Keeping up with the pathogens: improved antimicrobial resistance detection and prediction from Pseudomonas aeruginosa genomes.

Background: Antimicrobial resistance (AMR) is an intensifying threat that requires urgent mitigation to avoid a post-antibiotic era. Pseudomonas aeruginosa represents one of the greatest AMR concerns due to increasing multi- and pan-drug resistance rates. Shotgun sequencing is gaining traction for in silico AMR profiling due to its unambiguity and transferability; however, accurate and comprehensive AMR prediction from P.

Bicarbonate as a predictor of successful insulin transition in critically ill patients with diabetic ketoacidosis: A retrospective cohort study.

Background: Treatment of diabetic ketoacidosis with intravenous insulin is effective but resource intensive. Treatment guidelines recommend transitioning to subcutaneous insulin when the anion gap closes, but transition failures due to recrudescent ketoacidosis are common despite adherence to treatment protocols following such guidance.

Study Objective: The primary objective of our study was to evaluate the ability of serum bicarbonate levels of ≤16 mEq/L to predict intravenous to subcutaneous transition failures among those with a normal anion gap at the time of transition.

Wood from Hardwood Angiosperms and Coniferous Gymnosperms Shows Distinctive Lignin Peaks in Direct Analysis in Real Time (DART) Mass Spectra.

A data set was constructed consisting of 3021 mass spectra randomly selected from all available families in the ForeST© (Forensic Spectra of Trees) database of mass spectra for wood analyzed by Direct Analysis in Real Time ionization coupled with time-of-flight mass spectrometry (DART-TOFMS). Clear and reproducible differences were observed between the lignin peaks for hardwood angiosperms and coniferous gymnosperms, with DART-TOFMS spectra of angiosperms showing significantly higher relative abundances for peaks associated with syringyl subunits. Application of the method to processed wood samples demonstrated that these differences can be used to provide support for enforcing trade laws by accurately identifying the source of finished wood products from hardwood angiosperms and coniferous gymnosperms.

Rapid fluoroquinolone resistance detection in using mismatch amplification mutation assay-based real-time PCR.

Antimicrobial resistance (AMR) is an ever-increasing global health concern. One crucial facet in tackling the AMR epidemic is earlier and more accurate AMR diagnosis, particularly in the dangerous and highly multi-drug-resistant ESKAPE pathogen, . We aimed to develop two SYBR Green-based mismatch amplification mutation assays (SYBR-MAMAs) targeting GyrA T83I (248) and GyrA D87N, D87Y and D87H (259).

Comparative genomics of reveals recent importation and subsequent widespread dissemination in mariculture farms in the South Central Coast region, Vietnam.

Between 2010 and 2015, nocardiosis outbreaks caused by affected many permit farms throughout Vietnam, causing mass fish mortalities. To understand the biology, origin and epidemiology of these outbreaks, 20 . strains collected from farms in four provinces in the South Central Coast region of Vietnam, along with two Taiwanese strains, were analysed using genetics and genomics.

Express Yourself: Quantitative Real-Time PCR Assays for Rapid Chromosomal Antimicrobial Resistance Detection in Pseudomonas aeruginosa.

The rise of antimicrobial-resistant (AMR) bacteria is a global health emergency. One critical facet of tackling this epidemic is more rapid AMR diagnosis in serious multidrug-resistant pathogens like Pseudomonas aeruginosa. Here, we designed and then validated two multiplex quantitative real-time PCR (qPCR) assays to simultaneously detect differential expression of the resistance-nodulation-division efflux pumps MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM, the AmpC β-lactamase, and the porin OprD, which are commonly associated with chromosomally encoded AMR.

Tools, Strains, and Strategies To Effectively Conduct Anaerobic and Aerobic Transcriptional Reporter Screens and Assays in Staphylococcus aureus.

Transcriptional reporters are reliable and time-tested tools to study gene regulation. In Staphylococcus aureus, β-galactosidase ()-based genetic screens are not widely used because of the necessity of selectable markers for strain construction and the production of staphyloxanthin pigment, which obfuscates results. We describe a series of vectors that allow for markerless insertion of codon-optimized -based transcriptional reporters.

Bacterial approaches to sensing and responding to respiration and respiration metabolites.

Bacterial respiration of diverse substrates is a primary contributor to the diversity of life. Respiration also drives alterations in the geosphere and tethers ecological nodes together. It provides organisms with a means to dissipate reductants and generate potential energy in the form of an electrochemical gradient.

Taking the next-gen step: Comprehensive antimicrobial resistance detection from Burkholderia pseudomallei.

Background: Antimicrobial resistance (AMR) poses a major threat to human health. Whole-genome sequencing holds great potential for AMR identification; however, there remain major gaps in accurately and comprehensively detecting AMR across the spectrum of AMR-conferring determinants and pathogens.

Methods: Using 16 wild-type Burkholderia pseudomallei and 25 with acquired AMR, we first assessed the performance of existing AMR software (ARIBA, CARD, ResFinder, and AMRFinderPlus) for detecting clinically relevant AMR in this pathogen.

A Persisting Nontropical Focus of Burkholderia pseudomallei with Limited Genome Evolution over Five Decades.

is the causative agent of the high-mortality disease melioidosis. Although melioidosis is classified as a tropical disease, rare autochthonous cases have been reported from temperate climatic regions, with uncertainty as to whether is persistent in the local environment and whether specific genetic mechanisms facilitate the survival of outside the tropics. Sporadic cases of melioidosis occurred in a valley region (latitude 31.

