Category: Statistics

Microbiol Spectr. 2022 Jul 7:e0117622. doi: 10.1128/spectrum.01176-22. Online ahead of print.

ABSTRACT

Chlorhexidine (CHX) is widely used to control the spread of pathogens (e.g., human/animal clinical settings, ambulatory care, food industry). Enterococcus faecalis, a major nosocomial pathogen, is broadly distributed in diverse hosts and environments facilitating its exposure to CHX over the years. Nevertheless, CHX activity against E. faecalis is understudied. Our goal was to assess CHX activity and the variability of ChlR-EfrEF proteins (associated with CHX tolerance) among 673 field isolates and 1,784 E. faecalis genomes from the PATRIC database from different sources, time spans, clonal lineages, and antibiotic-resistance profiles. The CHX MIC (MIC_CHX) and minimum bactericidal concentration (MBC_CHX) against E. faecalis presented normal distributions (0.5 to 64 mg/L). However, more CHX-tolerant isolates were detected in the food chain and recent human infections, suggesting an adaptability of E. faecalis populations in settings where CHX is heavily used. Heterogeneity in ChlR-EfrEF sequences was identified, with isolates harboring incomplete ChlR-EfrEF proteins, particularly the EfrE identified in the ST40 clonal lineage, showing low MIC_CHX (≤1mg/L). Distinct ST40-E. faecalis subpopulations carrying truncated and nontruncated EfrE were detected, with the former being predominant in human isolates. This study provides a new insight about CHX susceptibility and ChlR-EfrEF variability within diverse E. faecalis populations. The MIC_CHX/MBC_CHX of more tolerant E. faecalis (MIC_CHX = 8 mg/L; MBC_CHX = 64 mg/L) remain lower than in-use concentrations of CHX (≥500 mg/L). However, increased CHX use, combined with concentration gradients occurring in diverse environments, potentially selecting multidrug-resistant strains with different CHX susceptibilities, signals the importance of monitoring the trends of E. faecalis CHX tolerance within a One Health approach. IMPORTANCE Chlorhexidine (CHX) is a disinfectant and antiseptic used since the 1950s and included in the World Health Organization’s list of essential medicines. It has been widely applied in hospitals, the community, the food industry, animal husbandry and pets. CHX tolerance in Enterococcus faecalis, a ubiquitous bacterium and one of the leading causes of human hospital-acquired infections, remains underexplored. Our study provides novel and comprehensive insights about CHX susceptibility within the E. faecalis population structure context, revealing more CHX-tolerant subpopulations from the food chain and recent human infections. We further show a detailed analysis of the genetic diversity of the efrEF operon (previously associated with E. faecalis CHX tolerance) and its correlation with CHX phenotypes. The recent strains with a higher tolerance to CHX and the multiple sources where bacteria are exposed to this biocide alert us to the need for the continuous monitoring of E. faecalis adaptation toward CHX tolerance within a One Health approach.

PMID:35862993 | DOI:10.1128/spectrum.01176-22

Microbiol Spectr. 2022 Jul 7:e0121822. doi: 10.1128/spectrum.01218-22. Online ahead of print.

