Pathogens Of Interest Research Articles

In Silico Evaluation of Lawsonia intracellularis Genes Orthologous to Genes Associated with Pathogenesis in Other Intracellular Bacteria.

Proliferative enteropathy is an enteric disease caused by the bacterium Lawsonia intracellularis, which affects several species of domestic and wild animals. The mechanisms underlying the mechanisms employed by L. intracellularis to cause host cell proliferation are poorly understood, mostly because this bacterium is extremely difficult to isolate and propagate in vitro. Comparative genomics methods for searching for genes orthologous to genes known to be associated with pathogenesis allow identification of genes potentially involved in pathogenesis by the pathogen of interest. The goal of this study was to carry out in silico research on L. intracellularis genes orthologous to genes required for intracellular invasion and survival present in other pathogenic bacteria, particularly Brucella abortus, B. melitensis, B. suis, Listeria monocytogenes, Mycobacterium tuberculosis, Mycobacterium avium subspecies paratuberculosis, Salmonella enterica, Yersinia pestis, Y. enterocolitica, and Y. pseudotuberculosis. A total of 127 genes associated with invasion and intracellular survival from five known intracellular bacteria were mapped against the predicted proteomes of all L. intracellularis strains publicly available on GenBank, using the OrthoFinder program. A total of 45 L. intracellularis genes were orthologous to genes associated with pathogenesis of other intracellular bacteria. Genes putatively associated with signal the transduction of chemotaxis and cell motility were identified. Genes related to DNA binding and repair were also identified, with some of them supporting a possible association of bacteria with macrophages or inducing pro-inflammatory responses. The homology-based identification of these genes suggests their potential involvement in the virulence and pathogenicity of L. intracellularis, opening avenues for future research and insights into the molecular mechanisms of Lawsonia-elicited proliferative enteropathy.

Impact of terminal cleaning in rooms previously occupied by patients with healthcare-associated infections.

Healthcare associated infections (HAIs) are costly but preventable. A limited understanding of the effects of environmental cleaning on the riskiest HAI associated pathogens is a current challenge in HAI prevention. This project aimed to quantify the effects of terminal hospital cleaning practices on HAI pathogens via environmental sampling in three hospitals located throughout the United States. Surfaces were swabbed from 36 occupied patient rooms with a laboratory-confirmed, hospital- or community-acquired infection of at least one of the four pathogens of interest (i.e., Acinetobacter baumannii (A. baumannii), methicillin resistant Staphylococcus aureus (MRSA), vancomycin resistant Enterococcus faecalis/faecium (VRE), and Clostridioides difficile (C. difficile)). Six nonporous, high touch surfaces (i.e., chair handrail, bed handrail, nurse call button, desk surface, bathroom counter near the sink, and a grab bar near the toilet) were sampled in each room for Adenosine Triphosphate (ATP) and the four pathogens of interest before and after terminal cleaning. The four pathogens of interest were detected on surfaces before and after terminal cleaning, but their levels were generally reduced. Overall, C. difficile was confirmed on the desk (n = 2), while MRSA (n = 24) and VRE (n = 25) were confirmed on all surface types before terminal cleaning. After cleaning, only MRSA (n = 6) on bed handrail, chair handrail, and nurse call button and VRE (n = 5) on bathroom sink, bed handrail, nurse call button, toilet grab bar, and C. difficile (n = 1) were confirmed. At 2 of the 3 hospitals, pathogens were generally reduced by >99% during terminal cleaning. One hospital showed that VRE increased after terminal cleaning, MRSA was reduced by 73% on the nurse call button, and VRE was reduced by only 50% on the bathroom sink. ATP detections did not correlate with any pathogen concentration. This study highlights the importance of terminal cleaning and indicates room for improvement in cleaning practices to reduce surface contamination throughout hospital rooms.

