Antimicrobial resistance profiles and genetic basis of resistance among non-fastidious Gram-negative bacteria recovered from ready-to-eat foods in Kibera informal housing in Nairobi, Kenya

Abstract

Objective. This cross-sectional study conducted in Kibera, Kenya, sought to gain insights on relative microbial contamination levels of popular unprocessed food types, determine antimicrobial resistance (AMR) burden and the carriage of integrons that are essential elements for spreading antimicrobial resistance genes (ARG). Foods analysed consisted of cooked vegetables (kale, cabbage, and nightshades), boiled cereal foods (beans, rice, and Githeri, which is a mixture of beans and maize), meat, Omena fish (fried silver cyprinids), and Ugali (a product of simmered maize flour in boiled water). Results. The analysis detected contamination levels exceeding 2×104 c.f.u. ml−1 in 106 (38 %) of the 281 ready-to-eat foods analysed. The majority of food types had microbial contaminations of between 4.0×104 and 2.3×106 c.f.u. ml−1. Kale was the most contaminated with a mean of 2.3×106 c.f.u. ml−1, while Omena was the least contaminated with 4.0×104 c.f.u. ml−1. Foods sold close to open sewage and refuse sites were more contaminated than those sold in relatively ‘cleaner’ settings (P <0.0001, O.R 0.1162, C.I 0.1162–0.120). A total of 405 bacterial isolates were recovered and included; Klebsiella spp 116 (29 %), Escherichia coli 104 (26 %), Enterobacter agglomerans 88 (22 %), Proteus mirabilis 30 (7 %), Salmonella spp 28 (7 %), Citrobacter freundii 27 (7 %) and Serratia marcescens 12 (3 %). Imipenem (IPM, 100 %) was the most effective antimicrobial agent, followed by cefepime (98 %). Ampicillin (AMP, 33 %), trimethoprim (TMP, 27 %), and sulfamethoxazole (SMX, 23 %) on the other hand, were the least effective antimicrobials. The analysis also found ten isolates (2 %) that had co-resistance to third-generation cephalosporins, fluoroquinolone (CIP), quinolones (NAL) and aminoglycosides (GEN); hereby we refer to this phenotype as the βFQA. The prevalence of multidrug-resistant (MDR) strains was 23 % (93), while that of extended-spectrum β-lactamases (ESBL) producing strains was 4 % (17). The bla TEM was the most prevalent (55 %) β-lactamase (bla) gene among the screened 93 MDR-strains. Carriage of class one integrons (intI1) was more common (23 %) than intl2 (3 %) among these MDR-strains. Bacterial diversity analysis using the GTG5-PCR found no significant clusters for analysed E. coli and K. pneumoniae, suggesting recovered isolates were genetically diverse and not due to non-clonal expansion. The findings of this study are an indication that contaminated foods can be a reservoir for enteric pathogens and a source of AMR strains.

Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing

“…More recently, Musila et al (2021) identified K. pneumoniae isolates with the bla OXA-181 carbapenemase gene. In addition, K. pneumoniae resistance to aminoglycosides, tetracyclines, chloramphenicol, and fluoroquinolones has also been observed in Kenya, typically associated with ESBL production in MDR [ 6 , 10 , 18 ]. Aminoglycosides are widely used to treat bacterial infections due to the ease of administration and access in Kenya [ 19 ].…”

“…Aminoglycosides are widely used to treat bacterial infections due to the ease of administration and access in Kenya [ 19 ]. Musila et al (2021) also reported the 16S rRNA methyltransferase genes, rmtF and rmtC , in K. pneumoniae isolates which confer pan-aminoglycoside resistance [ 18 ]. Resistance to chloramphenicol and sulfonamides is high in part due to its use as a first-line treatment option for enteric infections such as typhoid and HIV prophylaxis in Kenya [ 10 ].…”

Molecular Characterization and Diversity of Bacteria Isolated from Fish and Fish Products Retailed in Kenyan Markets

“…In each quadrant, proportionate sampling based on the number of fish products vendors in each cluster was done to get the number of participants. Random tables were used to randomly identify the participants, while the convenient sampling strategy described by Maina et al [ 15 ] was used to randomly sample the fish and fish products in the selected fish retail markets in the county. These markets included Kerugoya, Ndia, Kianyaga, Mwea, Sagana, and Tebere.…”

Antimicrobial resistance and virulence characteristics of Klebsiella pneumoniae isolates in Kenya

“…For library preparation, the extracted DNA was end-repaired using the NEBNext® UltraII End Repair/dA-Tailing kit using the manufacturer's instructions. LSK 109 ligation kit, EXP-NBD 104 (1-12), and EXP-NBD 114 (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24) Native Barcoding kits were used to barcode each DNA sample and adapters added. The DNA library was loaded onto a FLO-MIN106 R9.…”

“…In addition, KP resistance to aminoglycosides, tetracyclines, chloramphenicol, and fluoroquinolones has also been observed in Kenya, typically associated with ESBL-production in MDR (6,10). Aminoglycosides are widely used to treat bacterial infections due to the ease of administration and access in Kenya (18). Musila et al (2021) also reported the 16S rRNA methyltransferase genes, rmtF, and rmtC, in KP isolates which confer pan-aminoglycoside resistance.…”