ABSTRACT

A total of 232 goat fecal samples (124 diarrheic and 108 nondiarrheic) collected from 12 farms in Southwest China were tested for astrovirus using RT-PCR. A total of 16.9% (21/124) of diarrheic and 20.4% (22/108) of nondiarrheic samples were astrovirus-positive, and no statistical difference was found in the detection rate between healthy and sick goats. Furthermore, 28 obtained complete ORF2 sequences could be classified into six genotypes according to the species classification criteria of the International Committee on Taxonomy of Viruses (ICTV). It is worth noting that, in addition to four known caprine astrovirus genotypes (MAstV-33, MAstV-34, Caprine Astrovirus G5.1, and Caprine Astrovirus G3.1), MAstV-13 and MAstV-24 genotypes were identified in goats. Interestingly, five of 19 ORF2 sequences in the Caprine Astrovirus G3.1 genotype showed possible intragenotypic recombination events. Furthermore, nearly complete caprine astrovirus genomes of MAstV-13 and MAstV-24 genotypes were obtained. The genome of the SWUN/ECJK3/2021 strain shared the highest similarity (62.0% to 73.9%) with astrovirus in MAstV-13, and clustered in the so-called human-mink-ovine (HMO) clade, which contained the majority of the neurotropic astrovirus strains. Moreover, the SWUN/LJK2-2/2020 strain showed the highest similarity (69.7% to 78.6%) and the closest genetic relationship to the known porcine and bovine astroviruses in MAstV-24. In conclusion, this study confirmed six genotypes of astrovirus circulating among goats in Southwest China, including MAstV-13 and MAstV-24 genotypes. These findings enhance our knowledge of the prevalence and diversity of astroviruses. IMPORTANCE Caprine astrovirus is a newly emerging virus, and information regarding its prevalence and molecular characteristics remains limited. In this study, six genotypes of astrovirus, including MAstV-13 and MAstV-24, were identified in goats, adding two novel caprine astrovirus genotypes to the four previously known genotypes, thereby enriching the diversity of the caprine astrovirus. Moreover, genomes of MAstV-13 SWUN/ECJK3/2021 and MAstV-24 SWUN/LJK2-2/2020 strains were obtained from goats, which aids in the understanding of the infection spectrum and host range of the two genotypes. This study is the first to demonstrate the presence of neurotropic-like astrovirus (MAstV-13) in goats, which has significant implications for the diagnosis of neurological diseases in goats.

PMID:35862967 | DOI:10.1128/spectrum.01218-22

J Spec Oper Med. 2022 Jul 21:A10N-KTMD. doi: 10.55460/A10N-KTMD. Online ahead of print.

ABSTRACT

BACKGROUND: Transfusion of whole blood (WB) is a lifesaving treatment that prolongs life until definitive surgical intervention can be performed; however, collecting WB is a time-consuming and resource-intensive process. Furthermore, it may be difficult to collect sufficient WB at the point of injury to treat critically wounded patients or multiple hemorrhaging casualties. This study is a follow-up to the proof-of-concept study on the effect of airdrop on WB. In addition, this study confirms the statistical significance for the plausibility of using airdrop to deliver WB to combat medics treating casualties in the pre-hospital setting when Federal Drug Administration (FDA)-approved cold-stored blood products are not available.

METHODS: Forty-eight units of WB were collected and loaded into a blood cooler that was dropped from a fixed-wing aircraft under a Standard Airdrop Training Bundle (SATB) parachute or 68-in pilot chute. Twenty-four of these units were dropped from a C-145 aircraft, and 24 were dropped from a C-130 aircraft. A control group of 15 units of WB was stored in a blood cooler that was not dropped. Baseline and post-intervention laboratory tests were measured in both airdropped and control units, including complete blood count; prothrombin time/partial thromboplastin time (PT/PTT); pH, lactate, potassium, bilirubin, glucose, fibrinogen, and lactate dehydrogenase (LDH) levels; and peripheral blood smears.

RESULTS: The blood cooler, cooling packs, and all 48 WB units did not sustain any major damage from the airdrop. There was no evidence of hemolysis. Except for the one slightly damaged bag that was not sampled, all airdropped blood met parameters for transfusion per the Joint Trauma System Whole Blood Transfusion Clinical Practice Guideline and the Association for the Advancement of Blood and Biotherapies (AABB) Circular of Information for the Use of Human Blood and Blood Components.

CONCLUSIONS: Airdrop of fresh or stored WB in a blood cooler with a chute is a viable way of delivering blood products to combat medics treating hemorrhaging patients in the pre-hospital setting. This study also demonstrated the portability of this technique for multiple aircraft. The techniques evaluated in this study have the potential for utilization in other austere settings such as wilderness medicine or humanitarian disasters where an acute need for WB delivery by airdrop is the only option.

PMID:35862850 | DOI:10.55460/A10N-KTMD

mSystems. 2022 Jul 5:e0025822. doi: 10.1128/msystems.00258-22. Online ahead of print.

