CHARACTERIZATION OF Salmonella spp. AND Escherichia coli ISOLATED FROM SOME POULTRY FARMS IN BENIN METROPOLIS USING THE 16S rRNA SEQUENCE ANALYSIS

ABSTRACT

Poultry is an important agricultural business in Nigeria with over 70% of livestock farms into chicken production and its products. Salmonella sp. and E. coli are leading causes of infection in poultry and subsequently man. The aim of this research is to investigate the presence of Salmonella sp. and E. coli in poultry farms in Benin City, Edo State and to characterize the isolates using the 16S rRNA sequence analysis. A total of forty eight (48) samples were collected from wall, feed, water and droppings of poultry farms. The bacteria, Salmonella sp. and E. coli counts, biochemical tests and antibiotics pattern of the bacterial isolates associated with the poultry samples were evaluated using standard analytical methods. Polymerase chain reaction (PCR) and 16S RNA sequencing were further used in identification of the bacterial isolates up to the strain level. The DNA extraction and sequencing guided in identification of specific strains of organisms isolated from the various poultry. A phylogenetic tree was established in showing the inferred evolutionary relationships among Salmonella sp. and E. coli isolated. On Eosine methylene blue agar (EMB) E.coli showed a metallic green sheen while Salmonella sp. showed a transparent color with a black center on Salmonella-Shigella agar (SSA). Highest THBC count of 21.5x10³ CFU/g was observed in the feed of Sokponba road poultry, while the lowest THBC count was also obtained in the wall samples of Sokponba road poultry farm (2.7x10³ CFU/g). Furthermore, average bacterial population in all farms was highest in poultry droppings (15.2x10³ CFU/g) and lowest in the poultry walls (4x10³ CFU/g).Total Salmonella count (TSC) was highest in droppings of Sokponba road poultry farm (12.6x10³ CFU/g), no Salmonella sp. was isolated in the walls, feed and water samples of all the four poultry farms. The antibiotics test showed the susceptibility pattern of Salmonella sp. and E. coli isolated from different poultry sample by showing zone of clearing around each antibiotics disk which was measured in millimeter (mm). Antibiotic resistance plasmid was expressed in nine (09) E. coli strains, while all Salmonella enterica strains expressed resistance plasmid. After DNA extraction and sequencing the Salmonella sp. were identified as S. enterica subsp. enterica serovar typhi and S. enterica subsp. enterica serovar typhimurium and the E. coli strains as E. coli 0157:H7, E. coli K-12, E. coli 0104:H4, E. coli 083:H1, E. coli 1A139 and E. coli UMN026. It is therefore recommended that good hygiene and sanitary practices be encouraged in poultry farming which will help reduce the risk of infection in poultry farms in Benin City metropolis.