David C. Alexander

Nontuberculous mycobacteria (NTM) is a generic term for the >200 species of environmental mycobacteria . NTM are ubiquitous, but there is extensive variation in the distribution of individual species. In a recent article published in Applied and Environmental Microbiology , Wilsey et al. describe how community-based citizen science efforts helped map the distribution of NTM in Hawai’i (R. N. Wilsey, L.-H. Ding, S. N. Dawrs, C. K. Raulerson, et al., Appl Environ Microbiol 92:e00269-26, 2026, https://doi.org/10.1128/aem.00269-26 ). Mycobacterium chimaera , an opportunistic pathogen and the leading cause of NTM pulmonary disease in Hawai’i, was among the most common species isolated.

The incidence of disseminated gonococcal infection (DGI) has remained low since the advent of antibiotics; however, a recent surge in DGI has inexplicably emerged during the past decade. In an effort to understand whether Neisseria gonorrhoeae that cause disseminated disease can be differentiated from non-invasive strains, we have performed a phenotypic and genotypic analysis on a selection of isolates obtained from invasive and uncomplicated infections in Canada. The increase in DGI was initially associated with a single antibiotic-susceptible gonococcal lineage, but later cases have been caused by diverse strains. Phenotypic analysis of a matched subset of 20 isolates obtained since 2013 found that these varied in their capacity to aggregate in suspension and in their association with serum complement proteins; however, these interactions did not discriminate between the invasive and mucosal isolates. Sequence typing of 360 Canadian isolates revealed that two variant porBa alleles are significantly associated with the DGI strains, one of these being present throughout the past decade, whereas the other emerged more recently. A PopNet-based population dynamics analysis, which instead establishes relationships based upon variance among discrete chromosomal segments, revealed that DGI isolates were restricted to distinct subpopulations within their phylogenetic distribution, implying a genetically linked potential to cause invasive disease. Consistent with this, a large number of genetic determinants are enriched in the DGI strains, making these enticing candidates to explain the increased capacity of N. gonorrhoeae to cause systemic infection and/or reduce the presentation of clinical symptoms from localized infection so that it remains untreated. IMPORTANCE: The re-emergence of disseminated gonococcal infections (DGIs) has raised concern that the virulence of some strains has increased due to their acquisition of a new capacity to remain asymptomatic during uncomplicated mucosal infection and/or to invade the bloodstream and persist upon establishing colonization at distal tissue sites. The molecular epidemiology of a very large incidence of DGI in Canada, which began from a single strain but then diversified with time, provided an opportunity to understand whether the invasive isolates were either phenotypically or genotypically related. While classical phenotypic analysis did not discriminate between mucosal and invasive isolates, a population dynamics-based approach established that the DGI isolates are present within distinct subpopulations of Neisseria gonorrhoeae and reveals genetic determinants that are linked to this phenotype. This suggests that the DGI phenotype emerged multiple times independently and/or the genetic features responsible have been transmitted among the populations.

Macrolides (clarithromycin and azithromycin) are a mainstay of therapy for infections caused by rapidly growing mycobacteria (RGM). Historically, macrolide resistance in RGM species is associated with mutations in the 23S rRNA gene and chromosomal erythromycin ribosome methylase (erm) genes. We recently described macrolide resistance in the RGM species, Mycobacterium chelonae, due to a novel, plasmid–encoded erm(55) gene. For this study, we expanded our search to pigmented RGM species. Clinical isolates from two U.S. reference laboratories were screened. Isolates were collected between 1997 and 2024 from diverse clinical sites and multiple geographic locales. Here, we describe the genetic diversity of 30 erm(55)–containing plasmids from six different RGM species. The plasmids share a common 126 kb backbone but, due to insertions and deletions, vary in size from 119 to 173 kb. Six plasmids carry heavy metal resistance operons in addition to erm(55). These results imply that erm(55)–containing plasmids are highly promiscuous, conjugative, and have been spreading unnoticed for decades. They are present in M. chelonae as well as pathogenic pigmented RGM species, including M. bacteremicum, M. grossiae, M. iranicum, M. neoaurum and M. obuense. Their spread to other RGM species seems inevitable and has serious implications for antimicrobial therapy.

