Characterization of antibiogram fingerprints in Listeria monocytogenes recovered from irrigation water and agricultural soil samples

Listeria monocytogenes (L. monocytogenes) is a foodborne pathogen and the etiologic agent of listeriosis, which can be disseminated within the agricultural environment particularly soil and irrigation water, contaminate farm produce and cause high mortality and morbidity among vulnerable individuals. This study assessed the incidence and antibiogram of L. monocytogenes recovered from irrigation water and agricultural soil samples collected from Chris Hani and Amathole District Municipalities (DMs) in Eastern Cape Province, South Africa. The distribution of presumptive L. monocytogenes in irrigation water and agricultural soil samples was done using the standard plate count method, while polymerase chain reaction (PCR) was used to identify the isolates. The confirmed isolates were screened for 9 key virulence markers using PCR after which they were subjected to antibiotic susceptibility testing against 18 antibiotics used for the alleviation of listeriosis using the disk diffusion method. Relevant putative antibiotic resistance genes in the resistant variants were screened for using PCR. The distribution of L. monocytogenes in irrigation water samples was statistically significant (P ≤ 0.05) and ranged from log10 1.00 CFU/100ml to log10 3.75 CFU/100 ml. In agricultural soil samples, the distribution ranged significantly (P ≤ 0.05) from log10 2.10 CFU/g to log10 3.51 CFU/g. Of the 117 presumptive L. monocytogenes recovered from irrigation water samples and 183 presumptive L. monocytogenes isolated from agricultural soil samples, 8 (6.8%) and 12 (6.6%) isolates were confirmed respectively. Nine virulence genes including inlA, inlB, inlC, inlJ, actA, hlyA, plcA, plcB, and iap were detected in all the isolates. The proportion of the isolates exhibiting phenotypic resistance against the test antimicrobials followed the order: tetracycline (90%), doxycycline (85%), cefotaxime (80%), penicillin (80%), chloramphenicol (70%), linezolid (65%), erythromycin (60%) and trimethoprim/sulfamethoxazole (55%). The isolates exhibited multiple antibiotic resistance against 3 or more antibiotics and the MAR indices of all the multidrug isolates were ≥0.2. The isolates harboured antibiotic resistance genes including tetA, tetB, tetC, sulI, sulII, aadA, aac(3)-IIa and ESBLs including blaTEM, blaCTX-M group 9, blaVEB as well as AmpC. None of the isolates harboured the carbapenemases. We conclude that irrigation water and agricultural soil collected from Chris Hani and Amathole District Municipalities (DMs) in Eastern Cape Province of South Africa are reservoirs and potential transmission routes of multidrug-resistant L. monocytogenes to the food web and consequently threat to public health.


Irrigation water
Irrigation water is sourced from a river. Soil samples were not collected due to the inaccessibility of agricultural farms Animal intrusion, dumping of refuse, recreational activities, swimming, and domestic activities in the source river.

Irrigation water and soil
Irrigation water is sourced from a dam. Type of irrigation used is a sprinkler irrigation system. Irrigation is done once in 3 days between 8 am and 3 pm on each day. Soil type is loam and crops grown on it include cabbage, broccoli, butternut, spinach and lettuce.
Animal intrusion in the dam. Soil amendment is with inorganic fertilizer (LAN).

Irrigation water and soil
Irrigation water is sourced from an artificial pond which receives water from both rainfall and downstream river. Type of irrigation used is the sprinkler irrigation system. Irrigation is done once a day between 8 am and 12 pm, and none on rainy days. Soil type is clay-loam and crops grown on it include cabbage, broccoli, lettuce and onions. Irrigation water is sourced from an artificial pond, which primarily receives water from the effluents of a poultry and piggery farm. Type of irrigation used is the sprinkler irrigation system. Irrigation is done once every day between 8 am and 5 pm except on rainy days. Soil type is loam and crops grown on it include spinach and cabbage.
Discharge of swine and poultry effluents into the pond. Soil amendment is with poultry and swine faeces.
Irrigation water Irrigation water is sourced from a river. Soil samples were not collected due to the inaccessibility of agricultural farms Animal intrusion, recreational activities, swimming, and domestic activities in the source river.

