BugSeq Report

Automated bioinformatics for microbiology labs.

Analysis Name: ZymoBIOMICS Gut Microbiome Standard D6331
Sample Name: SRR13128014.fastq
Sample Type: Bacterial isolate
Isolate Taxon: Mixed
Run ID: 880c588d-3a20-4b06-abad-4efc81dedba3
BugSeq Pipeline Version: Latest
Metagenomic Database: BugSeq Default
Contact E-mail: support@bugseq.com

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Report generated on 2023-03-01, 07:18 UTC

General Statistics

Showing ²⁰/₂₀ rows and ⁵/₈ columns.

Sample Name	N50 (Kbp)	Assembly Length (Kbp)	≥ 100X	≥ 20X	≥ 300X	≥ 400X	≥ 50X	Median
Akkermansia muciniphila	2851.6Kbp	2851.6Kbp	95.0%	95.0%			95.0%	132.0X
Bacteroides fragilis	5181.5Kbp	5212.3Kbp	88.0%	88.0%	88.0%	88.0%	88.0%	738.0X
Bifidobacterium adolescentis	2028.4Kbp	2089.7Kbp	92.0%	92.0%			92.0%	172.0X
Candida	55.9Kbp	8106.9Kbp
Candida albicans	11.8Kbp	132.7Kbp						0.0X
Clostridioides difficile	4209.2Kbp	4209.2Kbp	96.0%	96.0%			96.0%	114.0X
Enterobacteriaceae	110.0Kbp	364.5Kbp
Escherichia coli	189.8Kbp	17135.0Kbp	90.0%	90.0%	82.0%	77.0%	90.0%	607.0X
Faecalibacterium prausnitzii	2913.9Kbp	2913.9Kbp	38.0%	38.0%	38.0%	38.0%	38.0%	0.0X
Fusobacterium nucleatum	2448.2Kbp	2448.2Kbp	64.0%	64.0%	64.0%		64.0%	327.0X
Limosilactobacillus fermentum	1905.4Kbp	1905.4Kbp		88.0%			88.0%	84.0X
Methanobrevibacter smithii	415.3Kbp	1858.9Kbp
Plasmids	5.4Kbp	5.4Kbp
Prevotella corporis	2162.8Kbp	2927.3Kbp	79.0%	79.0%	79.0%	79.0%	79.0%	495.0X
Root	196.5Kbp	249.9Kbp
Roseburia hominis	3463.3Kbp	3463.3Kbp	87.0%	87.0%			87.0%	277.0X
Saccharomyces	50.1Kbp	6072.7Kbp
Saccharomyces cerevisiae	35.1Kbp	1836.6Kbp						0.0X
Salmonella enterica	21.2Kbp	70.1Kbp						0.0X
Veillonella rogosae	2158.0Kbp	2158.0Kbp	88.0%	88.0%	88.0%	88.0%	88.0%	1619.0X

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Sort	Group	Column	Description	ID	Scale
\|\|	Assembly Statistics	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly (kilo base pairs)	`N50`	None
\|\|	Assembly Statistics	Assembly Length (Kbp)	The total number of bases in the assembly (Kbp).	`Total length`	None
\|\|	Depth of Sequencing	≥ 100X	Fraction of genome with at least 100X coverage	`100_x_pc`	None
\|\|	Depth of Sequencing	≥ 20X	Fraction of genome with at least 20X coverage	`20_x_pc`	None
\|\|	Depth of Sequencing	≥ 300X	Fraction of genome with at least 300X coverage	`300_x_pc`	None
\|\|	Depth of Sequencing	≥ 400X	Fraction of genome with at least 400X coverage	`400_x_pc`	None
\|\|	Depth of Sequencing	≥ 50X	Fraction of genome with at least 50X coverage	`50_x_pc`	None
\|\|	Depth of Sequencing	Median	Median coverage	`median_coverage`	None

Plasmid Detection

Cluster IDs reflect unique taxonomic identifiers for plasmids and are stable across time. Cluster IDs are generated separately from bacterial host identification and therefore may be used to track plasmid spread across species. Novel plasmids not found in the BugSeq database are labelled "Novel_-like". If a detected replicon cannot be assigned to a known incompatibility group, it is assigned to a replicon cluster ("rep_cluster_*"). These replicon cluster types also remain stable over time.