Clinical features and viral load variations of Mpox: a retrospective study in Chongqing, China

PurposeSince May 2022, Mpox has spread extensively outside of Africa, posing a serious threat to the health of people globally, and particularly to the men who have sex with men (MSM) population. Chongqing, a province in Southwest China, has relatively large MSM and people living with HIV (PLWH) populations, presenting conditions conducive to the wide dissemination of Mpox. In this study, we investigated the clinical characteristics of Mpox patients among MSM and PLWH in Chongqing, aiming to inform the development of targeted prevention, control, and treatment strategies for Mpox.MethodWe evaluated the clinical characteristics, travel history, time of onset, distribution and number of skin lesions of Mpox patients admitted to the Chongqing Public Health Medical Center between September 2022 and October 2023. Meanwhile, a series of clinical samples were collected and the pathogen of interest was identified as Mpox virus using quantitative polymerase chain reaction (qPCR). The results were presented in the form of cycle thresholds (Ct), which help to approximate the quantification of viral load.ResultsAs of October 11, 2023, the Chongqing Public Health Medical Center reported a total of nine Mpox virus infections. All the patients identified were male and belonged to the MSM population, among whom seven (77.8%) were living with HIV, and maintained a preserved immune system while achieving viral suppression via effective ART. We observed no discernible clinical differences between MSM with Mpox with or without HIV, and no fatalities were recorded. Viral loads were observed to be higher in samples taken from the skin than those from the throat, nasopharynx, blood, or semen.ConclusionIn this retrospective study, the clinical manifestations of MPXV infection appeared consistent among MSM patients, regardless of HIV status. Elevated MPXV viral loads in the skin and mucosal tissues, particularly at genital and anal sites, indicate that transmission is more likely to occur via direct physical contact as opposed to respiratory pathways or through exposure to bodily fluids.

Efficacy and mechanisms of Pseudomonas aeruginosa PAO1 biofilm inactivation using high-power pulsed microwave

Foodborne pathogens and biofilm formation pose a critical threat to food safety. Pseudomonas aeruginosa is a pathogen of interest in the food industry. High-power pulsed microwave (HPPM) is a non-thermal technology with proven efficacy towards bacterial inactivation. This study investigated the inactivation mechanisms and performance of different HPPM treatments (50, 100, 150, 200, and 250 Hz for 3, 5, 7, 9, and 11 min, respectively) to identify the optimum conditions to inactivate P. aeruginosa PAO1 biofilms. The results showed significant cell inactivation at increasing frequency/time (p < 0.05). Hence, HPPM treatment (200 Hz, 9 min) was selected following its efficacy and limited thermal sublethal effects to elucidate further the inactivation mechanisms against P. aeruginosa and its biofilm-forming ability. Cell viability, scanning (SEM) and transmission electron microscopy (TEM) results demonstrated severe morphological disruptions, cell disintegration, and cell lysis in the treated cells. From the confocal laser scanning micrographs (CLSM), biofilm thickness was calculated, showing a significant reduction after treatment (17.56 vs. 42.16 μm in the treated and untreated groups, respectively), indicating that HPPM effectively compromised the integrity of the biofilm envelope. This study outlines useful insights into better understanding HPPM's efficacy on microbial inactivation and biofilm proliferation in the food industry.

Comparative genomics identifies genetic markers linked to structural variations that differentiate Puccinia graminis tritici and secalis formae speciales

AbstractStem rust is a serious disease of many gramineous plants including small grain staples such as wheat, barley, rye and triticale. Separate formae speciales (ff. spp.) of the causal fungus, Puccinia graminis, predominantly infect certain host plant genera. However, despite these taxonomic subdivisions, many P. graminis ff. spp. are genetically too similar to distinguish using existing genetic markers. For those infecting cereals, this is particularly challenging for P. graminis f. sp. tritici (Pgt) and P. graminis f. sp. secalis (Pgs). Herein we harnessed newly available genomic data for 39 Pgt and Pgs isolates and identified four regions of structural variation that were used to design four simple PCR‐based assays to distinguish the aforementioned formae speciales. These genomic regions display large presence/absence variation between Pgt and Pgs isolates, and yet a high degree of sequence conservation within shared neighbouring regions, facilitating primer design. We also confirmed lack of amplification in host plant genera analysed, which included assessment of the shared alternate host of Pgt and Pgs, Berberis vulgaris. Accurate classification of P. graminis ff. spp. infections on B. vulgaris is exceptionally valuable to rapidly define plants harbouring P. graminis inoculum when adjacent to cereal crops. Finally, we demonstrated utility of these four genetic markers to correctly distinguish a genetically diverse array of Pgt and Pgs isolates. This strategy could now be readily applied to other pathogens of interest, which will be of increasing value as genomic resources continue to rapidly expand for many key biotic threats to agricultural productivity.

