A high-performance polymer composite column for coronavirus nucleic acid purification

Here, we report the development of a novel polymer composite (PC) purification column and kit. The performance of the PC columns was compared to conventional silica gel (SG) columns for the purification of nucleic acids from coronaviruses, including SARS-CoV-2, in 82 clinical samples. The results shows that PC-based purification outperforms silica gel (SG)-based purification by enabling a higher sensitivity (94%), accuracy (97%), and by eliminating false positives (100% specificity). The high specificity is critical for efficient patient triage and resource management during pandemics. Furthermore, PC-based purification exhibits three times higher analytical precision than a commonly used SG-based nucleic acid purification thereby enabling a more accurate quantification of viral loads and higher reproducibility.

A High-Performance Polymer Composite Column for Coronavirus Nucleic Acid Purification

Here, we report the development of a novel polymer composite (PC) purification column and kit. The performance of the PC columns was compared to conventional silica gel (SG) columns for the purification of nucleic acids from coronaviruses, including SARS-CoV-2, in 82 clinical samples. The results shows that PC-based purification outperforms silica gel (SG)-based purification by enabling a higher sensitivity (94%), accuracy (97%), and by eliminating false positives (100% selectivity). The high selectivity is critical for efficient patient triage and resource management during pandemics. Furthermore, PC-based purification exhibits three times higher analytical precision than a commonly used SG-based nucleic acid purification thereby enabling a more accurate quantification of viral loads and higher reproducibility.

Optimized Replication of Arrayed Bacterial Mutant Libraries Increases Access to Biological Resources

Biological collections, including arrayed libraries of single transposon (Tn) or deletion mutants, greatly accelerate the pace of bacterial genetic research. Despite the importance of these resources, few protocols exist for the replication and distribution of these materials. Here, we describe a protocol for creating multiple replicates of an arrayed bacterial Tn library consisting of approximately 6,800 mutants in 96-well plates (73 plates). Our protocol provides multiple checkpoints to guard against contamination and minimize genetic drift caused by freeze/thaw cycles. This approach can also be scaled for arrayed culture collections of various sizes. Overall, this protocol is a valuable resource for other researchers considering the construction and distribution of arrayed culture collection resources for the benefit of the greater scientific community. IMPORTANCE Arrayed mutant collections drive robust genetic screens, but few protocols exist for replication of these resources and subsequent quality control. Increasing the distribution of arrayed biological collections will increase the accessibility and use of these resources. Developing standardized techniques for replication of these resources is essential for ensuring their quality and usefulness to the scientific community.

Optimized replication of arrayed bacterial mutant libraries increase access to biological resources

Biological collections, including arrayed libraries of single transposon or deletion mutants, greatly accelerate the pace of bacterial genetics research. Despite the importance of these resources, few protocols exist for the replication and distribution of these materials. Here, we describe a protocol for creating multiple replicates of an arrayed bacterial Tn library consisting of approximately 6,800 mutants in 73 × 96-well plates. Our protocol provides multiple checkpoints to guard against contamination and minimize genetic drift caused by freeze/thaw cycles. This approach can also be scaled for arrayed culture collections of various sizes. Overall, this protocol is a valuable resource for other researchers considering the construction and distribution of arrayed culture collection resources for the benefit of the greater scientific community.

Importance

Arrayed mutant collections drive robust genetic screens, yet few protocols exist for replication of these resources and subsequent quality control. Increasing distribution of arrayed biological collections will increase accessibility to and use of these resources. Developing standardized techniques for replication of these resources is essential for ensuring their quality and usefulness to the scientific community.

