. 2020 Feb 10;5(3):455–464. doi: 10.1038/s41564-019-0656-6

Table 1.

Predicted phenotypes of S. pneumoniae for database isolates (a), non-database isolates (b) and metagenomes (c)

(a) Database isolates
Sample	Lineage confidently detected	Matched k-mers (%)	Serotype		Antibiogram CRO		Antibiogram ERY		Antibiogram PEN		Antibiogram SXT		Antibiogram TET		MLST match	CC match
Sample	Lineage confidently detected	Matched k-mers (%)	Actual	Best match	Actual	Best match	Actual	Best match	Actual	Best match	Actual	Best match	Actual	Best match	MLST match	CC match
SP01	Yes	16	11D	11D^a	S	S^a	S	S^a	S	S^a	S	S^a	S⁽¹⁾	S^(1)a	Yes^a	Yes^a
SP02	Yes	9.6	19A	19A^a	R	R^a	R	R^a	R	R^a	R	R^a	R⁽²⁾	R^(2)a	Yes^a	Yes^a

(b) Non-database isolates
Sample	Lineage confidently detected	Matched k-mers (%)	Serotype		Antibiogram CRO		Antibiogram ERY		Antibiogram PEN		Antibiogram SXT		Antibiogram TET		MLST match	CC match
Sample	Lineage confidently detected	Matched k-mers (%)	Actual	Best match	Actual	Best match	Actual	Best match	Actual	Best match	Actual	Best match	Actual	Best match	MLST match	CC match
SP03	Yes	3.1	23F	23F^a	R	R^a	R	S^(3)b	R	R^a	R	R^a	S	S^a	OoD^c	Yes^a
SP04	Yes	12	19A	19A^a	R	R^a	R	R^a	R	R^a	R	R^a	R	R^(4)a	OoD^c	Yes^a
SP05	No	1.8	19F	19F^a	R	R^a	R	R^a,d	R	R^a	R	R^a^,d	R	R^a,d	OoD^c	Yes^a
SP06	Yes	8.3	23F	23F^a	R	R^a	R	S^(3)b	R	R^a	R	R^a	S	S^a	OoD^c	Yes^a

(c) Metagenomes
Sample	Lineage confidently detected	SP (%)	Matched k-mers (%)	Antibiogram ERY		Antibiogram PEN		Antibiogram TET
Sample	Lineage confidently detected	SP (%)	Matched k-mers (%)	Actual	Best match	Actual	Best match	Actual	Best match
SP07	No	2.3	0.2	NA	S^c	S	S^a	R	S^(5)b
SP08	No	2.5	0.9	S	S^a	S	S^a,d	S	S^(6)a
SP09	No	4.0	1.2	NA	S^c	S	S^a	S	S^(7)a
SP10	Yes	21	5.2	R	R^a	R	R^a	R	R^(8)a
SP11	Yes	70	14	R	R^a	R	R^a	R	R^(8)a
SP12	Yes	86	17	S	S^a	S	S^a	R	S^(5)b

The table displays actual and predicted resistance phenotypes (where ‘S’ represents susceptible and ‘R’ represents non-susceptible) for individual experiments and information on the match of the predicted MLST-identified sequence type and the clonal complex (CC). Resistance categories in bold were inferred using ancestral reconstruction and were confirmed using phenotypic testing (see Methods and Supplementary Table 2). Metagenomic samples were sorted by the estimated fraction of S. pneumoniae reads (SP).

^aCorrect prediction.

^bIncorrect prediction.

^cCannot be evaluated.

^dLow confidence call. OoD, out of database; ⁽ⁿ⁾, identity of a retested sample; NA, not available. For definitions of antibiotics see Fig. 2.