Showing ⁵/₅ rows and ¹¹/₁₁ columns.

Cluster ID	Circular	Length (bp)	Number of Contigs	Coverage	Predicted Host Range	Nearest NCBI Accession	Replicon Type(s)	Relaxase Type(s)	MPF Type	oriT Type(s)
AA619	Yes	10283bp	1	93.0	Enterobacteriaceae	KY471146	-	-	None	-
AA174	Yes	122305bp	1	144.0	Enterobacteriaceae	CP009860	IncFIA; IncFIB; IncFII	MOBF	MPF_F	MOBF
AA747	Yes	110007bp	1	216.0	Enterobacterales	CP039754	IncFIB	-	None	-
AA474	Yes	61337bp	1	323.0	Enterobacterales	CP002968	IncI-gamma/K1	-	None	-
AA150	Yes	5360bp	1	43.0	Actinobacteria/Firmicutes/Proteobacteria	CP002518	rep_cluster_2335	MOBP	None	MOBP

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Sort	Column	Description	ID	Scale
\|\|	Circular	Circular	`Circular`	None
\|\|	Length (bp)	Length (bp)	`Length (bp)`	None
\|\|	Number of Contigs	Number of Contigs	`Number of Contigs`	None
\|\|	Coverage	Coverage	`Coverage`	None
\|\|	Predicted Host Range	Predicted Host Range	`Predicted Host Range`	None
\|\|	Detected Resistance Markers	Detected Resistance Markers	`Detected Resistance Markers`	None
\|\|	Nearest NCBI Accession	Nearest NCBI Accession	`Nearest NCBI Accession`	None
\|\|	Replicon Type(s)	Replicon Type(s)	`Replicon Type(s)`	None
\|\|	Relaxase Type(s)	Relaxase Type(s)	`Relaxase Type(s)`	None
\|\|	MPF Type	MPF Type	`MPF Type`	None
\|\|	oriT Type(s)	oriT Type(s)	`oriT Type(s)`	None

Detection of Genotypic Markers Predicting Antimicrobial Resistance

Note: Genotype does not necessarily predict phenotypic antimicrobial resistance. Laboratory and/or clinical correlation are required.
Confidence explanation:

Very high confidence reflects a 100% identity match across 100% of the reference gene sequence.
High confidence reflects a 100% identity match across less than 100% of the reference gene sequence.
Moderate confidence reflects less than 100% identity match across less than 100% of the reference gene sequence.

Bacteroides fragilis

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance	Confidence	Genotypic Determinant
Unknown beta-lactam	Beta-Lactam	Present	High	cepA
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Doxycycline	Tetracycline	Present	High	tet(Q)
Minocycline	Tetracycline	Present	High	tet(Q)
Tetracycline	Tetracycline	Present	High	tet(Q)
Tigecycline	Tetracycline	Not Detected
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected

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Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Faecalibacterium prausnitzii

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance	Confidence	Genotypic Determinant
Doxycycline	Tetracycline	Present	High	tet(W)
Minocycline	Tetracycline	Present	High	tet(W)
Tetracycline	Tetracycline	Present	High	tet(W)
Tigecycline	Tetracycline	Not Detected
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Prevotella corporis

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance	Confidence	Genotypic Determinant
Doxycycline	Tetracycline	Present	Very High	tet(Q)
Minocycline	Tetracycline	Present	Very High	tet(Q)
Tetracycline	Tetracycline	Present	Very High	tet(Q)
Tigecycline	Tetracycline	Not Detected
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Plasmids

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Salmonella enterica

Showing ²⁷/₂₇ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Azithromycin	Macrolide	Not Detected
Colistin	Polymyxin	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Fusobacterium nucleatum

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Limosilactobacillus fermentum

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Roseburia hominis

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Veillonella rogosae

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Akkermansia muciniphila

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Bifidobacterium adolescentis

