Diarrheagenic Escherichia coli in Stool Specimens Collected from Patients Attending Primary Healthcare Facilities in Ethiopia: Whole-Genome Sequencing-Based Molecular Characterization
Abstract
:1. Introduction
2. Results
2.1. Whole-Genome Sequencing of DEC Isolates
2.2. Serotypes, Phylogenetic Groups, and Multilocus Sequence Typing of DEC Isolates
2.3. Virulence-Associated Genes of DEC Isolates
2.4. Antimicrobial Resistance Genes in DEC Isolates
2.5. Plasmids and Other Mobile Genetic Elements
3. Discussion
4. Materials and Methods
4.1. Bacterial Isolates
4.2. DNA Extraction and PCR Detection of E. coli Pathotypes Genes
4.3. Whole-Genome Sequencing, Raw Data Pre-Processing, De Novo Assembly and Quality Control
4.4. Phylogenetic Groups, In Silico Multilocus Sequence Typing, and In Silico Serotyping
4.5. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Characteristics | Number of DEC Isolates (%) | |||
---|---|---|---|---|
EPEC (n = 10) | EAEC (n = 6) | ETEC (n = 5) | STEC (n = 3) | |
Study site | ||||
Addis Ababa (n = 12) | 4 (16.7) | 3 (12.5) | 2 (8.3) | 3 (12.5) |
Hossana (n = 12) | 6 (25) | 3 (12.5) | 3 (12.5) | 0 |
Sex | ||||
Male (n = 10) | 6 (25.0) | 3 (12.5) | 0 | 1 (4.2) |
Female (n = 14) | 4 (16.7) | 3 (12.5) | 5 (20.8) | 2 (8.3) |
Participants | ||||
Diarrheic (n = 14) | 7 (29.2) | 3 (12.5) | 4 (16.7) | 0 |
Non-diarrheic (n = 10) | 3 (12.5) | 3 (12.5) | 1 (4.2) | 3 (12.5) |
Age group | ||||
0–4 (n = 3) | 2 (8.3) | 0 | 1 (4.2) | 0 |
5–9 (n = 2) | 1 (4.2) | 1 (8.3) | 0 | 0 |
10–14 (n = 3) | 2 (8.3) | 0 | 0 | 1 (4.2) |
15–19 (n = 2) | 0 | 1 (4.2) | 1 (4.2) | 0 |
20–45 (n = 11) | 5 (20.8) | 3 (12.5) | 2 (8.3) | 1 (4.2) |
46–65 (n = 3) | 0 | 1 (4.2) | 1 (4.2) | 1 (4.2) |
Pathotype as Determined by WGS | Phylogroup | ST | Serotype | Pathotype Specific Virulence Genes |
---|---|---|---|---|
EPEC | A | 10 | O90:H40 | eae-g02-θ |
A | 10 | O90:H40 | eae-g02-θ | |
A | 382 | H5 | eae-e08-π | |
B1 | 40 | O21:H21 | eae-b01a-β | |
B1 | 517 | O111:H19 | eae-e02-ε | |
B1 | 517 | H19 | eae-e02-ε | |
B1 | 616 | H21 | eae-e06-η | |
B1 | 4038 | O93:H28 | eae-e06-η | |
B2 | 2346 | O142:H34 | eae-a01-α | |
E | 8508 | O136:H49 | eae-g02-θ | |
EAEC | A | 10 | O65:H12 | aggR |
A | 34 | O99:H33 | aggR | |
B1 | 295 | O171:H5 | aggR | |
B1 | 678 | O104:H4 | aggR | |
B1 | 1136 | O59:H19 | aggR | |
B1 | 1136 | O167:H19 | aggR | |
ETEC | A | 10 | O159:H21 | estah-STa3 |
A | 1564 | H21 | estah-STa3 | |
B1 | 155 | O58:H51 | eltIAB-8 | |
B1 | 314 | O112ab:H21 | eltIAB-11 | |
B1 | 314 | O112ab:H21 | eltIAB-11 | |
STEC | B1 | 101 | O117:H12 | stx1 (stx1a) |
B1 | 155 | H25 | stx2 (stx2c) | |
B1 | 737 | O81:H21 | stx1 (stx1c) |
Virulence-Associated Genes and Their Encoded Proteins/Functions | Prevalence in Each Pathotypes N (%), N = 24 | |||||
