We previously developed Multilevel Genome Typing (MGT), a typing system encompassing multiple MLST schemes, and enabling epidemiological and microbiological investigations at multiple levels of resolutions. The publicly available typing system MGTdb (mgtdb.unsw.edu.au), currently comprises >65,000 isolates of Salmonella enterica serovar Typhimurium (STM) - one of the most frequent serovars causing infections worldwide.
In this study, we analysed the antimicrobial resistance (AMR) profiles of the public STM isolates in MGTdb. We used abritAMR to identify resistance genes and predict phenotypic resistance to 14 major drug classes in 58,563 isolates in MGTdb. High resistance (>30%) was observed to four antibiotic classes, intermediate resistance (<20% and >1%) to seven classes, and low resistance (≤1%) to three classes. Six drugs (azithromycin, ciprofloxacin, amoxicillin, trimethoprim-sulfamethoxazole, cefotaxime and ceftriaxone) are commonly prescribed in certain cases such as in invasive disease or infection in children. Evaluating resistance to the first four drugs was straightforward using abritAMR, resistance to the last two was evaluated by considering the reported resistance mechanisms of extended spectrum β-lactamases (ESBL) and the specific AmpC β-lactamases (AmpC). We found low global resistance to azithromycin (1%) and ESBL (1%); followed by relatively low resistance to AmpC (4.3%), ciprofloxacin (6.9%) and trimethoprim-sulfamethoxazole (9.6%); but high level of resistance to amoxicillin (33.9%). Resistance to each of these six drugs was also present in Australian isolates in MGTdb. Upon analysing the MGT sequence types (MGT STs), we identified 14 MGT STs, comprising 328 isolates, as being multidrug resistant (MDR) with resistance to ≥ three prescribed drugs. Atmost resistance was observed to four prescribed drugs. Additionally, we identified 10 MGT STs comprising 1,349 isolates as being susceptible to all six drugs.
In summary, we analysed the global patterns of AMR in STM isolates within MGTdb. Although, resistance to commonly prescribed drugs is moderate or relatively low - with the exception of ampicillins, isolates with resistance to all drugs are present within Australia - highlighting the need for continued surveillance of resistance in this pathogen.