Respiratory Pathogen Panel - Illumina

Respiratory Pathogen ID/AMR Enrichment Kit od spoločnosti Illumina je panel založený na NGS („Next Generation Sequencing“) technológii. Poskytuje vysoko citlivé a komplexné informácie o detekcii kritických patogénov a antimikrobiálnej rezistencii (AMR). Tento enrichmentový panel dokáže detegovať viac ako 280 respiračných patogénov, vrátane SARS-CoV-2 a ďalších vírusov, húb a baktérií a tiež viac ako 1 200 alel AMR.

Príprava samotnej NGS knižnice pozostáva zo syntézy cDNA z RNA, BLT („Bead-linked transposomes“) technológie – fragmentácia vlákna na magnetických guličkách a súčasné naviazanie adaptérov, tzv. tagovanie. Nasleduje vychytávanie oblastí záujmu, tzv. enrichment. Po pridaní indexov, normalizácii a kvantifikácii je knižnica pripravená na sekvenáciu. Súčasťou riešenia je aj softvér na analýzu dát, konkrétne IDbyDNA Explify Analysis Software, dostupný aj na BaseSpace Sequence Hub vo forme aplikácie IDbyDNA Explify RPIP Analysis App.

Základné špeficikácie k Illumina Respiratory Pathogen panelu:

Umožňuje detegovať RNA a DNA pre 187 baktérií, 53 húb a 42 vírusov
Identifikuje až 1 218 AMR alel
Poskytuje informáciu o celom genóme SARS-CoV-2 a Influenza A/ B vírusov
Zahŕňa próby cielené na 10 komerčne dostupných spike-in kontrol (fágy, vírusy, baktérie, syntetická RNA)
Flexibilné množstvo vtupného materiálu: 10 - 100 ng
Panel je kompatibilný so všetkými sekvenátormi spoločnosti Illumina
Doporučenie pre sekvenáciu: 1M čítaní/ vzorka
Využitím MiniSeq Rapid Reagent kitu trvá sekvenácia menej ako 5 hodín

Viac informácií sa dozviete na stránkach výrobcu

Zoznam targetov zachytávaných pomocou Illumina Respiratory Pathogen panelu:

