We tested the hypothesis that the time course of the evolution of antifungal drug resistance depends on the ploidy of the fungus. The experiments were designed to measure the initial response to the selection imposed by the antifungal drug fluconazole up to and including the fixation of the first resistance mutation in populations of Saccharomyces cerevisiae. Under conditions of low drug concentration, mutations in the genes PDR1 and PDR3, which regulate the ABC transporters implicated in resistance to fluconazole, are favored. In this environment, diploid populations of defined size consistently became fixed for a resistance mutation sooner than haploid populations. Experiments manipulating population sizes showed that this advantage of diploids was due to increased mutation availability relative to that of haploids; in effect, diploids have twice the number of mutational targets as haploids and hence have a reduced waiting time for mutations to occur. Under conditions of high drug concentration, recessive mutations in ERG3, which result in resistance through altered sterol synthesis, are favored. In this environment, haploids consistently achieved resistance much sooner than diploids. When 29 haploid and 29 diploid populations were evolved for 100 generations in low drug concentration, the mutations fixed in diploid populations were all dominant, while the mutations fixed in haploid populations were either recessive (16 populations) or dominant (13 populations). Further, the spectrum of the 53 nonsynonymous mutations identified at the sequence level was different between haploids and diploids. These results fit existing theory on the relative abilities of haploids and diploids to adapt and suggest that the ploidy of the fungal pathogen has a strong impact on the evolution of fluconazole resistance.

Extended overuse and misuse of antibiotics and other antibacterial agents has resulted in an antimicrobial resistance crisis. Bacteriophages, viruses that infect bacteria, have emerged as a legitimate alternative antibacterial agent with a wide scope of applications which continue to be discovered and refined. However, the potential of some bacteriophages to aid in the acquisition, maintenance, and dissemination of negatively associated bacterial genes, including resistance and virulence genes, through transduction is of concern and requires deeper understanding in order to be properly addressed. In particular, their ability to interact with mobile genetic elements such as plasmids, genomic islands, and integrative conjugative elements (ICEs) enables bacteriophages to contribute greatly to bacterial evolution. Nonetheless, bacteriophages have the potential to be used as therapeutic and biocontrol agents within medical, agricultural, and food processing settings, against bacteria in both planktonic and biofilm environments. Additionally, bacteriophages have been deployed in developing rapid, sensitive, and specific biosensors for various bacterial targets. Intriguingly, their bioengineering capabilities show great promise in improving their adaptability and effectiveness as biocontrol and detection tools. This review aims to provide a balanced perspective on bacteriophages by outlining advantages, challenges, and future steps needed in order to boost their therapeutic and biocontrol potential, while also providing insight on their potential role in contributing to bacterial evolution and survival.

Streptococcus suis is ubiquitous in swine, and yet, only a small percentage of pigs become clinically ill. The objective of this study was to describe the distribution of serotypes, virulence-associated factor (VAF), and antimicrobial resistance (AMR) genes in S. suis isolates recovered from systemic (blood, meninges, spleen, and lymph node) and non-systemic (tonsil, nasal cavities, ileum, and rectum) sites of sick and healthy pigs using whole-genome sequencing. In total, 273 S. suis isolates recovered from 112 pigs (47 isolates from systemic and 136 from non-systemic sites of 65 sick pigs; 90 isolates from non-systemic sites of 47 healthy pigs) on 17 Ontario farms were subjected to whole-genome sequencing. Using in silico typing, 21 serotypes were identified with serotypes 9 (13.9%) and 2 (8.4%) as the most frequent serotypes, whereas 53 (19.4%) isolates remained untypable. The relative frequency of VAF genes in isolates from systemic (Kruskal–Wallis, p < 0.001) and non-systemic (Kruskal–Wallis, p < 0.001) sites in sick pigs was higher compared with isolates from non-systemic sites in healthy pigs. Although many VAF genes were abundant in all isolates, three genes, including dltA [Fisher's test (FT), p < 0.001], luxS (FT, p = 0.01), and troA (FT, p = 0.02), were more prevalent in isolates recovered from systemic sites compared with non-systemic sites of pigs. Among the isolates, 98% had at least one AMR gene, and 79% had genes associated with at least four drug classes. The most frequently detected AMR genes were tetO conferring resistance to tetracycline and ermB conferring resistance to macrolide, lincosamide, and streptogramin. The wide distribution of VAFs genes in S. suis isolates in this study suggests that other host and environmental factors may contribute to S. suis disease development.

The goal of this study was to determine the frequency of resistance to extended-spectrum cephalosporins (ESCs) in Escherichia coli and other Enterobacterales from turkeys in Canada and characterize the associated resistance determinants. Pooled fecal samples were collected in 77 turkey farms across British Columbia, Québec, and Ontario. Isolates were obtained with and without selective enrichment cultures and compared to isolates from diagnostic submissions of suspected colibacillosis cases in Ontario. Isolates were identified using MALDI-TOF and susceptibility to ESCs was assessed by disk diffusion. The presence of bla_CMY, bla_CTX-M, bla_TEM, and bla_SHV was tested by PCR. Transformation experiments were used to characterize bla_CMY plasmids. Genome sequencing with short and long reads was performed on a representative sample of bla_CTX-M-positive isolates to assess isolates relatedness and characterize bla_CTX-M plasmids. For the positive enrichment cultures (67% of total samples), 93% (587/610) were identified as E. coli, with only a few other Enterobacterales species identified. The frequency of ESC resistance was low in E. coli isolates from diagnostic submission (4%) and fecal samples without selective enrichment (5%). Of the ESC-resistant Enterobacterales isolates from selective enrichments, 71%, 18%, 14%, and 8% were positive for bla_CMY, bla_TEM, bla_CTX-M, and bla_SHV, respectively. IncI1 followed by IncK were the main incompatibility groups identified for bla_CMY plasmids. The bla_CTX-M-1 gene was found repeatedly on IncI1 plasmids of the pMLST type 3, while bla_CTX-M-15, bla_CTX-M-55, and bla_CTX-M-65 were associated with a variety of IncF plasmids. Clonal spread of strains carrying bla_CTX-M genes between turkey farms was observed, as well as the presence of an epidemic bla_CTX-M-1 plasmid in unrelated E. coli strains. In conclusion, Enterobacterales resistant to ESCs were still widespread at low concentration in turkey feces two years after the cessation of ceftiofur use. Although bla_CMY-2 is the main ESC resistance determinant in E. coli from Canadian turkeys, bla_CTX-M genes also occur which are often carried by multidrug resistance plasmids. Both clonal spread and horizontal gene transfer are involved in parallel in the spread of bla_CTX-M genes in Enterobacterales from Canadian turkeys.