---|---|---|---|---|---|---|
EPEC (n = 10) | EAEC (n = 6) | ETEC (n = 5) | STEC (n = 3) | |||
Adhesins | aap | Dispersin, antiaggregation protein | 0 | 6 (25) | 0 | 0 |
afaA | Transcriptional regulator | 1 (4.2) | 0 | 0 | 0 | |
afaC | Outer membrane usher protein | 1 (4.2) | 0 | 0 | 0 | |
afaD | Afimbrial adhesion | 1 (4.2) | 3 (12.5) | 0 | 0 | |
agg3A | AAF/III major fimbrial subunit | 0 | 3 (12.5) | 0 | 0 | |
agg3B | AAF/III minor adhesin | 0 | 3 (12.5) | 0 | 0 | |
agg3C | Usher, AAF/III assembly unit | 0 | 3 (12.5) | 0 | 0 | |
agg3D | Chaperone, AAF/III assembly unit | 0 | 3 (12.5) | 0 | 0 | |
agg4A | AAF/IV major fimbrial subunit | 0 | 2 (8.3) | 0 | 0 | |
agg4C | Usher, AAF/IV assembly unit | 0 | 2 (8.3) | 0 | 0 | |
aggA | AAF/I major fimbrial subunit | 0 | 1 (4.2) | 0 | 0 | |
aggC | Usher, AAF/I assembly unit | 0 | 1 (4.2) | 0 | 0 | |
aggD | Chaperone, AAF/I assembly unit | 0 | 1 (4.2) | 0 | 0 | |
aggR | AraC transcriptional activator | 0 | 6 (25) | 0 | 0 | |
cif | Type III secreted effector | 4 (16.7) | 0 | 0 | 0 | |
csgA | Curli major subunit CsgA | 9 (37.5) | 6 (25) | 5 (20.8) | 2 (8.3) | |
cswR | CS12 Transcriptional activator | 0 | 0 | 2 (8.3) | 0 | |
eaeA | Intimin | 10 (41.7) | 0 | 0 | 0 | |
efa1 | EHEC factor for adherence; lymphostatin Efa1-LifA | 1 (4.2) | 0 | 0 | 0 | |
etpB | EtpB Nonfimbrial adhesin/TPS transporter | 0 | 0 | 1 (4.2) | 0 | |
faeC | F4 (K88) Minor fimbrial subunit | 0 | 0 | 0 | 1 (4.2) | |
fdeC | Intimin-like adhesin FdeC | 5 (20.8) | 2 (8.3) | 3 (12.5) | 3 (12.5) | |
fimH | Type 1 fimbriae | 8 (33.3) | 5 (20.8) | 4 (16.7) | 3 (12.5) | |
hra | Heat-resistant agglutinin | 0 | 2 (8.3) | 1 (4.2) | 0 | |
iha | Adherence protein | 0 | 2 (8.3) | 0 | 3 (12.5) | |
lpfA | Long polar fimbriae | 4 (16.7) | 4 (16.7) | 3 (12.5) | 3 (12.5) | |
nlpI | Lipoprotein NlpI precursor | 10 (41.7) | 6 (25) | 5 (20.8) | 3 (12.5) | |
perA | EPEC adherence factor | 1 (4.2) | 0 | 0 | 0 | |
tir | Translocated intimin receptor protein | 9 (37.5) | 0 | 0 | 0 | |
yehA | Outer membrane lipoprotein, YHD fimbrial cluster | 6 (25) | 3 (12.5) | 4 (16.7) | 2 (8.3) | |
yehB | Usher, YHD fimbrial cluster | 8 (33.3) | 6 (25) | 5 (20.8) | 3 (12.5) | |
yehC | Chaperone, YHD fimbrial cluster | 8 (33.3) | 6 (25) | 5 (20.8) | 3 (12.5) | |
yehD | Major pilin subunit, YHD fimbrial cluster | 8 (33.3) | 5 (20.8) | 5 (20.8) | 3 (12.5) | |
yfcV | Fimbrial protein | 1 (4.2) | 0 | 0 | 0 | |
Protectins | aaiC | Type VI secretion protein | 0 | 3 (12.5) | 0 | 0 |
aar | AggR-activated regulator | 0 | 4 (16.7) | 0 | 0 | |
aatA | Dispersin transporter protein | 0 | 6 (25) | 0 | 0 | |
aamR:FN554766 | Not defined | 0 | 1 (4.2) | 0 | 0 | |
anr | AraC negative regulator | 3 (12.5) | 5 (20.8) | 1 (4.2) | 0 | |
aslA | Arylsulfatase-like protein | 1 (4.2) | 2 (8.3) | 0 | 0 | |