ABSTRACT

Malaria symptoms are caused by the development of the parasites within the blood of an infected host. Bulk RNA sequencing (RNA-seq) of infected blood can reveal interactions between parasites and the host immune system during an infection, but because multiple developmental stages with distinct transcriptional profiles are concurrently present in infected blood, it is necessary to correct such analyses for differences in cell composition among samples. Gene expression deconvolution is a statistical approach that has been developed for inferring the cell composition of complex tissues characterized by bulk RNA-seq using gene expression profiles from reference cell types. Here, we describe the evaluation of a species-agnostic reference data set that can be used for efficient and accurate gene expression deconvolution of bulk RNA-seq data generated from any Plasmodium species and for correct gene expression analyses for biases caused by differences in stage composition among samples. IMPORTANCE Differences in cell type proportions among samples can introduce artifacts in gene expression analyses and mask genuine differences in gene regulation. Gene expression deconvolution allows estimation of the proportion of each cell type present in one sample directly from bulk RNA sequencing data, but this approach requires a reference data set with the signature profile of each cell type. Here, we evaluate the suitability of a rodent malaria parasite gene expression data set for estimating the proportions of each parasite developmental stage present in bulk RNA sequencing data generated from blood-stage infections with the human parasites Plasmodium falciparum and Plasmodium vivax. These analyses provide a species-agnostic approach for reliably estimating stage proportions in infected human blood and correcting subsequent gene expression analyses for these variations.

PMID:35862820 | DOI:10.1128/msystems.00258-22

mSystems. 2022 Jul 12:e0034822. doi: 10.1128/msystems.00348-22. Online ahead of print.

ABSTRACT

Microbial tolerance to organic solvents such as ionic liquids (ILs) is a robust phenotype beneficial for novel biotransformation. While most microbes become inhibited in 1% to 5% (vol/vol) IL (e.g., 1-ethyl-3-methylimidazolium acetate), we engineered a robust Yarrowia lipolytica strain (YlCW001) that tolerates a record high of 18% (vol/vol) IL via adaptive laboratory evolution. Yet, genotypes conferring high IL tolerance in YlCW001 remain to be discovered. In this study, we shed light on the underlying cellular processes that enable robust Y. lipolytica to thrive in inhibitory ILs. By using dynamic transcriptome sequencing (RNA-Seq) data, we introduced Gene Coexpression Connectivity (GeCCo) as a metric to discover genotypes conferring desirable phenotypes that might not be found by the conventional differential expression (DE) approaches. GeCCo selects genes based on their number of coexpressed genes in a subnetwork of upregulated genes by the target phenotype. We experimentally validated GeCCo by reverse engineering a high-IL-tolerance phenotype in wild-type Y. lipolytica. We found that gene targets selected by both DE and GeCCo exhibited the best statistical chance at increasing IL tolerance when individually overexpressed. Remarkably, the best combination of dual-overexpression genes was genes selected by GeCCo alone. This nonintuitive combination of genes, BRN1 and OYE2, is involved in guiding/regulating mitotic cell division, chromatin segregation/condensation, microtubule and cytoskeletal organization, and Golgi vesicle transport. IMPORTANCE Cellular robustness to cope with stressors is an important phenotype. Y. lipolytica is an industrial robust oleaginous yeast that has recently been discovered to tolerate record high concentrations of ILs, beneficial for novel biotransformation in organic solvents. However, genotypes that link to IL tolerance in Y. lipolytica are largely unknown. Due to the complex IL-tolerant phenotype, conventional gene discovery and validation based on differential gene expression approaches are time-consuming due to a large search space and might encounter a high false-discovery rate. Here, using the developed Gene Coexpression Connectivity (GeCCo) method, we identified and validated a subset of most promising gene targets conferring the IL-tolerant phenotypes and shed light on their potential mechanisms. We anticipate GeCCo being a useful method to discover the genotype-to-phenotype link.

PMID:35862814 | DOI:10.1128/msystems.00348-22

mSystems. 2022 Jul 18:e0012022. doi: 10.1128/msystems.00120-22. Online ahead of print.

