The New Zealand Institute for Public Health and Forensic Science (PHF Science) was formerly named The Institute of Environmental Science and Research (ESR).

References for poster paper being presented at the Queenstown Research Week Antimicrobial Resistance Satellite Meeting 2-3 September 2025, Christchurch.

Validation of genomic antimicrobial resistance markers (AMR) for national AMR surveillance for Salmonella spp. identifies discrepancies in azithromycin resistance for S. Paratyphi A

Antimicrobial Health AMR

References

1.         The Clinical and Laboratory Standards Institute (CLSI). Performance Standards for Antimicrobial Susceptibility Testing. 35th ed. CLSI supplement M100. 35 ed. USA: Clinical and Laboratory Standards Institute; 2025.

2.         EUCAST European Committee on Antimicrobial Susceptibility Testing. Clinical breakpoints - breakpoints and guidance. European Committee on Antimicrobial Susceptibility Testing. Updated 01 January 2025. Accessed 8 April 2025, 2025. https://www.eucast.org/clinical_breakpoints

3.         EUCAST European Committee on Antimicrobial Susceptibility Testing. EUCAST Disk Diffusion Test Methodology. EUCAST. Updated 1 January 2025. Accessed 8 April 2025, 2025. https://www.eucast.org/ast_of_bacteria/disk_diffusion_methodology

4.         Humphries R. AST News Update June 2023: New! CLSI M100-Ed33: Updated Aminoglycoside Breakpoints for Enterobacterales and Pseudomonas aeruginosa (Clinical and Laboratory Standards Institute;. 2025. https://clsi.org/about/news/ast-news-update-june-2023-new-clsi-m100-ed33-updated-aminoglycoside-breakpoints-for-enterobacterales-and-pseudomonas-aeruginosa/

5.         EUCAST European Committee on Antimicrobial Susceptibility Testing. EUCAST Expert Rules v 3.2, Salmonella. 2025. https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2019/Salmonella_ExpertRules_V3.2_20190613.pdf

6.         Chen S, Zhou Y, Chen Y, Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884-i890. doi:10.1093/bioinformatics/bty560

7.         Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res. Dec 2016;26(12):1721-1729. doi:10.1101/gr.210641.116

8.         Souvorov A, Agarwala R, Lipman DJ. SKESA: strategic k-mer extension for scrupulous assemblies. Genome Biology. 2018/10/04 2018;19(1):153. doi:10.1186/s13059-018-1540-z

9.         Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072-1075. doi:10.1093/bioinformatics/btt086

10.       Seemann T, Stroehleina A, Goncalves da Silva A. MLST. Github. 2023. https://github.com/tseemann/mlst

11.       Yoshida CE, Kruczkiewicz P, Laing CR, et al. The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies. PLoS One. 2016;11(1):e0147101. doi:10.1371/journal.pone.0147101

12.       Sherry NL, Horan KA, Ballard SA, et al. An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance. Nature communications. 2023/01/04 2023;14(1):60. doi:10.1038/s41467-022-35713-4

13.       Feldgarden M, Brover V, Gonzalez-Escalona N, et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Scientific Reports. 2021/06/16 2021;11(1):12728. doi:10.1038/s41598-021-91456-0

14.       Kahlmeter G, Turnidge J. Wild-type distributions of minimum inhibitory concentrations and epidemiological cut-off values—laboratory and clinical utility. Clinical Microbiology Reviews. 2023;36(4):e00100-22. doi:doi:10.1128/cmr.00100-22

15.       EUCAST European Committee on Antimicrobial Susceptibility Testing. Antimicrobial wild type distributions of microorganisms. EUCAST. 2025. https://mic.eucast.org/search/

16.       Dyson ZA, Ashton PM, Khanam F, et al. Pathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study. The Lancet Microbe. 2024;5(8)doi:10.1016/S2666-5247(24)00047-8

17.       Poppe C, Smart N, Khakhria R, Johnson W, Spika J, Prescott J. Salmonella typhimurium DT104: a virulent and drug-resistant pathogen. Can Vet J. Sep 1998;39(9):559-65.

18.       Threlfall EJ. Epidemic Salmonella Typhimurium DT 104—a truly international multiresistant clone. Journal of Antimicrobial Chemotherapy. 2000;46(1):7-10. doi:10.1093/jac/46.1.7

19.       Mandilara G, Sideroglou T, Chrysostomou A, et al. The Rising Burden of Salmonellosis Caused by Monophasic Salmonella Typhimurium (1,4,[5],12:i:-) in Greece and New Food Vehicles. Antibiotics (Basel). Feb 13 2021;10(2)doi:10.3390/antibiotics10020185

20.       Qin X, Yang M, Cai H, et al. Antibiotic Resistance of Salmonella Typhimurium Monophasic Variant 1,4,[5],12:i:-in China: A Systematic Review and Meta-Analysis. Antibiotics (Basel). Apr 16 2022;11(4)doi:10.3390/antibiotics11040532

21.       Mather AE, Gilmour MW, Reid SWJ, French NP. Foodborne bacterial pathogens: genome-based approaches for enduring and emerging threats in a complex and changing world. Nature Reviews Microbiology. 2024/05/24 2024;doi:10.1038/s41579-024-01051-z

22.       Argimón S, Yeats CA, Goater RJ, et al. A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch. Nature communications. 2021/05/17 2021;12(1):2879. doi:10.1038/s41467-021-23091-2

23.       Poppe C, Ziebell K, Martin L, Allen K. Diversity in Antimicrobial Resistance and Other Characteristics Among Salmonella Typhimurium DT104 Isolates. Microbial drug resistance (Larchmont, NY). 02/01 2002;8:107-22. doi:10.1089/107662902760190653

24.       Carey ME, Dyson ZA, Ingle DJ, et al. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife. 2023/09/12 2023;12:e85867. doi:10.7554/eLife.85867

25.       Petrosino J, Cantu C, Palzkill T. β-Lactamases: protein evolution in real time. Trends in Microbiology. 1998/08/01/ 1998;6(8):323-327. doi:https://doi.org/10.1016/S0966-842X(98)01317-1

26.       Weill F-X, Perrier-Gros-Claude J-D, Demartin M, Coignard S, Grimont PAD. Characterization of extended-spectrum-β-lactamase (CTX-M-15)-producing strains of Salmonella enterica isolated in France and Senegal. FEMS Microbiology Letters. 2004;238(2):353-358. doi:10.1111/j.1574-6968.2004.tb09776.x