Molecular methods that enable the detection of antimicrobial resistance determinants are critical... more Molecular methods that enable the detection of antimicrobial resistance determinants are critical surveillance tools that are necessary to aid in curbing the spread of antibiotic resistance. In this study, we describe the use of the Antimicrobial Resistance Determinant Microarray (ARDM) that targets 239 unique genes that confer resistance to 12 classes of antimicrobial compounds, quaternary amines and streptothricin for the determination of multidrug resistance (MDR) gene profiles. Fourteen reference MDR strains, which either were genome, sequenced or possessed well characterized drug resistance profiles were used to optimize detection algorithms and threshold criteria to ensure the microarray's effectiveness for unbiased characterization of antimicrobial resistance determinants in MDR strains. The subsequent testing of Acinetobacter baumannii, Escherichia coli and Klebsiella pneumoniae hospital isolates revealed the presence of several antibiotic resistance genes [e.g. belonging to TEM, SHV, OXA and CTX-M classes (and OXA and CTX-M subfamilies) of blactamases] and their assemblages which were confirmed by PCR and DNA sequence analysis. When combined with results from the reference strains, ,25% of the ARDM content was confirmed as effective for representing allelic content from both Gram-positive and-negative species. Taken together, the ARDM identified MDR assemblages containing six to 18 unique resistance genes in each strain tested, demonstrating its utility as a powerful tool for molecular epidemiological investigations of antimicrobial resistance in clinically relevant bacterial pathogens.
Journal of the American Chemical Society, Mar 5, 2021
Melanin is a ubiquitous natural pigment found in a diverse array of organisms. Allomelanin is a c... more Melanin is a ubiquitous natural pigment found in a diverse array of organisms. Allomelanin is a class of nitrogen-free melanin often found in fungi. Herein, we find artificial allomelanin analogues exhibit high intrinsic microporosity and describe an approach for further increasing and tuning that porosity. Notably, the synthetic method involves an oxidative polymerization of 1,8-DHN in water, negating the need for multiple complex templating steps and avoiding expensive or complex chemical precursors. The well-defined morphologies of these nanomaterials were elucidated by a combination of electron microscopy and scattering methods, yielding to high-resolution 3D reconstruction based on small-angle X-ray scattering (SAXS) results. Synthetic allomelanin nanoparticles exhibit high BET areas, up to 860 m 2 /g, and are capable of ammonia capture up to 17.0 mmol/g at 1 bar. In addition, these nanomaterials can adsorb nerve agent simulants in solution and as a coating on fabrics with high breathability where they prevent breakthrough. We also confirmed that naturally derived fungal melanin can adsorb nerve gas simulants in solution efficiently despite lower porosity than synthetic analogues. Our approach inspires further analysis of yet to be discovered biological materials of this class where melanins with intrinsic microporosity may be linked to evolutionary advantages in relevant organisms and may in turn inspire the design of new high surface area materials.
Introduction: In spite of promising medical, sociological, and engineering strategies and interve... more Introduction: In spite of promising medical, sociological, and engineering strategies and interventions to reduce the burden of disease, malaria remains a source of significant morbidity and mortality, especially among children in sub-Saharan Africa. In particular, progress in the development and administration of chemotherapeutic agents is threatened by evolved resistance to most of the antimalarials currently in use, including artemisinins. Methods: This study analyzed the prevalence of mutations associated with antimalarial resistance in Plasmodium falciparum from 95 clinical samples collected from individuals with clinically confirmed malaria at a hospital in Bo, Sierra Leone between May 2017 and December 2018. The combination of polymerase chain reaction amplification and subsequent high throughput DNA sequencing was used to determine the presence of resistanceassociated mutations in five P. falciparum genes-pfcrt, pfmdr1, pfdhfr, pfdhps and pfkelch13. The geographic origin of parasites was assigned using mitochondrial sequences. Results: Relevant mutations were detected in the pfcrt (22%), pfmdr1 (>58%), pfdhfr (100%) and pfdhps (>80%) genes while no resistance-associated mutations were found in the pfkelch13 gene. The mitochondrial barcodes were consistent with a West African parasite origin with one exception indicating an isolate imported from East Africa. Discussion: Detection of the pfmdr1 NFSND haplotype in 50% of the samples indicated the increasing prevalence of strains with elevated tolerance to Frontiers in Microbiology 01 frontiersin.org Leski et al. 10.3389/fmicb.2022.1059695 artemeter + lumefantrine (AL) threatening the combination currently used to treat uncomplicated malaria in Sierra Leone. The frequency of mutations linked to resistance to antifolates suggests widespread resistance to the drug combination used for intermittent preventive treatment during pregnancy.
Here we present the complete genome sequence of Lactobacillus acidophilus ATCC 53544. The assembl... more Here we present the complete genome sequence of Lactobacillus acidophilus ATCC 53544. The assembly contains 1,991,906 bp and is 99.7% similar to L. acidophilus NCFM. This strain was isolated from a rectal swab specimen of an infant and has previously been used as a feed supplement for animals.
