Submitted:
26 April 2024
Posted:
28 April 2024
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Abstract
Keywords:
1. Introduction
2. Materials and Methods
2.1. Ethical Approval
2.2. Collection, Processing and Transportation of Sample
2.3. Isolation and Purification of E. coli
2.4. MALDI-TOF
2.5. VAGs-Based Detection
2.6. Antibiotic Susceptibility Testing
2.7. Phenotypic Confirmation of Colistin Resistance
2.8. CarbaNPCLSI Test
2.9. Molecular Characterization of ARGs
2.10. O Typing
2.11. Statistical Analysis
3. Results
3.1.1. Distribution of E. coli from Various Food Origin
3.1.2. Distribution of NON-O157 STEC among Various Sample Sources
3.1.3. Distribution of Non-O157 STEC Co-Harboring blaNMD-1-1 & mcr-1 among Various Sample Sources
3.1.4. VAGs Detection
- (a)
- Heat map showing the distribution of five major categories of food specimen from various food origin showing in coloured boxes on the right side, along with Antibiotic resistance genes including ESBLs, MBLs, qnrs, sul, tet, mcr (1,11) and fos showing in colored boxes on right size. These genes were grouped as low, intermediate and high frequency.
- (b)
- Heat map showing the placement of virulence genes associated with Fimbrae, mobility, toxin and iron uptake etc. in E. coli isolates from various food groups mainly livestock (mutton, beef, veal), poultry (chicken meat, cloacal/nasal swabs & dropping), environment (slaughter house & transport means), and from dairy (raw milk & cheese) shown as low, intermediate and high on the right side.
- (c)
- Heat map showing Co-existence of NDM and mcr-1 with VRGs based E. coli detection as in this case VRGs detected mainly from livestock (mutton, beef, veal), poultry (chicken meat, cloacal/nasal swabs & dropping) and one from environmental sample (slaughter house) show high, low and intermediate values along with co-occurrence of ARGs (NDM & mcr-1).
3.1.5. Resistance Profiling of the Isolates
- (a)
- Scatter plot showing the presence of ESBLs genes in various food sources. The high number of blaCTX-M was detected in fisheries via transport means whereas blaSHV is more in beef. Among blaTEM, blaOXA, blaCMY highest prevalence observed in raw milk, poultry waste and slaughter housing sample respectively.
- (b)
- Scatter plot in MBLs showcasing highest prevalence of blaNDM-1 and blaOXA in poultry droppings and lowest in poultry farm waste while blaIMP in fisheries market waste.
- (c)
- Scatter plot describing qnrs, among which qnrS was highest in poultry farm waste followed by qnrA which is more in open market waste. Along with qnrB which is more in raw milk. Between gyrs, gyrA is more prevalent than gyrB and detected more in open market waste.
- (d)
- Scatter plot elaborating sul and tet genes. Here sul1 and sul2 are more prevalent in environmental waste samples while tetA is more in number in dairy waste as compared to tetB that is more in open market waste.
3.1.6. ARGs
4. Discussion
- (a)
- Linear regression/correlation (multiple R = 0.72) showed the co-existence of blaNDM-1 and mcr-1 in VRGs based confirmed E. coli. Here in chicken meat showing the highest percentage in marker VAGs (stx1, stx2, eae, hylA, fimH) along with blaNDM-1 and mcr-1 co harboring E. coli followed by beef, mutton, poultry droppings and cloacal /anal swabs. As same increase pattern was observed in both cases.
- (b)
- Linear regression of Non O157, blaNDM-1 and mcr-1 harboring STEC isolates revealed the correlation among MICs of the isolates from chicken meat and chicken droppings.
- (c)
- Linear regression shows correlation of different selected sources and various Serotypes. In livestock category (beef samples) exhibited high percentage and same sample sources showing the high level of O26 in STEC cohobring blaNDM-1 and mcr-1 followed by chicken meat, cloacal/anal swabs and poultry dropping. Along with other Otypes, O103, O121 were also present along with O111 and O145 among selected food sources showing same rise pattern.