ABSTRACT

Pathogenic fungal infections in plants may, in some cases, lead to downstream systematic impacts on the plant metabolome and microbiome that may either alleviate or exacerbate the effects of the fungal pathogen. While Sphaerulina musiva is a well-characterized fungal pathogen which infects Populus tree species, an important wood fiber and biofuel feedstock, little is known about its systematic effects on the metabolome and microbiome of Populus. Here, we investigated the metabolome of Populus trichocarpa and Populus deltoides leaves and roots and the microbiome of the leaf and root endospheres, phylloplane, and rhizosphere to understand the systematic impacts of S. musiva abundance and infection on Populus species in a common garden field setting. We found that S. musiva is indeed present in both P. deltoides and P. trichocarpa, but S. musiva abundance was not statistically related to stem canker onset. We also found that the leaf and root metabolomes significantly differ between the two Populus species and that certain leaf metabolites, particularly the phenolic glycosides salirepin and salireposide, are diminished in canker-infected P. trichocarpa trees compared to their uninfected counterparts. Furthermore, we found significant associations between the metabolome, S. musiva abundance, and microbiome composition and α-diversity, particularly in P. trichocarpa leaves. Our results show that S. musiva colonizes both resistant and susceptible hosts and that the effects of S. musiva on susceptible trees are not confined to the site of canker infection. IMPORTANCE Poplar (Populus spp.) trees are ecologically and economically important trees throughout North America. However, many western North American poplar plantations are at risk due to the introduction of the nonnative fungal pathogen Sphaerulina musiva, which causes leaf spot and cankers, limiting their production. To better understand the interactions among the pathogen S. musiva, the poplar metabolome, and the poplar microbiome, we collected leaf, root, and rhizosphere samples from poplar trees consisting of 10 genotypes and two species with differential resistance to S. musiva in a common garden experiment. Here, we outline the nuanced relationships between the poplar metabolome, microbiome, and S. musiva, showing that S. musiva may affect poplar trees in tissues distal to the site of infection (i.e., stem). Our research contributes to improving the fundamental understanding of S. musiva and Populus sp. ecology and the utility of a holobiont approach in understanding plant disease.

PMID:35862808 | DOI:10.1128/msystems.00120-22

Am J Bot. 2022 Jul 21. doi: 10.1002/ajb2.16040. Online ahead of print.

ABSTRACT

BACKGROUND AND AIMS: Antheridiogen systems are a set of pheromonal mechanisms that control sex expression in fern gametophytes. However, antheridiogen has rarely been studied outside of the laboratory and little is known about its function in natural settings. Combining predictions based on field and laboratory study, we test if the sexual structure of tree fern gametophyte colonies is attributable to antheridiogen.

METHODS: Gametophyte colonies of the antheridiogen-producing tree fern species Cyathea multiflora were collected at La Selva Biological Station in Costa Rica in January 2019. The sex of each gametophyte was determined, mapped, and spatial statistic approaches were used to examine the distribution of sex in each colony.

KEY RESULTS: In all gametophyte colonies, males were most common, representing 62%-68% of individuals. No hermaphroditic gametophytes were identified in any colony. A quadrat-based method showed female gametophytes were not clustered in each colony while male gametophytes were clustered. In two of the colonies, the K(r) test statistic for males was greater than expected compared to random simulations of sex, indicating male sex expression was spatially associated with females.

CONCLUSIONS: This study provides the first documentation of spatial sex expression in natural gametophyte settings of an antheridiogen-producing tree fern species. The profound impact of antheridiogen on gametophyte sex expression in field settings suggests this system is intimately tied to mating system, fitness, and genetic diversity in Cyathea multiflora. This article is protected by copyright. All rights reserved.

PMID:35862812 | DOI:10.1002/ajb2.16040

mSphere. 2022 Jul 11:e0029422. doi: 10.1128/msphere.00294-22. Online ahead of print.

NO ABSTRACT

PMID:35862806 | DOI:10.1128/msphere.00294-22

Antimicrob Agents Chemother. 2022 Jul 6:e0224421. doi: 10.1128/aac.02244-21. Online ahead of print.

