Antimicrobial Resistance in Endemic Enteric Infections in Kenya and the Region, and Efforts Toward Addressing the Challenges

Abstract

Resistance to commonly available antimicrobials is a major threat to the fight against endemic bacterial diseases in sub-Saharan Africa (SSA), with majority of the population unable to afford alternative effective antimicrobial options for management of these diseases. Diseases such as typhoid, cholera and invasive non-typhoidal salmonella (NTS) are among the key enteric infections endemic in most parts of SSA, especially in displaced populations and among the urban populations living in overcrowded informal settlements. Here, we explore the prevalence and the genomic epidemiology of these infections and the growing problem of multidrug resistance (MDR) including emerging resistance to the last line of treatment for these infections. Prevalence rates to commonly available antimicrobials including ampicillin, chloramphenicol, co-trimoxazole and tetracycline, now range between 65-80%, while 15-20% of recently studied isolates show reduced susceptibility to fluoroquinolones and emerging resistance to extended spectrum beta-lactams (ESBLs) mediated by the CTX-M-15 gene carried on a highly mobile genetic element. The high prevalence of MDR isolates including resistance to reserve antibiotics, calls for enhanced control and management options. It will be important for governments in the region to enhance the implementation of National Action Plans as guided by the Global Action Plan championed by the World Health Organisation (WHO) to combat the threat of antimicrobial resistance. However, these efforts will require a strong commitment and enhanced at all different levels of healthcare in order to yield meaningful results. In addition, utilization of WHO approved vaccines in the short-to-medium term and improvement of water and sanitation in the long term will reduce burden of disease and AMR in the region.

Antimicrobial Susceptibility Profiles of Diarrheagenic Escherichia coli Strains Isolated in Children Below Five Years and Food Animals Kisumu County, Kenya

“…In Kenya, antibiotic therapy is recommended for treatment of dysentery and salmonellosis for children below five years, while oral rehydration solutions and zinc sulphate are recommended for the management of DEC-related diarrhea (MOH 2016). However, low diagnostic capacities in lowmiddle income countries promote empiric treatment of childhood diarrhoea with antibiotics, which likely contributes to the emergence of resistant strains [20]. This study reports on low prevalence of resistance towards Gentamicin and ciprofloxacin to EAEC, EPEC and ETEC isolates which contrast certain studies in Burkhina faso [21].…”

<i>Escherichia coli</i> Pathotypes in Children with Acute Diarrhea in an Informal Settlement in Nairobi, Kenya

“…In Kenya, antibiotic therapy for infant or childhood diarrhoea is recommended for the treatment of dysentery and salmonellosis, while oral rehydration solutions and zinc sulphate are recommended for the management of DEC-related diarrhoea [41]. However, low diagnostic capacities in low-middle income countries promote empiric treatment of childhood diarrhoea with antibiotics, which likely contributes to the emergence of resistant strains [42]. For informal settlements, where dense populations and unsanitary environmental conditions can facilitate the transmission of multidrug-resistant bacteria [43] [44] [45], antibiotic stewardship efforts are best complemented with water, sanitation and hygiene interventions to reduce childhood diarrhea-related deaths.…”

Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58

“…Our data also suggest a population replacement of the historical genotypes by H58; similar to what has previously been observed in different countries of Asia and sSA [ 51 – 53 ]. Genotype 4.3.1 has emerged in Asia and has shown intercontinental transmission from South Asia to East Africa where it established [ 20 , 22 , 51 , 54 ]. Our data suggest a separate introduction in Rwanda giving rise to a stable population, possibly directly from Asia.…”

“…This haplotype showed intercontinental transmission from South Asia to East Africa and is associated with high levels of MDR and DCS [ 20 ]. While genotype 4.3.1 is dominant in East sSA [ 21 , 22 ], genotype 3.1.1 dominates West sSA [ 21 ].…”