Releated new study:
onlinelibrary.wiley.com/doi/10.1111/tmi.13003/full

Over a period of 2 months, paired (exposed and non-exposed) containers with cooked rice were placed on the ground in kitchen areas in an urban slum area in Dhaka, Bangladesh, and the numbers of flies landing on the exposed rice were counted. Following exposure, the surface of the rice was microbiologically and molecularly analysed for the presence of Escherichia coli and genes of diarrhoeagenic E. coli and Shigella strains.

Results:
Rice was at greater risk (P < 0·001) of being contaminated with E. coli if flies landed on the rice than if no flies landed on the rice (odds ratio 5·4 (P < 0·001, 95% CI: 2·5–11·7). Mean contamination in exposed rice samples (n = 60) was 3·1 × 103 CFU/g (95% CI: 2·2 × 103–4·0 × 103). Furthermore, for approximately half of the observed fly landings, the average CFU per fly landing was >0·6 × 103 CFU. Genes of diarrhoeagenic E. coli and Shigella species were detected in 39 of 60 (65%) of exposed rice samples. Two fly species were identified: the common housefly (Musca domestica) and the oriental latrine fly (Chrysomya megacephala).

Conclusion:
Flies may transmit large quantities of E. coli to food under field settings. The findings highlight the importance of implementing control measures to minimise exposure of food to flies to ensure food safety. Fly control measures should be considered for the prevention of diarrhoeal diseases caused by E. coli.

Interesting article on a recent study regarding the microbiome found on flies. It seems like this was the first time anyone actually studied this using modern molecular techniques. See:

Flies' disease-carrying potential may be greater than thought, researchers say

In a study of the microbiomes of 116 houseflies and blowflies from three different continents, researchers found, in some cases, these flies carried hundreds of different species of bacteria, many of which are harmful to humans. Because flies often live close to humans, scientists have long suspected they played a role in carrying and spreading diseases, but this study, which was originally initiated at Penn State's Eberly College of Science, adds further proof, as well as insights into the extent of that threat.

and further:

Blowflies and houseflies — both carrion fly species — are often exposed to unhygienic matter because they use feces and decaying organic matter to nurture their young, where they could pick up bacteria that could act as pathogens to humans, plants and animals. The study also indicates that blowflies and houseflies share over 50 percent of their microbiome, a mixture of host-related microorganisms and those acquired from the environments they inhabit. Surprisingly, flies collected from stables carried fewer pathogens than those collected from urban environments.

The researchers, who report their findings in the current issue of Scientific Reports, found 15 instances of the human pathogen Helicobacter pylori, a pathogen often causing ulcers in the human gut, largely in the blowfly samples collected in Brazil. The known route of transmission of Helicobacter has never considered flies as a possible vector for the disease, said Schuster.

Of course nothing ground braking, but it is nice to have some actual scientific evidence on this as well.