Mastitis is one of the most frequent and costly production diseases of dairy cattle. It is frequently treated with broad-spectrum antimicrobials. The objectives of this work were to investigate the prevalence of
Staphylococcus aureus
and
Escherichia coli
, find out the antimicrobials used in mastitis treatment, and explore the antimicrobial resistance profile including detection of resistance genes. Bacterial species and antimicrobial resistance genes were confirmed by the polymerase-chain reaction. A total of 450 cows were screened, where 23 (5.11%) and 173 (38.44%) were affected with clinical and sub-clinical mastitis, respectively. The prevalence of
S. aureus
was 39.13% (n = 9) and 47.97%(n = 83) while,
E. coli
was 30.43% (n = 7) and 15.60% (n = 27) in clinical and sub-clinical mastitis affected cows, respectively. The highest antimicrobials used for mastitis treatment were ciprofloxacin (83.34%), amoxycillin (80%) and ceftriaxone (76.67%). More than, 70% of
S. aureus
showed resistance against ampicillin, oxacillin, and tetracycline and more than 60% of
E. coli
exhibited resistance against oxacillin and sulfamethoxazole-trimethoprim. Selected antimicrobial resistance genes (
mec
A,
tet
K,
tet
L,
tet
M,
tet
A,
tet
B,
tet
C,
sul
1,
sul
2 and
sul
3) were identified from
S. aureus
and
E. coli
. Surprisingly, 7 (7.61%)
S. aureus
carried the
mec
A gene and were confirmed as methicillin-resistant
S. aureus
(MRSA). The most prevalent resistance genes were
tet
K 18 (19.57%) and
tet
L 13 (14.13%) for
S. aureus
, whereas
sul
1 16 (47.06%),
tet
A 12 (35.29%),
sul
2 11 (32.35%) and
tet
B 7 (20.59%) were the most common resistance genes in
E. coli
. Indiscriminate use of antimicrobials and the presence of multidrug-resistant bacteria suggest a potential threat to public health.