Candida glabrata ( Nakaseomyces glabratus ) is an important cause of invasive fungal infections and may exhibit reduced susceptibility toward antifungal drugs. Here, we used whole-genome sequencing to investigate the genomic phylogeny and identify genetic determinants of antifungal resistance in a collection of 142 clinical C. glabrata isolates obtained from the 10 provinces of Canada between 2013 and 2020. Our study prioritized resistant isolates ( n = 62, 43.7%) from invasive infections to better understand antifungal resistance and represents the largest national genomic survey of clinical C. glabrata isolates performed to date in Canada. Phylogenomic analysis based on single-nucleotide variants in the core genome revealed 15 genetically related clusters of C. glabrata . The largest cluster (cluster I, n = 29) was significantly associated with antifungal resistance ( P value = 0.0112). Antifungal-resistant isolates were present in almost all clusters, suggesting that resistance most likely arises from selective pressure during antifungal therapy, rather than dissemination of resistant clones. Thirty-six unique PDR1 variants were found in 38/52 (73.1%) fluconazole-resistant C. glabrata isolates, with more than half identified in this study as potential novel azole resistance variants. Well-characterized hot-spot variants in FKS genes ( n = 5) were found in 12/13 (92.3%) micafungin-resistant C. glabrata isolates. Our genomic analysis highlights the diversity in strain types and sheds light on potential genetic mechanisms of resistance in Canadian isolates of C. glabrata . IMPORTANCE: Candida glabrata , also known as Nakaseomyces glabratus , is a type of yeast that can cause infections in individuals with weakened immune systems. Invasive infections can be difficult to treat since some C. glabrata isolates may not respond well to common antifungals. We studied a large collection of C. glabrata isolates collected from across Canada to better understand how C. glabrata spreads and why this fungal pathogen sometimes resists treatment. Using whole-genome sequence analysis, we found that drug resistance appears in different strains independently, likely as a result of treatment, rather than spreading from a single clone. We also identified specific mutations that may be linked to resistance to commonly used antifungal drugs, such as fluconazole and micafungin. Our research shows how valuable whole-genome sequencing is for understanding the spread and drug resistance of C. glabrata , which can help improve treatment and infection control.

Mycobacterium avium subsp. hominissuis (MAH) is a clinically important species of non-tuberculous mycobacteria that causes infections in a variety of hosts. This opportunistic pathogen is widespread in the environment, including natural and engineered water systems across the globe. To examine the current genetic diversity of this organism, we analysed 702 MAH genomes isolated from humans, pigs and environmental sources across six countries and three continents. Through Bayesian population structure analysis, we identified ten distinct global lineages, including seven previously described and three new ones. Several lineages exhibited regional clustering, including sequence cluster 6 (SC6) in Germany and SC8 in both the USA and Germany. Further analysis identified recombination hotspots in membrane proteins associated with virulence, antimicrobial resistance and immune modulation, driven by insertion sequences and other elements that frequently integrate at tRNA gene sites. This work demonstrates the remarkable genomic diversity of MAH and provides insight into the evolutionary mechanisms that contribute to its success as a pathogen in both humans and animals.

We report complete genome sequences of four Burkholderia cepacia complex isolates from cystic fibrosis patients which consist of three circular chromosomes and zero to two plasmids.

Colistin is a last-resort treatment for highly drug-resistant bacterial infections. Of 47,184 Salmonella isolates collected from 2017 to 2022 in Canada from human and animal/food sources, mobile colistin resistance ( mcr ) variants conferring colistin resistance were detected exclusively in humans ( n = 15). These variants were mcr -1.1 ( n = 7), mcr -3.1 ( n = 5), mcr -3.2 ( n = 2), and mcr -1.2 ( n = 1). The most common mcr -containing serotypes were I 4,[5],12:i:- ( n = 8) and Typhimurium ( n = 3). The proportion of Salmonella carrying mcr genes remains low in Canada (0.03%). IMPORTANCE: Colistin can be used in combination with other drugs as salvage therapy for extensively drug-resistant infections. If mobile colistin resistance ( mcr ) becomes widely disseminated in Enterobacterales , colistin will no longer be an option for salvage therapy in otherwise untreatable infections. While colistin is not commonly used to treat human Salmonella infections, Salmonella represents an important reservoir of mcr genes that may be transmitted to other gram-negative bacteria. Our aim was to determine the occurrence of mcr genes in Salmonella isolates collected from humans, food animals, and retail meats in Canada.

