TABLE 1.
Summary of the demographic and travel-related (if any) data along with the results of WGS analyses of the S. sonnei strains analyzed in the present studyh
| Strain | Yr of isolation | Age (yr)/sexa | Sample | Origin of infectiona | Groupb | Coresistanceb | STc | Antimicrobial resistance genes/plasmid replicons (pMLST, approximate size)c | No. (%) of called alleles among a total of 2,513d | No. (%) of allele matches in cgSTd | cgSTd |
|---|---|---|---|---|---|---|---|---|---|---|---|
| L4094 | 2018 | NA/NA | NA | NA | ESC-R | ST152 | blaCTX-M-3, aadA1, mdf(A), dfrA1/l1 (pST57, 86 kb), Col156, Col(BS512) | 2,503 (99.60) | 2,496 (99.32) | cgST113036 | |
| 1205-3131 | 2018 | 35/M | Stool | Unknown | ESC-R | ST152 | blaCTX-M-3, aadA1, mdf(A), dfrA1/l1 (pST57, 86 kb), Col156, Col(BS512) | 2,500 (99.48) | 2,492 (99.16) | cgST113036 | |
| 7111-69 | 2019 | 20/M | Stool | Turkey | ESC-R | ST152 | blaCTX-M-3, aadA1, mdf(A), dfrA1/l1 (pST57, 86 kb), Col156, Col(BS512) | 2,499 (99.44) | 2,491 (99.12) | cgST113036 | |
| LC-1477-18e | 2018 | 10/F | Stool | Albania | ESC-R | SXT | ST152 | blaCTX-M-3, aadA1, aph(3'')-Ib, aph(6)-Id, mdf(A), dfrA1, sul2, tet(A)/I1 (pST57, 85 kb), Col156, Col(BS512) | 2,505 (99.68) | 2,498 (99.40) | cgST118753 |
| 509-1022 | 2019 | 50/F | Stool | Unknown | ESC-R | SXT | ST152 | blaCTX-M-3, aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, sul2, tet(A)/l1 (pST57, 88 kb), Col156, Col(BS512) | 2,503 (99.60) | 2,495 (99.28) | cgST115537 |
| 19-0822-3296 | 2019 | 5/F | Stool | Unknown | ESC-R | SXT | ST152 | blaCTX-M-3, aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, sul2, tet(A)/l1 (pST57, 88 kb), Col156, Col(BS512) | 2,504 (99.64) | 2,495 (99.28) | cgST115537 |
| 6607-69 | 2017 | 60/F | Stool | Sri Lanka | ESC-R | SXT | ST1503f | blaCTX-M-15, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, tet(A), sul2/I1 (pST16, 90 kb), FII, Col156, Col(BS512) | 2,504 (99.64) | 2,496 (99.32) | cgST64457 |
| 19-0821-3486 | 2019 | 45/M | Stool | Egypt | ESC-R | SXT | ST152 | blaCTX-M-15, aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, qnrS1, sul2, tet(A)/FII (F2:A-:B-, 83 kb), Col156, Col(BS512) | 2,500 (99.48) | 2,493 (99.20) | cgST112958 |
| 0401930105 | 2019 | 50/M | Stool | Egypt | ESC-R | SXT | ST152 | blaCTX-M-15, aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, qnrS1, tet(A), sul2/FII (F2:A-:B-, 83 kb), Col156, Col(BS512) | 2,502 (99.56) | 2,496 (99.32) | cgST112958 |
| 6904-27 | 2018 | 35/M | Stool | Local | ESC-R | SXT | ST152 | blaCTX-M-15, aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, qnrS1, tet(A), sul2/FII (F2:A-:B-, 83 kb), Col156, Col(BS512) | 2,502 (99.56) | 2,497 (99.36) | cgST112958 |
| 19-1125-3493 | 2019 | 40/F | Stool | Unknown | ESC-R | SXT | ST152 | blaCTX-M-15, aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, qnrS1, tet(A), sul2/FII (F2:A-:B-, 83 kb), Col156, Col(BS512) | 2,496 (99.32) | 2,489 (99.04) | cgST112958 |
| 19-0820-1561 | 2019 | 15/F | Stool | Nepal | ESC-R | SXT, CIP, AZT | ST152 | blaCTX-M-15, aadA5, mdf(A), mph(A), dfrA1, dfrA17, qnrS1, sul1/FII (F2: A-:B-, 83 kb), Col156, Col(BS512) | 2,493 (99.20) | 2,477 (98.57) | cgST117387 |
| 0401952027 | 2019 | 45/M | Stool | Egypt | ESC-R | SXT, AZT | ST152 | blaCTX-M-55, aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), mph(A), dfrA1, sul2, tet(A)/I1, FII (F2:A-:B-, 74 kb), Col156, Col(BS512) | 2,498 (99.40) | 2,489 (99.04) | cgST20888 |
| 09163633 | 2019 | 50/M | Stool | Unknown | ESC-R | SXT | ST152 | blaCTX-M-27, aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, sul2, tet(A)/FII (F2:A-:B-, 68 kb), B/O/K/Z, Col156, Col(BS512) | 2,497 (99.36) | 2,489 (99.04) | cgST67380 |
