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1. Comparative survival of environmental and clinical Mycobacterium abscessus isolates in a variety of diverse host cells

   https://doi.org/10.1111/jam.15416  

   Vang, Charmie K.; Dawrs, Stephanie N.; Oberlag, Nicole M.; Gilmore, Anah E.; Hasan, Nabeeh A.; Honda, Jennifer R. (April 2022, Journal of Applied Microbiology)

   Abstract AimsMycobacterium abscessus subsp. abscessus (MABS) is an emerging, opportunistic pathogen found globally in freshwater biofilms and soil. Typically, isolates are treated as a uniform group of organisms and very little is known about their comparative survival in healthy host cells. We posit that environmentally- and clinically derived isolates, show differential infectivity in immune cells and resistance to innate defenses. Methods and ResultsSix MABS isolates were tested including three water biofilm/soil and three sputum-derived isolates. A clinical MABS type strain and an environmental isolate of Arthrobacter were also included. MABS counts were significantly higher compared to Arthrobacter after co-culture with Acanthamoeba lenticulata, BEAS-2B epithelial cells, alveolar macrophages and the THP-1 macrophage cell line. A rough sputum-derived MABS isolate emerged as an isolate with higher virulence compared to others tested, as both a pellicle and cord former, survivor in the human cell models tested, inducer of high and prolonged production of pro-inflammatory cytokines, and the capacity to evade LL-37. ConclusionsFindings support intraspecies variation between MABS isolates. Significance and Impact of the StudyThese data indicate subversion of host immune defenses by environmental and clinical MABS isolates is nuanced and maybe isolate dependent, providing new information regarding the pathogenesis of NTM infections. 

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2. Genomic and in vitro pharmacodynamic analysis of rifampicin resistance in multidrug‐resistant canine Staphylococcus pseudintermedius isolates

   https://doi.org/10.1111/vde.12959  

   Hicks, Karly; Tan, Yongjun; Cao, Wenqi; Hathcock, Terri; Boothe, Dawn; Kennis, Robert; Zhang, Dapeng; Wang, Xu; White, Amelia (April 2021, Veterinary Dermatology)

   BackgroundAntimicrobial resistance is a growing concern in canineStaphylococcus pseudintermediusdermatitis. Treatment with rifampicin (RFP) is considered only in meticillin‐resistant and multidrug‐resistantS. pseudintermedius(MDR‐MRSP). Hypothesis/ObjectivesTo determine an optimal RFP dosing for MDR‐MRSP treatment without induction of RFP resistance and identify causal mutations for antimicrobial resistance. Methods and materialsTime–kill assays were performed in a control isolate and three MDR‐MRSP isolates at six clinically relevant concentrations [32 to 1,024 × MIC (the minimum inhibitory concentration)]. Whole‐genome resequencing and bioinformatic analysis were performed in the resistant strains developed in this assay. ResultsThe genomic analysis identified nine antimicrobial resistance genes (ARGs) in MDR‐MRSP isolates, which are responsible for resistance to seven classes of antibiotics. RFP activity against all four isolates was consistent with a time‐dependent and bacteriostatic response. RFP resistance was observed in six of the 28 time–kill assays, including concentrations 64 × MIC in MDR‐MRSP1 isolates at 24 h, 32 × MIC in MDR‐MRSP2 at 48 h, 32 × MIC in MDR‐MRSP3 at 48 h and 256 × MIC in MDR‐MRSP3 at 24 h. Genome‐wide mutation analyses in these RFP‐resistant strains discovered the causal mutations in the coding region of therpoBgene. Conclusions and clinical relevanceA study has shown that 6 mg/kg per os results in plasma concentrations of 600–1,000 × MIC ofS. pseudintermedius. Based on our data, this dose should achieve the minimum MIC (×512) to prevent RFP resistance development; therefore, we recommend a minimum daily dose of 6 mg/kg for MDR‐MRSP pyoderma treatment when limited antibiotic options are available. 

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3. Draft genome sequences of six high pH adapted Marinobacter shengliensis strains isolated from Mariana forearc serpentinite mud volcanoes

   https://doi.org/10.1128/mra.01045-24  

   Elkassas, Sabrina M; Serres, Margrethe H; Navarro, Michael; Patterson, Amina; Zhivkova, Teodora; Petersen, Madelyn; Weeks, Katelyn; Lang, Susan; Seewald, Jeffrey; Wheat, Geoffrey; et al (February 2025, Microbiology Resource Announcements)

   Hudson, André O (Ed.)

