Differing burden and epidemiology of non-Typhi Salmonella bacteremia in rural and urban Kenya, 2006-2009

Abstract

Background: The epidemiology of non-Typhi Salmonella (NTS) bacteremia in Africa will likely evolve as potential co-factors, such as HIV, malaria, and urbanization, also change.

Methods: As part of population-based surveillance among 55,000 persons in malaria-endemic, rural and malaria-nonendemic, urban Kenya from 2006-2009, blood cultures were obtained from patients presenting to referral clinics with fever ≥38.0°C or severe acute respiratory infection. Incidence rates were adjusted based on persons with compatible illnesses, but whose blood was not cultured.

Results: NTS accounted for 60/155 (39%) of blood culture isolates in the rural and 7/230 (3%) in the urban sites. The adjusted incidence in the rural site was 568/100,000 person-years, and the urban site was 51/100,000 person-years. In both sites, the incidence was highest in children <5 years old. The NTS-to-typhoid bacteremia ratio in the rural site was 4.6 and in the urban site was 0.05. S. Typhimurium represented >85% of blood NTS isolates in both sites, but only 21% (urban) and 64% (rural) of stool NTS isolates. Overall, 76% of S. Typhimurium blood isolates were multi-drug resistant, most of which had an identical profile in Pulse Field Gel Electrophoresis. In the rural site, the incidence of NTS bacteremia increased during the study period, concomitant with rising malaria prevalence (monthly correlation of malaria positive blood smears and NTS bacteremia cases, Spearman's correlation, p = 0.018 for children, p = 0.16 adults). In the rural site, 80% of adults with NTS bacteremia were HIV-infected. Six of 7 deaths within 90 days of NTS bacteremia had HIV/AIDS as the primary cause of death assigned on verbal autopsy.

Conclusions: NTS caused the majority of bacteremias in rural Kenya, but typhoid predominated in urban Kenya, which most likely reflects differences in malaria endemicity. Control measures for malaria, as well as HIV, will likely decrease the burden of NTS bacteremia in Africa.

Figure 1. Antimicrobial resistance patterns among invasive S. Typhimurium (n = 45) in rural western Kenya, 2006–2009.

Chl is chloramphenicol, sxt is trimethoprim-sulfamethoxazole, Tetr is tetracycline, Cip is ciprofloxacin, Nal is nalidixic acid, Amp is ampicillin, Sxz is sulfisoxazole, Strep is streptomycin, Kan is kanamycin, Genta is gentamycin, Ctx is ceftriazone, Amc is amoxicillin-clavulinic acid, Multi Drug Resistance (MDR) defined as resistance to chloramphenicol, trimethoprim-sulfamethoxazole and ampicillin.

Figure 2. PFGE Gel patterns from XbaI restriction enzyme of Salmonella typhimurium isolates from blood and stool, western Kenya, 2006–2009.

Figure 3. Numbers of NTS bacteremia, smear-positive malaria cases and blood cultures done by quarter of the year, rural western Kenya, 2006–2009.

A. All persons (spearman rank correlation coefficient, 0.87, p = 0.0003). B. Children <5 years old (spearman rank correlation coefficient, 0.66, p = 0.018). C. Persons ≥5 years of age (spearman rank correlation coefficient, 0.43, p = 0.18).