ABSTRACT
Neisseria gonorrhoeae is the causative agent of gonorrhea and was identified by the World Health Organization as an urgent public health threat due to emerging antibiotic resistance. Here, we report 13 draft genome sequences of N. gonorrhoeae isolates derived from two epidemiologically linked cases from Austria.
GENOME ANNOUNCEMENT
Neisseria gonorrhoeae is the etiological agent of the sexually transmitted disease gonorrhea, and it poses a public health threat due to the emergence of multidrug-resistant strains (1–4). Whole-genome sequencing is considered a powerful strategy to elucidate chains of transmission (5). Here, we announce the draft genome sequences of 13 epidemiologically linked N. gonorrhoeae isolates.
Two vaginal swabs, taken from a 3-year-old girl on 10 January 2018, and her rectal swab, gained on 13 January 2018, yielded N. gonorrhoeae colonies on Chocolat PolyViteX VCAT3 agar plates (bioMérieux, Marcy-l’Étoile, France). A 46-year-old male household member was sampled on 13 January 2018, and N. gonorrhoeae colonies grew from a rectal swab. Eight single colonies from the child and five from the adult were further analyzed.
For each isolate, antimicrobial susceptibility was determined according to the EUCAST recommendations for gonococci (6). All 13 isolates showed resistance to penicillin G (median MIC, 6 µg/ml; range, 1.5 to 32 µg/ml), tetracycline (median MIC, 24 µg/ml; range, 24 to 64 µg/ml), and ciprofloxacin (median MIC, 0.75 µg/ml; range, 0.5 to 1.5 µg/ml), but were susceptible to ceftriaxone, cefixime, and azithromycin.
Genomic DNA isolation, whole-genome sequencing, assembly, and contig filtering were performed as described previously (7). Paired-end sequencing (2 × 300 bp) generated 348,172 to 847,328 reads, with a mean coverage of 41- to 89-fold. The NCBI Prokaryotic Genome Automatic Annotation Pipeline identified 2,654 to 2,720 genes, 2,604 to 2,664 coding sequences, 273 to 305 pseudogenes, 3 to 6 rRNA genes, and 47 to 51 tRNA genes.
Antimicrobial resistance genes were identified using the Comprehensive Antibiotic Resistance Database (CARD) (8). All 13 isolates had gyrA, N. meningitidis PBP2 and rpsJ, and the efflux genes farA, farB, macA, macB, mtrC, mtrD, and mtrR. In addition, blaTEM-1 was detected in three child and three household member isolates. Three isolates from the child and one from the household member carried blaTEM-90. One child isolate had blaTEM-150, and another one carried blaTEM-150 plus the efflux gene patA.
All 13 isolates belonged to multilocus sequence type (MLST) 1588 (ST1588). An ad hoc core genome MLST (cgMLST) scheme comprising 1,524 targets was established using strain MS11 (ATCC BAA-1833) as a reference. Child isolates differed by zero to three alleles and household member isolates by zero to one alleles; the maximum interindividual variability of the isolates was five allelic differences. In the course of comparison with the Austrian Agency for Health and Food Safety (AGES) N. gonorrhoeae whole-genome database (currently covering 452 isolates from the years 2014 to 2018), all but one isolate differed by at least 303 alleles. An isolate gained in 2016 (strain 980016-16) from a urethral swab of an epidemiologically unrelated 32-year-old male patient, registered in the same Austrian province as the two described case patients, showed a six-allele difference. From these results, we propose a complex-type threshold of a maximum of five allelic differences for direct transmission events of N. gonorrhoeae. Our findings underline the considerable potential of whole-genome sequencing (WGS) to document chains of transmission.
Accession number(s).
This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession numbers shown in Table 1. The versions described in this paper are the first versions.
TABLE 1.
