- Volume 69, Issue 6, 2020

Introduction. Bloodstream infections (BSI) are growing in incidence and present a serious health threat. Most patients wait up to 48 h before microbiological cultures can confirm a diagnosis. Low numbers of circulating bacteria in patients with BSI mean we need to develop new methods and optimize current methods to facilitate efficient recovery of bacteria from the bloodstream. This will allow detection of positive blood cultures in a more clinically useful timeframe. Many bacterial blood recovery methods are available and usually include a combination of techniques such as centrifugation, filtration, serum separation or lysis treatment. Here, we evaluate nine different bacteria recovery methods performed directly from blood culture.

Aim. We sought to identify a bacterial recovery method that would allow for a cost-effective and efficient recovery of common BSI pathogens directly from blood culture.

Methods. Simulated E. coli ATCC 25922 blood culture was used as a model system to evaluate nine different bacteria recovery methods. Each method was assessed on recovery yield, cost, hands-on time, risk of contamination and ease of use. The highest scoring recovery method was further evaluated using simulated blood cultures spiked with seven of the most frequently occurring bloodstream pathogens. The recovery yield was calculated based on c.f.u. count before and after each recovery method. Independent t-tests were performed to determine if the recovery methods evaluated were significantly different based on c.f.u. ml−1 log recovery.

Results. All nine methods evaluated successfully recovered E. coli ATCC 25922 from simulated blood cultures although the bacterial yield differed significantly. The MALDI-TOF intact cell method offered the poorest recovery with a mean loss of 2.94±0.37 log c.f.u. ml−1. In contrast, a method developed by Bio-Rad achieved the greatest bacterial yield with a mean bacteria loss of 0.27±0.013 log c.f.u. ml−1. Overall, a low-speed serum-separation method was demonstrated to be the most efficient method in terms of time, cost and recovery efficiency and successfully recovered seven of the most frequent BSI pathogens with a mean bacteria loss of 0.717±0.18 log c.f.u. ml−1.

Conclusion. The efficiency of bacterial recovery can vary significantly between different methods and thereby can have a critical impact on downstream analysis. The low-speed serum-separation method offered a simple and effective means of recovering common BSI pathogens from blood culture and will be further investigated for use in the rapid detection of bacteraemia and susceptibility testing in clinical practice.

Introduction. Identification of typhoidal Salmonella (TS) serovars and their discrimination from non-typhoidal Salmonella (NTS) is conventionally performed by seroagglutination. This method is labour-intensive, requires technical experience and can be inconclusive in some cases. Molecular assays may be reliable alternative diagnostic tools.

Aim. This study was designed to evaluate the eazyplex TyphiTyper based on loop-mediated isothermal amplification (LAMP) for fast identification of TS and S. Choleraesuis in culture.

Methodology. A total of 121 Salmonella strains and 33 isolates of other Enterobacterales species were tested by the eazyplex TyphiTyper. Simulated and clinical blood cultures (BCs) were used to examine the performance of the assay for diagnosis of systemic infection. Sample preparation took about 5 min and the test running time was 20 min. Amplification was measured by real-time fluorescence detection.

Results. All TS and S. Choleraesuis strains were correctly identified. The most common NTS S. Typhimurium (n=34) and S. Enteritidis (n=15) were detected as Salmonella species without any false positive result for TS targets. Cross-reactions of NTS with TS were only rarely observed. Direct testing of positive BCs gave correct results. Sensitivities and specificities of the assay were as follows: 100 and 99.3 % for S. Typhi, 100 and 98.7 % for S. Paratyphi A, 100 and 97.3 % for S. Paratyphi B, 100 and 100 % for S. Paratyphi C, 100 and 100 % for S. Choleraesuis, and 100 and 100 % for Salmonella species, respectively.

Conclusion. The eazyplex TyphiTyper is very easy to perform and allows the rapid identification of TS and S. Choleraesuis isolates.

Introduction. Candida auris is an emerging fungal pathogen. The organism can cause invasive infections associated with high mortality, has been implicated in outbreaks in healthcare settings and is frequently resistant to multiple antifungal agents, making it a significant challenge to infection prevention and patient treatment.

Aim. To implement a real-time PCR assay for detection of C. auris in patient surveillance samples collected with the Copan Liquid Amies elution swab (ESwab) collection and transport system.

Methodology. We optimized a real-time PCR testing procedure based on the sample collection device used in our institution.

Results . ESwab transport medium was strongly inhibitory to the real-time PCR. Removing the medium with centrifugation, followed by suspending the pellet in PBS-BSA buffer (concentration 1 %), sufficiently eliminated the inhibition. The manual sample preparation method, freeze–thaw followed by mechanical disruption, allowed the detection of C. auris at the lowest cell concentration.

Conclusion . The optimized procedure was used to test 1414 patient surveillance samples. The real-time PCR detected all culture-positive samples with 100 % sensitivity and 100 % specificity.

