Fresh fruits are susceptible to rot by different types of molds such as Penicillium, Aspergillus, Alternaria, Botrytis, Rhizopus, Cladosporium, Tricothecium, Phytophthora, Aureobasidium, Colletotrichum, and others.  Yeast from the genera Saccharomyces, Candida, Torulopsis, and Hansenula have been associated with fermentation of fruits.  Bacterial spoilage associated with the souring of berries and figs has been attributed to the growth of lactic and acetic acid bacteria.

Pathogens on fresh fruits and vegetables are Salmonella, Shigella, Listeria monocytogenes, E. coli 0157:H1, gastrointestinal viruses, Entamoeba histolytica, and Ascaris spp.  Usually these pathogens are incorporated by polluted irrigation water.  Fruits are generally too acidic for growth of the more common foodborne pathogens such as Salmonella and Shigella (in citrus juices).  Listeria monocytogenes can survive well on both chopped and whole tomatoes.  Toxigenic molds are also a problem since they can produce mycotoxins. 

Fresh cut up melons used in salad bars must be kept at 5^oC (41^oF) since they may contain pathogens such as E. coli 0157:H1 if they are not properly washed before they are cut up in pieces.  

The contaminants on frozen fruits originate from the equipment.  Geotrichum candidum has been termed "machinery mold" because it may accumulate on fruit-processing equipment.  Some acid tolerant bacteria such as Acetobacter, Gluconobacter, and Zymomonas may also develop in the environment of fruit-processing lines.  Coliform bacteria can be recovered even though the pH may be too low to support growth of these organisms.  Their presence usually does not indicate a public health problem.

In concentrated fruit drinks and preserves, due to low a_w (0.90), only osmophilic yeasts can grow; molds can also grow if oxygen is available.

The microorganisms most significant in fruit juices are the lactic acid bacteria (Lactobacillus, Leuconostoc), yeasts, and molds.  High levels of mold contamination are generally attributed to unsound fruit entering the processing plant.  Machinery mold, Geotrichum candidum, may be introduced from unsanitary equipment.  Low numbers of heat-resistant molds such as Byssochlamys spp. and Neosartorya fischeri often are present in the raw fruit and can survive the thermal processing steps.  Pathogenic bacteria are usually not a problem in pasteurized fruit juices since they are killed by the heating step.  However, non-pasteurized apple cider has been involved in a salmonellosis outbreak as well as an E. coli 0157:H1 outbreak.  Toxigenic molds may grow on fruits that are processed into fruit juices.  Traces of the mycotoxin patulin have been found in apple juice.

Fresh vegetables contain microorganisms coming from soil, water, air, and other environmental sources, and can include some plant pathogens.  Most of them have high pH (between 5.5 and 6.4) except for the tomatoes; therefore, they are not only spoiled by yeasts and molds but also by bacteria.  Mold spoilage is caused by Penicillium, Phytophthora, Alternaria, Botrytis, Fusarium, Cladosporium, Phoma, Trichoderma, and Aspergillus.  Among the bacteria, species of Pseudomonas, Erwinia, Xanthomonas, Enterobacter, Flavobacterium, Chromobacter, Lactobacillus, Bacillus, and Clostridium are the most important as well as non fecal enterococci and lactic acid streptococci.  

Foil-wrapped baked potatoes, chopped garlic in oil and onions sauteed in butter mixtures have been involved in outbreaks of Clostridium botulinum.  In all cases, these products were held at room temperature for several days.

Pickles can be spoiled by yeasts and halophilic bacteria, especially if the acidity is not sufficient.  Candida, Torulopsis, Debaromyces, Hansenula, Rhodotorula, and Saccharomyces are the most common spoilage yeasts.  Dill pickles with low salt (<5%) can have a bloating defect from carbon dioxide gas production by yeasts, lactic acid bacteria, and coliforms.  If the vinegar is kept in wooden tanks, these products can be spoiled by the mold Monilliela acetoabutans.  Sweet and sour pickles can be spoiled by yeasts and lactic acid bacteria.  Sauerkraut can be spoiled by coliforms and other gram-negative bacteria, yeasts and molds if the fermentation process was  not adequated.  Olives can also have problems with gassiness due to lactic acid bacteria, coliforms, and yeasts.  Softening of texture can be caused by pectinases of yeasts such as Rhodotorula spp.   

The major source of organisms in frozen vegetables is contaminated equipment since the blanching step destroys most contaminating microorganisms (except spores).  Coliforms and enterococci are common contaminants and may be present in large numbers.  Their presence does not usually indicate fecal contamination.  They are part of the processing line.  Escherichia coli is a relatively rare contaminant of blanched vegetables and its presence may indicate fecal contamination.

Recommended tests:  

Aerobic plate count.
Total coliform count.  
E. coli.
Yeast and molds.
 

Additional tests:

Geotrichum count (sanitation index for fruits and tomato products).
Listeria monocytogenes (for fruits and vegetables destined for chronically ill or immunocompromised persons).
Salmonella.
E. colo0157/H7.

Adapted from:

Brackett, R. E. and Splittstoesser, D. F.  2001.  Fruits and Vegetables, p. 515.  In F. P. Downes and K. Ito (eds.), Compendium of Methods for the Microbiological Examination of Foods.  American Public Health Association, Washington, DC.