The clerks confronted the couple at the door, and Fresno Police Chief Jerry Dyer says the argument led to a fight.
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"That physical fight ultimately led out into the front of the store, and at one point, the male suspect pulled out a handgun from his waistband fired it one time and struck the store employee in the stomach."
The suspects drove away from the store in a black Audi.
The victim, 38-year-old Steve Austin was rushed to the hospital. His father Larry says he cried when he first learned his son, a Marine Corps veteran of Desert Storm had been shot.
But, Larry said he was relieved when he learned the gunshot wound went clean through, and so far it looks like his son will recover.
"When I saw him in the hospital bed I felt good because he looked normal."
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Chief Dyer says it's disturbing because now even some shoplifters must be considered possibly armed and dangerous.
"This is initially a shoplifting that turned into a violent crime which is not uncommon."
But Chief Dyer says surveillance cameras and other evidence have him believing the suspects will be caught.
"I am very confident we are going to be able to solve this case quickly and to be able to arrest the male and female responsible for this crime."
Larry Austin says doctors have told him his son Steve could soon be released from the hospital and be recovering at home.