📄RPIP

Abbreviation	Definition
AMR	antimicrobial resistance
CLSI	Clinical and Laboratory Standards Institute
ESBL	extended spectrum beta-lactamase
EUCAST	European Committee on Antimicrobial Susceptibility Testing
mL	milliliter
NAI	neuraminidase inhibitor
NGS	next-generation sequencing
PAI	polymerase acidic endonuclease inhibitor
pangolin	phylogenetic assignment of named global outbreak lineages
RPIP	Respiratory Pathogen ID/AMR Panel
RPKM	targeted Reads mapped Per Kilobase of targeted sequence per Million quality-filtered reads

Category	Test information
RUO	For Research Use Only. Not for use in diagnostic procedures.
URL	See https://www.illumina.com/ for additional information.
Quantification - when a quantitative Internal Control {ic_name} and concentration {ic_concentration} is specified	RPIP data analysis using DRAGEN Microbial Enrichment Plus detects 41 viruses, 187 bacteria, 53 fungi, and 4,079 AMR markers, unless filtered reporting options are selected, based on target enriched next-generation sequencing (NGS) of microorganism DNA and cDNA sequences. Sequencing data are interpreted by the DRAGEN software platform and microorganisms that pass detection thresholds are reported. Absolute quantification assumes use of {ic_name} as an Internal Control spiked at {ic_concentration} copies/mL of sample. Relative abundance is calculated based on absolute quantities and is expressed as proportion of absolute quantities within each pathogen class (i.e., bacteria, viruses, fungi). If RPKM for the Internal Control is zero, no absolute quantification is provided, and relative abundance is expressed as proportion of microorganism RPKM values within each pathogen class.
Quantification - when a quantitative Internal Control is NOT specified	RPIP data analysis using DRAGEN Microbial Enrichment Plus detects 41 viruses, 187 bacteria, 53 fungi, and 4,079 AMR markers, unless filtered reporting options are selected, based on target enriched next-generation sequencing (NGS) of microorganism DNA and cDNA sequences. Sequencing data are interpreted by the DRAGEN software platform and microorganisms that pass detection thresholds are reported. Relative abundance is expressed as proportion of microorganism RPKM values within each pathogen class (i.e., bacteria, viruses, fungi). Internal Control not specified; no absolute quantification provided.
AMR - when "Report bacterial AMR markers only when an associated microorganism is reported" is selected	This test detects 4,079 antimicrobial resistance (AMR) markers and reports associations for 99 microorganisms, 181 antimicrobials, and 35 drug classes, unless filtered reporting options are selected. Bacterial AMR markers are based on the Comprehensive Antibiotic Research Database (CARD, version 3.2.8) and viral AMR markers are based on World Health Organization (WHO) Influenza virus neuraminidase inhibitor (NAI) and polymerase acidic protein inhibitor (PAI) Reduced Susceptibility Marker Tables (07 March 2023 version). Detection of an AMR marker is reported if the AMR marker passes a minimum detection threshold and if one or more of the microorganisms associated with the AMR marker is also detected, in alignment with guidance provided by the College of American Pathologists (CAP) MIC.21855. However, reported AMR markers may originate from microorganisms that did not meet detection thresholds or microorganisms not targeted by the test. Association between microorganisms and bacterial AMR marker is based on scientific literature and the Comprehensive Antibiotic Research Database Prevalence Data (CARD Prevalence, version 4.0.1) from McMaster University. Reported AMR markers have been associated with antimicrobial resistance but may not always indicate phenotypic resistance. Failure to detect AMR markers does not always indicate phenotypic susceptibility. Results should be interpreted in the context of all available information.
AMR - when "Report bacterial AMR markers only when an associated microorganism is reported" is NOT selected	This test detects 4,079 antimicrobial resistance (AMR) markers and reports associations for 99 microorganisms, 181 antimicrobials, and 35 drug classes. Bacterial AMR markers are based on the Comprehensive Antibiotic Research Database (CARD, version 3.2.8) and viral AMR markers are based on World Health Organization (WHO) Influenza virus neuraminidase inhibitor (NAI) and polymerase acidic protein inhibitor (PAI) Reduced Susceptibility Marker Tables (07 March 2023 version). Association between microorganisms and bacterial AMR marker is based on scientific literature and the Comprehensive Antibiotic Research Database Prevalence Data (CARD Prevalence, version 4.0.1) from McMaster University. Detection of a bacterial AMR marker is reported if the marker passes a minimum detection threshold, regardless of associated microorganism detection. Reported AMR markers may originate from microorganisms that did not meet detection thresholds or microorganisms not targeted by the test. Reported AMR markers have been associated with antimicrobial resistance but may not always indicate phenotypic resistance. Failure to detect AMR markers does not always indicate phenotypic susceptibility. Results should be interpreted in the context of all available information.