Enterococcus faecalis colonizes and forms persistent biofilm microcolonies on undamaged endothelial surfaces in a rabbit endovascular infection model

Infectious endocarditis (IE) is an uncommon disease with significant morbidity and mortality. The pathogenesis of IE has historically been described as a cascade of host-specific events beginning with endothelial damage and thrombus formation and followed by bacterial colonization of the nascent thrombus. Enterococcus faecalis is a Gram-positive commensal bacterial member of the gastrointestinal tract microbiota in most terrestrial animals and a leading cause of opportunistic biofilm-associated infections, including endocarditis. Here, we provide evidence that E. faecalis can colonize the endocardial surface without pre-existing damage and in the absence of thrombus formation in a rabbit endovascular infection model. Using previously described light and scanning electron microscopy techniques, we show that inoculation of a well-characterized E. faecalis lab strain in the marginal ear vein of New Zealand White rabbits resulted in rapid colonization of the endocardium throughout the heart within 4 days of administration. Unexpectedly, ultrastructural imaging revealed that the microcolonies were firmly attached directly to the endocardium in areas without morphological evidence of gross tissue damage. Further, the attached bacterial aggregates were not associated with significant cellular components of coagulation or host extracellular matrix damage repair (i.e. platelets). These results suggest that the canonical model of mechanical surface damage as a prerequisite for bacterial attachment to host sub-endothelial components is not required. Furthermore, these findings are consistent with a model of initial establishment of stable, endocarditis-associated E. faecalis biofilm microcolonies that may provide a reservoir for the eventual valvular infection characteristic of clinical endocarditis. The similarities between the E. faecalis colonization and biofilm morphologies seen in this rabbit endovascular infection model and our previously published murine gastrointestinal colonization model indicate that biofilm production and common host cell attachment factors are conserved in disparate mammalian hosts under both commensal and pathogenic contexts.

Enterococcal Endocarditis: Hiding in Plain Sight

Enterococcus faecalis is a major opportunistic bacterial pathogen of increasing clinical relevance. A substantial body of experimental evidence suggests that early biofilm formation plays a critical role in these infections, as well as in colonization and persistence in the GI tract as a commensal member of the microbiome in most terrestrial animals. Animal models of experimental endocarditis generally involve inducing mechanical valve damage by cardiac catheterization prior to infection, and it has long been presumed that endocarditis vegetation formation resulting from bacterial attachment to the endocardial endothelium requires some pre-existing tissue damage. Here we review both historical and contemporary animal model studies demonstrating the robust ability of E. faecalis to directly attach and form stable microcolony biofilms encased within a bacterially-derived extracellular matrix on the undamaged endovascular endothelial surface. We also discuss the morphological similarities when these biofilms form on other host tissues, including when E. faecalis colonizes the GI epithelium as a commensal member of the normal vertebrate microbiome - hiding in plain sight where it can serve as a source for systemic infection via translocation. We propose that these phenotypes may allow the organism to persist as an undetected infection in asymptomatic individuals and thus provide an infectious reservoir for later clinical endocarditis.

Early E. casseliflavus gut colonization and outcomes of allogeneic hematopoietic cell transplantation

Gut dysbiosis has been associated with worse allogeneic hematopoietic cell transplantation (allo-HCT) outcomes. We reported an association between intrinsically vancomycin-resistant enterococci (iVRE: E. gallinarum and E. casseliflavus) gut colonization and lower post-transplant mortality. In this study, using an expanded cohort, we evaluated whether our previously observed association is species-specific. We included allo-HCT recipients with ≥1 positive rectal swab or stool culture for iVRE between days -14 and +14 of transplant. To investigate whether iVRE modulate the gut microbiota, we performed agar diffusion assays. To investigate whether iVRE differ in their ability to activate the aryl hydrocarbon receptor, we analyzed iVRE genomes for enzymes in the shikimate and tryptophan pathways. Sixty six (23 E. casseliflavus and 43 E. gallinarum) of the 908 allograft recipients (2011-2017) met our inclusion criteria. Overall survival was significantly higher in patients with E. casseliflavus (91% vs. 62% at 3 years, P = 0.04). In multivariable analysis, E. casseliflavus gut colonization was significantly associated with reduced all-cause mortality (hazard ratio 0.20, 95% confidence interval 0.04-0.91, P = 0.04). While agar assays were largely unremarkable, genome mining predicted that E. casseliflavus encodes a larger number of enzymes in the tryptophan metabolism pathway. In conclusion, E. casseliflavus gut colonization is associated with reduced post-HCT morality. Further research is needed to understand the mechanisms for this association.