Rapid loss of maternal immunity and increase in environmentally mediated antibody generation in urban gulls

Monitoring pathogen circulation in wildlife sentinel populations can help to understand and predict the spread of disease at the wildlife-livestock-human interface. Immobile young provide a useful target population for disease surveillance, since they can be easily captured for sampling and their levels of antibodies against infectious agents can provide an index of localized circulation. However, early-life immune responses include both maternally-derived antibodies and antibodies resulting from exposure to pathogens, and disentangling these two processes requires understanding their individual dynamics. We conducted an egg-swapping experiment in an urban-nesting sentinel seabird, the yellow-legged gull, and measured antibody levels against three pathogens of interest (avian influenza virus AIV, Toxoplasma gondii TOX, and infectious bronchitis virus IBV) across various life stages, throughout chick growth, and between nestlings raised by biological or non-biological parents. We found that levels of background circulation differed among pathogens, with AIV antibodies widely present across all life stages, TOX antibodies rarer, and IBV antibodies absent. Antibody titers declined steadily from adult through egg, nestling, and chick stages. For the two circulating pathogens, maternal antibodies declined exponentially after hatching at similar rates, but the rate of linear increase due to environmental exposure was significantly higher in the more prevalent pathogen (AIV). Differences in nestling antibody levels due to parental effects also persisted longer for AIV (25 days, vs. 14 days for TOX). Our results suggest that yellow-legged gulls can be a useful sentinel population of locally transmitted infectious agents, provided that chicks are sampled at ages when environmental exposure outweighs maternal effects.

Dairy farmers' knowledge about milk-borne zoonosis in the Eastern Cape province, South Africa.

Foodborne zoonosis is a longstanding global issue that limits and continues to threaten the food production industry and public health in several countries. The study's objective was to evaluate the dairy farmers' knowledge, attitudes, and practices about milkborne pathogens in the Eastern Cape province, South Africa. A total of 139 dairy farmers were interviewed using a semi-structured online questionnaire. The pathogens of interest were Brucella spp., Escherichia coli, Listeria monocytogenes, Salmonella spp., Staphylococcus aureus, and Cryptosporidium. Only 20.9% of dairy farmers reported knowledge of Brucella spp. as a milk-borne pathogen. The most known pathogen was E. coli (54.7%), followed by Listeria spp. (41.0%), Staphylococcus spp. (38.8%), and Salmonella spp. (35.3%). In this study, knowledge of milk-borne pathogens was statistically associated (p<0.05) with workplace position. Only a few participants (37.2%) showed knowledge of abortion as an important clinical sign of foodborne pathogens. Also, 84.1% of dairy farmers indicated that they consume unpasteurized milk and sour milk (77%). Some respondents (18.0%) do not believe assisting a cow during calving difficulty without wearing gloves is a risk factor for zoonosis. Knowledge assessment is essential in developing countries that have experienced a foodborne outbreak, such as South Africa. There is an urgent need to educate dairy farmers about milk-borne zoonosis to minimize the threat to food security and public health.

Dual RNA-seq Analysis of Patients' Cells and Viral Genome After Measles Infection.

During the infection of a host cell by an infectious agent, a series of gene expression changes occurs as a consequence of host-pathogen interactions. Unraveling this complex interplay is the key for understanding of microbial virulence and host response pathways, thus providing the basis for new molecular insights into the mechanisms of pathogenesis and the corresponding immune response. Dual RNA sequencing (dual RNA-seq) has been developed to simultaneously determine pathogen and host transcriptomes enabling both differential and coexpression analyses between the two partners as well as genome characterization in the case of RNA viruses. Here, we provide a detailed laboratory protocol and bioinformatics analysis guidelines for dual RNA-seq experiments focusing on - but not restricted to - measles virus (MeV) as a pathogen of interest. The application of dual RNA-seq technologies in MeV-infected patients can potentially provide valuable information on the structure of the viral RNA genome and on cellular innate immune responses and drive the discovery of new targets for antiviral therapy.