Introduction. Sporotrichosis, caused by species of the Sporothrix schenckii complex, is the most prevalent subcutaneous mycosis in many areas of Latin America. Statins are a class of drugs widely used for lowering high sterol levels through their action on 3-hydroxy-3-methylglutaryl-CoA reductase, a key enzyme in the synthesis of sterol.

Aim. In this study, the antifungal activity of statins (simvastatin, atorvastatin, pravastatin) against planktonic cells and biofilms of S. schenckii complex species was evaluated, as well as the interaction of pravastatin with classical antifungals (amphotericin B, itraconazole, terbinafine).

Methodology. Eighteen strains of Sporothrix species were used. The antifungal susceptibility assay was performed using the broth microdilution method. Mature biofilms were exposed to statins and metabolic activity was measured by the XTT reduction assay.

Results. MICs of statins ranged from 8 to 512 μg ml−1 and from 8 to 256 μg ml−1 for filamentous and yeast forms, respectively. Regarding mature biofilms, MICs of 50 % inhibition (SMIC50) were 128 μg ml−1 for simvastatin and atorvastatin and >2048 μg ml−1 for pravastatin. MICs of 90 % inhibition (SMIC90) were 512 μg ml−1 for simvastatin and >2048 μg ml−1 for atorvastatin and pravastatin.

Conclusion. These results highlight the antifungal and antibiofilm potential of statins against S. schenckii complex species.

Introduction. Signal transducer and activator of transcription 3 (STAT3) deficiency is a rare primary immunodeficiency associated with increased susceptibility to bacterial and fungal infections, notably pulmonary aspergillosis.

Aim. We describe the emergence of azole-resistant Aspergillus fumigatus infections in STAT3-deficient patients.

Methodology. During a retrospective study of 13 pulmonary aspergillosis cases in STAT3-deficient patients conducted in France, we identified patients infected with azole-resistant A. fumigatus isolates.

Results. Two out of the 13 STAT3-deficient patients with aspergillosis had azole-resistant A. fumigatus infection, indicating an unexpectedly high prevalence of resistance. The first patient with STAT3 deficiency presented several flares of allergic bronchopulmonary aspergillosis-like episodes. He was chronically infected with two azole-resistant A. fumigatus isolates (TR34/L98). Despite prolonged antifungal treatment, including caspofungin and amphotericin B, the patient was not able to clear the azole-resistant A. fumigatus. The second patient had chronic cavitary pulmonary aspergillosis (CCPA). The A. fumigatus isolate was initially azole susceptible but harboured three F46Y, M172V and E427K point mutations. Despite prolonged antifungal therapies, lesions worsened and the isolate became resistant to all azoles. Surgery and caspofungin treatments were then required to cure CCPA. Resistance was probably acquired from the environment (TR34/L98) in the first case whereas resistance developed under antifungal treatments in the second case. These infections required long-term antifungal treatments and surgery.

Conclusions. The emergence of azole-resistant A. fumigatus infections in STAT3-deficiency dramatically impacts both curative and prophylactic antifungal strategies. Physicians following patients with primary immune-deficiencies should be aware of this emerging problem as it complicates management of the patient.

Introduction. The emergence of SARS-CoV-2 has taken humanity off guard. Following an outbreak of SARS-CoV in 2002, and MERS-CoV about 10 years later, SARS-CoV-2 is the third coronavirus in less than 20 years to cross the species barrier and start spreading by human-to-human transmission. It is the most infectious of the three, currently causing the COVID-19 pandemic. No treatment has been approved for COVID-19. We previously proposed targets that can serve as binding sites for antiviral drugs for multiple coronaviruses, and here we set out to find current drugs that can be repurposed as COVID-19 therapeutics.

Aim. To identify drugs against COVID-19, we performed an in silico virtual screen with the US Food and Drug Administration (FDA)-approved drugs targeting the RNA-dependent RNA polymerase (RdRP), a critical enzyme for coronavirus replication.

Methodology. Initially, no RdRP structure of SARS-CoV-2 was available. We performed basic sequence and structural analysis to determine if RdRP from SARS-CoV was a suitable replacement. We performed molecular dynamics simulations to generate multiple starting conformations that were used for the in silico virtual screen. During this work, a structure of RdRP from SARS-CoV-2 became available and was also included in the in silico virtual screen.

Results. The virtual screen identified several drugs predicted to bind in the conserved RNA tunnel of RdRP, where many of the proposed targets were located. Among these candidates, quinupristin is particularly interesting because it is expected to bind across the RNA tunnel, blocking access from both sides and suggesting that it has the potential to arrest viral replication by preventing viral RNA synthesis. Quinupristin is an antibiotic that has been in clinical use for two decades and is known to cause relatively minor side effects.

Conclusion. Quinupristin represents a potential anti-SARS-CoV-2 therapeutic. At present, we have no evidence that this drug is effective against SARS-CoV-2 but expect that the biomedical community will expeditiously follow up on our in silico findings.

