Biology subjects

Barry, K. E.

Publications and source records attributed to Barry, K. E..

10 recordsLinked to original sources

bioRxiv2025

Variable Chlorhexidine Tolerance Across Klebsiella Species from a Single Facility

We assessed in vitro chlorhexidine tolerance across Klebsiella species from a hospital with widespread chlorhexidine use. Isolates underwent MIC testing and whole genome sequencing. Klebsiella species showed varying tolerance, with K. quasipneumoniae having the highest MICs. No clear link to acquired resistance was found, though chromosomal efflux pumps appeared in some traditionally environmental species. Differences in chlorhexidine tolerance between species highlight the role that biocides could have in shaping microbial populations in the hospital environment.

microbiology↗

bioRxiv2024

Impact of media brand on cefiderocol disk diffusion results

IntroductionCefiderocol is a siderophore cephalosporin that utilizes iron transport systems to cross cell membranes. This unique strategy complicates antimicrobial susceptibility testing (AST) due to variable iron content in media. While guidance for using iron-depleted media exists for broth microdilution (BMD), disk diffusion (DD) with commercial media is a common AST method in the clinical laboratory. We investigated cefiderocol DD result variability using multiple Mueller-Hinton agar (MHA) brands. MethodsDD results using Remel (Thermo Fisher Scientific, San Diego, CA), Hardy (Hardy Diagnostics, Springboro, OH), and BBL (Becton Dickenson, East Rutherford, NJ) MHA were compared to BMD using iron-depleted cation-adjusted Mueller-Hinton broth. BMD reproducibility, BMD trailing endpoints, and DD intra- and inter-brand variability in zones of inhibition were investigated. ResultsForty-seven multidrug-resistant clinical isolates and three Antibiotic Resistance bank isolates composed of Pseudomonas aeruginosa, carbapenemase (CP-) and non-carbapenemase-producing (non-CP-) carbapenem-resistant Enterobacterales (CRE), Acinetobacter baumannii complex, Stenotrophomonas maltophilia, and Burkholderia cepacia complex were tested. Categorical agreement (CA) [≥]90% was only demonstrated using CLSI breakpoints with BBL agar. Intra- and inter-brand variability in DD were greatest for P. aeruginosa and CRE, with 30% (6/20) and 16.7% (3/18) exhibiting discrepant AST interpretations, respectively. Isolates not susceptible to cefiderocol via BMD were commonly associated with AST interpretation errors and lower CA. ConclusionsUsing commercial MHA for DD resulted in frequent AST interpretation discrepancies, particularly for isolates that were not susceptible to cefiderocol by BMD. Methods and quality control may need to be revisited to ensure the reliability of DD for cefiderocol AST. IMPORTANCE STATEMENTThe novel mechanism of action of cefiderocol overcomes a variety of resistance mechanisms associated with gram-negative bacteria and positions the agent as an attractive option for infections involving multidrug-resistant pathogens. The availability of accurate, timely antimicrobial susceptibility testing methods for cefiderocol in clinical microbiology laboratories is critical as cefiderocol-resistant isolates have been described and may contribute to treatment failure. Iron-depleted broth microdilution testing may not be feasible for many clinical laboratories. While disk diffusion is an appealing, practical method to implement, our data demonstrate reproducibility issues across agar brands, most notably for organisms that do not test susceptible to cefiderocol via broth microdilution. Discrepant errors and misclassifications of resistant isolates as susceptible, and susceptible isolates as resistant, may mislead clinicians and compromise treatment efficacy. More work is needed to standardize practical yet reproducible methods for cefiderocol antimicrobial susceptibility testing.

microbiology↗

bioRxiv2024

Tree diversity increases carbon stocks and fluxes above- but not belowground in a tropical forest experiment

