Antibiogram of isolated bacteria and overview of resistome and virulome of multi-drug resistant Escherichia coli from ready-to-eat foods vended in Lagos, Nigeria

TL;DR

This study found antibiotic-resistant and virulent bacteria in ready-to-eat foods in Lagos, Nigeria, highlighting a public health risk.

Contribution

The study provides new insights into the resistome and virulome of multi-drug resistant Escherichia coli in Nigerian RTE foods.

Findings

Multiple bacterial species, including MDR Escherichia coli, were identified in RTE food samples.

Recovered strains showed high resistance to antibiotics like ciprofloxacin and aztreonam.

Genome sequencing revealed numerous antibiotic resistance and virulence genes in MDR E. coli strains.

Abstract

Ready-to-eat (RTE) foods are popular fast-foods due to their convenience and affordability. However, they pose huge public health risks due to the presence of antibiotic-resistant and virulent pathogens. Nevertheless, such data is sparse in Nigeria where RTE food consumption is widespread. This study determined antibiotic susceptibility patterns, and identified antibiotic resistance and virulence genes in bacteria from 199 RTE food samples (aadun, biscuits, bread, eko, kokoro and shawarma) vended within Lagos State, Nigeria. Bacteria were recovered on nutrient agar and MacConkey agar and identified by 16 S rRNA gene sequencing. Antibiotic susceptibility testing of recovered isolates was performed against eight antibiotics using the disc diffusion method. Antibiotic resistance and virulence genes in two multidrug resistant (MDR) E. coli strains were determined by whole genome sequencing.

Eight bacterial species, Kosakonia cowanii (n = 167), Yokenella regensburgei (n = 106), Proteus mirabilis (n = 104), Bacillus subtilis (n = 101), Klebsiella pneumoniae (n = 66), Acinetobacter baumannii (n = 48), Kurthia gibsonii (n = 37) and Escherichia coli (n = 2), were recovered from the foods. Klebsiella pneumoniae and E. coli recorded the highest (30%) and least (0.9%) occurrences in the RTE foods. The recovered strains revealed the most resistance to ciprofloxacin (38%), aztreonam (30%) and gentamicin (30%) belonging to carbapenems, monobactams and aminoglycosides, respectively. Co-resistance to ampicillin, aztreonam and ampicillin/clavulanic acid was recorded in 25% of the MDR strains with MAR index > 0.3. Sixty-three antibiotic resistance genes (ARGs), including acrD, emrA, (Bla) EC-18, (Bla)AmpC2_Ecoli, and (Bla)ampH, were identified in enterotoxigenic Escherichia coli D1 and D2 strains. The strains exhibited resistance mechanisms, such as antibiotic efflux, antibiotic target alteration and antibiotic inactivation, against the tested antibiotics. In addition, the strains possessed virulence genes responsible for attachment and adherence (espX1, fimH, espL1, upaG/ehaG), acid resistance (gadX and cadA), biofilm formation (csgB, and ehaA), toxin production (hlyE) and invasion/cell penetration factor (ibeB).

RTE food vended in Lagos, Nigeria, is a major reservoir of pathogenic Gram-positive and -negative bacteria including MDR strains with multiple potent ARGs and virulence gene determinants. The findings therefore suggest an urgent need for enhanced routine surveillance, monitoring, and education of food handlers and vendors to ensure the safety of consumers and reduce the public health risks associated with pathogenic bacteria in RTE foods.

The online version contains supplementary material available at 10.1186/s12866-025-04694-x.

Figures