Dot plots showing the detection efficiency (with lines indicating the mean and 95% confidence intervals from 100 simulations) for resistance variants RplD G70D (A–B), 23S rRNA C2611T (C–D), and penA …
Maximum-likelihood phylogeny produced from the pseudogenome alignment (with predicted regions of recombination removed) of isolates from dataset 2 (A). Patient travel history is indicated by the …
Scatter dot plots showing the detection efficiency (with lines indicating the mean and 95% confidence intervals from 100 simulations) for resistance variants RplD G70D (A), 23S rRNA C2611T (B), and p…
Scatter dot plots showing the detection efficiency (with lines indicating the mean and 95% confidence intervals from 100 simulations) for resistance variants RplD G70D (A), 23S rRNA C2611T (B), and p…
Bar charts showing the proportions of ceftriaxone reduced susceptibility (CRO-RS) isolates, ceftriaxone susceptible (CRO-S) isolates, cefixime resistant (CFX-R) isolates, and cefixime susceptible …
Dataset | Temporal range | Nisolates | Geographic range | Metadata available | SRA study ID/Reference |
---|---|---|---|---|---|
1 | 2011–2015 | 896 | New York, NY, US | Gender, sexual behavior, anatomical site of isolation | ERP011192 (Mortimer et al., 2020) |
2 | 2016–2017 | 2186 | Victoria, Australia | Gender, sexual behavior, anatomical site of isolation, travel history, sex worker status | SRP185594 (Williamson et al., 2019) |
3 | 2013 | 1054 | Europe | Country of sample collection | ERP010312 (Harris et al., 2018) |
4 | 2015 | 244 | Japan | Prefecture of sample collection | DRP004052 (Yahara et al., 2018) |
5 | 2014–2015 | 398 | New Zealand | N/A | SRP111927 (Lee et al., 2018b) |
Variant | Genetic | Phenotypic | ||||
---|---|---|---|---|---|---|
RplD G70D | 23S rRNA C2611T (2–4 alleles) | penA XXXIV | CRO-RS (≥0.12 μg/mL) | CFX-R (>0.25 μg/mL) | ||
Drug | AZM (Grad et al., 2016) | AZM (Lk et al., 2002) | ESCs (Grad et al., 2014) | N/A | N/A | |
Prevalence of variant in dataset | 1 | 10.04%* | 0.11% | 5.25% | 1.47% | 0.11% |
2 | 1.14% | 1.24% | 1.69% | 0% | 0% | |
3 | 2.47% | 0.95% | 15.68%* | 1.04% | 0.76% | |
4 | 11.07%* | 1.23% | 0.41% | 6.56% | 8.20% | |
5 | 0.75% | 0.50% | 2.26% | 0.25% | 0% | |
Phylogenetic D statistic for variant in dataset | 1 | −0.18 | 17.50 | −0.29 | N/A | N/A |
2 | −0.10 | 0.46 | −0.24 | N/A | N/A | |
3 | 0.05 | 0.30 | −0.20 | N/A | N/A | |
4 | −0.16 | 1.83 | 1.81 | N/A | N/A | |
5 | 0.83 | 1.12 | −0.15 | N/A | N/A |
*Given the >10% prevalence of RplD G70D in datasets 1 and 4 and penA XXXIV in dataset 3, these variants were excluded from sampling simulations.
AZM, azithromycin; ESC, extended-spectrum cephalosporin; CRO-RS, ceftriaxone reduced susceptibility; CFX-R, cefixime resistance.
Variant | Diagnostic assay | Documented association with diagnostic failure | Prevalence in dataset | ||||
---|---|---|---|---|---|---|---|
1 | 2 | 3 | 4 | 5 | |||
16S rRNA C1209A (four alleles) | Aptima GC Combo | Yes (Guglielmino et al., 2019) | 0.11% | 0.09% | 0% | 0% | 0% |
N. meningitidis-like porA | In-house (Whiley et al., 2004; Whiley et al., 2005) | Yes (Whiley et al., 2011; Golparian et al., 2012) | 0.11% | 0.05% | 0% | 0% | 0% |
cppB deletion | In-house (Diemert et al., 2002; Van Dyck et al., 2001) | Yes (Bruisten et al., 2004) | 1.12% | 0.05% | 0.47% | 0% | 7.29% |
DR-9A G168A | Roche COBAS 4800 CT/NG | No | 0% | 0.09% | 0% | 0% | 0% |
Variant | Reference accession | Coordinates of genetic locus in reference entry | Position of mutation in reference locus |
---|---|---|---|
RplD G70D | NC_011035.1 | 2033052–2033672 | amino acid 70 |
23S rRNA C2611T | NC_011035.1 | 1263408–1266305 | nucleotide 2603 |
penA XXXIV | NZ_LT906440.1 | 1588456–1590201 | N/A (assessed presence/absence of this allele) |
16S rRNA C1209A | NC_011035.1 | 1266903–1268450 | nucleotide 1192 |
N. meningitidis-like porA | NC_011035.1 | 735796–737125 | N/A (assessed nucleotide similarity across the full locus with a threshold of ≤ 90%)* |
cppB deletion | LT592149.1 | 2912–3553 | N/A (assessed presence/absence of full locus) |
DR-9A G168A | NC_011035.1 | 530088–530277 | nucleotide 168 |
*Isolates with a porA pseudogene with ≤90% similarity to the NC_011035.1 porA pseudogene were called positive for N. meningitidis-like porA. Note that all such isolates were confirmed to have a porA pseudogene that was ≥92% similar to the N. meningitidis porA (GenBank Accession: GQ173789.1), while all other isolates had ≤89% similarity to the N. meningitidis porA.
Metadata and resistance variant profiles for isolates assessed in this study.
M, men; W, women; MSM, men who have sex with men; MSW, men who have sex with women; WSM, women who have sex with men; CFX-R, cefixime resistance; CRO-RS, ceftriaxone reduced susceptibility; AZM-R, azithromycin resistance.
Dataset bias and targeted sampling results.
(A) Demographic and geographic sampling biases in datasets 1–3. (B) Detection efficiency of random, demography-, niche-, and geography-aware sampling approaches for resistance variants. (C) Detection efficiency of random sampling, as well as preferential sampling of patients that had recently engaged in overseas sex or in sex work, for resistance variants in dataset 2. (D) Detection efficiency of random and phylogeny-aware sampling approaches for resistance variants. (E) Detection efficiency of random and phylogeny-aware sampling approaches for variants associated with diagnostic escape. (F) Detection efficiency of random and genomic background-aware sampling approaches for resistance variants.