International commitments advocate large-scale forest restoration as a nature-based solution to climate change mitigation through carbon (C) sequestration. Mounting evidence suggests that mixed compared to monospecific planted forests may sequester more C, exhibit lower susceptibility to climate extremes and offer a broader range of ecosystem services. However, experimental studies comprehensively examining the control of tree diversity on multiple C stocks and fluxes above- and belowground are lacking. To address this gap, we leverage data from the Sardinilla experiment in Panama, the oldest tropical tree diversity experiment which features a gradient of one-, two-, three- and five-species mixtures of native tree species. Over 16 years, we measured multiple above- and belowground C stocks and fluxes, ranging from tree aboveground C, over leaf litter C production, to soil organic carbon (SOC). We show that tree diversity significantly increased aboveground C stocks and fluxes, with a 57% higher gain in aboveground tree C in five-species mixtures compared to monocultures (35.7{+/-}1.8 vs 22.8{+/-}3.4 Mg C ha-1) 16 years after planting. In contrast, we observed a net reduction in SOC (on average -11.2{+/-}1.1 Mg C ha-1) and no significant difference in SOC3 stocks (the predominantly tree-derived, i.e., C3 plant-derived SOC fraction) between five-species mixtures and monocultures (13.0{+/-}0.9 vs 15.1{+/-}1.3 Mg C ha-1). Positive tree diversity effects persisted despite repeated climate extremes and strengthened over time for aboveground tree growth. Structural equation models showed that higher tree growth in mixtures enhanced leaf litter and coarse woody debris C fluxes to the soil, resulting in a tightly linked C cycle aboveground. However, we did not observe significant links between above- and belowground C stocks and fluxes. Our study elucidates the mechanisms through which higher tree diversity bolsters the climate mitigation potential of tropical forest restoration. Restoration schemes should prioritize mixed over monospecific planted forests.

ecology↗

bioRxiv2022

Neighbourhood species richness and drought-tolerance traits modulate tree growth and δ13C responses to drought

O_LIMixed-species forests are promoted as a forest management strategy for climate change adaptation, but whether they are more resistant to drought than monospecific forests remains contested. Particularly, the trait-based mechanisms driving the role of tree diversity under drought remain elusive. C_LIO_LIUsing tree cores from a large-scale biodiversity experiment, we investigated tree growth and physiological stress responses (i.e. increase in wood carbon isotopic ratio; {delta}13C) to changes in climate-induced water availability (wet to dry years) along gradients in neighbourhood tree species richness and drought-tolerance traits. We hypothesized that neighbourhood species richness increases growth and decreases {delta}13C and that these relationships are modulated by the abiotic (i.e. climatic conditions) and the biotic context. We characterized the biotic context using drought-tolerance traits of focal trees and their neighbours. These traits are related to cavitation resistance vs resource acquisition and stomatal control. C_LIO_LITree growth increased with neighbourhood species richness. However, we did not observe a universal relief of water stress in species-rich neighbourhoods. Neighbourhood species richness effects on growth and {delta}13C did not strengthen from wet to dry years. Instead, richness-growth and richness-{delta}13C relationships were modulated by climatic conditions and the traits of trees and their neighbours. At either end of each drought-tolerance gradient, species responded in opposing directions during drought and non-drought years. C_LIO_LIWe show that species drought-tolerance traits can explain the strength and nature of biodiversity-ecosystem functioning relationships in experimental tree communities experiencing drought. Mixing tree species can increase growth but may not universally relieve drought stress. C_LI One-sentence summaryThe drought-tolerance traits of trees and their neighbours determine biodiversity-ecosystem functioning relationships in experimental tree communities.

ecology↗

bioRxiv2021

Hydraulic diversity stabilizes productivity in a large-scale subtropical tree biodiversity experiment

Extreme climatic events threaten forests and their climate mitigation potential globally. Understanding the drivers promoting ecosystem stability is therefore considered crucial to mitigate adverse climate change effects on forests. Here, we use structural equation models to explain how tree species richness, asynchronous species dynamics and diversity in hydraulic traits affect the stability of forest productivity along an experimentally manipulated biodiversity gradient ranging from 1 to 24 tree species. Tree species richness improved stability by increasing species asynchrony. That is, at higher species richness, inter-annual variation in productivity among tree species buffered the community against stress-related productivity declines. This effect was mediated by the diversity of species hydraulic traits regarding drought tolerance and stomatal control, but not by the community-weighted means of these traits. The identified mechanisms by which tree species richness stabilizes forest productivity emphasize the importance of hydraulically diverse, mixed-species forests to adapt to climate change.