capU | Hexosyltransferase homolog | 2 (8.3) | 3 (12.5) | 1 (4.2) | 0 | |
cba | Colicin B | 0 | 0 | 0 | 1 (4.2) | |
cea | Colicin E1 | 0 | 1 (4.2) | 0 | 0 | |
cia | Colicin Ia | 1 (4.2) | 0 | 0 | 1 (4.2) | |
cib | Colicin Ib | 0 | 0 | 2 (8.3) | 0 | |
cma | Colicin M | 0 | 0 | 0 | 1 (4.2) | |
colE2 | Colicin E2 | 0 | 0 | 0 | 1 (4.2) | |
colE5 | Colicin E5 lysis protein Lys | 0 | 2 (8.3) | 0 | 0 | |
cvaC | Microcin C | 1 (4.2) | 0 | 0 | 0 | |
eilA | Salmonella HilA homolog | 1 (4.2) | 0 | 0 | 0 | |
espA | Type III secretions system | 10 (41.7) | 0 | 0 | 0 | |
espB | Secreted protein B | 1 (4.2) | 0 | 0 | 0 | |
espC | Escherichia coli enterotoxin EspC | 1 (4.2) | 0 | 0 | 0 | |
espF | EPEC secreted protein F; Type III secretion system | 4 (16.7) | 0 | 0 | 0 | |
espI | Serine protease autotransporters of Enterobacteriaceae (SPATE) EspI | 0 | 1 (4.2) | 0 | 1 (4.2) | |
espJ | Prophage-encoded type III secretion system effector | 5 (20.8) | 0 | 0 | 0 | |
espP | Extracellular serine protease plasmid-encoded | 0 | 0 | 0 | 1 (4.2) | |
espY2 | Non-LEE-encoded type III secreted effector | 1 (4.2) | 0 | 0 | 0 | |
etpC | EtpC Glycotransferase | 2 (8.3) | 0 | 0 | 0 | |
etpD | Type II secretion protein EtpD | 1 (4.2) | 0 | 1 (4.2) | 0 | |
etsC | Putative type I secretion outer membrane protein | 1 (4.2) | 0 | 1 (4.2) | 0 | |
gad | Glutamate decarboxylase | 3 (12.5) | 2 (8.3) | 2 (8.3) | 0 | |
hha | Hemolysin expression modulator Hha (previous rmoA) | 5 (20.8) | 1 (4.2) | 0 | 0 | |
iss | Increased serum survival | 4 (16.7) | 2 (8.3) | 1 (4.2) | 2 (8.3) | |
kpsE | Capsule polysaccharide export inner-membrane protein | 0 | 0 | 0 | 1 (4.2) | |
mchB | Precursor of microcin H47 | 0 | 1 (4.2) | 0 | 1 (4.2) | |
mchC | MchC protein | 0 | 1 (4.2) | 0 | 1 (4.2) | |
mchF | ABC transporter protein MchF | 1 (4.2) | 1 (4.2) | 0 | 1 (4.2) | |
mcmA | Microcin M | 0 | 1 (4.2) | 0 | 1 (4.2) | |
neuC | Polysialic acid capsule biosynthesis protein | 0 | 2 (8.3) | 0 | 0 | |
nleB | Non-LEE encoded effector B | 6 (25) | 0 | 0 | 0 | |
ompT | Outer membrane protease (protein protease 7) | 3 (12.5) | 0 | 1 (4.2) | 2 (8.3) | |
ORF3 | Isoprenoid Biosynthesis | 0 | 6 (25) | 0 | 0 | |
ORF4 | Putative isopentenyl-diphosphate delta-isomerase | 0 | 6 (25) | 0 | 0 | |
shiA | Homologue of the Shigella flexneri SHI-2 pathogenicity island gene shiA | 0 | 2 (8.3) | 1 (4.2) | 0 | |
shiB | Homologue of the Shigella flexneri SHI-2 pathogenicity island gene shiB | 1 (4.2) | 3 (12.5) | 0 | 1 (4.2) | |
tia | Tia invasion determinant | 0 | 0 | 0 | 1 (4.2) | |
traJ | Protein TraJ (Positive regulator of conjugal transfer operon) | 4 (16.7) | 3 (12.5) | 3 (12.5) | 0 | |
traT | Outer membrane protein complement resistance | 3 (12.5) | 3 (12.5) | 3 (12.5) | 3 (12.5) | |
