Biology subjects

Tisthammer, K.

Publications and source records attributed to Tisthammer, K..

3 recordsLinked to original sources

bioRxiv2022

Sequence type diversity amongst antibiotic-resistant bacterial strains is lower than amongst antibiotic-susceptible strains

The increasing number of antibiotic resistant bacterial infections is a global threat to human health. Antibiotic resistant bacterial strains generally evolve from susceptible strains by either horizontal gene transfer or chromosomal mutations. After evolving within a host, such resistant strains can be transmitted to other hosts and increase in frequency in the population at large. Population genetic theory postulates that the increase in frequency of an adaptive trait can lead to signatures of selective sweeps. One would thus expect to observe reduced genetic diversity amongst that part of the population that carries the adaptive trait. Specifically, if the evolution of new resistant strains is rare, it is expected that resistant strains represent only a subset of the diversity of susceptible strains. It is currently unknown if diversity of resistant strains is indeed lower than diversity of susceptible strains when considering antibiotic resistance. Here we show that in several bacterial species in several different datasets, sequence-type diversity amongst antibiotic-resistant bacterial strains is indeed lower than amongst antibiotic-susceptible strains in most cases. We re-analysed eight existing clinical datasets with Escherichia coli, Staphylococcus aureus and Enterococcus faecium samples. These datasets consisted of 53 - 1094 patient samples, with multi-locus sequence types and antibiotic resistance phenotypes for 3 - 19 different antibiotics. Out of 59 comparisons, we found that resistant strains were significantly less diverse than susceptible strains in 51 cases (86%). In addition, we show that sequence-type diversity of antibiotic-resistant strains is lower if resistance is rare, compared to when resistance is common, which is consistent with rare resistance being due to fewer evolutionary origins. Our results show that for several different bacterial species, we observe reduced diversity of resistant strains, which is consistent with the evolution of resistance driven by selective sweeps stemming from a limited number of evolutionary origins. In future studies, more detailed analysis of such sweep signatures is warranted.

evolutionary biology↗

bioRxiv2019

Physiological and Molecular Responses Suggest Local Adaptation of the Lobe Coral Porites lobata to the Nearshore Environment

Corals in nearshore marine environments are increasingly exposed to reduced water quality, which is the primary local threat to Hawaiian coral reefs. It is unclear if corals surviving in such conditions have adapted to withstand sedimentation, pollutants, and other environmental stressors. Lobe coral populations from Maunalua Bay, Hawaii showed clear genetic differentiation between the polluted, high-stress nearshore site and the lower-stress offshore site. To understand the driving force of the observed genetic partitioning, reciprocal transplant and common-garden experiments were conducted to assess phenotypic differences between these two populations. Physiological responses were significantly different between the populations, revealing more stress-resilient traits in the nearshore corals. Changes in protein profiles between the two populations highlighted the inherent differences in the cellular metabolic processes and activities; nearshore corals did not significantly alter their proteome between the sites, while offshore corals responded to nearshore transplantation with increased abundances of proteins associated with detoxification, antioxidant defense, and regulation of cellular metabolic processes. The response differences across multiple phenotypes between the populations suggest local adaptation of nearshore corals to reduced water quality. Our results provide insight into corals adaptive potential and its underlying processes, and reveal potential protein biomarkers that could be used to predict resiliency.

ecology↗

bioRxiv2019

CpG-creating Mutations are Costly in Many Human Viruses

Mutations can occur throughout the virus genome and may be beneficial or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly that similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.

evolutionary biology↗