Antimicrobial Profiles of Selected Gram-Negative Bacteria Recoverable from Sewage and Sludge from Juja and Kibera Informal Settlements of the Larger Nairobi Metropolis

Africa has experienced rapid urban migration in the past two decades. New informal settlements continue to emerge and expand but the sanitation provision of facilities has not improved at the same pace and this poses a serious health concern to the public especially the urban poor. Open sewage systems and sludge-clogged drainage systems as well as soil contaminated with industrial and domestic wastes are possible sources of germs that probably cause clinical infections and epidemics. In this cross-sectional study, we recorded diverse genera of Gram-negative non-fastidious bacteria that included;Escherichia coli (23%), Klebsiella spp (21%), Enterobacter spp (19%), Citrobacter spp (10%), Pseudomonas aeruginosa (8%), Proteus spp (7%), Salmonella (3%), Yersinia spp (3%), Shigella spp (2%), Morganella morganii (2%), Edwardisella spp (1%), Hafnia spp (1%), Serratia marcesence (0.5%), and Acinetobacter baumannii (0.5%). Most of these isolates were resistant to ampicillin while imipenem and ciprofloxacin were the most effective antimicrobial agents. Resistance combination towards ampicillin, trimethoprim, sulfamethoxazole and streptomycin was also noted in recovered isolates (16%). An overall high antimicrobial resistance was recorded among isolates from slum as compared to those recovered from Juja, a middle-class settlement located at the edge of Nairobi metropolis. The prevalence of isolates with a combined resistance to 3rd generation cephalosporins (cefotaxime, ceftriaxone and ceftazidime), gentamicin and ciprofloxacin was the highest among P. aeruginosa isolates (13%) but none of the Yersinia species and Edwardisella tarda exhibited this resistance. Carriage of blaTEM (52%) was most prevalent in all bacteria species followed by blaCTX-M (20%), blaSHV (18%) while blaOXA (17%) was the least common. The phylogeny analysis revealed significant genetic similarity among strains belonging to E. coli, K. pneumoniae, E. agglomerans and P. mirabilis strains but less relatedness was noted among strains belonging to C. freundii. Further analysis showed possible clonal expansion of E. agglomerans and K. pneumoniae within the environmental ecosystems.

Phenotypic and Genotypic Characterisation of Antibiotic Resistance in Escherichia coli, Klebsiella spp., and Listeria monocytogenes Isolates from Raw Meat Sold in Nairobi

Worldwide, the increase in antimicrobial resistance (AMR) is a public health concern. Food-borne associated antibiotic-resistant pathogens can contaminate raw meat during slaughter, transportation, and at sale points. A cross-sectional study was conducted from March 2021 to December 2021 to determine antimicrobial susceptibility patterns and characterize the molecular basis of resistance in E. coli, Klebsiella spp., and L. monocytogenes contaminating raw meat collected from retail outlets in Nairobi. Isolation and identification of the strains were done using the standard culture methods and PCR. Antimicrobial susceptibilities of the recovered strains were determined using disk diffusion while the presence of antibiotic resistance gene determinants;blaTEM, blaCTX-M, blaOXA, sul, and qnrS was done using PCR. Of 270 samples collected, 163 (60%) Escherichia coli, 19 (7%) Klebsiella spp., and L. monocytogenes 3 (1.1%) were recovered. Among Escherichia coli, high antibiotic resistance was found to Erythromycin 161 (98%) and ampicillin 88 (54%) while low resistance was found against imipenem 2 (1%). Similarly, high resistance was found among Klebsiella spp. to Erythromycin 19 (100%) and ampicillin 12 (63%) low resistance to ceftazidime 1 (5%), cefotaxime 1 (5%), aztreonam 1 (5%), and chloramphenicol 1 (5%). One isolate among the three Listeria monocytogenes strains isolated was resistant to Trimethoprim-sulfamethoxazole. No resistance was exhibited to gentamycin by all Klebsiella spp. The prevalence of multidrug-resistant (resistance to three or more classes of antibiotics) isolates was 95/182 (52.2%). The common resistance pattern observed was Erythromycin, ampicillin, tetracycline, and trimethoprim-sulfamethoxazole with a prevalence of 19 (20%). ESBL was confirmed in isolates that harbored: blaTEM (65%), blaCTX-M (44%), blaOXA (33%) while sul and qnrS were detected in 46.7% and 13.6% respectively. Circulation of antibiotic-resistant and MDR isolates found in this study could play a role in the dissemination of AMR among food-borne bacteria and suggest potential food safety and public health risk. Therefore, enhanced surveillance for antibiotic-resistant organisms in raw meat for early detection of emerging resistant bacteria species in the food chain is recommended.