Table 3.

Concordance rates between genotypic and phenotypic AMR data

False positive is referred to as ‘major discrepancy' by the US-FDA, while false negative is referred to as ‘very major discrepancy’ by the US-FDA. Overall, the prevalence of predicted AMR in Cambodia is summarized in Table 4) . There was no significant difference in AMR or multidrug resistance from the pre-PCV13 (79 % MDR) to post-PCV13 (76 % MDR) populations (Table 4); however, there was a higher prevalence of mutlidrug resistance in the VT serotypes (91 % MDR) compared with the NVT serotypes (62 % MDR) (Table 5). Assuming the previously demonstrated vaccine effectiveness for pneumococcal colonization of 39.2 % (95 % confidence interval 26.7–46.1) for VT serotypes in Cambodia maintains, the prevalence of AMR should decrease [16]. Alternatively, despite high vaccine efficacy, the genetic backgrounds containing VT and AMR may persist via serotype switching and expansion of previously low prevalence NVT lineages, resulting in vaccine escape (Fig. 1).

Antibiotic	Concordance (%)	Discordance (%)
		False positive by WGS	False negative by WGS
Multidrug resistance	651 (94.9)	16 (2.3)	6 (0.9)
Penicillin (meningitis threshold)	685 (99.9)	0	1 (0.1)
Erythromycin	682 (99.4)	3 (0.4)	1 (0.1)
Chloramphenicol	684 (99.7)	2 (0.3)	0
Tetracycline	646 (94.2)	22 (3.2)	18 (2.6)
Co-trimoxazole	661 (96.4)	25 (3.6)	–