tsh | Serine protease autotransporter of Enterobacteriaceae (SPATE)-Immunoglobulin A1 protease- Temperature-sensitive hemagglutinin | 1 (4.2) | 0 | 0 | 0 | |
Iron uptake | aalF | CS23 Minor structural subunit | 0 | 0 | 0 | 1 (4.2) |
chuA | Outer membrane hemin receptor | 2 (8.3) | 0 | 0 | 0 | |
fyuA | Yersiniabactin siderophore receptor | 0 | 3 (12.5) | 0 | 1 (4.2) | |
ireA | Iron-regulated outer membrane protein IreA | 0 | 2 (8.3) | 0 | 0 | |
iroN | Salmochelin siderophore receptor protein | 1 (4.2) | 0 | 0 | 0 | |
irp2 | Yersiniabactin non-ribosomal peptide synthetase | 0 | 2 (8.3) | 0 | 1 (4.2) | |
iucC | Aerobactin synthetase | 1 (4.2) | 4 (16.7) | 0 | 1 (4.2) | |
iutA | Ferric aerobactin receptor | 1 (4.2) | 4 (16.7) | 0 | 1 (4.2) | |
sitA | Iron transport protein | 1 (4.2) | 2 (8.3) | 1 (4.2) | 0 | |
terC | Tellurium ion resistance protein | 9 (37.5) | 6 (25) | 5 (20.8) | 3 (12.5) | |
Toxins | astA | Heat-stable enterotoxin EAST-1 | 1 (4.2) | 4 (16.7) | 4 (16.7) | 0 |
cdt-IIIB | Cytolethal distending toxin III subunit B | 0 | 0 | 0 | 1 (4.2) | |
cnf2 | Cytotoxic necrotizing factor 2 | 0 | 0 | 0 | 1 (4.2) | |
ehxA | Enterohaemolysin | 0 | 0 | 0 | 1 (4.2) | |
eltIAB-8 | Heat-labile enterotoxin LTIh-8 | 0 | 0 | 3 (12.5) | 0 | |
eltIAB-11 | Heat-labile enterotoxin LTIh-11 | |||||
estah-STa3 | Heat-stable enterotoxin STa3 human variant | 0 | 0 | 2 (8.3) | 0 | |
hlyA | Hemolysin A | 1 (4.2) | 0 | 0 | 0 | |
hlyE | Avian E. coli haemolysin | 8 (33.3) | 6 (25) | 4 (16.7) | 3 (12.5) | |
hlyF | Hemolysin F | 1 (4.2) | 0 | 1 (4.2) | 0 | |
pet | Autotransporter enterotoxin | 1 (4.2) | 0 | 0 | 0 | |
pic | Serine protease autotransporter of Enterobacteriaceae (SPATE) Pic | 0 | 2 (8.3) | 0 | 0 | |
sat | Serine protease autotransporter of Enterobacteriaceae (SPATE) Sat | 2 (8.3) | 2 (8.3) | 0 | 0 | |
senB | Plasmid-encoded enterotoxin | 2 (8.3) | 0 | 0 | 0 | |
sigA | Serine protease autotransporter of Enterobacteriaceae (SPATE) Shigella IgA-like protease homologue | 0 | 3 (12.5) | 0 | 0 | |
stx1 | Shiga toxin 1 | 0 | 0 | 0 | 2 (8.3) | |
stx2 | Shiga toxin 2 | 0 | 0 | 0 | 1 (4.2) | |
subA | Subtilase toxin subunit | 0 | 0 | 0 | 1 (4.2) | |
toxB | Toxin B | 1 (4.2) | 0 | 0 | 0 | |
vat | Serine protease autotransporter of Enterobacteriaceae (SPATE) Vat | 0 | 0 | 0 | 1 (4.2) |
Virulence-Associated Genes and Their Encoded Proteins/Functions | Prevalence in Each Phylogenetic Group N (%), N = 24 | |||||
---|---|---|---|---|---|---|
A (n = 7) | B1 (n = 15) | B2 (n = 1) | E (n = 1) | |||
Adhesins | aap | Dispersin, antiaggregation protein | 2 (8.3) | 4 (16.7) | 0 | 0 |
afaA | Transcriptional regulator | 1 (4.2) | 0 | 0 | 0 | |
afaC | Outer membrane usher protein | 1 (4.2) | 0 | 0 | 0 | |
afaD | Afimbrial adhesion | 2 (8.3) | 2 (8.3) | 0 | 0 | |