We identified a novel enzyme that may allow the bioluminescent marine bacterium Vibrio campbellii... more We identified a novel enzyme that may allow the bioluminescent marine bacterium Vibrio campbellii to exploit some of the most abundant polysaccharides associated with deteriorating phytoplankton blooms.
Figure S1. (a) Archaeal and bacterial subfamily richness across individual samples. Archaeal subf... more Figure S1. (a) Archaeal and bacterial subfamily richness across individual samples. Archaeal subfamily richness ranged from 7 to 24; bacterial subfamily richness ranged from 346 to 602. All seawater samples were less rich in bacterial taxa compared to the hull biofilms. (b) Proportions of OTUs classified at the family level (nine richest families). Each color block represents the percentage of OTUs detected within a family compared to the total number of OTUs detected within the top nine richest families. Data acquired using the PhyloChip™ Array, version G3.
Culture-independent techniques such as LC-MS/MS-based metaproteomic analyses are being increasing... more Culture-independent techniques such as LC-MS/MS-based metaproteomic analyses are being increasingly utilized for the study of microbial composition and function in complex environmental samples. Although several studies have documented the many challenges and sources of bias that must be considered in these types of analyses, none have systematically characterized the effect of protein extraction bias on the biological interpretation of true environmental biofilm metaproteomes. In this study, we compared three protein extraction methods commonly used in the analyses of environmental samples [guanidine hydrochloride (GuHCl), B-PER, sequential citrate-phenol (SCP)] using nano-LC-MS/ MS and an environmental marine biofilm to determine the unique biases introduced by each method and their effect on the interpretation of the derived metaproteomes. While the protein extraction efficiencies of the three methods ranged from 2.0 to 4.3%, there was little overlap in the sequence (1.9%), function (8.3% of total assigned protein families) and origin of the identified proteins from each extract. Each extraction method enriched for different protein families (GuHCl-photosynthesis, carbohydrate metabolism; B-PER-membrane transport, oxidative stress; SCP-calcium binding, structural) while 23.7-45.4% of the identified proteins lacked SwissProt annotations. Taken together, the results demonstrated that even the most basic interpretations of this complex microbial assemblage (species composition, ratio of prokaryotic to eukaryotic proteins, predominant functions) varied with little overlap based on the protein extraction method employed. These findings demonstrate the heavy influence of protein extraction on biofilm metaproteomics and provide caveats for the interpretation of such data sets when utilizing single protein extraction methods for the description of complex microbial assemblages.
For three years, part of DARPA has funded two teams for each project: one for research and one fo... more For three years, part of DARPA has funded two teams for each project: one for research and one for reproducibility. The investment is paying off.
Microarrays are a valuable tool for analysis of both bacterial and eukaryotic nucleic acids. As m... more Microarrays are a valuable tool for analysis of both bacterial and eukaryotic nucleic acids. As many of these applications use non-specific amplification to increase sample concentration prior to analysis, the methods used to fragment and label large amplicons are important to achieve the desired analytical selectivity and specificity. Here, we used eight sequenced ESKAPE pathogens to determine the effect of two methods of whole genome amplicon fragmentation and three methods of subsequent labeling on microarray performance; nick translation was also assessed. End labeling of both initial DNase I-treated and sonication-fragmented amplicons failed to provide detectable material for a significant number of sequence-confirmed genes. However, processing of amplicons by nick translation, or by sequential fragmentation and labeling by Universal Labeling System or Klenow fragment/random primer provided good sensitivity and selectivity, with marginally better results obtained by Klenow fragment labeling. Nick-translation provided 91-100% sensitivity and 100% specificity in the tested strains, requiring half as many manipulations and less than 4h to process samples for hybridization; full sample processing from whole genome amplification to final data analysis could be performed in less than 10h. The method of template denaturation before amplification did affect detection sensitivity/selectivity of nicklabeled amplicons, however.
Oral anti-idiotypic antibody to Chlamydial GLXA reduces genital infection and dissemination to joints
<i>Vibrio natriegens</i> genome‐scale modeling reveals insights into halophilic adaptations and resource allocation
Molecular Systems Biology, Feb 27, 2023
Microbial invasions and inoculants: a call to action
The use of non-genetically modified microbial inoculants for beneficial purposes in agriculture, ... more The use of non-genetically modified microbial inoculants for beneficial purposes in agriculture, bioremediation, medicine, and infrastructure is increasing. The intentional introduction of plants and animals for similar purposes has a long history, but despite successes, has resulted in thousands of plant and animal species becoming invasive, with catastrophic consequences for the environment, public health, and society. Hundreds of microbial invasions are known, and although microbial inoculants can provide benefits, they have similar potential to negatively impact ecosystems. Little action has been taken to guard against the threat of microbial invasions from non-genetically modified microbial inoculants. Now is the time to develop an effective research and management infrastructure for these microbial inoculants to avoid catastrophic outcomes similar to those caused by intentionally-introduced plants and animals. Here, we propose a unified research and management approach to spur...
Antimicrobial resistance determinant microarray for analysis of multi-drug resistant isolates
Proceedings of SPIE - The International Society for Optical Engineering, 2012
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