Table 1.
Summary of sequences used to investigate the emergence of fluoroquinolone-resistant Shigella sonnei
| Country | Number of sequences | In CenAsiaIII clade | CIP resistant isolates | Study or Institute of origin | Patient group | Region of recent travel history (N) | Sequencing platform | CIP susceptibility test |
|---|---|---|---|---|---|---|---|---|
| Bhutan | 71 | 71 | 71 | Diarrhoeal disease surveillance in JDWNRH, Thimphu, Bhutan (AFRIMS) | Hospitalised children <5 years old | NA | Illumina HiSeq 2000 | Disk diffusion/E-test |
| Vietnam | 24 | 22 (−2 poor sequencing quality) | 22 | Diarrhoeal disease surveillance in HCMC, Vietnam | Hospitalised children <5 years old | NA | Illumina MiSeq | Disk diffusion |
| Thailand | 8 | 8 | 1 | Cross-sectional study of S. sonnei diversity in Southeast Asia (AFRIMS) | Hospitalised children <5 years old | NA | Illumina HiSeq 2000 | Disk diffusion |
| Cambodia | 1 | 1 | 1 | Cross-sectional study of S. sonnei diversity in Southeast Asia (AFRIMS) | Hospitalised children <5 years old | NA | Illumina HiSeq 2000 | Disk diffusion |
| Ireland | 20 | 20 | 16 | National Salmonella, Shigella and L. monocytogenes Reference Laboratory, Galway, Ireland | Primarily patients with recent travel history | South Asia (9), Africa (1), Europe (1), No travel (5), Unknown (4) | Illumina HiSeq 2000 | Broth microdilution |
| Australia | 85 | 77 | 46 | Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, Australia | Primarily patients with recent travel history | Africa (2), America (1), Southeast Asia (12), Middle East (2), Oceania (1), South Asia (60), Unknown (4) | Illumina NextSeq | Agar dilution |
| France | 97 | 95 | 72 | French National Reference Centre for E. coli, Shigella, and Salmonella, Paris, France | Primarily patients with recent travel history | Africa (4) America (1) Southeast Asia (4) South Asia (88) | Illumina HiSeq 2000 | Disk diffusion |
| England | 91 | 90 | 82 | Gastrointestinal Bacteria Reference Unit, Public Health England, London, UK | Primarily patients with recent travel history | Africa (3), East Asia (1), Europe (13), Middle East (1), South Asia (73) | Illumina HiSeq 2000 | Disk diffusion |
| Global references | 14 | 11 | 0 | NA | NA | NA | Illumina HiSeq 2000 | NA |
| Total | 411 | 395 | 311 |
CIP ciprofloxacin, JDWNRH Jigme Dorji Wangchuk National Reference Hospital, AFRIMS Armed Forces Research Institute of Medical Sciences, HCMC Ho Chi Minh City