AMR	Linkage between bacterial AMR marker, antimicrobial, and drug class is based on the Comprehensive Antibiotic Research Database (CARD, version 3.2.8) from McMaster University, ResFinder (version 2.2.1), NCBI Reference Gene Catalog (version 2023-09-26.1), EUCAST expert rules on indicator agents (2019-2023), and CLSI Performance Standards for Antimicrobial Susceptibility Testing (M100 34th Edition). Linkage between viral AMR marker, antimicrobial, and drug class is based on the publications provided in the JSON report - see PubMed IDs (pmids) field. Not all antimicrobials and drug classes that are listed may be relevant. Detected AMR markers may also confer resistance to antimicrobials and drug classes that are not listed.
AMR	A representative list of associated microorganisms known to harbor the detected or similar bacterial AMR markers, based on the Comprehensive Antibiotic Research Database Prevalence Data (CARD Prevalence, version 4.0.1) from McMaster University, can be found in the Associated Microorganisms field.
AMR	Mutations connected with a '+' form an epistatic group. Epistatic groups are two or more mutations that need to be present concurrently to confer the associated resistance.
AMR	All intrinsic resistance described in CLSI Performance Standards for Antimicrobial Susceptibility Testing, M100 34th Edition, Appendix B for detected microorganism(s) is reported. Additional comments regarding CLSI intrinsic resistance definitions may be reported in footnotes specific to the detected microorganism(s). Some intrinsic resistance is described with reference to drug classes rather than specific antimicrobials. Users may reference CLSI Glossary I (Part 1 and Part 2): Class and Subclass Designations and Generic Names for information on how CLSI categorizes antimicrobials and drug classes.
AMR	Confidence of bacterial AMR marker detection is shown as High, Medium, or Low and is based on the available sequencing data. High confidence indicates that a bacterial AMR marker has 100% protein sequence coverage and 100% protein sequence percent identity (PID). Medium confidence indicates that a bacterial AMR marker has ≥90% protein sequence coverage and ≥90% protein sequence percent identity (PID). Low confidence indicates that a bacterial AMR marker has ≥60% protein sequence coverage and ≥80% protein sequence percent identity (PID).
Phenotypic group	Targeted microorganisms are classified into three Phenotypic Groups based on general association with normal flora, colonization, or contamination from the environment or other sources, as well as based on general association with disease. Phenotypic grouping DOES NOT INDICATE PATHOGENICITY IN A GIVEN CASE and results need to be interpreted in the context of all available information. Phenotypic Group 1: Microorganisms that are frequently considered part of the normal flora, colonizers, or contaminants but may be associated with disease in certain settings. Phenotypic Group 2: Microorganisms that may represent normal flora, colonizers, or contaminants but that are frequently associated with disease. Phenotypic Group 3: Microorganisms that are not generally considered part of the normal flora, colonizers, or contaminants and are generally considered to be associated with disease.
Pango lineage	The most likely Pango (phylogenetic assignment of named global outbreak) lineage is assigned to the majority consensus SARS-CoV-2 genome sequence using pangolin 4.3.1 (Áine O'Toole & Emily Scher et al. 2021 Virus Evolution DOI:10.1093/ve/veab064).
Read classification	This test differentiates sequencing reads classified to microorganism and Internal Control regions that are targeted by capture probes (“Targeted Microbial” and “Targeted Internal Control”) from those that are not targeted (“Untargeted”), are low complexity (“Low Complexity”), cannot be unambiguously assigned to one category (“Ambiguous”), or cannot be classified with confidence (“Unclassified”).
Limitations	Non-detected results do not rule out the presence of viruses, bacteria, fungi, and AMR markers. Contamination with microorganisms is possible during specimen collection, transport, and processing. Closely related microorganisms may be misidentified based on sequence homology to species present in the database. The identification of cDNA or DNA sequences from a microorganism does not confirm that the identified microorganism is causing symptoms, is viable, or is infectious. Recombinant viral strains may not be reported or may be reported as one or more individual viruses. Should one or more individual viruses be reported for a recombinant viral strain, antiviral resistance results may be inaccurate.
Limitations	The best matching allele is reported for each detected bacterial AMR gene family. If two or more alleles within the same bacterial AMR gene family are detected, only the allele with the higher confidence will be reported as the best match unless multiple alleles have a High confidence interpretation (100% coverage and PID). In strains containing insertion-deletion mutations (indels), there is a risk of false positive or false negative results for other resistance mutations within a region of 100 nucleotides around the indel.
Limitations	Information provided by DRAGEN Microbial Enrichment Plus is based on scientific knowledge and has been curated; however, scientific knowledge evolves and information about associated microorganism and associated resistance may not always be complete and/or correct. Results should be interpreted in the context of all available information. Other sources of data may be required for confirmation.