agg3A | AAF/III major fimbrial subunit | 1 (4.2) | 2 (8.3) | 0 | 0 | |
agg3B | AAF/III minor adhesin | 1 (4.2) | 2 (8.3) | 0 | 0 | |
agg3C | Usher, AAF/III assembly unit | 1 (4.2) | 2 (8.3) | 0 | 0 | |
agg3D | Chaperone, AAF/III assembly unit | 1 (4.2) | 2 (8.3) | 0 | 0 | |
agg4A | AAF/IV major fimbrial subunit | 0 | 2 (8.3) | 0 | 0 | |
agg4C | Usher, AAF/IV assembly unit | 0 | 2 (8.3) | 0 | 0 | |
aggA | AAF/I major fimbrial subunit | 1 (4.2) | 0 | 0 | 0 | |
aggC | Usher, AAF/I assembly unit | 1 (4.2) | 0 | 0 | 0 | |
aggD | Chaperone, AAF/I assembly unit | 1 (4.2) | 0 | 0 | 0 | |
aggR | AraC transcriptional activator | 2 (8.3) | 4 (16.7) | 0 | 0 | |
cif | Type III secreted effector | 2 (8.3) | 1 (4.2) | 0 | 1 (4.2) | |
csgA | Curli major subunit CsgA | 7 (29.2) | 15 (62.5) | 1 (4.2) | 1 (4.2) | |
cswR | CS12 Transcriptional activator | 0 | 2 (8.3) | 0 | 0 | |
eaeA | Intimin | 3 (12.5) | 4 (16.7) | 1 (4.2) | 1 (4.2) | |
efa1 | EHEC factor for adherence; lymphostatin Efa1-LifA | 0 | 1 (4.2) | 0 | 0 | |
etpB | EtpB nonfimbrial adhesin/TPS transporter | 1 (4.2) | 0 | 0 | 0 | |
faeC | F4 (K88) Minor fimbrial subunit | 0 | 1 (4.2) | 0 | 0 | |
fdeC | Intimin-like adhesin FdeC | 0 | 12 (50) | 0 | 1 (4.2) | |
fimH | Type 1 fimbriae | 6 (25) | 13 (54.2) | 0 | 1 (4.2) | |
hra | Heat-resistant agglutinin | 1 (4.2) | 2 (8.3) | 0 | 0 | |
iha | Adherence protein | 0 | 5 (20.8) | 0 | 0 | |
lpfA | Long polar fimbriae | 0 | 14 (58.3) | 0 | 0 | |
nlpI | Lipoprotein NlpI precursor | 6 (25) | 12 (50) | 1 (4.2) | 1 (4.2) | |
perA | EPEC adherence factor | 0 | 0 | 1 (4.2) | 0 | |
tir | Translocated intimin receptor protein | 3 (12.5) | 5 (20.8) | 0 | 1 (4.2) | |
yehA | Outer membrane lipoprotein, YHD fimbrial cluster | 7 (29.2) | 7 (29.2) | 1 (4.2) | 0 | |
yehB | Usher, YHD fimbrial cluster | 5 (20.8) | 15 (62.5) | 1 (4.2) | 1 (4.2) | |
yehC | Chaperone, YHD fimbrial cluster | 5 (20.8) | 15 (62.5) | 1 (4.2) | 1 (4.2) | |
yehD | Major pilin subunit, YHD fimbrial cluster | 5 (20.8) | 14 (58.3) | 1 (4.2) | 1 (4.2) | |
yfcV | Fimbrial protein | 0 | 0 | 1 (4.2) | 1 (4.2) | |
Protectins | aaiC | Type VI secretion protein | 1 (4.2) | 1 (4.2) | 0 | 0 |
aar | AggR-activated regulator | 1 (4.2) | 1 (4.2) | 0 | 0 | |
aatA | Dispersin transporter protein | 1 (4.2) | 2 (8.3) | 0 | 0 | |
aamR:FN554766 | Not defined | 0 | 1 (4.2) | 0 | 0 | |
anr | AraC negative regulator | 4 (16.7) | 2 (8.3) | 0 | 0 | |
aslA | Arylsulfatase-like protein | 1 (4.2) | 0 | 1 (4.2) | 0 | |
capU | Hexosyltransferase homolog | 1 (4.2) | 3 (12.5) | 0 | 0 | |
cba | Colicin B | 0 | 1 (4.2) | 0 | 0 | |
cea | Colicin E1 | 1 (4.2) | 0 | 0 | 0 | |
cia | Colicin Ia | 1 (4.2) | 1 (4.2) | 0 | 0 | |
cib | Colicin Ib | 2 (8.3) | 0 | 0 | 0 | |
cma | Colicin M | 0 | 1 (4.2) | 0 | 0 | |