Widespread Lichtheimia Infection in a Patient with Extensive Burns: Opportunities for Novel Antifungal Agents

The Mucorales fungi-formerly classified as the zygomycetes-are environmentally ubiquitous fungi, but generally rare causes of clinical infections. In the immunocompromised host, however, they can cause invasive, rapidly spreading infections that confer a high risk of morbidity and mortality, often despite surgical and antifungal therapy. Patients with extensive burn injuries are particularly susceptible to skin and soft-tissue infections with these organisms. Here, we present a case of Lichtheimia infection in a patient with extensive full-thickness burns that required significant and repeated surgical debridement successfully treated with isavuconazole and adjunctive topical amphotericin B washes. We also review the available literature on contemporary antifungal treatment for Lichtheimia species and related Mucorales fungi.

A Noninvasive Rhizopus Infection With a Bladder Fungal Ball in a Patient With Poorly Controlled Diabetes Mellitus

Here we present the first reported case of a noninvasive Rhizopus fungal ball confined to the bladder of a patient with poorly controlled diabetes and right flank pain. The patient developed bilateral hydronephrosis after several hospital admissions for urinary tract infections with multiple failed courses of antibiotics. During cystoscopy to replace a ureteral stent, he was found to harbor a fungal ball in the bladder that was removed and grew Rhizopus in culture. Patient received treatment with amphotericin B and transitioned to long-term posaconazole therapy. This case highlights the importance of considering fungal agents in urinary tract infections, especially in persistent or refractory cases, and the role of the clinical microbiology laboratory in correct identification of the infectious source.

Enterococcus faecalis readily colonizes the entire gastrointestinal tract and forms biofilms in a germ-free mouse model

The mammalian gastrointestinal (GI) tract is a complex organ system with a twist-a significant portion of its composition is a community of microbial symbionts. The microbiota plays an increasingly appreciated role in many clinically-relevant conditions. It is important to understand the details of biofilm development in the GI tract since bacteria in this state not only use biofilms to improve colonization, biofilm bacteria often exhibit high levels of resistance to common, clinically relevant antibacterial drugs. Here we examine the initial colonization of the germ-free murine GI tract by Enterococcus faecalis-one of the first bacterial colonizers of the naïve mammalian gut. We demonstrate strong morphological similarities to our previous in vitro E. faecalis biofilm microcolony architecture using 3 complementary imaging techniques: conventional tissue Gram stain, immunofluorescent imaging (IFM) of constitutive fluorescent protein reporter expression, and low-voltage scanning electron microscopy (LV-SEM). E. faecalis biofilm microcolonies were readily identifiable throughout the entire lower GI tract, from the duodenum to the colon. Notably, biofilm development appeared to occur as discrete microcolonies directly attached to the epithelial surface rather than confluent sheets of cells throughout the GI tract even in the presence of high (>10⁹) fecal bacterial loads. An in vivo competition experiment using a pool of 11 select E. faecalis mutant strains containing sequence-defined transposon insertions showed the potential of this model to identify genetic factors involved in E. faecalis colonization of the murine GI tract.

Multiple roles for Enterococcus faecalis glycosyltransferases in biofilm-associated antibiotic resistance, cell envelope integrity, and conjugative transfer

The emergence of multidrug-resistant bacteria and the limited availability of new antibiotics are of increasing clinical concern. A compounding factor is the ability of microorganisms to form biofilms (communities of cells encased in a protective extracellular matrix) that are intrinsically resistant to antibiotics. Enterococcus faecalis is an opportunistic pathogen that readily forms biofilms and also has the propensity to acquire resistance determinants via horizontal gene transfer. There is intense interest in the genetic basis for intrinsic and acquired antibiotic resistance in E. faecalis, since clinical isolates exhibiting resistance to multiple antibiotics are not uncommon. We performed a genetic screen using a library of transposon (Tn) mutants to identify E. faecalis biofilm-associated antibiotic resistance determinants. Five Tn mutants formed wild-type biofilms in the absence of antibiotics but produced decreased biofilm biomass in the presence of antibiotic concentrations that were subinhibitory to the parent strain. Genetic determinants responsible for biofilm-associated antibiotic resistance include components of the quorum-sensing system (fsrA, fsrC, and gelE) and two glycosyltransferase (GTF) genes (epaI and epaOX). We also found that the GTFs play additional roles in E. faecalis resistance to detergent and bile salts, maintenance of cell envelope integrity, determination of cell shape, polysaccharide composition, and conjugative transfer of the pheromone-inducible plasmid pCF10. The epaOX gene is located in a variable extended region of the enterococcal polysaccharide antigen (epa) locus. These data illustrate the importance of GTFs in E. faecalis adaptation to diverse growth conditions and suggest new targets for antimicrobial design.