DETECTION OF SARS-COV-2 NEUTRALIZING ANTIBODIES IN RETROPHARYNGEAL LYMPH NODE EXUDATES OF WHITE-TAILED DEER (ODOCOILEUS VIRGINIANUS) FROM NEBRASKA, USA.

Disease surveillance testing for emerging zoonotic pathogens in wildlife is a key component in understanding the epidemiology of these agents and potential risk to human populations. Recent emergence of SARS-CoV-2 in humans, and subsequent detection of this virus in wildlife, highlights the need for developing new One Health surveillance strategies. We used lymph node exudate, a sample type that is routinely collected in hunter-harvested white-tailed deer (WTD, Odocoileus virginianus) for surveillance of chronic wasting disease, to assess anti-SARS-CoV-2 neutralizing antibodies. A total of 132 pairs of retropharyngeal lymph nodes collected from Nebraska WTD harvested in Nebraska, US, in 2019 (pre-SARS-CoV-2 pandemic) and 2021 (post-SARS-CoV-2 pandemic) were tested for SARS-CoV-2 with reverse transcription PCR. Thereafter, exudates obtained from these same lymph nodes were tested for SARS-CoV-2 neutralizing antibodies using a surrogate virus neutralization test. Neutralizing antibodies were detected in the exudates with high diagnostic specificity (100% at proposed cutoff of 40% inhibition). Application of this testing approach to samples collected for use in other disease surveillance activities may provide additional epidemiological data on SARS-CoV-2 exposure, and there is further potential to apply this sample type to detection of other pathogens of interest.

Cost-effectiveness of a real-time spatiotemporal mapping surveillance system for meticillin-resistant Staphylococcus aureus prevention

An infection surveillance system based on a hospital's digital twin [4D-Disease Outbreak Surveillance System (4D-DOSS)] is being developed in Singapore. It offers near-real-time infection surveillance and mapping capabilities. This early economic modelling study was conducted, using meticillin-resistant Staphylococcus aureus (MRSA) as the pathogen of interest, to assess the potential cost-effectiveness of 4D-DOSS. A Markov model that simulates the likelihood of MRSA colonization and infection was developed to evaluate the cost-effectiveness of adopting 4D-DOSS for MRSA surveillance from the hospital perspective, compared with current practice. The cycle duration was 1 day, and the model horizon was 30 days. Probabilistic sensitivity analysis was conducted, and the probability of cost-effectiveness was reported. Scenario analyses and a value of information analysis were performed. In the base-case scenario, with 10-year implementation/maintenance costs of 4D-DOSS of $0, there was 68.6% chance that 4D-DOSS would be cost-effective. In a more pessimistic but plausible scenario where the effectiveness of 4D-DOSS in reducing MRSA transmission was one-quarter of the base-case scenario with 10-year implementation/maintenance costs of $1 million, there was 47.7% chance that adoption of 4D-DOSS would be cost-effective. The value of information analysis showed that uncertainty in MRSA costs made the greatest contribution to model uncertainty. This early-stage modelling study revealed the circumstances for which 4D-DOSS is likely to be cost-effective at the current willingness-to-pay threshold, and identified the parameters for which further research will be worthwhile to reduce model uncertainty. Inclusion of other drug-resistant organisms will provide a more thorough assessment of the cost-effectiveness of 4D-DOSS.

Viability and Desiccation Resistance of Bartonella henselae in Biological and Non-Biological Fluids: Evidence for Pathogen Environmental Stability.