ABSTRACT

Reduction of Clostridioides difficile infection (CDI) recurrence is an essential endpoint for CDI-directed antibiotic development that is often not evaluated until Phase III trials. The purpose of this project was to use a functional and metagenomic approach to predict the potential anti-CDI recurrence effect of ibezapolstat, a DNA polymerase IIIC inhibitor, in clinical development for CDI. As part of the Phase I ibezapolstat clinical study, stool samples were collected from 22 healthy volunteers, who were given either ibezapolstat or vancomycin. Stool samples were evaluated for microbiome changes and bile acid concentrations. Ibezapolstat 450 mg and vancomycin, but not ibezapolstat 300 mg, showed statistically significant changes in alpha diversity over time compared to that of a placebo. Beta diversity changes confirmed that microbiota were significantly different between study groups. Vancomycin had a more wide-ranging effect on the microbiome, characterized by an increased proportion of Gammaproteobacteria. Ibezapolstat demonstrated an increased proportion of Actinobacteria, including the Bifidobacteriaceae family. Using a linear regression analysis, vancomycin was associated with significant increases in primary bile acids as well as primary:secondary bile acid ratios. An overabundance of Enterobacteriaceae was most highly correlated with primary bile acid concentrations (r = 0.63; P < 0.0001). Using Phase I healthy volunteer samples, beneficial changes suggestive of a lower risk of CDI recurrence were associated with ibezapolstat compared to vancomycin. This novel omics approach may allow for better and earlier prediction of anti-CDI recurrence effects for antibiotics in the clinical development pipeline.

PMID:35862742 | DOI:10.1128/aac.02244-21

Am J Sports Med. 2022 Jul 21:3635465221108975. doi: 10.1177/03635465221108975. Online ahead of print.

ABSTRACT

BACKGROUND: Patients with femoroacetabular impingement syndrome (FAIS) may frequently have co-existing sacroiliac joint (SIJ) pain. It is known that patients with lower back pain undergoing total hip arthroplasty (THA) have inferior outcomes; however, it is unclear what the effect of SIJ pain is on outcomes after hip arthroscopy.

PURPOSE: To determine whether patients undergoing hip arthroscopy with SIJ pain either subjectively or on physical examination achieve similar postoperative improvement in patient-reported outcomes (PROs) compared with patients without SIJ pain at 2-year follow-up.

STUDY DESIGN: Cohort study; Level of evidence, 3.

METHODS: Patients with a minimum 2-year follow-up who underwent primary hip arthroscopy for FAIS with SIJ pain were matched in a 1:2 ratio to controls without SIJ pain. Baseline demographics, as well as postoperative PROs and rates of achievement of the minimal clinically important difference (MCID) or Patient Acceptable Symptom State (PASS) at 2-year follow-up were compared between the 2 groups.

RESULTS: A total of 73 patients (75 hips) with SIJ pain were matched to 150 control patients (150 hips) without SIJ pain. Both groups demonstrated statistically significant improvement in all PROs at 2 years (P < .05 for all). Patients with SIJ pain had significantly lower postoperative PRO scores for the Hip Outcome Score-Activities of Daily Living (HOS-ADL) (SIJ pain: 80.4 ± 22.4 vs no SIJ pain: 88.0 ± 15.1; P = .006), modified Harris Hip Score (mHHS) (SIJ pain: 73.2 ± 22.8 vs no SIJ pain: 80.0 ± 17.3; P < .001), and International Hip Outcome Tool-12 questionnaire (iHOT-12) (SIJ pain: 61.7 ± 25.9 vs no SIJ pain: 73.7 ± 23.7; P = .008). There were no statistically significant differences in improvement (delta) in PRO scores between the 2 groups (P > .05 for all). The SIJ pain group had significantly lower achievement of MCID for the HOS-ADL (SIJ pain: 65.2% vs no SIJ pain: 80.5%; P = .044) but not HOS-SS, mHHS, or iHOT-12 (P > .05 for all). The SIJ pain group had significantly lower achievement of PASS for the mHHS (SIJ pain: 27.5% vs no SIJ pain: 45.3%; P = .030) and iHOT-12 (SIJ pain: 31.0% vs no SIJ pain: 56.0%; P = .010) but not the HOS-ADL and HOS-SS (P > .05 for both). Only 4.1% of patients with SIJ pain and 2.4% of controls required revision surgery or converted to THA at the time of final follow-up (P = .69).

CONCLUSION: Patients with FAIS and SIJ pain on history or physical examination experience significant improvement in PROs at 2 years after hip arthroscopy. However, they may be less likely to achieve the MCID or PASS and have significantly lower postoperative PROs compared with a matched cohort of patients without SIJ pain. Overall rates of revision and conversion to THA were similarly low in both groups.

PMID:35862645 | DOI:10.1177/03635465221108975