Characterization of Escherichia coli from Water and Food Sold on the Streets of Maputo: Molecular Typing, Virulence Genes, and Antibiotic Resistance
Abstract
:1. Introduction
2. Material and Methods
2.1. E. coli Isolates
2.2. Pulsed Field Gel Electrophoresis (PFGE)
2.3. Multiplex-PCR (MPCR) for Identification of Virulence and Antibiotic Resistance Genes
2.4. Antibiotic Susceptibility Profile
2.5. Data Analysis and Interpretation
3. Results
3.1. Pulse Typing and the Presence of Virulence Genes
3.2. Antibiotic Resistance Profiles
3.3. Antibiotic Resistance Genes
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Primer Name | Sequence | Target Gene/ (Virulence Factor) | Size (bp) | Reference |
---|---|---|---|---|
LT—1: For | ATT TAC GGC GTT ACT ATC CTC | lt (LT) | 280 | [25] |
LT—2: Rev | TTT TGG TCT CGG TCA GAT ATG | |||
ST—PR1: For | TCT GTA TTG TCT TTT TCA CC | st (ST) | 195 | [26] |
ST—PR2: Rev | TTA ATA GCA CCC GGT ACA AGC | |||
EAE 23F: For | ACC AGA TCG TAA CGG CTG CCT | eae (Intimin) | 499 | |
EAE 25R: Rev | AGT TTG GGT TAT AAC GTC TTC ATT G | |||
ES—151: For | GAG CGA AAT AAT TTA TAT GT | stx (VT) | 323 | [27] |
ES—149: Rev | CGA AAT CCC CTC TGT ATT TGC C | |||
EAST 11: For | CCA TCA ACA CAG TAT ATC CGA | astA (EAST1) | 114 | [28] |
EAST 11: Rev | GGT CGC GAG TGA CGG CTT TGT |
Primer Name | Sequence | Target Gene | Size (bp) | Final Concentration | Ref |
---|---|---|---|---|---|
MultiTSO-T-For | CATTTCCGTGTCGCCCTTATTC | TEM variantes (TEM-1 and TEM-2) | 800 | 0.4 µM | [29] |
MultiTSO-T-Rev | CGTTCATCCATAGTTGCCTGAC | ||||
MultiTSO-S-For | AGCCGCTTGAGCAAATTAAAC | SHV variants (including SHV-1) | 713 | 0.4 µM | |
MultiTSO-S-Rev | ATCCCGCAGATAAATCACCAC | ||||
MultiTSO-O-For | GGCACCAGATTCAACTTTCAAG | OXA-variants (OXA-1, OXA-4, OXA-30) | 564 | 0.4 µM | |
MultiTSO-O-Rev | GACCCCAAGTTTCCTGTAAGTG | ||||
CTX-MGrp1—For | TTAGGAARTGTGCCGCTGYA | Multi CTX-MGrp1 (CTX-M-1, CTX-M-3, CTX-M-15) | 688 | 0.4 µM | |
CTX-MGrp1—Rev | CGATATCGTTGGTGGTRCCAT | ||||
CTX-MGrp9—For | TCAAGCCTGCCGATCTGGT | CTX-M Group 9 (CTX-M-9, CTX-M-14) | 561 | 0.4 µM | |
CTX-MGrp9—Rev | TGATTCTCGCCGCTGAAG | ||||
MultiACC-For | CACCTCCAGCGACTTGTTAC | ACC variants (ACC-1 and ACC-2) | 346 | 0.2 µM | [29] |
MultiACC-Rev | GTTAGCCAGCATCACGATCC | ||||
MultiFOX-For | CTACAGTGCGGGTGGTTT | FOX variants (FOX-1 to FOX-5) | 162 | 0.5 µM | |
MultiFOX-Rev | CTATTTGCGGCCAGGTGA | ||||
MultiMOX_For | GCAACAACGACAATCCATCCT | MOX variants (MOX-1, MOX-2, CMY-1, CMY-8 to CMY-11, and CMY-19) | 895 | 0.2 µM | |
MultiMOX_Rev | GGGATAGGCGTAACTCTCCCAA | ||||
MultiCIT-For | CGAAGAGGCAATGACCAGAC | CIT variants (LAT-1 to 3, BIL-1, CMY-2 to 7, CMY-12 to -18, and CMY-21 -23) | 538 | 0.3 µM | |
MultiCIT-Rev | ACGGACAGGGTTAGGATAGY | ||||
MultiDHA_For | TGATGGCACAGCAGGATATTC | DHA variants | 997 | 0.5 µM | |
MultiDHA-Rev | GCTTTGACTCTTTCGGTATTCG | ||||
Tetracyclines (A)-For | GCTACATCCTGCTTGCCTTC | tetA | 210 | 1 µM | [30] |
Tetracyclines (A)-Rev | CATAGATCGCCGTGAAGAGG | ||||