5. Conclusions
6. Patents
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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| Specimen Category | Sources | Collected Samples |
Total Samples |
Positive Sample |
Distribution of E. coli positive Samples | Distribution of E. coli from selected categories |
P-value | ||
|---|---|---|---|---|---|---|---|---|---|
| Livestock products | Beef | 25 | 75 | 8 | 32% | 19/75 (25.34%) |
|||
| Mutton | 25 | 7 | 28% | .001* | |||||
| Veal | 25 | 4 | 16% | ||||||
| Poultry | Chicken meat | 25 | 75 | 11 | 44% | 29/75 (38.67%) |
|||
| Cloacal/anal swabs | 25 | 10 | 40% | ||||||
| Droppings | 25 | 8 | 32% | ||||||
| Environmental samples | Slaughterhouse | 25 | 125 | 4 | 16% | 37/125 (29.6%) |
|||
| Open market waste | 25 | 10 | 40% | ||||||
| Transport Means | 25 | 6 | 24% | ||||||
| Dairy farm waste | 25 | 8 | 32% | ||||||
| Poultry farm waste | 25 | 9 | 36% | ||||||
| Fisheries | Fish | 25 | 100 | 6 | 24% | 32/100 (32%) |
|||
| Shrimps | 25 | 2 | 8% | ||||||
| Market waste | 25 | 7 | 28% | ||||||
| Transport means | 25 | 17 | 68% | ||||||
| Dairy | Raw milk | 25 | 125 | 12 | 48% | 37/125 (29.6%) |
|||
| Yogurt | 25 | 9 | 36% | ||||||
| Dairy cream | 25 | 4 | 16% | ||||||
| Cheese | 25 | 7 | 28% | ||||||
| Outlet waste | 25 | 5 | 20% | ||||||
| Grand Total | 500 | 154 | 154/500 (30.8%) |
||||||
| Specimen category | VAGs based confirmed E. coli |
STEC % out of E. coli | Non O157 STEC co harboring blaNDM-1 & mcr-1 | O Type | Statistical analysis |
|---|---|---|---|---|---|
| Beef | 8(32%) | 6/8(75%) | 2/6(33.33%) | O26 , O103 & O121 | 0.05* |
| Mutton | 7(28%) | 3/7(42.85%) | 1/3(33.33%) | O26, O103 & O111 | |
| Veal | 4(16%) | 1/4(25%) | 1/1(100%) | O121 | |
| Chicken meat | 11(44%) | 3/11(27.27%) | 3/3(100%) | O26 & O145 |
|
| Cloacal/anal swabs | 10(40%) | 4/10(40%) | 2/4(50%) | O26, O111 & O145 |
|
| Droppings | 8(32%) | 2/8(25%) | 2/2(100%) | O26 |
|
| Slaughterhouse | 4(16%) | 2/4(50%) | 1/1(100%) | O103& O12 |
|
| Overall | 52(29.71%) | 21/52(40.38%) | 12/21(57.14%) |
| Sources | STEC | Non-O157 O types | Co-existence of ARGs | P value | ||||
| O26 | O103 | O111 | O121 | O145 |
0.05* |
|||
| Beef | 6 | 4 | 1 | -- | 1 | -- | blaNDM,mcr-1, blaTEM,blaOXA, blaKPC, blaqnrA, | |
| Mutton | 3 | 1 | 1 | 1 | -- | blaNDM,mcr-1, blaSHV, blaOXA, | ||
| Veal | 1 | -- | -- | -- | 1 | -- | blaNDM,mcr-1, blaCTX-M, blaTEM, blatetB | |
| Chicken meat | 3 | 2 | -- | -- | -- | 1 | blaNDM,mcr-1, blaCTX-M,blaqnrS, | |
| Cloacal/anal swabs | 4 | 2 | -- | 1 | -- | 1 | blaNDM,mcr-1, blaqnrB, | |
| Droppings | 2 | 2 | -- | -- | -- | -- | blaNDM,mcr-1, blatetA | |
| Slaughterhouse |
2 |
