
Researchers from the Ineos Oxford Institute for antimicrobial research (IOI) have found that flies present in Nigerian hospitals are carriers of bacteria resistant to clinically important antibiotics, including last-resort antibiotics.
Scientists at the IOI in collaboration with researchers in Nigeria collected 1,396 flies from eight hospitals in six Nigerian cities. They found 17 different species of bacteria in the fly samples. The bacteria were isolated and characterised using antibiotic susceptibility testing and whole genome sequencing (WGS) methods to identify their resistance profiles.
Antimicrobial resistance genes (ARGs) were found in all 17 species of bacteria isolated from fly samples across all hospital sites. Many bacterial samples showed resistance to multiple classes of antibiotics, including beta-lactams and last-resort antibiotics such as carbapenems and colistin.
Researchers found a high prevalence of ARGs across all sites, with 40% of flies carrying bacteria with at least one extended-spectrum beta-lactamase gene and 8% carrying bacteria with the blaNDM gene. These genes are associated with resistance to commonly used antibiotics, making infections harder and more costly to treat.
In addition to this, mecA (a bacterial gene associated with methicillin resistance), was found in bacteria carried by 6.4% of flies. Multiple species of bacteria carried the gene, including Staphylococcus aureus, a common cause of hospital-acquired infections. 86.8% of Staphylococcus aureus samples were multidrug resistant.
Multidrug resistance was also observed in other bacterial species isolated from flies across the eight hospitals, including Providencia spp., Escherichia. coli and Klebsiella. pneumoniae, all of which are known to cause human infections.
Insect pests such as flies can move between hospitals, urban settings and the natural environment. Our latest findings imply that flies circulating in hospital wards could pose a threat to patients who are vulnerable to infection during their stay, especially as flies commonly land on patients in these settings.
Our study is one of the largest surveillance studies looking at the bacteria carried by flies in hospitals in low- and middle-income countries to date. We utilised high-throughput methods to analyse a large number of fly samples and isolated a range of resistant bacterial species, many of which cause significant clinical illness.

Flies were collected using sticky traps placed on hospital wards. Information about the hospital environment was recorded, as well as their antibiotic usage. Samples were stored and labelled before being shipped to the IOI labs in Oxford for microbiological processing.
In Oxford, samples were first homogenised in saline to release bacteria from flies. After this, the team inoculated samples on selective agar plates and identified a range of antibiotic resistant bacteria.
The team then screened bacterial growth for the presence of ARGs using PCR (polymerase chain reaction) tests. The species of bacteria that tested positive for ARGs were identified before undergoing further testing. Researchers measured the susceptibility of bacteria to numerous antibiotics and used whole genome sequencing to study the genetic make-up of the drug-resistant bacteria.
The widespread presence of a variety of multidrug-resistant bacteria in flies in Nigerian hospitals is very worrying. Even more concerning is the fact that there may be many more flies carrying multiple resistance genes out there than our study was able to find. The data we’ve gathered is valuable evidence of the need for improved insect control measures in hospitals. We hope this study will provide a blueprint for future research into the role of flies in spreading AMR in hospitals in Nigeria and other low- and middle-income countries.