Achromobacter denitrificans	Dialister pneumosintes	Neisseria meningitidis
Achromobacter xylosoxidans	Dolosigranulum pigrum	Neisseria mucosa
Acinetobacter baumannii	Eikenella corrodens	Nocardia abscessus
Acinetobacter lwoffii	Elizabethkingia anophelis	Nocardia arthritidis
Acinetobacter nosocomialis	Elizabethkingia meningoseptica	Nocardia beijingensis
Acinetobacter pittii	Enterobacter cloacae complex	Nocardia brasiliensis
Actinomyces graevenitzii	Enterococcus faecalis	Nocardia cyriacigeorgica
Actinomyces israelii	Enterococcus faecium	Nocardia farcinica
Actinomyces meyeri	Escherichia coli	Nocardia nova
Actinomyces naeslundii	Eubacterium brachy	Nocardia otitidiscaviarum
Actinomyces odontolyticus	Eubacterium limosum	Nocardia transvalensis
Aeromonas caviae	Eubacterium nodatum	Nocardia veterana
Aeromonas hydrophila	Finegoldia magna	Ochrobactrum anthropi
Aeromonas sobria	Francisella tularensis	Orientia tsutsugamushi
Aeromonas veronii	Fusobacterium necrophorum	Pandoraea pulmonicola
Aggregatibacter actinomycetemcomitans	Fusobacterium nucleatum	Pantoea agglomerans
Aggregatibacter aphrophilus	Gemella haemolysans	Parvimonas micra
Arcanobacterium haemolyticum	Gemella morbillorum	Pasteurella multocida
Bacillus anthracis	Gordonia araii	Pediococcus acidilactici
Bacillus cereus	Gordonia bronchialis	Peptostreptococcus anaerobius
Bacillus thuringiensis	Haemophilus haemolyticus	Prevotella buccae
Bacteroides fragilis	Haemophilus influenzae	Prevotella intermedia
Bartonella henselae	Haemophilus parahaemolyticus	Prevotella melaninogenica
Bartonella quintana	Haemophilus parainfluenzae	Prevotella pleuritidis
Bordetella bronchiseptica	Haemophilus pittmaniae	Proteus mirabilis
Bordetella hinzii	Hafnia alvei	Proteus penneri
Bordetella holmesii	Kingella kingae	Proteus vulgaris
Bordetella parapertussis	Klebsiella aerogenes (Enterobacter aerogenes)	Providencia stuartii
Bordetella pertussis	Klebsiella oxytoca	Pseudomonas aeruginosa
Bordetella petrii	Klebsiella pneumoniae	Pseudomonas fluorescens
Brucella abortus	Klebsiella quasipneumoniae	Pseudomonas stutzeri
Brucella canis	Klebsiella variicola	Ralstonia pickettii
Brucella melitensis	Kytococcus sedentarius	Raoultella ornithinolytica
Brucella suis	Leclercia adecarboxylata	Raoultella planticola
Burkholderia cepacia complex	Legionella anisa	Rhodococcus hoagii
Burkholderia gladioli	Legionella feeleii	Rickettsia rickettsii
Burkholderia glumae	Legionella longbeachae	Rothia mucilaginosa
Burkholderia mallei	Legionella maceachernii	Salmonella enterica
Burkholderia pseudomallei	Legionella pneumophila	Serratia marcescens
Burkholderia thailandensis	Legionella wadsworthii	Shewanella putrefaciens
Campylobacter concisus	Leptospira interrogans	Slackia exigua
Capnocytophaga gingivalis	Leptotrichia buccalis	Sphingomonas paucimobilis
Capnocytophaga leadbetteri	Listeria monocytogenes	Staphylococcus aureus
Capnocytophaga sputigena	Moraxella catarrhalis	Stenotrophomonas maltophilia
Cardiobacterium hominis	Moraxella osloensis	Streptococcus agalactiae
Cardiobacterium valvarum	Morganella morganii	Streptococcus anginosus
Chlamydia pneumoniae	Mycobacterium avium complex	Streptococcus constellatus
Chlamydia psittaci	Mycobacterium fortuitum	Streptococcus dysgalactiae
Chlamydia trachomatis	Mycobacterium gordonae	Streptococcus intermedius
Chromobacterium violaceum	Mycobacterium kansasii	Streptococcus mitis
Citrobacter freundii	Mycobacterium malmoense	Streptococcus pneumoniae
Citrobacter koseri	Mycobacterium parascrofulaceum	Streptococcus pyogenes
Corynebacterium diphtheriae	Mycobacterium scrofulaceum	Tatlockia micdadei (Legionella micdadei)
Corynebacterium jeikeium	Mycobacterium szulgai	Treponema denticola
Corynebacterium propinquum	Mycobacterium tuberculosis	Tropheryma whipplei
Corynebacterium pseudodiphtheriticum	Mycobacterium xenopi	Tsukamurella pulmonis
Corynebacterium pseudotuberculosis	Mycobacteroides abscessus (Mycobacterium abscessus)	Tsukamurella tyrosinosolvens
Corynebacterium striatum	Mycobacteroides chelonae (Mycobacterium chelonae)	Ureaplasma parvum
Corynebacterium ulcerans	Mycobacteroides immunogenum (Mycobacterium immunogenum)	Ureaplasma urealyticum
Coxiella burnetii	Mycoplasma pneumoniae	Veilonella parvula
Cronobacter sakazakii	Neisseria flavescens	Williamsia muralis
Delftia acidovorans	Neisseria lactamica	Yersinia enterocolitica
		Yersinia pestis