-- | 1 | -- | 1 | -- | blaNDM,mcr-1, blaTEM,blaqnrS,blatetA,blaSul2,blatetB | |
| Total | 21 | 11 | 3 | 2 | 3 | 2 | ||
| Sample Source |
Positive VAGs in E. coli |
NDM | mcr-1 | Stx | Pap | P value | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| stx1 | stx2 | Eae | hylA | Iss | papA | papC | fimH | TraT | OmpT | AmpC | |||||
| Beef | 8 | 3 37.5% |
2 25% |
1 12.5% |
6 75% |
ND | 2 25% |
3 37.50% |
1 12.5% |
ND |
6 75% |
2 25% |
ND | ND |
.001* |
| Mutton | 7 |
1 14.28% |
1 14.28% |
3 42.85% |
1 14.28% |
1 14.28% |
3 42.85% |
ND | ND | ND | ND | ND | ND | 1 14.28% |
|
| Veal | 4 | ND | 1 25% |
1 25% |
ND | 1 25% |
ND | ND | ND | ND | ND | 2 50% |
2 50% |
ND | |
| Chicken Meat |
11 | 3 27.27% |
8 72.72% |
2 18.18% |
1 9.09% |
ND | 8 88.89% |
9 81.81% |
ND | 4 36.36% |
7 63.63.% |
9 81.81% |
7 63.63% |
ND | |
| Cloacal /anal Swabs |
10 | 1 10% |
2 20% |
2 20% |
4 40% |
5 50% |
ND | ND | ND | ND | ND | ND | ND | 1 10% |
|
|
Droppings |
8 | 5 62.5% |
2 25% |
2 25% |
2 25% |
2 25% |
ND | ND | ND | ND | 1 12.5% |
ND | ND | ND | |
| Slaughter House |
4 | 1 25% |
1 25% |
ND | 2 50% |
ND | 2 50% |
1 25% |
ND | ND | ND | ND | 2 50% |
ND | |
| Total |
52 |
14 | 17 | 11 | 16 | 9 | 15 | 13 | 1 | 4 | 14 | 13 | 11 | 2 | |
| Antibiotics | Conc. |
CLSI EUCAST/FDA Resistance Breakpoint |
Beef samples (n=2) |
Mutton sample (n=1) |
Veal sample (n=1) |
Chicken meat (n=3) |
Poultry Cloacal /anal swabs (n=2) |
Poultry droppings (n=2) |
Slaughter house (n=1) |
|||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Ampicillin | 10 µg | ≥32 | 128 | 256 |
512 |
256 | 256 | 512 | 256 | 512 | 512 | 256 | 128 | 128 |
| Cefepime | 30µg | ≥16 | 256 | 128 |
256 |
256 | 128 | 128 | 32 | 32 | 16 | 128 | 64 | 256 |
| Ciprofloxacin | 5µg | ≥4 | 64 | 32 |
64 |
128 | 64 | 128 | 128 | 64 | 64 | 128 | 64 | 32 |
| Levofloxacin | 5µg | ≥4 | 64 | 64 |
32 |
32 | 32 | 64 | 64 | 64 | 128 | 32 | 128 | 64 |
| Chloramphenicol | 30µg | ≥32 | 128 | 64 |
128 |
64 | 32 |
32 |
512 | 32 | 32 | 64 | 128 | 64 |
| Trimethoprim | 5µg | ≥16 | 32 | 32 |
64 |
32 | 128 |
256 |
128 | 64 | 32 | 128 | 64 | 32 |
| Imipenem | 10µg | ≥4 | 32 | 32 |
32 |
32 | 256 | 128 |
256 |
128 |
64 | 32 | 64 | 32 |
| Meropenem | 10µg | ≥4 | 64 | 32 |
64 |
64 | 128 | 64 | 128 | 8 | 8 | 32 | 32 | 32 |
| Colistin | 10µg | ≥8 | 128 | 128 |
128 |
32 | 4 | 4 | 4 | 4 | 4 | 64 | 32 | 4 |
| Tetracycline | 30µg | ≥16 | 64 | 32 |
64 |
64 | 128 | 128 | 128 | 32 | 64 | 32 | 32 | 32 |
| Tigecycline | 15µg | ≥8 | 4 | 4 |
8 |
8 | 4 | 4 | 8 | 4 | 8 | 4 | 4 | 4 |
| Fisfomycin | 200 μg | ≥64 | 512 | 256 |
128 |
128 | 128 | 256 | 512 | 128 | 256 | 128 | 128 | 128 |
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