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Clindamycin	Lincosamide	Not Detected
Azithromycin	Macrolide	Not Detected
Erythromycin	Macrolide	Not Detected
Spiramycin	Macrolide	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Pristinamycin ia	Streptogramin B	Not Detected
Quinupristin	Streptogramin B	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Clostridioides difficile

Showing ⁶⁵/₆₅ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance	Confidence	Genotypic Determinant
Clindamycin	Lincosamide	Present	Very High	erm(B)
Azithromycin	Macrolide	Present	Very High	erm(B)
Erythromycin	Macrolide	Present	Very High	erm(B)
Spiramycin	Macrolide	Not Detected
Pristinamycin ia	Streptogramin B	Present	Very High	erm(B)
Quinupristin	Streptogramin B	Present	Very High	erm(B)
Spectinomycin	Aminocyclitol	Not Detected
Amikacin	Aminoglycoside	Not Detected
Bleomycin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Kanamycin	Aminoglycoside	Not Detected
Paromomycin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Unknown aminoglycoside	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin	Beta-Lactam	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefotaxime clavulanic acid	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftaroline	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Cefuroxime	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Penicillin	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Teicoplanin	Glycopeptide	Not Detected
Vancomycin	Glycopeptide	Not Detected
Maduramicin	Ionophores	Not Detected
Narasin	Ionophores	Not Detected
Salinomycin	Ionophores	Not Detected
Metronidazole	Nitroimidazole	Not Detected
Linezolid	Oxazolidinone	Not Detected
Colistin	Polymyxin	Not Detected
Mupirocin	Pseudomonic Acid	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Fluoroquinolone	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Nalidixic acid	Quinolone	Not Detected
Rifampicin	Rifamycin	Not Detected
Fusidic acid	Steroid Antibacterial	Not Detected
Dalfopristin	Streptogramin A	Not Detected
Pristinamycin iia	Streptogramin A	Not Detected
Quinupristin dalfopristin	Streptogramin A	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Enterobacteriaceae

Showing ³²/₃₂ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Amikacin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Colistin	Polymyxin	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

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Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Escherichia coli

Showing ³³/₃₃ rows and ⁴/₄ columns.

Antimicrobial	Class	Genotypic Predictor of Resistance
Amikacin	Aminoglycoside	Not Detected
Gentamicin	Aminoglycoside	Not Detected
Streptomycin	Aminoglycoside	Not Detected
Tobramycin	Aminoglycoside	Not Detected
Chloramphenicol	Amphenicol	Not Detected
Amoxicillin clavulanic acid	Beta-Lactam	Not Detected
Ampicillin	Beta-Lactam	Not Detected
Aztreonam	Beta-Lactam	Not Detected
Cefazolin	Beta-Lactam	Not Detected
Cefepime	Beta-Lactam	Not Detected
Cefixime	Beta-Lactam	Not Detected
Cefotaxime	Beta-Lactam	Not Detected
Cefoxitin	Beta-Lactam	Not Detected
Ceftazidime	Beta-Lactam	Not Detected
Ceftazidime avibactam	Beta-Lactam	Not Detected
Ceftriaxone	Beta-Lactam	Not Detected
Ertapenem	Beta-Lactam	Not Detected
Imipenem	Beta-Lactam	Not Detected
Meropenem	Beta-Lactam	Not Detected
Piperacillin	Beta-Lactam	Not Detected
Piperacillin tazobactam	Beta-Lactam	Not Detected
Ticarcillin clavulanic acid	Beta-Lactam	Not Detected
Unknown beta-lactam	Beta-Lactam	Not Detected
Sulfamethoxazole	Folate Pathway Antagonist	Not Detected
Trimethoprim	Folate Pathway Antagonist	Not Detected
Fosfomycin	Fosfomycin	Not Detected
Colistin	Polymyxin	Not Detected
Ciprofloxacin	Quinolone	Not Detected
Levofloxacin	Quinolone	Not Detected
Doxycycline	Tetracycline	Not Detected
Minocycline	Tetracycline	Not Detected
Tetracycline	Tetracycline	Not Detected
Tigecycline	Tetracycline	Not Detected

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Sort	Column	Description	ID	Scale
\|\|	Class	Class	`Class`	None
\|\|	Genotypic Predictor of Resistance	Gene or variant conferring antimicrobial resistance	`Genotypic Predictor of Resistance`	None
\|\|	Confidence	Confidence of AMR gene detection. See notes.	`Confidence`	None
\|\|	Genotypic Determinant	Genotypic Determinant	`Genotypic Determinant`	None

Multilocus Sequence Typing

Schemes available on PubMLST.

