Urinary tract infections: a review of the current diagnostics landscape.

Urinary tract infections are the most common bacterial infections worldwide. Infections can range from mild, recurrent (rUTI) to complicated (cUTIs), and are predominantly caused by uropathogenic Escherichia coli (UPEC). Antibiotic therapy is important to tackle infection; however, with the continued emergence of antibiotic resistance there is an urgent need to monitor the use of effective antibiotics through better stewardship measures. Currently, clinical diagnosis of UTIs relies on empiric methods supported by laboratory testing including cellular analysis (of both human and bacterial cells), dipstick analysis and phenotypic culture. Therefore, development of novel, sensitive and specific diagnostics is an important means to rationalise antibiotic therapy in patients. This review discusses the current diagnostic landscape and highlights promising novel diagnostic technologies in development that could aid in treatment and management of antibiotic-resistant UTIs.

Outbreak investigation of NDM-producing Burkholderia cepacia causing neonatal sepsis in Pakistan.

Aim: To investigate the outbreak of Burkholderia cepacia complex (BCC), mortality, antimicrobial resistance and associated risk factors in the neonatal intensive care unit. Method: Eighteen blood culture samples from neonates and twenty swab samples from different neonatal intensive care unit surfaces were collected. The VITEK 2 was used to confirm the isolates and generate the antibiogram. PCR was used to identify blaNDM. Results: Eighteen samples tested positive for BCC, and 10/18 (55.5%) of the neonates died. 13/18 (72%) of the neonates had late-onset neonatal sepsis, and 10/18 (55%) had low birth weight. Resistance to minocycline and chloramphenicol was 100%, 72.2% to meropenem; 72.2% NDM gene was found in neonates and was 20% from the environment. Conclusion: Outbreak of NDM-producing BCC resulting in high neonatal mortality in NICU.

Neonatal septicemia, or blood poisoning, is a dangerous illness in newborns. It is caused by bacteria or other infections entering the blood and spreading. Pregnancy, labor, delivery and exposure after birth can result in infection of the newborn. Neonatal septicemia kills 700,000 babies worldwide, mostly in low- and middle-income countries. Burkholderia cepacia complex bacteria can cause infections in people with weaker immune systems or other disorders. They are particularly dangerous in hospitals, as they can cause chronic lung problems. This study collected blood samples from newborns with blood poisoning. Most samples that contained Burkholderia cepacia complex were not susceptible to drugs. Four of the newborns carried the same bacteria, indicating that hospital staff should practice hand washing and equipment and environmental cleaning to prevent the spread of the bacteria.

Dermatophyte resistance - on the rise.

Dermatophytes are group of filamentous fungi which have adapted to living on the skin of humans and other animals. In the last decade, reports have emerged from Asia of new dermatophyte strains showing resistance to the commonly used antifungal agent terbinafine and others. The spread of these resistant strains has been noted in many other countries globally. Little is known about the mechanisms or management of this emerging problem. Urgent research and changes to current practice are required if the spread of the infection is to be contained and managed effectively.

Hypervirulent R20291 Clostridioides difficile spores show disinfection resilience to sodium hypochlorite despite structural changes.

BACKGROUND: Clostridioides difficile is a spore forming bacterial species and the major causative agent of nosocomial gastrointestinal infections. C. difficile spores are highly resilient to disinfection methods and to prevent infection, common cleaning protocols use sodium hypochlorite solutions to decontaminate hospital surfaces and equipment. However, there is a balance between minimising the use of harmful chemicals to the environment and patients as well as the need to eliminate spores, which can have varying resistance properties between strains. In this work, we employ TEM imaging and Raman spectroscopy to analyse changes in spore physiology in response to sodium hypochlorite. We characterize different C. difficile clinical isolates and assess the chemical's impact on spores' biochemical composition. Changes in the biochemical composition can, in turn, change spores' vibrational spectroscopic fingerprints, which can impact the possibility of detecting spores in a hospital using Raman based methods. RESULTS: We found that the isolates show significantly different susceptibility to hypochlorite, with the R20291 strain, in particular, showing less than 1 log reduction in viability for a 0.5% hypochlorite treatment, far below typically reported values for C. difficile. While TEM and Raman spectra analysis of hypochlorite-treated spores revealed that some hypochlorite-exposed spores remained intact and not distinguishable from controls, most spores showed structural changes. These changes were prominent in B. thuringiensis spores than C. difficile spores. CONCLUSION: This study highlights the ability of certain C. difficile spores to survive practical disinfection exposure and the related changes in spore Raman spectra that can be seen after exposure. These findings are important to consider when designing practical disinfection protocols and vibrational-based detection methods to avoid a false-positive response when screening decontaminated areas.