| 3123885 | 2019 | 30/M | Stool | Israel | ESC-R | SXT, CIP, AZT | ST152 | blaCTX-M-134, aph(6)-ld, mdf(A), mph(A), dfrA1, sul2, tet(A)/FII (F35:A-:B-, 69 kb), B/O/K/Z, Col156, Col(BS512) | 2,489 (99.04) | 2,480 (98.69) | cgST114011 |
| 7103-58g | 2018 | 10/M | Stool | Romania | ESC-S | SXT, CIP, AZT | ST152 | blaTEM-1B, aadA5, aph(3″)-lb, aph(6)-ld, mdf(A), mph(A), erm(B), dfrA1/A17, sul1/2, tet(A)/Col156, Col(BS512) | 2,489 (99.04) | 2,482 (98.77) | cgST107674 |
| 7103-28g | 2018 | 50/M | Stool | Romania | ESC-S | SXT, CIP, AZT | ST152 | blaTEM-1B, aadA5, aph(3″)-lb, aph(6)-ld, mdf(A), mph(A), erm(B), dfrA1/A17, sul1/2, tet(A)/Col156, Col(BS512) | 2,490 (99.08) | 2,481 (98.73) | cgST107674 |
| 6407-57 | 2017 | 40/M | Stool | Local | ESC-S | SXT, CIP, AZT | ST152 | blaTEM-1B, aadA5, aph(3″)-lb, aph(6)-ld, mdf(A), mph(A), erm(B), dfrA1/A17, sul1/2, tet(A)/I1, Col156, Col(BS512) | 2,492 (99.16) | 2,484 (98.85) | cgST108068 |
| 6110-62 | 2016 | 60/F | Stool | Brazil | ESC-S | SXT | ST152 | blaTEM-1B, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA8, sul2/FII, Col156, Col(BS512) | 2,499 (99.44) | 2,492 (99.16) | cgST108083 |
| 6105-15 | 2016 | 35/M | Stool | Egypt | ESC-S | SXT | ST152 | aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, sul2, tet(A)/FII, Col156, Col(BS512) | 2,497 (99.36) | 2,487 (98.97) | cgST37499 |
| 6101-40 | 2016 | 40/F | Stool | Western Africa | ESC-S | SXT | ST152 | aadA1, aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, sul2, tet(A)/FII, Col156, Col(BS512) | 2,492 (99.16) | 2,479 (98.65) | cgST98334 |
| 6412-75 | 2017 | 50/M | Blood, stool | India | ESC-S | CIP | ST152 | mdf(A), dfrA1/Col156, Col(BS512) | 2,495 (99.28) | 2,487 (98.97) | cgST101592 |
| 6502-32 | 2017 | 40/F | Stool | Dominican Republic | ESC-S | SXT | ST152 | aph(3″)-lb, aph(6)-ld, mdf(A), dfrA1, sul2, tet(A)/I1, Col156, Col(BS512) | 2,494 (99.24) | 2,484 (98.85) | cgST108763 |
| 7111-23 | 2019 | 25/F | Stool | Philippines | ESC-S | ST152 | sul2, dfrA14, aph(3″)-lb, aph(6)-ld, mdf(A)/I1, FII, Col156 | 2,495 (99.28) | 2,481 (98.73) | cgST108909 | |
| 7109-28 | 2019 | 30/M | Stool | Colombia | ESC-S | SXT | ST152 | aadA1, aph(3″)-lb, aph(6)-ld, sul2, mdf(A), dfrA1, qnrB19, qnrB5, qnrB81, tet(A)/I1, Col156 | 2,499 (99.44) | 2,486 (98.93) | cgST109254 |
| 7001-38 | 2018 | 50/F | Stool | Local | ESC-S | SXT | ST152 | aadA1, mdf(A), dfrA1/Col156, Col(BS512) | 2,503 (99.60) | 2,494 (99.24) | cgST113036 |
Age and sex are based on the information provided to the clinical laboratory analyzing routine samples. Age has been approximated at ±5 years. The origin of infection has been attributed to a foreign country if symptoms (i.e., diarrhea) occurred during or after the patients returned from a specific country.
Groups are based on the MICs obtained with the Sensititre GNX2F panel and interpreted according to the EUCAST 2019 criteria. Only key antibiotics to which nonsusceptibility is shown are reported (see Table S1 in the supplemental material for full MIC results).
Performed by implementing the tools of the Center for Genomic Epidemiology (CGE), specifically, MLST (v2.0; E. coli scheme 1), ResFinder (v3.2), PlasmidFinder (v2.0), and pMLST (v2.0), when available. The main bla genes and the associated plasmids carrying these genes are indicated in bold.
Core-genome results obtained with cgMLSTFinder (v1.1).
Strain LC-1477-18 was detected in Italy (7). It was added to the analysis as a control.
ST1503 is a single allele variant of ST152.
The patients from whom strains 7103-58 and 7103-28 were isolated are relatives.
M, male; F, female; ESC-R, extended-spectrum cephalosporin resistant; ESC-S, extended-spectrum cephalosporin susceptible; SXT, trimethoprim-sulfamethoxazole; CIP, ciprofloxacin; AZT, azithromycin; ST, sequence type; cgST, core-genome sequence type; NA, not available.