Introduction. Biological adhesives and effective topical therapeutic agents that improve wound healing are urgently required for the treatment of chronic ulcers. A biodegradable adhesive based on a carbohydrate polymer with zinc oxide (CPZO) was shown to possess anti-inflammatory activity and enhance wound healing, but its bactericidal activity was unknown.

Aim. To investigate the bactericidal activity of CPZO against bacteria commonly present as infectious agents in chronic wounds.

Methodology. We examined the bactericidal activity of CPZO against three biofilm-producing bacteria ( Staphylococcus aureus , Escherichia coli and Pseudomonas aeruginosa ) through three strategies: bacterial suspension, biofilm disruption and in vitro wound biofilm model.

Results. In suspension cultures, CPZO had direct, potent bactericidal action against S. aureus within 24 h, whereas E. coli took 7 days to be eliminated. By contrast, P. aeruginosa survived up to 14 days with CPZO. CPZO had biofilm disruption activity against clinical isolates of S. aureus in the anti-biofilm test. Finally, in the in vitro wound biofilm model, CPZO dramatically reduced the bacterial viability of S. aureus and P. aeruginosa .

Conclusions. Together with its previously shown anti-inflammatory properties, the bactericidal activity of CPZO gives it the potential to be a first-line therapeutic option for chronic various ulcers and, possibly, other chronic ulcers, preventing or controlling microbial infections, and leading to the healing of such complicated chronic ulcers.

Introduction. Pseudomonas aeruginosa grows in extracellular DNA (eDNA)-enriched biofilms and infection sites. eDNA is generally considered to be a structural biofilm polymer required for aggregation and biofilm maturation. In addition, eDNA can sequester divalent metal cations, acidify growth media and serve as a nutrient source.

Aim. We wanted to determine the genome-wide influence on the transcriptome of planktonic P. aeruginosa PAO1 grown in the presence of eDNA.

Methodology. RNA-seq analysis was performed to determine the genome-wide effects on gene expression of PAO1 grown with eDNA. Transcriptional lux fusions were used to confirm eDNA regulation and to validate phenotypes associated with growth in eDNA.

Results. The transcriptome of eDNA-regulated genes included 89 induced and 76 repressed genes (FDR<0.05). A large number of eDNA-induced genes appear to be involved in utilizing DNA as a nutrient. Several eDNA-induced genes are also induced by acidic pH 5.5, and eDNA/acidic pH promoted an acid tolerance response in P. aeruginosa . The cyoABCDE terminal oxidase is induced by both eDNA and pH 5.5, and contributed to the acid tolerance phenotype. Quantitative metal analysis confirmed that DNA binds to diverse metals, which helps explain why many genes involved in a general uptake of metals were controlled by eDNA. Growth in the presence of eDNA also promoted intracellular bacterial survival and influenced virulence in the acute infection model of fruit flies.

Conclusion. The diverse functions of the eDNA-regulated genes underscore the important role of this extracellular polymer in promoting antibiotic resistance, virulence, acid tolerance and nutrient utilization; phenotypes that contribute to long-term survival.

Introduction. Indwelling medical devices such as endotracheal tubes (ETTs), urinary catheters, vascular access devices, tracheostomies and feeding tubes are often associated with hospital-acquired infections. Bacterial biofilm formed on the ETTs in intubated patients is a significant risk factor associated with ventilator-associated pneumonia. Pseudomonas aeruginosa is one of the four frequently encountered bacteria responsible for causing pneumonia, and the biofilm formation on ETTs. However, understanding of biofilm formation on ETT and interventions to prevent biofilm remains lagging. The ability to sense and adapt to external cues contributes to their success. Thus, the biofilm formation is likely to be influenced by the two-component systems (TCSs) that are composed of a membrane-associated sensor kinase and an intracellular response regulator.

Aim. This study aims to establish an in vitro method to analyse the P. aeruginosa biofilm formation on ETTs, and identify the TCSs that contribute to this process.

Methodology. In total, 112 P. aeruginosa PA14 TCS mutants were tested for their ability to form biofilm on ETTs, their effect on quorum sensing (QS) and motility.

Results. Out of 112 TCS mutants studied, 56 had altered biofilm biomass on ETTs. Although the biofilm formation on ETTs is QS-dependent, none of the 56 loci controlled quorum signal. Of these, 18 novel TCSs specific to ETT biofilm were identified, namely, AauS, AgtS, ColR, CopS, CprR, NasT, KdpD, ParS, PmrB, PprA, PvrS, RcsC, PA14_11120, PA14_32580, PA14_45880, PA14_49420, PA14_52240, PA14_70790. The set of 56 included the GacS network, TCS proteins involved in fimbriae synthesis, TCS proteins involved in antimicrobial peptide resistance, and surface-sensing. Additionally, several of the TCS-encoding genes involved in biofilm formation on ETTs were found to be linked to flagellum-dependent swimming motility.

Conclusions. Our study established an in vitro method for studying P. aeruginosa biofilm formation on the ETT surfaces. We also identified novel ETT-specific TCSs that could serve as targets to prevent biofilm formation on indwelling devices frequently used in clinical settings.