colE2 | Colicin E2 | 0 | 1 (4.2) | 0 | 0 | |
colE5 | Colicin E5 lysis protein Lys | 0 | 2 (8.3) | 0 | 0 | |
cvaC | Microcin C | 1 (4.2) | 0 | 0 | 0 | |
eilA | Salmonella HilA homolog | 0 | 0 | 0 | 1 (4.2) | |
espA | Type III secretions system | 3 (12.5) | 5 (20.8) | 1 (4.2) | 1 (4.2) | |
espB | Secreted protein B | 0 | 1 (4.2) | 0 | 0 | |
espC | Escherichia coli enterotoxin EspC | 0 | 0 | 1 (4.2) | 0 | |
espF | EPEC secreted protein F; Type III secretion system | 1 (4.2) | 3 (12.5) | 0 | 0 | |
espI | Serine protease autotransporter of Enterobacteriaceae (SPATE) EspI | 1 (4.2) | 1 (4.2) | 0 | 0 | |
espJ | Prophage-encoded type III secretion system effector | 0 | 3 (12.5) | 1 (4.2) | 1 (4.2) | |
espP | Extracellular serine protease plasmid-encoded | 0 | 1 (4.2) | 0 | 0 | |
espY2 | Non-LEE-encoded type III secreted effector | 0 | 0 | 0 | 1 (4.2) | |
etpC | EtpC Glycotransferase | 1 (4.2) | 0 | 0 | 0 | |
etpD | Type II secretion protein EtpD | 1 (4.2) | 1 (4.2) | 0 | 0 | |
etsC | Putative type I secretion outer membrane protein | 1 (4.2) | 0 | 0 | 0 | |
gad | Glutamate decarboxylase | 2 (8.3) | 4 (16.7) | 0 | 0 | |
hha | Hemolysin expression modulator Hha (previous rmoA) | 1 (4.2) | 3 (12.5) | 0 | 1 (4.2) | |
iss | Increased serum survival | 3 (12.5) | 5 (20.8) | 0 | 0 | |
kpsE | Capsule polysaccharide export inner-membrane protein | 0 | 1 (4.2) | 0 | 0 | |
mchB | Precursor of microcin H47 | 0 | 2 (8.3) | 0 | 0 | |
mchC | MchC protein | 0 | 2 (8.3) | 0 | 0 | |
mchF | ABC transporter protein MchF | 1 (4.2) | 2 (8.3) | 0 | 0 | |
mcmA | Microcin M | 0 | 2 (8.3) | 0 | 0 | |
neuC | Polysialic acid capsule biosynthesis protein | 0 | 1 (4.2) | 0 | 0 | |
nleB | Non-LEE encoded effector B | 3 (12.5) | 2 (8.3) | 0 | 1 (4.2) | |
ompT | Outer membrane protease (protein protease 7) | 1 (4.2) | 3 (12.5) | 1 (4.2) | 0 | |
ORF3 | Isoprenoid Biosynthesis | 2 (8.3) | 4 (16.7) | 0 | 0 | |
ORF4 | Putative isopentenyl-diphosphate delta-isomerase | 2 (8.3) | 4 (16.7) | 0 | ||
shiA | Homologue of the Shigella flexneri SHI-2 pathogenicity island gene shiA | 2 (8.3) | 1 (4.2) | 0 | 0 | |
shiB | Homologue of the Shigella flexneri SHI-2 pathogenicity island gene shiB | 1 (4.2) | 4 (16.7) | 0 | 0 | |
tia | Tia invasion determinant | 0 | 1 (4.2) | 0 | 0 | |
traJ | Protein TraJ (Positive regulator of conjugal transfer operon) | 4 (16.7) | 3 (12.5) | 1 (4.2) | 0 | |
traT | Outer membrane protein complement resistance | 3 (12.5) | 6 (25) | 0 | 0 | |
tsh | Serine protease autotransporter of Enterobacteriaceae (SPATE)-Immunoglobulin A1 protease- Temperature-sensitive hemagglutinin | 1 (4.2) | 0 | 0 | 0 | |
Iron uptake | aalF | CS23 Minor structural subunit | 0 | 1 (4.2) | 0 | 0 |
chuA | Outer membrane hemin receptor | 0 | 0 | 1 (4.2) | 1 (4.2) | |