Hospital surface disinfection using ultraviolet germicidal irradiation technology: A review.

Ultraviolet germicidal irradiation (UVGI) technologies have emerged as a promising alternative to biocides as a means of surface disinfection in hospitals and other healthcare settings. This paper reviews the methods used by researchers and clinicians in deploying and evaluating the efficacy of UVGI technology. The type of UVGI technology used, the clinical setting where the device was deployed, and the methods of environmental testing that the researchers followed are investigated. The findings suggest that clinical UVGI deployments have been growing steadily since 2010 and have increased dramatically since the start of the COVID-19 pandemic. Hardware platforms and operating procedures vary considerably between studies. Most studies measure efficacy of the technology based on the objective measurement of bacterial bioburden reduction; however, studies conducted over longer durations have examined the impact of UVGI on the reduction of healthcare associated infections (HCAIs). Future trends include increased automation and the use of UVGI technologies that are safer for use around people. Although existing evidence seems to support the efficacy of UVGI as a tool capable of reducing HCAIs, more research is needed to measure the magnitude of these effects and to establish recommended best practices.

Isolation of Clostridioides difficile PCR Ribotype 027 from single-use hospital gown ties.

Background. Clostridioides difficile is a spore-forming pathogen responsible for antibiotic-associated diarrhoea. In the USA high incidence of C. difficile infection (CDI) in clinical environments has led to interest in C. difficile spore transmission.Hypothesis. Single use hospital surgical gown ties act as a reservoir for C. difficile spores.Aim. This study sought to examine whether single-use hospital surgical gown ties used in surgery, from an acute healthcare facility, harboured C. difficile spores.Methodology. Used surgical gowns ties worn by clinicians in the healthcare facility were examined for C. difficile spore presence via spread plate and anaerobic culture. The colonies isolated from each gown tie were subcultured on C. difficile selective agar for phenotypic confirmation. Presumptive C. difficile colonies were examined using C. difficile Quik Check Complete, 16-23S PCR Ribotyping and MALDI-TOF analysis.Results. In total 17 suspected C. difficile colonies were isolated from 15 gown ties via culture. C. difficile Quik Check Complete found two isolates as possible C. difficile. MALDI-TOF and PCR Ribotyping confirmed one isolate as C. difficile PCR ribotype 027 associated with clinical outbreaks.Discussion. Our study revealed the presence of hypervirulent C. difficile ribotype 027 spores on single-use gown ties. This highlights the potential of gown ties as a vector of spore transmission across clinical environments, especially when gowns are not worn appropriately.Conclusions. Appropriate compliance to infection control procedures by healthcare workers is essential to prevent spore dissemination across clinical facilities and reduce CDI rates.

Single Virus Detection on Silicon Photonic Crystal Random Cavities.

On-chip silicon microcavity sensors are advantageous for the detection of virus and biomolecules due to their compactness and the enhanced light-matter interaction with the analyte. While their theoretical sensitivity is at the single-molecule level, the fabrication of high quality (Q) factor silicon cavities and their integration with optical couplers remain as major hurdles in applications such as single virus detection. Here, label-free single virus detection using silicon photonic crystal random cavities is proposed and demonstrated. The sensor chips consist of free-standing silicon photonic crystal waveguides and do not require pre-fabricated defect cavities or optical couplers. Residual fabrication disorder results in Anderson-localized cavity modes which are excited by a free space beam. The Q ≈105 is sufficient for observing discrete step-changes in resonance wavelength for the binding of single adenoviruses (≈50 nm radius). The authors' findings point to future applications of CMOS-compatible silicon sensor chips supporting Anderson-localized modes that have detection capabilities at the level of single nanoparticles and molecules.

SARS-CoV-2 Tests: Bridging the Gap between Laboratory Sensors and Clinical Applications.