Showing ³/₃ rows and ⁹/₉ columns.

Genome Name	Sequence Type	Scheme	Locus 1	Locus 2	Locus 3	Locus 4	Locus 5	Locus 6	Locus 7
Bacteroides fragilis	-	bfragilis	dnaJ(1)	fusA(44)	groL(5)	prfA(2)	recA(3)	rpoB(1)	rprX(1)
Clostridioides difficile	1	cdifficile	adk(1)	atpA(1)	dxr(1)	glyA(10)	recA(1)	sodA(3)	tpi(5)
Escherichia coli	-	ecoli_achtman_4	adk(6810)	fumC(711118)	gyrB(444)	icd(8888)	mdh(88)	purA(88121818)	recA(22)

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Sort	Column	Description	ID	Scale
\|\|	Sequence Type	Defined by PubMLST scheme.	`ST`	None
\|\|	Scheme	Scheme	`Scheme`	None
\|\|	Locus 1	Locus 1	`Locus 1`	None
\|\|	Locus 2	Locus 2	`Locus 2`	None
\|\|	Locus 3	Locus 3	`Locus 3`	None
\|\|	Locus 4	Locus 4	`Locus 4`	None
\|\|	Locus 5	Locus 5	`Locus 5`	None
\|\|	Locus 6	Locus 6	`Locus 6`	None
\|\|	Locus 7	Locus 7	`Locus 7`	None

Salmonella Serotyping

Further detail on Salmonella serovar prediction is available here: https://github.com/phac-nml/sistr_cmd.

Showing ¹/₁ rows and ³/₃ columns.

Genome Name	Subspecies	Serovar	QC Status
Salmonella enterica	S. enterica subsp. None	-:-:-	FAIL

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Sort	Column	Description	ID	Scale
\|\|	Subspecies	Subspecies	`Subspecies`	None
\|\|	Serovar	Serovar	`Serovar`	None
\|\|	QC Status	QC Status	`QC Status`	None

Assembly Statistics

Assembly Statistics reports the length, contiguity and and quality of assemblies.DOI: 10.1093/bioinformatics/btt086.

Assembly Statistics

Showing ²⁰/₂₀ rows and ⁵/₈ columns.

Sample Name	N50 (Kbp)	L50	Largest contig (Kbp)	Length (Kbp)	Misassemblies	Mismatches/100kbp	Indels/100kbp	Genome Fraction
Akkermansia muciniphila	2851.6Kbp	1.0	2851.6Kbp	2851.6Kbp	94.0	2247.64	85.39	86.2%
Bacteroides fragilis	5181.5Kbp	1.0	5181.5Kbp	5212.3Kbp	132.0	791.93	35.54	83.0%
Bifidobacterium adolescentis	2028.4Kbp	1.0	2028.4Kbp	2089.7Kbp	45.0	996.69	56.79	82.3%
Candida	55.9Kbp	47.0	186.3Kbp	8106.9Kbp
Candida albicans	11.8Kbp	3.0	41.1Kbp	132.7Kbp	5.0	644.01	149.52	0.8%
Clostridioides difficile	4209.2Kbp	1.0	4209.2Kbp	4209.2Kbp	112.0	787.81	35.60	93.0%
Enterobacteriaceae	110.0Kbp	2.0	122.3Kbp	364.5Kbp
Escherichia coli	189.8Kbp	21.0	2641.0Kbp	17135.0Kbp	657.0	1794.27	44.95	80.6%
Faecalibacterium prausnitzii	2913.9Kbp	1.0	2913.9Kbp	2913.9Kbp	0.0	5876.07	368.51	13.3%
Fusobacterium nucleatum	2448.2Kbp	1.0	2448.2Kbp	2448.2Kbp	218.0	7141.24	324.25	56.9%
Limosilactobacillus fermentum	1905.4Kbp	1.0	1905.4Kbp	1905.4Kbp	138.0	623.31	22.13	85.4%
Methanobrevibacter smithii	415.3Kbp	2.0	544.9Kbp	1858.9Kbp
Plasmids	5.4Kbp	1.0	5.4Kbp	5.4Kbp
Prevotella corporis	2162.8Kbp	1.0	2162.8Kbp	2927.3Kbp	501.0	1859.39	60.03	80.1%
Root	196.5Kbp	1.0	196.5Kbp	249.9Kbp
Roseburia hominis	3463.3Kbp	1.0	3463.3Kbp	3463.3Kbp	101.0	1401.24	54.72	81.2%
Saccharomyces	50.1Kbp	38.0	141.3Kbp	6072.7Kbp
Saccharomyces cerevisiae	35.1Kbp	17.0	114.2Kbp	1836.6Kbp	9.0	492.58	61.87	15.0%
Salmonella enterica	21.2Kbp	2.0	21.3Kbp	70.1Kbp	2.0	1192.09	73.76	1.0%
Veillonella rogosae	2158.0Kbp	1.0	2158.0Kbp	2158.0Kbp	131.0	2903.88	120.04	84.0%

