Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing

Fluoroquinolone (FQ)-resistant Salmonella spp. were listed by the WHO in 2017 as priority pathogens for which new antibiotics were urgently needed. The overall global burden of Salmonella infections is high, but differs per region. Whereas typhoid fever is most prevalent in South and South-East Asia, non-typhoidal salmonellosis is prevalent across the globe and associated with a mild gastroenteritis. By contrast, invasive non-typhoidal Salmonella cause bloodstream infections associated with high mortality, particularly in sub-Saharan Africa. Most Salmonella strains from clinical sources are resistant to first-line antibiotics, with FQs now being the antibiotic of choice for treatment of invasive Salmonella infections. However, FQ resistance is increasingly being reported in Salmonella, and multiple molecular mechanisms are already described. Whole-genome sequencing (WGS) is becoming more frequently used to analyse bacterial genomes for antibiotic-resistance markers, and to understand the phylogeny of bacteria in relation to their antibiotic-resistance profiles. This mini-review provides an overview of FQ resistance in Salmonella, guided by WGS studies that demonstrate that WGS is a valuable tool for global surveillance.

• Surrogate disk diffusion test: the results of pefloxacin disk diffusion testing are predicting susceptibility and resistance of Salmonella to ciprofloxacin [2] and is therefore an alternative for low-resource settings. Pefloxacin disk diffusion testing is however not indicative for the aac(6')-Ib-cr PMQR mechanism [2]. Prior to pefloxacin, nalidixic acid (a nonfluorinated quinolone) disk diffusion was used as a predictor for ciprofloxacin susceptibility testing, but its susceptibility was not affected by gyrB and PMQR mechanisms. Zone diameters and MICs are interpreted based on 'cut-off values' or 'breakpoints'. The following interpretative categories can be distinguished. The breakpoints for fluoroquinolone activity against Salmonella are given in Table SB1 and Table SB2.

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Bacteria with a MIC at or below (or with a zone diameter at or above) the susceptibility breakpoint are categorized as Susceptible (S): at the recommended dosage, clinical efficacy is predicted.

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Bacteria with a MIC at or above (or with a zone diameter at or below) the resistance breakpoint are categorized as Resistant (R): at the recommended dosage, clinical efficacy is not assured. • Bacteria with a MIC or a zone diameter in between the susceptible and resistance breakpoints are categorized as Intermediate (I): this category implies clinical efficacy in body sites where antibiotics are physiologically concentrated (e.g. urine) or when a higher than normal dosage of an antibiotic can safely be used. For invasive Salmonella infections, this clinical use and category are not applicable.

Molecular mechanisms
No mutations in the QRDR regions of the gyrA and parC genes [10].
Single chromosomal point mutations in the QRDR regions of the gyrA, gyrB, parC or parE genes [3] Two or more mutations in the gyrA gene, and an additional par mutation [3,10] PMQR genes (qnr variants and aac(6')-Ib-cr) Efflux pump mechanisms can be involved [11] Clinical implications Treatment with FQ (ciprofloxacin) is predicted to be successful The fourth-generation gatifloxacin remained efficacious for treatment of non-complicated infections caused by DCS Salmonella Typhi strains [12,13].
Salmonella Typhi isolates, with ciprofloxacin MIC values ≥ 16 µg/ml and gatifloxacin MIC values ≥ 1 µg/mL were associated with therapeutic failure of gatifloxacin during a clinical trial in Nepal [14].

Occurrence of resistance
Salmonella Typhi DCS strains are now worldwide dominating, partly catalyzed by the spread of the H58 clade [15] Until recently, full resistance to ciprofloxacin was rare; it was mainly confined to Salmonella Typhi/Paratyphi A in India and Tajikistan [7].