Irrigation water and soil
Irrigation water is sourced from a river. Type of irrigation used is a sprinkler irrigation system. Irrigation is done twice a week between 8 am and 4 pm each day. Soil type is clay and crops grown on it include pumpkin.
Animal intrusion, washing of cloths, bathing and other domestic activities in the source river. Soil amendment is with organic compost of livestock origin.

Irrigation water and soil
Irrigation water is sourced from a river. Type of irrigation used is a sprinkler irrigation system. Irrigation is done twice a day between 8 am and 12 pm and between 2 pm and 5 pm and none on days with heavy rainfall. Soil type is clay-loam and crops grown on it include cabbage, lettuce and spinach.
Animal intrusion in both river and close to farm sites. Soil amendment is with cow dung.

E026°54.062ˡ
Irrigation water Irrigation water is sourced from a dam. Type of irrigation used is a sprinkler irrigation system. Irrigation is done once a day and none on days with heavy rainfall.

Irrigation water and soil
Irrigation water is sourced from a river and manually irrigated on a backyard farm using watering cans. Soil type is loam and crops grown on it include spinach.
Animal intrusion, swimming, and washing of clothes in the source river. No soil amendment S12 S32°46.616ˡ E026°50.203ˡ

Irrigation water and soil
Irrigation water is sourced from treated municipal water. Type of irrigation used is a sprinkler irrigation system. Irrigation is done once a day from 8 am to 1 pm. Soil type is clayloam and crops grown on it include cabbage, lettuce, onions and spinach.
No visible anthropogenic activity in the water source. Soil amendment is done using inorganic fertilizer (LAN). S13 S32°35.783ˡ E027°26.880ˡ

Irrigation water and soil
Irrigation water is sourced from a river. Type of irrigation used is the sprinkler irrigation system. Irrigation is done once a day from 8 am to 12 pm. Soil type is clay-loam and crops grown on it include cabbage, broccoli, lettuce and spinach.

Irrigation water and soil
Irrigation water is sourced from a dam. Type of irrigation used is a sprinkler irrigation system. Irrigation is done once a day. Soil type is clay and crops grown on it include cabbage, lettuce and spinach.
No observed anthropogenic activity in the dam. Soil amendment is with inorganic fertilizer (LAN).

Irrigation water
Irrigation water is sourced from a river. Soil samples were not collected due to the inaccessibility of agricultural farms Animal intrusion S16 S32°01.927ˡ E027°04.619ˡ

Irrigation water and soil
Irrigation water is sourced from a river. Type of irrigation used is the sprinkler irrigation system. Irrigation is done once a day. Soil type is loam and crops grown on it include lettuce and spinach.
Animal intrusion. Soil amendment is with organic compost of animal origin S17 S31°55.297ˡ E026°49.882ˡ

Irrigation water and soil
Irrigation water is sourced from borehole groundwater. Types of irrigation used include sprinkler and drip irrigation system. Irrigation is done twice a day. Soil type is clay-loam and crops grown on it include cabbage, lettuce, broccoli and spinach.
No anthropogenic activity in the water source. Soil amendment is with inorganic fertilizer (LAN). S18 S31°53.203ˡ E026°47.764ˡ

Irrigation water and soil
Irrigation water is sourced from a river. Type of irrigation used is the centre pivot irrigation system. Irrigation is done once a day. Soil type is loam and crops grown on it is fodder Animal intrusion, receiving shed of WWTP effluent. Soil amendment is with inorganic fertilizer (LAN) S19 S32°00.855ˡ

E027°35.597ˡ
Irrigation water Irrigation water is sourced from a river. Soil samples were not collected due to the inaccessibility of agricultural farms Animal intrusion, dumping of refuse.
Note: For confidentiality sake, sampling sites are coded with S1-S19. All the information recorded in this table were gotten from the onsite survey as well as from farm owners and workers. Coordinates for each sampling site were retrieved using the "etrex-LEGENDH" GPS equipment. WWTP: Wastewater treatment plant. LAN: limestone ammonium nitrogen.