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Sort	Group	Column	Description	ID	Scale
\|\|	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly.	`N50`	None
\|\|	QUAST	L50	L50 is the number of contigs larger than N50, i.e. the minimum number of contigs comprising 50% of the total assembly length.	`L50`	None
\|\|	QUAST	Largest contig (Kbp)	The size of the largest contig of the assembly	`Largest contig`	None
\|\|	QUAST	Length (Kbp)	The total number of bases in the assembly.	`Total length`	None
\|\|	QUAST	Misassemblies	The number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (relocation) or they overlap on more than 1 kbp (relocation) or flanking sequences align on different strands (inversion) or different chromosomes (translocation).	`# misassemblies`	None
\|\|	QUAST	Mismatches/100kbp	The number of mismatches per 100 kbp	`# mismatches per 100 kbp`	None
\|\|	QUAST	Indels/100kbp	The number of indels per 100 kbp	`# indels per 100 kbp`	None
\|\|	QUAST	Genome Fraction	The total number of aligned bases in the reference, divided by the genome size.	`Genome fraction (%)`	None

Number of Contigs

This plot shows the number of contigs found for each assembly, broken down by length.

Assembly Completeness

Assembly Completeness is assessed using universal single-copy orthologs.DOI: 10.1093/bioinformatics/btv351.

Lineage: bacteria_odb10

Depth of Sequencing

Depth of Sequencing is calculated relative to the reference genome of each species. Reference genomes are designated by NCBI.DOI: 10.1093/bioinformatics/btx699.

Cumulative coverage distribution

Proportion of bases in the reference genome with, at least, a given depth of coverage

For a set of DNA or RNA reads mapped to a reference sequence, such as a genome or transcriptome, the depth of coverage at a given base position is the number of high-quality reads that map to the reference at that position, while the breadth of coverage is the fraction of the reference sequence to which reads have been mapped with at least a given depth of coverage (Sims et al. 2014).

Defining coverage breadth in terms of coverage depth is useful, because sequencing experiments typically require a specific minimum depth of coverage over the region of interest (Sims et al. 2014), so the extent of the reference sequence that is amenable to analysis is constrained to lie within regions that have sufficient depth. With inadequate sequencing breadth, it can be difficult to distinguish the absence of a biological feature (such as a gene) from a lack of data (Green 2007).

For increasing coverage depths (1×, 2×, …, N×), coverage breadth is calculated as the percentage of the reference sequence that is covered by at least that number of reads, then plots coverage breadth (y-axis) against coverage depth (x-axis). This plot shows the relationship between sequencing depth and breadth for each read dataset, which can be used to gauge, for example, the likely effect of a minimum depth filter on the fraction of a genome available for analysis.