ecology↗

bioRxiv2019

Plant traits are poor predictors of long-term ecosystem functioning

Earth is home to over 350,000 vascular plant species1 that differ in their traits in innumerable ways. Yet, a handful of functional traits can help explaining major differences among species in photosynthetic rate, growth rate, reproductive output and other aspects of plant performance2-6. A key challenge, coined "the Holy Grail" in ecology, is to upscale this understanding in order to predict how natural or anthropogenically driven changes in the identity and diversity of co-occurring plant species drive the functioning of ecosystems7, 8. Here, we analyze the extent to which 42 different ecosystem functions can be predicted by 41 plant traits in 78 experimentally manipulated grassland plots over 10 years. Despite the unprecedented number of traits analyzed, the average percentage of variation in ecosystem functioning that they jointly explained was only moderate (32.6%) within individual years, and even much lower (12.7%) across years. Most other studies linking ecosystem functioning to plant traits analyzed no more than six traits, and when including either only six random or the six most frequently studied traits in our analysis, the average percentage of explained variation in across-year ecosystem functioning dropped to 4.8%. Furthermore, different ecosystem functions were driven by different traits, with on average only 12.2% overlap in significant predictors. Thus, we did not find evidence for the existence of a small set of key traits able to explain variation in multiple ecosystem functions across years. Our results therefore suggest that there are strong limits in the extent to which we can predict the long-term functional consequences of the ongoing, rapid changes in the composition and diversity of plant communities that humanity is currently facing.

ecology↗

bioRxiv2019

A universal scaling method for biodiversity-ecosystem functioning relationships

Global biodiversity is declining at rates faster than at any other point in human history. Experimental manipulations of biodiversity at small spatial scales have demonstrated that communities with fewer species consistently produce less biomass than higher diversity communities. However, understanding how the global extinction crisis is likely to impact global ecosystem functioning will require applying these local and largely experimental findings to natural systems at substantially larger spatial and temporal scales. Here we propose that we can use two simple macroecological patterns - the species area curve and the biomass-area curve - to upscale the species richness-biomass relationship. We demonstrate that at local spatial scales, each additional species will contribute more to biomass production with increasing area sampled because the species-area curve saturates and the biomass-area curve increases monotonically. We use species-area and biomass-area curves from a Minnesota grassland and a Panamanian tropical dry forest to examine the species richness - biomass relationship at three and ten sampling extents, respectively. In both datasets, the observed relationship between biodiversity and biomass production at every sampling extent was predicted from simple species-area and biomass-area relationships. These findings suggest that macroecological patterns like the species-area curve underpin the scaling of biodiversity-ecosystem functioning research and can be used to predict these relationships at the global scales where they are relevant for species loss.

ecology↗

bioRxiv2019

The Role of fosA in Challenges with Fosfomycin Susceptibility Testing of Multispecies Klebsiella pneumoniae Carbapenemase-Producing Clinical Isolates

With multidrug resistant (MDR) Enterobacteriales on the rise, a non-toxic agent with a unique mechanism of action such as fosfomycin seems attractive. However, establishing accurate fosfomycin susceptibility testing for non-E. coli in a clinical microbiology laboratory remains problematic. We evaluated fosfomycin susceptibility by multiple methods with multiple strains and species of KPC-producing clinical isolates collected at a single center between 2008 and 2016. In addition, we assessed the presence of fosfomycin resistance genes from whole genome sequencing (WGS) data using NCBIs AMRFinder and custom HMM search. Susceptibility testing was performed using glucose-6-phosphate supplemented fosfomycin E-Test and Kirby-Bauer disk diffusion (DD) assays, and compared to agar dilution. Clinical Laboratory and Standards Institute (CLSI) breakpoints for E. coli were applied for interpretation. Overall, 63% (60/96) of isolates were susceptible by E-Test, 70% (67/96) by DD, and 88% (84/96) by agar dilution. FosA was detected in 80% (70/88) of previously sequenced isolates, with species-specific associations and alleles, and fosA-positive isolates were associated with higher MIC distributions. Disk potentiation testing was performed using sodium phosphonoformate to inhibit fosA and showed significant increases in the zone diameter of DD testing for isolates that were fosA-positive compared to fosA-negative. The addition of sodium phosphonoformate (PPF) corrected 10/14 (71%) major errors in categorical agreement with agar dilution. Our results indicate that fosA influences the inaccuracy of susceptibility testing by methods readily available in a clinical laboratory when compared to agar dilution. Further research is needed to determine the impact of fosA on clinical outcomes.

