus respectively, based on their content.

“Records without species names were classified as “Yeast”, “Mold” and “Fungus” based on their content.”

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex F1.

AMASS reportAntifungal resistance (AFR)

The antifungal analogue of AMR — the proportion of fungal isolates non-susceptible/resistant to an antifungal. Annex F2 reports the AFR proportion by organism and antifungal; Annex F3 reports mortality involving AFR and antifungal-susceptible infections.

AMASS AMR Surveillance Report (Example_dataset_5, AMASS v4.0), Annex F2–F3.

9Country-specific healthcare systems

Health-system and setting terms used when AMASS is applied at national scale. Each entry notes its source: the World Bank (income groups) and Thailand (MoPH hospital classifications, Service Plan levels, and health regions).

EditorialLMIC

Editorial Low- and middle-income country. AMASS was designed for hospitals in LMICs that lack the time, staff or software to deduplicate data and generate stratified AMR surveillance reports. The LMIC grouping follows the World Bank country-income classification.

Source: World Bank (country income groups).

QuotedTertiary-care (TCH) & secondary-care hospital (SCH)

“Based on the WHO definitions, class A hospitals are generally TCHs and referred to as regional hospitals, and classes S and M1 are generally SCHs and referred to as provincial or large district hospitals.”

Srisuphan V, et al. JAC Antimicrob Resist. 2023;5(4):dlad088. PMC10349292

Source: Thailand — MoPH hospital classes (A, S, M1); WHO hospital definitions applied to Thailand.

EditorialLevel A / S / M1 hospitals (Thailand)

Editorial Thailand’s Ministry of Public Health (MoPH) classifies public hospitals by service capability under its Service Plan:

Level A — advanced-level referral hospital (regional hospital); the largest, offering sub-specialty care. Generally a tertiary-care hospital (TCH).
Level S — standard-level referral hospital (general / provincial hospital), with most major specialties. Generally a secondary-care hospital (SCH).
Level M1 — middle-level referral hospital (large district hospital) with some specialist services. Generally a secondary-care hospital (SCH).

Smaller MoPH levels (M2, F1–F3) are community/district hospitals. The AMASS studies group Level A as TCH and Levels S and M1 as SCH.

Source: Thailand — MoPH Service Plan hospital levels; as used in Srisuphan 2023 (PMC10349292) and Tuamsuwan 2024 (PMC11409609).

EditorialMoPH, NARST, DDC (Thailand)

Editorial Thai health-system terms used in the national-scale papers: MoPH — Ministry of Public Health; NARST — National Antimicrobial Resistance Surveillance Thailand; DDC — Department of Disease Control (under the MoPH).

Source: Thailand (MoPH). Used in: Srisuphan 2023, Tuamsuwan 2024, Jitpeera 2025.

EditorialHealth regions (Thailand)

Editorial Thailand’s Ministry of Public Health groups the provinces into 12 health regions (groups of provinces), plus the capital Bangkok as health region 13, using the concept of decentralization to organize and compare health-service delivery. In 2022, the MoPH supervised 127 public referral hospitals across health regions 1–12; Bangkok (region 13) hospitals are managed by the Department of Medical Services (not the Health Administration Division). AMASS studies compare AMR by health region — e.g. region 4 (lower central region) had the highest frequency of community-origin 3GC-resistant E. coli BSI.

Source: Thailand (MoPH). Used in: Tuamsuwan 2024 (PMC11409609) and Jitpeera 2025 (PMC11936208).

§Source publications

The eight peer-reviewed papers this glossary quotes (their supplementary files were also reviewed). Verbatim definitions above link back to the relevant paper.

Lim 2020	Lim C, et al. Automating the Generation of Antimicrobial Resistance Surveillance Reports: Proof-of-Concept Study Involving Seven Hospitals in Seven Countries. J Med Internet Res. 2020;22(10):e19762. PMC7568216 · doi:10.2196/19762
Sinto 2022	Sinto R, et al. Blood culture utilization and epidemiology of antimicrobial-resistant bloodstream infections before and during the COVID-19 pandemic in the Indonesian national referral hospital. Antimicrob Resist Infect Control. 2022;11(1):73. PMC9117993 · doi:10.1186/s13756-022-01114-x
Srisuphan 2023	Srisuphan V, et al. Local and timely antimicrobial resistance data for local and national actions: the early implementation of an automated tool for data analysis at local hospital level in Thailand. JAC Antimicrob Resist. 2023;5(4):dlad088. PMC10349292 · doi:10.1093/jacamr/dlad088
Lim 2024	Lim C, et al. Frequency and mortality rate following antimicrobial-resistant bloodstream infections in tertiary-care hospitals compared with secondary-care hospitals. PLoS One. 2024;19(5):e0303132. PMC11104583 · doi:10.1371/journal.pone.0303132
Tuamsuwan 2024	Tuamsuwan K, et al. Frequency of antimicrobial-resistant bloodstream infections in 111 hospitals in Thailand, 2022. J Infect. 2024;89(4):106249. PMC11409609 · doi:10.1016/j.jinf.2024.106249
Lim 2024 (AJTMH)	Lim C, et al. Automating the Generation of Notifiable Bacterial Disease Reports: Proof-of-Concept Study and Implementation in Six Hospitals in Thailand. Am J Trop Med Hyg. 2024;111(1):151–155. PMC11229635 · doi:10.4269/ajtmh.23-0848 · PMID 38806021
Jitpeera 2025	Jitpeera C, et al. Epidemiology of Burkholderia pseudomallei, Streptococcus suis, Salmonella spp., Shigella spp. and Vibrio spp. infections in 111 hospitals in Thailand, 2022. PLOS Glob Public Health. 2025;5(3):e0003995. PMC11936208 · doi:10.1371/journal.pgph.0003995
Werayingyong 2026	Werayingyong P, et al. Trends and correlations in antimicrobial resistance indicators in 110 hospitals in Thailand, 2022–2024. Int J Infect Dis. 2026. ijidonline.com · doi:10.1016/j.ijid.2026.108830 · PMID 42202898

Note on provenance: quotations are reproduced from the open-access full text of each paper for reference and education. Where a term is used across several papers with consistent wording, one representative quotation is shown and the others are cited. Editorial and tool definitions are the AMASS team’s own wording, not quotations.