Prevalence, risk factors and antimicrobial resistance of escherichia coli pathotypes isolated from livestock and rats in slums areas of Nairobi

Abstract

E. coli is a facultative aerobic commensal microflora in livestock and human. Its detrimental effects in human and animal has attracted the most research interest. The current study was conducted to determine the antimicrobial resistance, and risk factors for occurrence of pathogenic E. coli in livestock and rats. Two slums areas were selected, Korogocho and Viwandani. Two hundred and six households were randomly selected for this study. Fecal samples were aseptically collected from a total of 795 animals and 13 rats from households in the two slums. The samples were cultured for isolation of E. coli using standards methods. The isolates were characterized to various pathotypes and tested for antimicrobial resistance phenotypes using disc diffusion method. Risk factors for occurrence of pathogenic E. coli pathotype in livestock and rats were assessed using a questionnaire administered to the household heads of the selected 206 households. Data was analyzed using STATA (R) and SPSS(R) for descriptive statistics and logistic regression to estimate the prevalence, risk factors for occurrence of E. coli pathotypes and to analyze household attributes in the two regions. Different attributes were analyzed and significant differences compared between the two areas of study at <0.05 level of significance. A total of 1171 E. coli were isolated from livestock and 85 from rats. The prevalence of E. coli n=795 was (49%), with chicken recording the highest prevalence of (35%) and doves and rabbits recording the lowest percentage of (1%) each. There was a significantly higher number of E. coli isolated from rabbits in Korogocho as compared to Viwandani (p < 0.05). Significantly more animals fed close to the dump site in Viwandani (45%) compared to Korogocho (24%) (p = 0.02) and more animals feed next to open sewer in Viwandani (48%) compared to Korogocho (26%) (P = 0.001). Significantly more animals accessed clean water in Korogocho (67%) than Viwandani (44%) (p = 0.001), while more animals in Viwandani (73%) mixed with other animals from other households compared to (30%) Korogocho (p = 0.00) Multiplex PCR was done on 231 E. coli pools. One pool represented six E. coli isolates from the same sample. Eighteen virulence genes were used to identify virulence characteristics for EHEC, EPEC, EAEC, ETEC, EIEC and DAEC E. coli pathotypes. The overall prevalence of E. coli pathotypes was n=795 (5.91%). EHEC had a prevalence of (2.4%), EPEC (1.76%), ETEC (HL) (0.75%), ETEC (HS) (0.13%), EAEC (0.50%) and DAEC (0.38%). The prevalence of resistant E.coli isolated from livestock (n=1171) was (56%) for tetracycline, followed by Trimethoprime/sulfamethoxazole (53%) and Streptomycin (45%).The lowest prevalence was in ciprofloxacin, amoxicillin and clavulinic acid at (1%) each. The prevalence of resistance of E.coli isolated from rats (n=85) was (17%) for tetracycline, Trimethoprime/sulfamethoxazole( 9%) and Streptomycin at (13%), ampicillin(9%), chloramphenicol (4%), ceftazidime (1%), ceftriazone (5%) andcefuroxime (2%).The study indicated serious multidrug resistance with 446 isolates being resistant to three(3) or more antibiotics. One isolated showed resistance to ten (10) antibiotics. In rodents five (5) E. coli isolates showed resistance to three (3) or more antibiotics with one isolate showing resistance to six (6) antibiotics. Risk factor analysis for occurrence of E. coli pathotypes indicated that goats, and over the counter sale of antibiotics to farmers to be significantly associated with the occurrence of E. coli pathotypes (odds ratio >1) and (p < 0.05). This study found the prevalence of E. coli pathotypes in livestock to be 5.9% with a diverse antimicrobial–resistant E. coli population distributed in various livestock species and rats. This poses a potential risk of transfer of antibiotic-resistant E. coli pathogens and antibiotic resistant commensal bacteria into human population during contact. To control transfer of antibiotic-resistant pathogens, the community should be educated on simple concepts like hygiene (hand washing) after handling livestock. Farmers should not buy drugs over the counter but consult a qualified veterinary for animal treatment. Also after handling livestock especially goats, people should wash hands thoroughly. Also due to multidrug resistance demonstrated in this study, the public should be enlightened on the importance of drug withdrawal on meat and milk products after antibiotics are administered to livestock. Government institutions dealing with medicine both veterinary and human need to come together and create policies that will govern the use of antimicrobial agents. Sensitization of the public on dangers of misuse of antimicrobial agents in both human and animals should be done. The importance of culture and antimicrobial sensitivity testing in the management of bacterial diseases should be stressed and closely monitored in hospitals and veterinary laboratories. Bodies regulating drugs used in agriculture as antimicrobials should be included in policy making. Other methods of reducing infection should be adopted. This includes vaccination, proper hygiene and avoiding overcrowding. This will significantly reduce the need for antibiotic use.