Tetracyclines (B)-For | TTGGTTAGGGGCAAGTTTTG | tetB | 659 | 0.25 µM | |
Tetracyclines (B)-Rev | GTAATGGGCCAATAACACCG | ||||
Tetracyclines (M)-For | GTGGACAAAGGTACAACGAG | tetM | 406 | 0.5 µM | |
Tetracyclines (M)-Rev | CGGTAAAGTTCGTCACACAC | ||||
Sulphonamides 1-For | CGGCGTGGGCTACCTGAACG | sul1 | 433 | 0.4 µM | [30] |
Sulphonamides 1-Rev | GCCGATCGCGTGAAGTTCCG | ||||
Sulphonamides 2-For | GCGCTCAAGGCAGATGGCATT | sul2 | 293 | 0.4 µM | |
Sulphonamides 2-Rev | GCGTTTGATACCGGCTCCCGT | ||||
Sulphonamides 3-For | GAGCAAGATTTTGGAATCG | sul3 | 790 | 0.4 µM | |
Sulphonamides 3-Rev | CATCTGCAGCTAACCTAGGGCTTTGGA |
Group | Antibiotic | RTE Street Food (n = 31) | Water (n = 28) | ||
---|---|---|---|---|---|
Susceptible | Resistant | Susceptible | Resistant | ||
ß-lactams | AMX (10 μg) | 25 (80.6%) | 6 (19.4%) | 18 (64.3%) | 10 (35.7%) |
AMC (20/10 μg) | 27 (87.1%) | 4 (12.9%) | 24 (85.7%) | 4 (14.3%) | |
CAZ (30 μg) | 25(80.6%) | 6 (19.4%) | 25 (89.3%) | 3 (10.7%) | |
IPM (10 μg) | 20 (64.5%) | 11 (35.5%) | 17 (60.7%) | 11 (39.3%) | |
CPO (30μg) | 31(100%) | 0 | 28 (100%) | 0 | |
ATM (30 μg) | 31(100%) | 0 | 27 (96.4%) | 1 (3.6%) | |
FOX (30 μg) | 31(100%) | 0 | 23 (81.1%) | 5 (17.8%) | |
AMP (10 μg) | 24 (77.4%) | 7 (22.6%) | 15 (53.6%) | 13 (46.4%) | |
CTX (30 μg) | 29 (93.5%) | 2 (6.5%) | 25 (89.3%) | 3 (10.7%) | |
Non-ß-lactams | CHL (30 μg) | 27(87.1%) | 4 (12.9%) | 22 (78.6%) | 6 (21.4%) |
TET (30 μg) | 13 (41.9%) | 18 (58.1%) | 14 (50%) | 14 (50%) | |
GEN (10 μg) | 29 (93.5%) | 2 (6.5%) | 25 (89.3%) | 3 (10.7%) | |
SXT (23.75/1.25 μg) | 28 (90.3%) | 3 (9.7%) | 17 (60.7%) | 11 (39.3%) | |
AZM (15 μg) | 30 (96.8%) | 1 (3.2%) | 24 (85.7%) | 4 (14.3%) | |
CIP (5 μg) | 31 (100%) | 0 | 28 (100%) | 0 |
Type of Resistance | Group of Antibiotics | Number of Isolates | |
---|---|---|---|
RTE Street Food | Drinking Water | ||
Multi-resistant | AMX, AMC, CAZ, AMP, CHL, SXT | - | 1 (4.5%) |
IPM, CHL, TET, AZM | - | 1 (4.5%) | |
AMX, FOX AMP, TET, SXT | - | 1 (4.5%) | |
IPM, GEN, SXT | - | 1 (4.5%) | |
TET, GEN, SXT | - | 1 (4.5%) | |
AMX, AMC, IPM, FOX, AMP, GEN, SXT, AMZ | - | 1 (4.5%) | |
AMX, AMC, CAZ, AMP, CHL, GEN, SXT | 1 (3.8%) | - | |
AMX, AMP, CHL, SXT | - | 1 (4.5%) | |
AMX, AMC, AMP, CHL, TET, SXT | 1 (3.8%) | - | |
AMP, TET, AZM | 1 (3.8%) | - | |
AMX, AMP, TET, SXT | - | 1 (4.5%) | |
AMX, AMP, TET, AZM | 1 (3.8%) | - | |
AMX, AMC, IPM, FOX, AMP, TET, GEN, SXT | - | 1 (4.5%) | |
AMX, CAZ, IPM, FOX, AMP, CHL, TET, AZM | - | 1 (4.5%) | |
AMX, AMC, AMP, CHL, SXT | 1 (3.8%) | - | |
Total | 5 (19.2%) | 10 (45.5%) | |
Non-multi resistant | CTX, TET | - | 1 (4.5%) |
IPM, AMP, CTX, TET | - | 1 (4.5%) | |
IPM, AMP, TET | - | 1 (3.6%) | |
CAZ, IPM, TET | 1 (3.8%) | - | |
AMX, CAZ, IMP, ATM, FOX, AMP, CTX, CHL | - | 1 (4.5%) | |
AMX, AMC, AMP, TET | - | 1 (4.5%) | |
AMX, IPM, AMP, TET | 1 (3.4%) | - | |
IPM, TET | 2 (7.7%) | - | |
IPM, CPO | 1 (3.8%) | - | |
TET, SXT | - | 1 (4.5%) | |
SXT | - | 1 (4.5%) | |
AMX, AMP, TET | - | 1 (4.5%) | |