This review covers emerging biosensors for SARS-CoV-2 detection together with a review of the biochemical and clinical assays that are in use in hospitals and clinical laboratories. We discuss the gap in bridging the current practice of testing laboratories with nucleic acid amplification methods, and the robustness of assays the laboratories seek, and what emerging SARS-CoV-2 sensors have currently addressed in the literature. Together with the established nucleic acid and biochemical tests, we review emerging technology and antibody tests to determine the effectiveness of vaccines on individuals.

Using alternative teaching and learning approaches to deliver clinical microbiology during the COVID-19 pandemic.

The COVID-19 (coronavirus disease 2019) pandemic has had significant impacts upon higher education teaching. Clinical microbiology teaching is primarily focused on a combination of practical skill development and didactic delivery of content. In the pandemic, the absence of in-person teaching has led to educators adapting in-person content for online platforms and delivery. This commentary covers alternative innovative and engaging teaching approaches to deliver clinical microbiology content during the COVID-19 pandemic.

Biocide Use in the Antimicrobial Era: A Review.

Biocides are widely used in healthcare and industry to control infections and microbial contamination. Ineffectual disinfection of surfaces and inappropriate use of biocides can result in the survival of microorganisms such as bacteria and viruses on inanimate surfaces, often contributing to the transmission of infectious agents. Biocidal disinfectants employ varying modes of action to kill microorganisms, ranging from oxidization to solubilizing lipids. This review considers the main biocides used within healthcare and industry environments and highlights their modes of action, efficacy and relevance to disinfection of pathogenic bacteria. This information is vital for rational use and development of biocides in an era where microorganisms are becoming resistant to chemical antimicrobial agents.

Applications of Microwave Energy in Medicine.

Microwaves are a highly utilized electromagnetic wave, used across a range of industries including food processing, communications, in the development of novel medical treatments and biosensor diagnostics. Microwaves have known thermal interactions and theorized non-thermal interactions with living matter; however, there is significant debate as to the mechanisms of action behind these interactions and the potential benefits and limitations of their use. This review summarizes the current knowledge surrounding the implementation of microwave technologies within the medical industry.

Biocide Resistance and Transmission of Clostridium difficile Spores Spiked onto Clinical Surfaces from an American Health Care Facility.

Clostridium difficile is the primary cause of antibiotic-associated diarrhea globally. In unfavorable environments, the organism produces highly resistant spores which can survive microbicidal insult. Our previous research determined the ability of C. difficile spores to adhere to clinical surfaces, finding that spores had markedly different hydrophobic properties and adherence abilities. Investigation into the effect of the microbicide sodium dichloroisocyanurate on C. difficile spore transmission revealed that sublethal concentrations increased spore adherence without reducing viability. The present study examined the ability of spores to transmit across clinical surfaces and their response to an in-use disinfection concentration of 1,000 ppm of chlorine-releasing agent sodium dichloroisocyanurate. In an effort to understand if these surfaces contribute to nosocomial spore transmission, surgical isolation gowns, hospital-grade stainless steel, and floor vinyl were spiked with 1 × 106 spores/ml of two types of C. difficile spore preparations: crude spores and purified spores. The hydrophobicity of each spore type versus clinical surface was examined via plate transfer assay and scanning electron microscopy. The experiment was repeated, and spiked clinical surfaces were exposed to 1,000 ppm sodium dichloroisocyanurate at the recommended 10-min contact time. Results revealed that the hydrophobicity and structure of clinical surfaces can influence spore transmission and that outer spore surface structures may play a part in spore adhesion. Spores remained viable on clinical surfaces after microbicide exposure at the recommended disinfection concentration, demonstrating ineffectual sporicidal action. This study showed that C. difficile spores can transmit and survive between various clinical surfaces despite appropriate use of microbicides.IMPORTANCEClostridium difficile is a health care-acquired organism and the causative agent of antibiotic-associated diarrhea. Its spores are implicated in fecal to oral transmission from contaminated surfaces in the health care environment due to their adherent nature. Contaminated surfaces are cleaned using high-strength chemicals to remove and kill the spores; however, despite appropriate infection control measures, there is still high incidence of C. difficile infection in patients in the United States. Our research examined the effect of a high-strength biocide on spores of C. difficile which had been spiked onto a range of clinically relevant surfaces, including isolation gowns, stainless steel, and floor vinyl. This study found that C. difficile spores were able to survive exposure to appropriate concentrations of biocide, highlighting the need to examine the effectiveness of infection control measures to prevent spore transmission and to consider the prevalence of biocide resistance when decontaminating health care surfaces.