   ABSTRACT Six marine bacterial isolates were obtained from fluid and sediments collected at alkaline serpentinite mud volcanoes of the Mariana forearc to examine life at high pH in a marine environment. Here, we present the draft genome sequences of these six isolates, classified as strains of the speciesMarinobacter shengliensis. 

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4. Using simulated wildland fire to assess microbial survival at multiple depths from biocrust and bare soils

   https://doi.org/10.3389/fmicb.2023.1123790  

   Palmer, Brianne; Pietrasiak, Nicole; Cobb, Polina; Lipson, David (March 2023, Frontiers in Microbiology)

   IntroductionSurface soil microbial communities are directly exposed to the heat from wildland fires. Due to this, the microbial community composition may be stratified within the soil profile with more heat tolerant microbes near the surface and less heat tolerant microbes, or mobile species found deeper in the soil. Biological soil crusts, biocrusts, are found on the soil surface and contain a diverse microbial community that is directly exposed to the heat from wildland fires. MethodsHere, we used a simulated fire mesocosm along with a culture-based approach and molecular characterization of microbial isolates to understand the stratification of biocrust and bare soil microbes after low severity (450°C) and high severity (600°C) fires. We cultured and sequenced microbial isolates from 2 to 6 cm depth from both fire types. ResultsThe isolates were stratified along the soil depth. Green algal isolates were less thermotolerant and found in the deeper depths (4–6 cm) and the control soils, while several cyanobacteria in Oscillatoriales, Synechococcales, and Nostocales were found at 2–3 cm depth for both fire temperatures. An Alphaproteobacteria isolate was common across several depths, both fire types, and both fire temperatures. Furthermore, we used RNA sequencing at three depths after the high severity fire and one control to determine what microbial community is active following a fire. The community was dominated by Gammaproteobacteria, however some Cyanobacteria ASVs were also present. DiscussionHere we show evidence of stratification of soil and biocrust microbes after a fire and provide evidence that these microbes are able to survive the heat from the fire by living just below the soil surface. This is a steppingstone for future work on the mechanisms of microbial survival after fire and the role of soil insulation in creating resilient communities. 

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5. Resolution of MALDI-TOF compared to whole genome sequencing for identification of Bacillus species isolated from cleanrooms at NASA Johnson Space Center

   https://doi.org/10.3389/fmicb.2025.1499516  

   Mazhari, Farnaz; Regberg, Aaron B; Castro, Christian L; LaMontagne, Michael G (April 2025, Frontiers in Microbiology)

   IntroductionBacteria are frequently isolated from surfaces in cleanrooms, where astromaterials are curated, at NASA’s Lyndon B. Johnson Space Center (JSC).Bacillusspecies are of particular interest because endospores can endure extreme conditions. Current monitoring programs at JSC rely on culturing microbes from swabs of surfaces followed by identification by 16S rRNA sequencing and the VITEK 2 Compact bacterial identification system. These methods have limited power to resolveBacillusspecies. Whole genome sequencing (WGS) is the current standard for bacterial identification but is expensive and time-consuming. Matrix-assisted laser desorption - time of flight mass spectrometry (MALDI-TOF MS), provides a rapid, low-cost, method of identifying bacterial isolates and has a higher resolution than 16S rRNA sequencing, particularly forBacillusspecies; however, few studies have compared this method to WGS for identification ofBacillusspecies isolated from cleanrooms. MethodsTo address this, we selected 15 isolates for analysis with WGS and MALDI-TOF MS. Hybrid next-generation (Illumina) and 3rd-generation (nanopore) sequencing were used to draft genomes. Mass spectra, generated with MALDI-TOF MS, were processed with custom scripts to identify clusters of closely related isolates. ResultsMALDI-TOF MS and WGS identified 13/15 and 9/14 at the species level, respectively, and clusters of species generated from MALDI-TOF MS showed good agreement, in terms of congruence of partitioning, with phylotypes generated with WGS. Pairs of strains that were > 94% similar to each other, in terms of average amino acid identity (AAI) predicted by WGS, consistently showed cosine similarities of mass spectra >0.8. The only discordance was for a pair of isolates that were classified asPaenibacillusspecies. This pair showed relatively high similarity (0.85) in terms of MALDI-TOF MS but only 85% similarity in terms of AAI. In addition, some strains isolated from cleanrooms at the JSC appeared closely related to strains isolated from spacecraft assembly cleanrooms. DiscussionSince MALDI-TOF MS costs less than whole genome sequencing and offers a throughput of hundreds of isolates per hour, this approach appears to offer a cost-efficient option for identifyingBacillusspecies, and related microbes, isolated during routine monitoring of cleanrooms and similar built environments. 

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