Geology topics

Christina A. Ahlstrom

Publications and source records attributed to Christina A. Ahlstrom.

22 records · Page 2Linked to original sources

USGS2020

Comparative genomics and genomic epidemiology of mycobacterium avium subsp. paratuberculosis strains

Two phenotypically distinct strains of Mycobacterium avium subsp. paratuberculosis (MAP) were recognized in the 1930s but it was not until the introduction of restriction endonuclease analysis (REA) in the mid-1980s that these two strains, MAP-C and MAP-S, could be distinguished genetically. Since then, a plethora of molecular typing techniques has been applied to MAP isolates (reviewed by Li et al. 2016; Fawzy et al., 2018) and a complex nomenclature for MAP strains has evolved. Currently, the most widely used genotyping method is Mycobacterial Interspersed Repetitive Units – Variable-Number Tandem Repeats (MIRU-VNTR). However, it has limited discriminatory power within the major lineages and does not always accurately reflect genetic relatedness since the repeat sequences are subject to homoplasy (Ahlstrom et al., 2015; Bryant et al., 2016). Whole genome sequencing (WGS) supplies the ultimate resolution and has revolutionized MAP research. It has enabled determination of single nucleotide polymorphism (SNP) level diversity, clarified phylogenetic relationships between divergent lineages and closely related strains and spawned the development of novel genotyping methods based on informative canonical SNPs (Leão et al. 2016; Ahlstrom et al. 2016b). This chapter presents an overview of comparative genomics and epidemiology of MAP strains and also highlights the role that WGS has played in increasing our understanding of MAP strain diversity.

Book chapter↗

USGS2019

Early emergence of mcr-1-positive Enterobacteriaceae in gulls from Spain and Portugal

We tested extended‐spectrum β‐lactamase producing bacteria from wild gulls ( Larus spp.) sampled in 2009 for the presence of mcr ‐1. We report the detection of mcr ‐1 and describe genome characteristics of four Escherichia coli and one Klebsiella pneumoniae isolate from Spain and Portugal that also exhibited colistin resistance. Results represent the earliest evidence for colistin‐resistant bacteria in European wildlife.

Environmental Microbiology Reports↗

USGS2019

Satellite tracking of gulls and genomic characterization of fecal bacteria reveals environmentally mediated acquisition and dispersal of antimicrobial resistant Escherichia coli on the Kenai Peninsula, Alaska

Gulls (Larus spp.) have frequently been reported to carry Escherichia coli exhibiting antimicrobial resistance (AMR E. coli); however, the pathways governing the acquisition and dispersal of such bacteria are not well-described. We equipped 17 landfill-foraging gulls with satellite transmitters and collected gull fecal samples longitudinally from four locations on the Kenai Peninsula, Alaska to assess: 1) gull attendance and transitions between sites, 2) spatiotemporal prevalence of fecally-shed AMR E. coli, and 3) genomic relatedness of AMR E. coli isolates among sites. We also sampled Pacific salmon (Oncorhynchus spp.) harvested as part of personal-use dipnet fisheries at two sites to assess potential contamination with AMR E. coli. Among our study sites, marked gulls most commonly occupied the lower Kenai River (61% of site locations) followed by the Soldotna landfill (11%), lower Kasilof River (5%), and upper Kenai River (<1%). Gulls primarily moved between the Soldotna landfill and the lower Kenai River (94% of transitions among sites), which were also the two locations with the highest prevalence of AMR E. coli. There was relatively high spatial and temporal variability in AMR E. coli prevalence in gull feces and there was no evidence of contamination on salmon harvested in personal-use fisheries. We identified E. coli sequence types and AMR genes of clinical importance, with some isolates possessing genes associated with resistance to as many as eight antibiotic classes. Our findings suggest that gulls acquire AMR E. coli at habitats with anthropogenic inputs and subsequent movements may represent pathways through which AMR is dispersed.

Alaska↗

USGS2019

Repeated detection of carbapenemase-producing Escherichia coli in gulls inhabiting Alaska, USA

We report the first detection of carbapenemase-producing Escherichia coli in Alaska and in wildlife in the United States. Wild bird (gull) feces sampled at three locations in Southcentral Alaska yielded isolates that harbored plasmid-encoded bla KPC-2 or chromosomally-encoded bla OXA-48 , and genes associated with antimicrobial resistance to up to eight antibiotic classes.

Alaska↗