TET | 7 (27%) | - | |
AMP, TET, AZM | 1 (3.8%) | - | |
TET, SXT | - | 1 (4.5%) | |
CAZ, GEN | 1 (3.8%) | - | |
AMP, TET | - | 1 (4.5%) | |
AMP, CTX | 1 (3.8%) | - | |
TET, GEN | 1 (3.8%) | - | |
CAZ | 1 (3.8%) | - | |
IMP | 3 (11.5%) | 1 (4.5%) | |
AMX, IPM, AMP, TET | 1 (3.8%) | - | |
CHL | - | 1 (4.5%) | |
Total | 21 (80.8%) | 12 (54.5%) |
Group | Subgroup | Antibiotic Resistance Gene Variants | Frequency | ||
---|---|---|---|---|---|
RTE Street Food | Water | Total | |||
ß-lactams | ESBL | blatem variants | 6 (15.8%) | 7 (17.5%) | 13 (16.7%) |
blaoxa variants | 0 | 4 (10%) | 4 (5.1%) | ||
blashv variants | 9 (23.7%) | 6 (15%) | 15 (33.3%) | ||
MCTX-M Group 1 variants | 1 (2.6%) | 2 (5%) | 3 (3.8%) | ||
MCTX-M Group 9 variants | 6 (15.8%) | 4 (10%) | 10 (12.8%) | ||
Total ESBL genes | 22 (57.9%) | 23 (57.5%) | 45 (57.7%) | ||
ß-lactams ampC | ACC variants | 9 (23.7%) | 5 (12.5%) | 14 (17.9%) | |
FOX variants | 7 (18.4%) | 4 (10%) | 11 (14.1%) | ||
MOX variants | 0 | 0 | 0 | ||
CIT variants | 0 | 8 (20%) | 8 (10.3%) | ||
DHA variants | 0 | 0 | 0 | ||
Total ampC genes | 16 (42.1%) | 17 (42.5%) | 33 (42.3%) | ||
Total ß-lactam coding genes | 38 (48.7%) | 40 (51.3%) | 78 (100%) | ||
non-ß-lactams | Tetracyclines | tet-A | 15 (71.4%) | 4 (23.5%) | 19 (50%) |
tet-B | 0 | 0 | 0 | ||
tet-M | 1 (4.8%) | 0 | 1 (2.6%) | ||
Total-TET genes | 16 (76.2%) | 4 (23.5%) | 20 (52.6%) | ||
Sulphonamides | sul-1 | 0 | 0 | 0 | |
sul-2 | 3 (14.3%) | 9 (52.9%) | 11 (28.9%) | ||
sul-3 | 2 (9.5%) | 4 (23.5%) | 6 (15.8%) | ||
Total-sul genes | 5 (23.8%) | 13 (76.5%) | 18 (47.4%) | ||
Total non-ß-lactams | 21 (55.3%) | 17 (44.7%) | 38 (100%) |
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Salamandane, A.; Alves, S.; Chambel, L.; Malfeito-Ferreira, M.; Brito, L. Characterization of Escherichia coli from Water and Food Sold on the Streets of Maputo: Molecular Typing, Virulence Genes, and Antibiotic Resistance. Appl. Microbiol. 2022, 2, 133-147. https://doi.org/10.3390/applmicrobiol2010008
Salamandane A, Alves S, Chambel L, Malfeito-Ferreira M, Brito L. Characterization of Escherichia coli from Water and Food Sold on the Streets of Maputo: Molecular Typing, Virulence Genes, and Antibiotic Resistance. Applied Microbiology. 2022; 2(1):133-147. https://doi.org/10.3390/applmicrobiol2010008
Chicago/Turabian StyleSalamandane, Acácio, Suse Alves, Lélia Chambel, Manuel Malfeito-Ferreira, and Luísa Brito. 2022. "Characterization of Escherichia coli from Water and Food Sold on the Streets of Maputo: Molecular Typing, Virulence Genes, and Antibiotic Resistance" Applied Microbiology 2, no. 1: 133-147. https://doi.org/10.3390/applmicrobiol2010008
APA StyleSalamandane, A., Alves, S., Chambel, L., Malfeito-Ferreira, M., & Brito, L. (2022). Characterization of Escherichia coli from Water and Food Sold on the Streets of Maputo: Molecular Typing, Virulence Genes, and Antibiotic Resistance. Applied Microbiology, 2(1), 133-147. https://doi.org/10.3390/applmicrobiol2010008