Forensic identification of the keratin fibers of South American camelids by ambient ionization mass spectrometry: Vicuña, alpaca and guanaco.

Rationale: The keratin fleece of the endangered vicuña (Vicugna vicugna) commands a high value in international markets, and this trade has caused illegal poaching and a substantial decrease in vicuña populations. Morphological analysis of hairs does not have the resolution to determine the species of origin of camelid natural fibers. In addition, commerce in camelid fleece also includes the legal trade of alpaca (Vicugna pacos) and guanaco (Lama guanicoe) wool.

Galvanizing for the future: a bottom-up departmental approach to diversity, equity, and inclusion.

As an academic department, we sought to identify effective strategies to engage our faculty and staff in diversity, equity, and inclusion initiatives and programs to build an inclusive department that would address our needs and those of our community and partners. Over a 4-year period, our faculty and staff have participated in town hall meetings, focus group discussions, surveys, and community-building activities to foster stakeholder engagement that will build a leading academic department for the future. We noted that our faculty and staff were committed to building diversity, equity, and inclusion, and our mission and vision were reflective of this.

Duplex real-time PCR assay for the simultaneous detection of and spp.

Several members of the Gram-negative environmental bacterial genus are associated with serious infections, with being the most common. Despite their pathogenic potential, little is understood about these intrinsically drug-resistant bacteria and their role in disease, leading to suboptimal diagnosis and management. Here, we performed comparative genomics for 158 spp.

Comparative Genomics and Antimicrobial Resistance Profiling of Isolates Reveal Nosocomial Transmission and Susceptibility to Fluoroquinolones, Tetracyclines, and Trimethoprim-Sulfamethoxazole.

The genus has gained global attention in recent years as containing sporadic, worldwide, nosocomial pathogens. spp. are intrinsically multidrug resistant, primarily infect immunocompromised individuals, and are associated with high mortality (∼20 to 40%).

Genetic Regulation of Metal Ion Homeostasis in Staphylococcus aureus.

The acquisition of metal ions and the proper maturation of holo-metalloproteins are essential processes for all organisms. However, metal ion homeostasis is a double-edged sword. A cytosolic accumulation of metal ions can lead to mismetallation of proteins and cell death.

Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection.

Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314's sputum despite intensive initial therapeutic regimens.

Comparative genomics confirms a rare melioidosis human-to-human transmission event and reveals incorrect phylogenomic reconstruction due to polyclonality.

Human-to-human transmission of the melioidosis bacterium, , is exceedingly rare, with only a handful of suspected cases documented to date. Here, we used whole-genome sequencing (WGS) to characterize one such unusual transmission event, which occurred between a breastfeeding mother with mastitis and her child. Two strains corresponding to multilocus sequence types (STs)-259 and -261 were identified in the mother's sputum from both the primary culture sweep and in purified colonies, confirming an unusual polyclonal infection in this patient.

Comparative genomic analysis identifies X-factor (haemin)-independent : a formal re-classification of ''.

The heterogeneous and highly recombinogenic genus comprises several species, some of which are pathogenic to humans. All share an absolute requirement for blood-derived factors during growth. Certain species, such as the pathogen and the commensal , are thought to require both haemin (X-factor) and nicotinamide adenine dinucleotide (NAD, V-factor), whereas others, such as the informally classified ' subsp.

Quantitative real-time PCR assay for the rapid identification of the intrinsically multidrug-resistant bacterial pathogen .

is emerging as an important cause of disease in nosocomial and community-acquired settings, including bloodstream, wound and catheter-associated infections. Cystic fibrosis (CF) airways also provide optimal growth conditions for various opportunistic pathogens with high antibiotic tolerance, including . Currently, there is no rapid, cost-effective and accurate molecular method for detecting this potentially life-threatening pathogen, particularly in polymicrobial specimens, suggesting that its true prevalence is underestimated.

Molecular Signatures of Non-typeable Lung Adaptation in Pediatric Chronic Lung Disease.

Non-typeable (NTHi), an opportunistic pathogen of the upper airways of healthy children, can infect the lower airways, driving chronic lung disease. However, the molecular basis underpinning NTHi transition from a commensal to a pathogen is not clearly understood. Here, we performed comparative genomic and transcriptomic analyses of 12 paired, isogenic NTHi strains, isolated from the nasopharynx (NP) and bronchoalveolar lavage (BAL) of 11 children with chronic lung disease, to identify convergent molecular signatures associated with lung adaptation.

Tracing the environmental footprint of the Burkholderia pseudomallei lipopolysaccharide genotypes in the tropical "Top End" of the Northern Territory, Australia.

The Tier 1 select agent Burkholderia pseudomallei is an environmental bacterium that causes melioidosis, a high mortality disease. Variably present genetic markers used to elucidate strain origin, relatedness and virulence in B. pseudomallei include the Burkholderia intracellular motility factor A (bimA) and filamentous hemagglutinin 3 (fhaB3) gene variants.

Lipopolysaccharide Genotype Does Not Correlate With Severity or Outcome in Melioidosis: Host Risk Factors Remain the Critical Determinant.

Background: The causative agent of melioidosis is the Gram-negative bacterium . Clinical presentations of melioidosis are notably diverse, with host risk factors considered central to progression from infection to disease and clinical outcome. Ubiquitous and variably present virulence determinants have been described for , with several variably present minority genotypes associated with specific disease presentations.