Coverage distribution

Proportion of bases in the reference genome with a given depth of coverage

Bases of a reference sequence (y-axis) are groupped by their depth of coverage (0×, 1×, …, N×) (x-axis). This plot shows the frequency of coverage depths relative to the reference sequence for each read dataset, which provides an indirect measure of the level and variation of coverage depth in the corresponding sequenced sample.

If reads are randomly distributed across the reference sequence, this plot should resemble a Poisson distribution (Lander & Waterman 1988), with a peak indicating approximate depth of coverage, and more uniform coverage depth being reflected in a narrower spread. The optimal level of coverage depth depends on the aims of the experiment, though it should at minimum be sufficiently high to adequately address the biological question; greater uniformity of coverage is generally desirable, because it increases breadth of coverage for a given depth of coverage, allowing equivalent results to be achieved at a lower sequencing depth (Sampson et al. 2011; Sims et al. 2014). However, it is difficult to achieve uniform coverage depth in practice, due to biases introduced during sample preparation (van Dijk et al. 2014), sequencing (Ross et al. 2013) and read mapping (Sims et al. 2014).

This plot may include a small peak for regions of the reference sequence with zero depth of coverage. Such regions may be absent from the given sample (due to a deletion or structural rearrangement), present in the sample but not successfully sequenced (due to bias in sequencing or preparation), or sequenced but not successfully mapped to the reference (due to the choice of mapping algorithm, the presence of repeat sequences, or mismatches caused by variants or sequencing errors). Related factors cause most datasets to contain some unmapped reads (Sims et al. 2014).

Average coverage per contig

Average coverage per contig or chromosome

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General Statistics

Plasmid Detection

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Bacteroides fragilis

Faecalibacterium prausnitzii

Prevotella corporis

Plasmids

Salmonella enterica

Fusobacterium nucleatum

Limosilactobacillus fermentum

Roseburia hominis

Veillonella rogosae

Akkermansia muciniphila

Bifidobacterium adolescentis

Clostridioides difficile

Enterobacteriaceae

Escherichia coli

Multilocus Sequence Typing

Salmonella Serotyping

Assembly Statistics

Assembly Statistics

Number of Contigs

Assembly Completeness

Lineage: bacteria_odb10

Depth of Sequencing

Cumulative coverage distribution

Coverage distribution

Average coverage per contig

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General Statistics

General Statistics: Columns

Plasmid Detection

Plasmids-Plot: Columns

Detection of Genotypic Markers Predicting Antimicrobial Resistance

Bacteroides fragilis

Bacteroides Fragilis Amr-Plot: Columns

Faecalibacterium prausnitzii

Faecalibacterium Prausnitzii Amr-Plot: Columns

Prevotella corporis

Prevotella Corporis Amr-Plot: Columns

Plasmids

Plasmids Amr-Plot: Columns

Salmonella enterica

Salmonella Enterica Amr-Plot: Columns

Fusobacterium nucleatum

Fusobacterium Nucleatum Amr-Plot: Columns

Limosilactobacillus fermentum

Limosilactobacillus Fermentum Amr-Plot: Columns

Roseburia hominis

Roseburia Hominis Amr-Plot: Columns

Veillonella rogosae

Veillonella Rogosae Amr-Plot: Columns

Akkermansia muciniphila

Akkermansia Muciniphila Amr-Plot: Columns

Bifidobacterium adolescentis

Bifidobacterium Adolescentis Amr-Plot: Columns

Clostridioides difficile

Clostridioides Difficile Amr-Plot: Columns

Enterobacteriaceae

Enterobacteriaceae Amr-Plot: Columns

Escherichia coli

Escherichia Coli Amr-Plot: Columns

Multilocus Sequence Typing

Mlst-Plot: Columns

Salmonella Serotyping

Salmonella Serovar-Plot: Columns

Assembly Statistics

Assembly Statistics

Quast Table: Columns

Number of Contigs

Assembly Completeness

Lineage: bacteria_odb10

Depth of Sequencing

Cumulative coverage distribution Help

Coverage distribution Help

Average coverage per contig

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Cumulative coverage distribution

Coverage distribution