Evaluation of the Enterococcus faecalis Biofilm-Associated Virulence Factors AhrC and Eep in Rat Foreign Body Osteomyelitis and In Vitro Biofilm-Associated Antimicrobial Resistance

Enterococcus faecalis can cause healthcare-associated biofilm infections, including those of orthopedic devices. Treatment of enterococcal prosthetic joint infection is difficult, in part, due to biofilm-associated antimicrobial resistance. We previously showed that the E. faecalis OG1RF genes ahrC and eep are in vitro biofilm determinants and virulence factors in animal models of endocarditis and catheter-associated urinary tract infection. In this study, we evaluated the role of these genes in a rat acute foreign body osteomyelitis model and in in vitro biofilm-associated antimicrobial resistance. Osteomyelitis was established for one week following the implantation of stainless steel orthopedic wires inoculated with E. faecalis strains OG1RF, ΩahrC, and ∆eep into the proximal tibiae of rats. The median bacterial loads recovered from bones and wires did not differ significantly between the strains at multiple inoculum concentrations. We hypothesize that factors present at the infection site that affect biofilm formation, such as the presence or absence of shear force, may account for the differences in attenuation in the various animal models we have used to study the ΩahrC and ∆eep strains. No differences among the three strains were observed in the planktonic and biofilm antimicrobial susceptibilities to ampicillin, vancomycin, daptomycin, linezolid, and tetracycline. These findings suggest that neither ahrC nor eep directly contribute to E. faecalis biofilm-associated antimicrobial resistance. Notably, the experimental evidence that the biofilm attachment mutant ΩahrC displays biofilm-associated antimicrobial resistance suggests that surface colonization alone is sufficient for E. faecalis cells to acquire the biofilm antimicrobial resistance phenotype.

Ultrastructure of a novel bacterial form located in Staphylococcus aureus in vitro and in vivo catheter-associated biofilms

Bacterial biofilms are ubiquitous in nature, industry, and medicine, and understanding their development and cellular structure is critical in controlling the unwanted consequences of biofilm growth. Here, we report the ultrastructure of a novel bacterial form observed by scanning electron microscopy in the luminal vegetations of catheters from patients with active Staphylococcus aureus bacteremia. This novel structure had the general appearance of a normal staphylococcal cell but up to 10 to 15 times as large. Transmission electron microscopy indicated that these structures appeared as sacs enclosing multiple normal-sized (~0.6 µm) staphylococcal forms. Using in vitro cultivated biofilms, cytochemical studies using fluorescent reagents revealed that these structures were rich in lipids and appeared within 15 min after S. aureus inoculation onto clinically relevant abiotic surfaces. Because they appeared early in biofilm development, these novel bacterial forms may represent an unappreciated mechanism for biofilm surface adherence, and their prominent lipid expression levels could explain the perplexing increased antimicrobial resistance of biofilm-associated bacteria.

Use of recombinase-based in vivo expression technology to characterize Enterococcus faecalis gene expression during infection identifies in vivo-expressed antisense RNAs and implicates the protease Eep in pathogenesis