fyuA | Yersiniabactin siderophore receptor | 2 (8.3) | 2 (8.3) | 0 | 0 | |
ireA | Iron-regulated outer membrane protein IreA | 0 | 1 (4.2) | 0 | 0 | |
iroN | Salmochelin siderophore receptor protein | 1 (4.2) | 0 | 0 | 0 | |
irp2 | Yersiniabactin non-ribosomal peptide synthetase | 1 (4.2) | 2 (8.3) | 0 | 0 | |
iucC | Aerobactin synthetase | 1 (4.2) | 4 (16.7) | 0 | 0 | |
iutA | Ferric aerobactin receptor | 1 (4.2) | 4 (16.7) | 0 | 0 | |
sitA | Iron transport protein | 1 (4.2) | 1 (4.2) | 0 | 0 | |
terC | Tellurium ion resistance protein | 7 (29.2) | 15 (62.5) | 1 (4.2) | 1 (4.2) | |
Toxins | astA | Heat-stable enterotoxin EAST-1 | 3 (12.5) | 4 (16.7) | 0 | 0 |
cdt-IIIB | Cytolethal distending toxin III subunit B | 0 | 1 (4.2) | 0 | 0 | |
cnf2 | Cytotoxic necrotizing factor 2 | 0 | 1 (4.2) | 0 | 0 | |
ehxA | Enterohaemolysin | 0 | 1 (4.2) | 0 | 0 | |
eltIAB-8 | Heat-labile enterotoxin LTIh-8 | 0 | 1 (4.2) | 0 | 0 | |
eltIAB-11 | Heat-labile enterotoxin LTIh-11 | 0 | 2 (8.3) | 0 | 0 | |
estah-STa3 | Heat-stable enterotoxin STa3 human variant | 2 (8.3) | 0 | 0 | 0 | |
hlyA | Hemolysin A | 0 | 1 (4.2) | 0 | 0 | |
hlyE | Avian E. coli haemolysin | 6 (25) | 15 (62.5) | 0 | 1 (4.2) | |
hlyF | Hemolysin F | 1 (4.2) | 0 | 0 | 0 | |
pet | Autotransporter enterotoxin | 0 | 1 (4.2) | 0 | 0 | |
pic | Serine protease autotransporter of Enterobacteriaceae (SPATE) Pic | 1 (4.2) | 1 (4.2) | 0 | 0 | |
sat | Serine protease autotransporter of Enterobacteriaceae (SPATE) Sat | 1 (4.2) | 3 (12.5) | 0 | 0 | |
senB | Plasmid-encoded enterotoxin | 0 | 2 (8.3) | 0 | 0 | |
sigA | Serine protease autotransporter of Enterobacteriaceae (SPATE), Shigella IgA-like protease homologue | 0 | 2 (8.3) | 0 | 0 | |
stx1 | Shiga toxin 1 | 0 | 2 (8.3) | 0 | 0 | |
stx2 | Shiga toxin 2 | 0 | 1 (4.2) | 0 | 0 | |
subA | Subtilase toxin subunit | 0 | 1 (4.2) | 0 | 0 | |
toxB | Toxin B | 0 | 0 | 1 (4.2) | 0 | |
vat | Serine protease autotransporter of Enterobacteriaceae (SPATE) Vat | 0 | 1 (4.2) | 0 | 0 |
Antimicrobial Class | Antimicrobial Resistance Gene (ARG) | Prevalence N (%) | Conferring Resistance to | Found in DEC Pathotype |
---|---|---|---|---|
β-lactams | blaTEM-1B | 12 (50) | amoxicillin, ampicillin, piperacillin, ticarcillin, cephalothin | EPEC, EAEC, ETEC |
blaTEM-122 | 1 (4.2) | amoxicillin, amoxicillin + clavulanic acid, ampicillin, ampicillin + clavulanic acid, piperacillin, piperacillin + tazobactam, ticarcillin, ticarcillin + clavulanic acid | ETEC | |
blaTEM-163 | 1 (4.2) | amoxicillin, amoxicillin + clavulanic acid, ampicillin, ampicillin + clavulanic acid, piperacillin, piperacillin + tazobactam, ticarcillin, ticarcillin + clavulanic acid | EPEC | |
blaCTX-M-3 | 1 (4.2) | amoxicillin, ampicillin, cefepime, cefotaxime, ceftazidime, piperacillin, aztreonam, ticarcillin, ceftriaxone | EPEC | |