Extraction and sensitive detection of toxins A and B from the human pathogen Clostridium difficile in 40 seconds using microwave-accelerated metal-enhanced fluorescence.

Clostridium difficile is the primary cause of antibiotic associated diarrhea in humans and is a significant cause of morbidity and mortality. Thus the rapid and accurate identification of this pathogen in clinical samples, such as feces, is a key step in reducing the devastating impact of this disease. The bacterium produces two toxins, A and B, which are thought to be responsible for the majority of the pathology associated with the disease, although the relative contribution of each is currently a subject of debate. For this reason we have developed a rapid detection assay based on microwave-accelerated metal-enhanced fluorescence which is capable of detecting the presence of 10 bacteria in unprocessed human feces within 40 seconds. These promising results suggest that this prototype biosensor has the potential to be developed into a rapid, point of care, real time diagnostic assay for C. difficile.

Contribution of spores to the ability of Clostridium difficile to adhere to surfaces.

Clostridium difficile is the commonest cause of hospital-acquired infection in the United Kingdom. We characterized the abilities of 21 clinical isolates to form spores; to adhere to inorganic and organic surfaces, including stainless steel and human adenocarcinoma cells; and to germinate. The composition of culture media had a significant effect on spore formation, as significantly more spores were produced in brain heart infusion broth (Student's t test; P = 0.018). The spore surface relative hydrophobicity (RH) varied markedly (14 to 77%) and was correlated with the ability to adhere to stainless steel. We observed no correlation between the ribotype and the ability to adhere to steel. When the binding of hydrophobic (DS1813; ribotype 027; RH, 77%) and hydrophilic (DS1748; ribotype 002; RH, 14%) spores to human gut epithelial cells at different stages of cell development was examined, DS1813 spores adhered more strongly, suggesting the presence of surface properties that aid attachment to human cells. Electron microscopy studies revealed the presence of an exosporium surrounding DS1813 spores that was absent from spores of DS1748. Finally, the ability of spores to germinate was found to be strain and medium dependent. While the significance of these findings to the disease process has yet to be determined, this study has highlighted the importance of analyzing multiple isolates when attempting to characterize the behavior of a bacterial species.

Oxidative stress of Burkholderia cenocepacia induces insertion sequence-mediated genomic rearrangements that interfere with macrorestriction-based genotyping.

Burkholderia cenocepacia can cause serious infections and epidemics in patients with cystic fibrosis (CF). A CF population in the Czech Republic experienced an epidemic outbreak caused by a B. cenocepacia ST-32 strain. The clonality of the isolates was evident by multilocus sequence typing; however, fingerprinting profiles obtained by pulsed-field gel electrophoresis (PFGE) showed substantial band variability. We investigated whether the PFGE pattern diversity resulted from genomic rearrangements mediated by insertion sequences (IS); in addition, we determined whether stressful growth conditions altered the transposition activity of these IS. DNA probes for IS commonly found in B. cenocepacia were designed using the B. cenocepacia J2315 genome. Southern hybridization analysis of ST-32 isolates demonstrated diversity in both the copy number and the insertion site for a homologue of ISBcen20. Movement of the ISBcen20 homologue was detected when the ST-32 isolate CZ1238 was exposed to oxidative stress (growth in the presence of H(2)O(2)). PFGE analysis of CZ1238 derivatives exposed to oxidative stress demonstrated genomic rearrangements. Interestingly, when the closely related B. cenocepacia strain J2315 was exposed to oxidative stress, no movement of ISBcen20 was detected. Since frameshift mutations are present within the transposases of all copies of this IS in J2315, our data suggest that the transposase is inactive. In summary, we have demonstrated for the first time that IS movement can be mediated by oxidative stress and can lead to genomic rearrangements in the CF pathogen B. cenocepacia. These IS movements may alter the PFGE fingerprints of isolates that are clonal by other typing methods.