Fourteen N. gonorrhoeae isolates included in BioProject PRJNA433931
| Strain | GenBank accession no. | No. of contigs | Total length (bp) |
|---|---|---|---|
| 980035-18 | PTPT00000000 | 173 | 2,234,140 |
| 980036-18 | PTPS00000000 | 155 | 2,227,585 |
| 980037-18 | PTPR00000000 | 203 | 2,214,439 |
| 980038-18 | PTPQ00000000 | 193 | 2,239,226 |
| 980039-18 | PTPP00000000 | 164 | 2,214,439 |
| 980040-18 | PTPO00000000 | 191 | 2,232,201 |
| 980041-18 | PTPN00000000 | 156 | 2,226,960 |
| 980042-18 | PTPM00000000 | 168 | 2,223,307 |
| 980043-18 | PTPL00000000 | 160 | 2,217,312 |
| 980044-18 | PTPK00000000 | 137 | 2,214,035 |
| 980045-18 | PTPJ00000000 | 141 | 2,210,712 |
| 980046-18 | PTPI00000000 | 140 | 2,217,914 |
| 980047-18 | PTPH00000000 | 199 | 2,209,742 |
| 980016-16 | PTPG00000000 | 178 | 2,233,553 |
ACKNOWLEDGMENT
A.C.R. was supported by a grant from the European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control (specific grant agreement 1 ECD.7550, implementing ECDC/GRANT/2017/003). No further funding was received from any funding agency in the public, commercial, or not-for-profit sectors.
Footnotes
Citation Hirk S, Lepuschitz S, Cabal Rosel A, Huhulescu S, Blaschitz M, Stöger A, Stadlbauer S, Hasenberger P, Indra A, Schmid D, Ruppitsch W, Allerberger F. 2018. Draft genome sequences of interpatient and intrapatient epidemiologically linked Neisseria gonorrhoeae isolates. Genome Announc 6:e00319-18. https://doi.org/10.1128/genomeA.00319-18.
REFERENCES
- 1.WHO 2014. Antimicrobial resistance: global report on surveillance. WHO, Geneva, Switzerland. [Google Scholar]
- 2.Newman L, Rowley J, Vander Hoorn S, Wijesooriya NS, Unemo M, Low N, Stevens G, Gottlieb S, Kiarie J, Temmerman M. 2015. Global estimates of the prevalence and incidence of four curable sexually transmitted infections in 2012 based on systematic review and global reporting. PLoS One 10:e0143304. doi: 10.1371/journal.pone.0143304. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 3.Unemo M, Shafer WM. 2014. Antimicrobial resistance in Neisseria gonorrhoeae in the 21st century: past, evolution, and future. Clin Microbiol Rev 27:587–613. doi: 10.1128/CMR.00010-14. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 4.Cole MJ, Spiteri G, Jacobsson S, Woodford N, Tripodo F, Amato-Gauci AJ, Unemo M. 2017. Overall low extended-spectrum cephalosporin resistance but high azithromycin resistance in Neisseria gonorrhoeae in 24 European countries, 2015. BMC Infect Dis 17:617. doi: 10.1186/s12879-017-2707-z. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 5.De Silva D, Peters J, Cole K, Cole MJ, Cresswell F, Dean G, Dave J, Thomas DR, Foster K, Waldram A, Wilson DJ, Didelot X, Grad YH, Crook DW, Peto TE, Walker AS, Paul J, Eyre DW. 2016. Whole-genome sequencing to determine Neisseria gonorrhoeae transmission: an observational study. Lancet Infect Dis 16:1295–1303. doi: 10.1016/S1473-3099(16)30157-8. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 6.European Committee on Antimicrobial Susceptibility Testing. 2018. Breakpoint tables for interpretation of MICs and zone diameters, version 8.0. http://www.eucast.org/clinical_breakpoints/.
- 7.Lepuschitz S, Sorschag S, Springer B, Allerberger F, Ruppitsch W. 2017. Draft genome sequence of carbapenemase-producing Serratia marcescens isolated from a patient with chronic obstructive pulmonary disease. Genome Announc 5:e01288-17. doi: 10.1128/genomeA.01288-17. [DOI] [PMC free article] [PubMed] [Google Scholar]
- 8.Jia B, Raphenya AR, Alcock B, Waglechner N, Guo P, Tsang KK, Lago BA, Dave BM, Pereira S, Sharma AN, Doshi S, Courtot M, Lo R, Williams LE, Frye JG, Elsayegh T, Sardar D, Westman EL, Pawlowski AC, Johnson TA, Brinkman FS, Wright GD, McArthur AG. 2017. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res 45:D566–D573. doi: 10.1093/nar/gkw1004. [DOI] [PMC free article] [PubMed] [Google Scholar]