Enterococcus faecalis is a member of the mammalian gastrointestinal microflora that has become a leading cause of nosocomial infections over the past several decades. E. faecalis must be able to adapt its physiology based on its surroundings in order to thrive in a mammalian host as both a commensal and a pathogen. We employed recombinase-based in vivo expression technology (RIVET) to identify promoters on the E. faecalis OG1RF chromosome that were specifically activated during the course of infection in a rabbit subdermal abscess model. The RIVET screen identified 249 putative in vivo-activated loci, over one-third of which are predicted to generate antisense transcripts. Three predicted antisense transcripts were detected in in vitro- and in vivo-grown cells, providing the first evidence of in vivo-expressed antisense RNAs in E. faecalis. Deletions in the in vivo-activated genes that encode glutamate 5-kinase (proB [EF0038]), the transcriptional regulator EbrA (ebrA [EF1809]), and the membrane metalloprotease Eep (eep [EF2380]) did not hinder biofilm formation in in vitro assays. In a rabbit model of endocarditis, the ΔebrA strain was fully virulent, the ΔproB strain was slightly attenuated, and the Δeep strain was severely attenuated. The Δeep virulence defect could be complemented by the expression of the wild-type gene in trans. Microscopic analysis of early Δeep biofilms revealed an abundance of small cellular aggregates that were not observed in wild-type biofilms. This work illustrates the use of a RIVET screen to provide information about the temporal activation of genes during infection, resulting in the identification and confirmation of a new virulence determinant in an important pathogen.

Relation between antibiotic susceptibility and ultrastructure of Staphylococcus aureus biofilms on surgical suture

BACKGROUND

Infectious biofilms are recalcitrant to antimicrobial therapy, but the mechanism(s) responsible for the greater resistance are unclear. Experiments were designed to clarify the association between antibiotic resistance and biofilm ultrastructure.

METHODS

Staphylococcus aureus was cultivated for 24 h on silk suture, where robust biofilms formed. Initial experiments compared the susceptibilities of planktonic (free-living) cells and mechanically dispersed biofilm cells to ampicillin, oxacillin, and vancomycin. Antibiotics in bactericidal concentrations were then incubated overnight with 24-h biofilms, and subsequent assays determined the viability of cells in mechanically dispersed biofilms, biofilm metabolic capacity and biomass, and biofilm ultrastructure (scanning electron microscopy).

RESULTS

Planktonic and biofilm cells had similar intrinsic antibiotic susceptibility. Nonetheless, a stable population of bacteria remained viable after biofilms were incubated with inhibitory drug concentrations, although biofilm metabolic capacity often was not detected, and biomass generally was reduced. Electron microscopy revealed that control (no drug) biofilms consisted primarily of bacterial clusters amid fibrillar elements. Antibiotic-treated biofilms had some staphylococci with smooth cells walls similar to planktonic cells, but other cocci were encased in extracellular material. This material was more abundant in antibiotic-treated than in control biofilms.

CONCLUSIONS

In the presence of high antibiotic concentrations, dense extracellular material may inhibit interaction of antibiotics with their bacterial targets.

Bacterial contamination of surgical suture resembles a biofilm

BACKGROUND

Although much attention is currently directed to studying microbial biofilms on a variety of surfaces, few studies are designed to study bacterial growth on surgical suture. The purpose of this study was to compare the kinetic development of Staphylococcus aureus and Enterococcus faecalis on five surgical suture materials and to clarify factors that might influence this growth.

METHODS

Pure cultures of S. aureus and E. faecalis were incubated with five types of suture for four days using either tissue culture medium or a bacterial growth medium. Suture-associated bacteria were quantified daily. In selected experiments, the bacterial growth medium was supplemented with heparin, a substance known to promote S. aureus biofilm formation. The ultrastructure of S. aureus biofilm developing on braided suture was studied with scanning electron microscopy.

RESULTS

Staphylococcus aureus and E. faecalis were recovered in greater numbers (typically p < 0.01) from braided than from monofilament suture, and the numbers of bacteria were greater (often p < 0.01) on sutures incubated in bacterial growth medium rather than tissue culture medium. Addition of heparin 1,000 U/mL to silk or braided polyglactin 910 suture incubated three days with S. aureus resulted in greater numbers of bacteria on day one but not on subsequent days. Scanning electron microscopy showed a maturing S. aureus biofilm that developed from small clusters of cells among amorphous material and fibrillar elements to larger clusters of cells that appeared covered by more consolidated extracellular material.

CONCLUSIONS

Bacterial growth was favored on braided vs. monofilament suture, and heparin enhanced bacterial adherence after day one, but not at subsequent times. Staphylococcus aureus adhered to suture material and formed a structure consistent with a bacterial biofilm.