A tale of two plasmids: contributions of plasmid associated phenotypes to epidemiological success among Shigella

Abstract

Dissemination of antimicrobial resistance (AMR) genes by horizontal gene transfer (HGT) mediated through plasmids is a major global concern. Genomic epidemiology studies have shown varying success of different AMR plasmids during outbreaks, but the underlying reasons for these differences are unclear. Here, we investigated two Shigella plasmids (pKSR100 and pAPR100) that circulated in the same transmission network but had starkly contrasting epidemiological outcomes to identify plasmid features that may have contributed to the differences. We used plasmid comparative genomics to reveal divergence between the two plasmids in genes encoding AMR, SOS response alleviation and conjugation. Experimental analyses revealed that these genomic differences corresponded with reduced conjugation efficiencies for the epidemiologically successful pKSR100, but more extensive AMR, reduced fitness costs, and a reduced SOS response in the presence of antimicrobials, compared with the less successful pAPR100. The discrepant phenotypes between the two plasmids are consistent with the hypothesis that plasmid-associated phenotypes contribute to determining the epidemiological outcome of AMR HGT and suggest that phenotypes relevant in responding to antimicrobial pressure and fitness impact may be more important than those around conjugation in this setting. Plasmid phenotypes could thus be valuable tools in conjunction with genomic epidemiology for predicting AMR dissemination.

The evolution and international spread of extensively drug resistant Shigella sonnei

“…The plasmid backbone encodes conjugation and stabilisation machinery and carries psiB (plasmid SOS inhibition), recently shown to inhibit the disruptive host SOS response to subminimal inhibitory concentrations of cipro oxacin. 19 Plasmids from single isolates from France and NSW also match the plasmid from the UK and searches revealed that all of these plasmids are also near identical to p893816, reported in MSM-associated CipR.MSM5 S. sonnei in London in 2020, 64 and perhaps more strikingly Plasmid 3 from an Australian S. exneri 3a isolated in 2018 (Table 2, Supplementary Fig. 1B).…”

“…18 The acquisition of resistance against recommended treatments for shigellosis and other STIs is a global public health concern, heralding an increased risk of treatment failure, and the emergence of pan-drug resistance (PDR) in S. sonnei. 70 Given the global transmission of the low the tness cost MDR pKSR100-type plasmids among various serotypes of Shigella, 19 we predict that the ESBL plasmid p893916, and others like it, will continue to spread via horizontal gene transfer to other species and serotypes of Shigella in MSM. Alternatively -or concurrently -other species and serotypes of Shigella could follow a similar journey of stepwise accumulation of AMR determinants, resulting in the acquisition of resistance to third-generation cephalosporins.…”

“…17,19 Our previous investigations suggested that pKSR100 (GenBank accession CP090162) conferred a lower tness cost on the bacterial host than another co-circulating AMR plasmid, pAPR100 (GenBank accession CP090161), which did not disseminate more broadly. 19 Repeating these experiments con rmed that a p893816-like plasmid is conjugative and had a similarly low tness cost as pKSR100 (Fig. 4).…”

“…E. coli MG1655 carrying pKSR100 or pAPR100 were from isolates obtained from the UKHSA, as previously described. 19 E. coli MG1655 and derivatives that each carry a different plasmid were inoculated into M9 minimal media supplemented with thiamine (10 µg/ml) and grown overnight with shaking at 220 rpm at 37˚C. These precultures were adjusted to OD 600 0.05 in a total volume of 1 ml and 150 µl aliquots inoculated into individual wells of a 96well plate (Greiner Bio One, UK).…”

“…17 The rst global transmission of azithromycin resistant shigellosis was described among MSM, driven by the acquisition of a low-tness cost AMR plasmid, and frequent use of antimicrobials for other sexually transmitted illnesses (STIs) leading to bystander resistance. 18,19 The acquisition of resistance to cipro oxacin, recommended by the World Health Organisation (WHO) for empirical treatment of shigellosis, 20 and increasing MDR in S. sonnei has earned it a place as a WHO priority organism for which new antimicrobials are urgently needed. 21 The extensive global dissemination of MDR S. sonnei subsequently led to periodic outbreaks of extensively drug resistant (XDR) S. sonnei that combine resistance to cipro oxacin, azithromycin and extended-spectrum β-lactam antibiotics (e.g., ceftriaxone).…”