blaCTX-M-15 | 2 (8.3) | amoxicillin, ampicillin, cefepime, cefotaxime, ceftazidime, piperacillin, aztreonam, ticarcillin, ceftriaxone | ETEC | |
Sulfonamides | sul1 | 2 (8.3) | sulfamethoxazole | EPEC |
sul2 | 8 (33.3) | sulfamethoxazole | EPEC, EAEC, ETEC | |
Aminoglycosides | aph(6)-Id | 6 (25) | streptomycin | EPEC, ETEC |
aph(3″)-Ib | 6 (25) | streptomycin | EPEC, ETEC | |
aac(3)-IIa | 1 (4.2) | gentamicin, tobramycin | EPEC | |
aadA1 | 2 (8.3) | streptomycin, spectinomycin | EAEC, ETEC | |
aadA5 | 1 (4.2) | streptomycin, spectinomycin | EPEC | |
aadA24 | 1 (4.2) | streptomycin, spectinomycin | EPEC | |
Tetracyclines | tet(A) | 4 (16.7) | tetracycline, doxycycline | EPEC |
tet(B) | 3 (12.5) | tetracycline, doxycycline, minocycline | EPEC, ETEC | |
Quinolones | qnrS1 | 2 (8.3) | ciprofloxacin | ETEC |
Trimethoprim | dfrA1 | 2 (8.3) | trimethoprim | EAEC, ETEC |
dfrA7 | 1 (4.2) | trimethoprim | EPEC | |
dfrA8 | 3 (12.5) | trimethoprim | EPEC, EAEC, ETEC | |
dfrA14 | 1 (4.2) | trimethoprim | EPEC | |
dfrA15 | 1 (4.2) | trimethoprim | ETEC | |
dfrA17 | 1 (4.2) | trimethoprim | EPEC | |
Macrolide/lincosamide/streptogramin (MLS) group | mph(A) | 6 (25) | erythromycin, azithromycin, spiramycin, telithromycin | EPEC, EAEC, ETEC |
erm(B) | 1 (4.2) | lincomycin, clindamycin, erythromycin, quinupristin, pristinamycin IA, virginiamycin S | EAEC |
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Wolde, D.; Eguale, T.; Medhin, G.; Haile, A.F.; Alemayehu, H.; Mihret, A.; Pirs, M.; Strašek Smrdel, K.; Avberšek, J.; Kušar, D.; et al. Diarrheagenic Escherichia coli in Stool Specimens Collected from Patients Attending Primary Healthcare Facilities in Ethiopia: Whole-Genome Sequencing-Based Molecular Characterization. Int. J. Mol. Sci. 2024, 25, 10251. https://doi.org/10.3390/ijms251910251
Wolde D, Eguale T, Medhin G, Haile AF, Alemayehu H, Mihret A, Pirs M, Strašek Smrdel K, Avberšek J, Kušar D, et al. Diarrheagenic Escherichia coli in Stool Specimens Collected from Patients Attending Primary Healthcare Facilities in Ethiopia: Whole-Genome Sequencing-Based Molecular Characterization. International Journal of Molecular Sciences. 2024; 25(19):10251. https://doi.org/10.3390/ijms251910251
Chicago/Turabian StyleWolde, Deneke, Tadesse Eguale, Girmay Medhin, Aklilu Feleke Haile, Haile Alemayehu, Adane Mihret, Mateja Pirs, Katja Strašek Smrdel, Jana Avberšek, Darja Kušar, and et al. 2024. "Diarrheagenic Escherichia coli in Stool Specimens Collected from Patients Attending Primary Healthcare Facilities in Ethiopia: Whole-Genome Sequencing-Based Molecular Characterization" International Journal of Molecular Sciences 25, no. 19: 10251. https://doi.org/10.3390/ijms251910251