**1. Introduction**

*Salmonella enterica* subsp. *enterica* include serotypes that are global foodborne pathogens significantly affecting public health and economy [1–3]. In humans, salmonellosis is classified into typhoid and non-typhoidal salmonellosis. Most cases of non-typhoidal *Salmonella* (NTS) disease are associated with consumption of contaminated foods of animal origin, particularly poultry, meat and in some instances vegetables [4–6]. Globally, NTS is estimated to cause 93.8 million cases of gastroenteritis annually, of which 80 million cases are foodborne and causing 155,000 deaths [7]. Although African countries have low estimated cases of NTS gastroenteritis compared to other parts of the world, they have a much higher level of invasive non-enteric NTS infections [7,8]. NTS bacteraemia

is an emerging opportunistic infection in individuals infected with HIV and is reported to be highly correlated with malaria, especially in children and elderly persons [9–13].

In poultry, transmission of NTS can occur by direct contacts with infected birds, consumption of contaminated feeds and water, and contact with environmental reservoirs [13]. Transmission can also occur through cross contamination anywhere along the production chain, and for specific serotypes, vertical transmission is also possible [14,15]. However, NTS infections in poultry is mainly asymptomatic [14], and may therefore not get the necessary attention with regard to prevention and control. The diversity of NTS circulating in poultry and livestock production environment in most developing countries is poorly understood, as very limited studies have been undertaken. Molecular typing is important for characterization of bacteria to establish genetic relatedness between isolates in order to elucidate the dynamics of the bacterial populations. Although whole genome sequencing is getting more established, pulsed-field gel electrophoresis (PFGE) technique is still considered an adequate molecular method suitable for subtyping of serotypes of *Salmonella*.

The increasing development of antimicrobial resistance (AMR) in NTS is complicating treatment of bacteraemia cases and results in poorer treatment outcomes. Even more worrying is the emergence of multidrug resistance (MDR) in NTS against commonly used antibiotics in human and animal treatment, which has become a serious public health challenge [15–18]. Resistance is increasing not only against first line antibiotics, but also against clinically important antimicrobial agents like fluoroquinolones and third generation cephalosporins [19]. Inappropriate use of antimicrobials in agriculture is known to be a key factor contributing to the development of AMR, and the influence of livestock environment in the development of MDR in NTS has been demonstrated [20]. Increased intensification of production in agriculture, use of antibiotics as feed additives, and prophylactic treatment are some of the practices that influence development of AMR [21,22]. MDR NTS can be transferred from the poultry reservoirs to humans through the food chain, but AMR can also be transferred from one bacterium to another through resistance genes associated with integrons and mobile genetic elements such as plasmids and transposons. Most studies on AMR in poultry are done in developed countries while in most developing countries, including Uganda, there are no surveillance and monitoring programs for important foodborne pathogens and AMR in primary production units. To date in Africa, only a few limited studies have documented AMR and corresponding genes in NTS isolated from humans, animal products, and poultry farms [23–29]. Therefore, data is scarce and the extent of NTS and AMR remains poorly known. As a result, development of appropriate mitigation measures and control efforts is compromised. The aim of this study was to characterize a collection of NTS isolates from poultry by using PFGE for molecular subtyping and to investigate the presence of integrons and acquired antimicrobial resistance genes from the phenotypically resistant isolates. The NTS were isolated from faecal samples collected from poultry farms in three districts (Wakiso, Lira, and Masaka) in Uganda between 2015 and 2016 [30].