Coxsackievirus A	Human parainfluenza virus 4
Coxsackievirus B	Human parechovirus
Cytomegalovirus (CMV)	Influenza A virus (H1N1)
EBV	Influenza A virus (H3N2)
Enterovirus A71	Influenza A virus (H5N1)
Enterovirus D68	Influenza A virus (H7N9)
Herpes simplex virus 1 (HSV-1)	Influenza A virus (H9N2)
HHV6	Influenza B virus
Human adenovirus B	Influenza C virus
Human adenovirus C	Measles Virus
Human adenovirus E	MERS coronavirus (MERS-CoV)
Human bocavirus 1	Mumps virus
Human Coronavirus 229E	Parvovirus B19
Human Coronavirus HKU1	Respiratory Syncytial Virus A
Human Coronavirus NL63	Respiratory Syncytial Virus B
Human Coronavirus OC43	Rhinovirus A
Human metapneumovirus	Rhinovirus B
Human parainfluenza virus 1	Rhinovirus C
Human parainfluenza virus 2	Rubella virus
Human parainfluenza virus 3	SARS coronavirus
	SARS-CoV-2

Alternaria alternata	Lomentospora prolificans (Scedosporium prolificans)
Alternaria infectoria	Microascus cinereus (Scopulariopsis cinereus)
Apophysomyces elegans	Microascus cirrosus (Scopulariopsis paisii)
Aspergillus flavus	Microasucus paisii (Scopulariopsis brumptii)
Aspergillus fumigatus	Mucor circinelloides
Aspergillus nidulans	Mucor indicus
Aspergillus niger	Mucor racemosus
Aspergillus terreus	Paecilomyces variotii
Aspergillus versicolor	Paracoccidioides brasiliensis
Blastomyces dermatitidis	Pneumocystis jirovecii
Candida auris	Purpureocillium lilacinum
Cladophialophora bantiana	Rasamsonia aegroticola
Coccidioides immitis	Rasamsonia argillacea
Coccidioides posadasii	Rhizomucor pusillus
Cryptococcus gattii	Rhizopus azygosporus
Cryptococcus neoformans	Rhizopus microsporus
Cunninghamella bertholletiae	Rhizopus oryzae
Curvularia geniculata	Saksenaea vasiformis
Curvularia lunata	Sarocladium kiliense (Acremonium kiliense)
Exophiala dermatitidis	Scedosporium apiospermum
Fusarium oxysporum	Schizophyllum commune
Fusarium proliferatum	Scopulariopsis brevicaulis
Fusarium solani	Sporothrix schenckii
Fusarium verticillioides	Syncephalastrum racemosum
Histoplasma capsulatum	Talaromyces marneffei
Lichtheimia corymbifera	Trichosporon asahii
Lichtheimia ramosa

16S rRNA methyltransferase (A1408)	IMP beta-lactamase
16S rRNA methyltransferase (G1405)	IND beta-lactamase
AAC(2')	KHM beta-latamase
AAC(3)	KPC beta-lactamase
AAC(6')	NDM beta-lactamase
ABC-F ATP-binding cassette ribosomal protection protein	NmcA beta-lactamase
ANT(3'')	OXA beta-lactamase
ANT(4')	SCO beta-lactamase
ANT(6)	SHV beta-lactamase
ANT(9)	SME beta-lactamase
APH(2'')	SPM beta-lactamase
APH(3')	TEM beta-lactamase
APH(4)	VIM beta-lactamase
ACC beta-lactamase	Cfr 23S ribosomal RNA methyltransferase
ADC beta-lactamase with carbapenemase activity	ciprofloxacin phosphotransferase
AIM beta-lactamase	trimethoprim resistant dihydrofolate reductase dfr
BIC Beta-lactamase	macrolide esterase
blaZ beta-lactamase	Erm 23S ribosomal RNA methyltransferase
CARB beta-lactamase	lincosamide nucleotidyltransferase (LNU)
CGB beta-lactamase	MCR phosphoethanolamine transferase
CMY beta-lactamase	macrolide phosphotransferase (MPH)
CphA beta-lactamase	methicillin resistant PBP2
CTX-M beta-lactamase	quinolone resistance protein (qnr)
DHA beta-lactamase	sulfonamide resistant sul
GES beta-lactamase	tetracycline inactivation enzyme
GIM beta-lactamase	tetracycline-resistant ribosomal protection protein
GOB beta-lactamase	glycopeptide resistance gene cluster
IMI beta-lactamase	van ligase

Respiratory Pathogen Panel - Illumina

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Respiratory Pathogen Panel

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