Antimicrobial resistance (AMR) is a global threat. The identification and characterization of novel resistance genes is integral to AMR surveillance. The erm (55) gene was originally identified through whole genome sequencing of macrolide-resistant strains of Mycobacterium chelonae . The gene was annotated as a ribosomal methyltransferase, but its role as a determinant of macrolide resistance was not formally demonstrated. Three erm (55) alleles have now been documented. The plasmid-borne erm (55) ^P , the transposon-associated erm (55) ^T , and the chromosomal encoded erm (55) ^C exhibit ≈82% amino acid sequence identity. Here, we confirm that, when expressed from plasmids in a macrolide-susceptible strain of Escherichia coli , all three erm (55) variants confer resistance to azithromycin and clarithromycin. IMPORTANCE: Macrolide antibiotics are often the only oral treatment option for infections with rapidly growing mycobacteria such as Mycobacterium abscessus and Mycobacterium chelonae . We previously identified three variants of a newly predicted macrolide resistance gene, erm (55), in M. chelonae , including the first case of a plasmid-mediated macrolide resistance in mycobacteria. The present study provides experimental evidence that the three erm (55) variants confer macrolide resistance and that each variant is unique in the degree to which it reduces susceptibility to clinically relevant macrolides.

Ciprofloxacin is important for treatment of severe or invasive Salmonella infections in humans. As laboratories transition from phenotypic to genomics-based methods for determining ciprofloxacin non-susceptibility, it is important to define the correlation between genetic determinants of resistance and phenotypic outcomes. Here, we examined ciprofloxacin resistance mechanisms in Salmonella and tested the hypothesis that isolates containing only one mechanism had intermediate resistance while isolates containing two or more mechanisms had full resistance according to breakpoints from the Clinical Laboratory Standards Institute. Among 13 750 human and food/animal Salmonella enterica isolates, 2325 were predicted to be non-susceptible to ciprofloxacin using whole genome sequencing and Staramr. The most common mechanisms of resistance were mutations in gyrA (especially S83F and D87N/D87Y) and the qnrB19 allele. Only 28% of ciprofloxacin resistant isolates had two or more resistance mechanisms; the remainder contained only one mechanism. Of isolates with two or more mechanisms, only 63% were resistant. Thus, the number of genetic determinants of ciprofloxacin resistance in an isolate could not reliably differentiate the ciprofloxacin intermediate or resistant categories when using North American breakpoints. Predicting ciprofloxacin intermediate/resistant as a single non-susceptible category would facilitate global standardization of data to inform public health surveillance, treatment guidelines, and stewardship.

Legionella is an underdiagnosed and underreported etiology of pneumonia. Legionella pneumophila serogroup 1 (LpSG1) is thought to be the most common pathogenic subgroup. This assumption is based on the frequent use of a urinary antigen test (UAT), only capable of diagnosing LpSG1. We aimed to explore the frequency of Legionella infections in individuals diagnosed with pneumonia and the performance of diagnostic methods for detecting Legionella infections. We conducted a scoping review to answer the following questions: (1) “Does nucleic acid testing (NAT) increase the detection of non-pneumophila serogroup 1 Legionella compared to non-NAT?”; and (2) “Does being immunocompromised increase the frequency of pneumonia caused by non-pneumophila serogroup 1 Legionella compared to non-immunocompromised individuals with Legionnaires’ disease (LD)?”. Articles reporting various diagnostic methods (both NAT and non-NAT) for pneumonia were extracted from several databases. Of the 3449 articles obtained, 31 were included in our review. The most common species were found to be L. pneumophila, L. longbeachae, and unidentified Legionella species appearing in 1.4%, 0.9%, and 0.6% of pneumonia cases. Nearly 50% of cases were caused by unspecified species or serogroups not detected by the standard UAT. NAT-based techniques were more likely to detect Legionella than non-NAT-based techniques. The identification and detection of Legionella and serogroups other than serogroup 1 is hampered by a lack of application of broader pan-Legionella or pan-serogroup diagnostics.