microbiology↗

bioRxiv2018

Klebsiella quasipneumonaiae provides a window into carbapenemase gene transfer, plasmid rearrangements and nosocomial acquisition from the hospital environment

Several emerging pathogens have arisen as a result of selection pressures exerted by modern healthcare. Klebsiella quasipneumoniae was recently defined as a new species, yet its prevalence, niche, and propensity to acquire antimicrobial resistance genes are not fully described. We have been tracking inter- and intra-species transmission of the Klebsiella pneumoniae carbapenemase (KPC) gene, blaKPC, between bacteria isolated from a single institution. We applied a combination of Illumina and PacBio whole-genome sequencing to identify and compare K. quasipneumoniae from patients and the hospital environment over 10 and five-year periods respectively. There were 32 blaKPC-positive K. quasipneumoniae isolates, all of which were identified as K. pneumoniae in the clinical microbiology laboratory, from eight patients and 11 sink drains, with evidence for seven separate blaKPC plasmid acquisitions. Analysis of a single subclade of K. quasipneumoniae subspecies quasipneumoniae (n=23 isolates) from three patients and six rooms demonstrated seeding of a sink by a patient, subsequent persistence of the strain in the hospital environment, and then probable transmission to another patient. Longitudinal analysis of this strain demonstrated the acquisition of two unique blaKPC plasmids and then subsequent within-strain genetic rearrangement through transposition and homologous recombination. Our analysis highlights the apparent molecular propensity of K. quasipneumoniae to persist in the environment as well as acquire carbapenemase plasmids from other species and enabled an assessment of the genetic rearrangements which may facilitate horizontal transmission of carbapenemases.

microbiology↗

bioRxiv2018

Droplet rather than Aerosol Mediated Dispersion is the Primary Mechanism of Bacterial transmission from Contaminated Hand Washing Sink Traps

An alarming rise in hospital outbreaks implicating hand-washing sinks has led to widespread acknowledgement that sinks are a major reservoir of antibiotic resistant pathogens in patient-care areas. An earlier study using a GFP-expressing Escherichia coli (GFP-E. coli) as a model organism demonstrated dispersal from drain biofilm in contaminated sinks. The present study further characterizes the dispersal of microorganisms from contaminated sinks. Replicate hand-washing sinks were inoculated with GFP-E. coli, and dispersion was measured using qualitative (settle plates) and quantitative (air sampling) methods. Dispersal caused by faucet water was captured with settle plates and air sampling methods when bacteria were present on the drain. In contrast, no dispersal was captured without or in between faucet events amending earlier theory that bacteria aerosolize from P-trap and disperse. Numbers of dispersed GFP-E. coli diminished substantially within 30 minutes after faucet usage, suggesting that the organisms were associated with larger droplet-sized particles that are not suspended in the air for long periods.\n\nIMPORTANCEAmong the possible environmental reservoirs in a patient care environment, sink drains are increasingly recognized as potential reservoir of multidrug resistant healthcare-associated pathogens to hospitalized patients. With increasing antimicrobial resistance limiting therapeutic options for patients, better understanding of how pathogens disseminate from sink drains is urgently needed. Once this knowledge gap has decreased, interventions can be engineered to decrease or eliminate transmission from hospital sink drains to patients. The current study further defines the mechanisms of transmission for bacteria colonizing sink drains.

microbiology↗