Screening for Carriage and Antimicrobial Resistance of HelicobacterPylori, Escherichia coli and Klebsiella species among Patients presenting with Gastritis in Kibera and Dagoretti areas in Nairobi, Kenya

Abstract

Helicobacter pylori is a global threat to the health sector affecting about a half of the entire population worldwide. In Kenya, 54.8% of people with gastrointestinal complications have been reported, however, this was data from a hospital-based study. Community acquired antimicrobial resistance (AMR) strains have emerged as a threat to public health and are associated with high morbidity and mortality rates. Escherichia coli and Klebsiella species are known reservoirs of resistant genes including Extended Spectrum Beta Lactamases (ESBL) and Klebsiella Pneumoniae Carbapenemases. H. pylori also, despite its pathogenicity, is rapidly increasing resistance towards available antimicrobial agents. Despite the threat to public health, limited data exist on prevalence, risk factors and AMR trends of H. pylori, E. coli, and Klebsiella. This study determined prevalence and AMR patterns of these three bacterial organisms as well as risk factors for H. pylori infection. A cross sectional study was conducted among outpatients presenting with gastritis-like symptoms in Mbagathi and Mutuini hospitals in Nairobi. A hundred and seventy-two identified patients were requested to consent to take part in the study. Follow-up visits were made and recruited 237 immediate contacts. Stool samples were collected and aseptically transported to the Mbagathi hospital laboratory for microbiological analysis. All stool samples were tested for H. pylori using rapid kit and the positive ones cultured on Columbia agar, and confirmed by PCR. For E. coli and Klebsiella isolation, all stool samples were cultured on MacConkey. Further identification was by Biochemical tests using standard methods including catalase and urease for H. pylori and Indole Methyl red Voges and Citrate for E. coli and Klebsiella. AMR genes were confirmed by Polymerase Chain Reaction. Risk factors were determined by the Logistic regression model using P-value (P) and odds ratio (OR). Infection was recorded in 83.3% of all participants. Of these, 73.8% were infected with E. coli, 28.6% with H. pylori and 39.1% with Klebsiella. Infection was predominant among Kibera participants (57.7%) when compared to those from Dagoretti (25.7%). Over 90% of patients were infected while 70.1% of contacts had infection. Co-infections among the three bacteria was reported in 25% participants. Antimicrobial resistance was observed in 64.2% isolates. Resistance in H. pylori was found against Amoxicillin (1%) Metronidazole (3.5%). Resistance in E. coli and Klebsiella was high against Sulfamethoxazole Trimethoprim (RL) 80% vs. 71% and Tetracycline (TET) 68% vs. 59% while low resistance was found in Imipenem (IPM), 16% vs 19%. Klebsiella exhibited high resistance (55%). Most isolates (25%) were resistant to more than three antimicrobial agents. ESBL was noted in 44% with Oxacillinases (OXA gene) being pre-dominant (65%). A person residing in Kibera was 1.8 more likely to acquire infection (P=0.014, OR:1.8 CI 1.1- 2.9. Similarly, smokers were at high risk of infection (P=0.03, OR=1.46 CI 1.13 - 2.88), and in those who had other bacterial infections (P<0.05, OR 1.07 CI 0.88-1.31) Most available antimicrobial agents including broad spectrum are rapidly becoming ineffective in fight against most bacterial isolates. Place of residence, presence of other microbial agents and unhealthy lifestyle were considered potential risk factors associated with H. pylori infection. Based on the findings, it can be concluded that symptoms of gastritis needs to be supported with laboratory testing during clinical diagnoses of H. pylori patients Mass screening is will be critical in early detection and subsequent treatment to reduce resistance rate. Enforcing the antimicrobial access regulations such as restricting the over counter sale and public awareness about drivers of AMR should be enacted to help fight against infection and AMR in line with vision 2030.