Pathogen environmental stability is an often-neglected research priority for pathogens that are known to be vector-transmitted. Bartonella henselae, the etiologic agent of Cat Scratch Disease, has become a "pathogen of interest" in several serious human illnesses, which include neoplastic, cardiovascular, neurocognitive, and rheumatologic conditions. Survival in the flea gut and feces as well as the association with a biofilm in culture-negative endocarditis provides insight into this organism's ability to adjust to environmental extremes. The detection of B. henselae DNA in blood and tissues from marine mammals also raises questions about environmental stability and modes of pathogen transmission. We investigated the ability of B. henselae to survive in fluid matrices chosen to mimic potential environmental sources of infective materials. Feline whole blood, serum and urine, bovine milk, and physiologic saline inoculated with a laboratory strain of B. henselae San Antonio 2 were subsequently evaluated by culture and qPCR at specified time intervals. Bacterial viability was also assessed following desiccation and reconstitution of each inoculated fluid matrix. Bartonella henselae SA2 was cultured from feline urine up to 24 h after inoculation, and from blood, serum, cow's milk, and physiologic saline for up to 7 days after inoculation. Of potential medical importance, bacteria were cultured following air-desiccation of all fluid inoculates. The viability and stability of Bartonella within biological and non-biological fluids in the environment may represent a previously unrecognized source of infection for animals and human beings.

Large‐scale eDNA monitoring of multiple aquatic pathogens as a tool to provide risk maps for wildlife diseases

AbstractMultiple parasites and pathogens cause disease in aquatic wildlife and in aquaculture species, generating a need for monitoring and management. Conventional disease monitoring methods involve laborious, costly, and invasive capture and examination of host species, and require specialized expertise for every host and pathogen of interest. Environmental DNA could provide simultaneous occurrence data for multiple pathogens across different host taxa, valuable for using parasite diversity as, for example, a bioindicator of ecosystem disturbance. Here, we tested the potential for simultaneous detection of four wildlife pathogens in water samples from 280, mainly riverine, sites across Switzerland. We targeted the crayfish pathogen Aphanomyces astaci, the amphibian pathogen Batrachochytrium dendrobatidis, and the fish pathogens Saprolegnia parasitica and Tetracapsuloides bryosalmonae. The eDNA detection showed a widespread distribution of A. astaci, S. parasitica, and T. bryosalmonae, although A. astaci and T. bryosalmonae were not detected in some alpine river catchments. B. dendrobatidis was detected only rarely, which was expected since the sampling did not target amphibian breeding sites. Co‐detection rates were higher in rivers than in lakes, likely reflecting the habitat preferences and distributions of the host species. We discuss the advantages and limitations of eDNA‐based pathogen monitoring and list a set of recommendations for managers. Our study illustrates how eDNA‐based techniques can monitor several pathogen species concurrently, thus facilitating more comprehensive disease monitoring schemes. Combined with metabarcoding approaches in the future, eDNA‐based sampling and detection can facilitate the incorporation of parasite and pathogen occurrence and diversity as an indicator for aquatic ecosystem health, and for revealing the hidden biodiversity and structure of parasite communities.

Prevalence of Babesia and Ehrlichia in owned dogs with suspected tick-borne infection in Hong Kong, and risk factors associated with Babesia gibsoni.

Babesiosis and ehrlichiosis are the most clinically significant tick-borne infections in dogs. Although epidemiological investigations of these diseases have been performed in some Asian regions, little data is available in Hong Kong, where competent vector tick species are endemic. The objectives of this study were to determine the molecular prevalence of Ehrlichia canis and Babesia species (B. canis, B. gibsoni, B. vogeli) in owned dogs suspected of tick-borne infection in Hong Kong and to identify risk factors associated with B. gibsoni infection. Electronic records from the Veterinary Diagnostic Laboratory of City University of Hong Kong were searched to identify canine blood samples submitted for molecular testing of these pathogens by real time PCR between March 2018 and May 2021. Electronic patient records from the affiliated veterinary hospital were searched to identify a subset of tested dogs to investigate the potential risk factors for B. gibsoni infection using logistic regression models. Among 1508 tested dogs for all four pathogens of interest, Babesia spp. were detected in 435 (28.8%) and E. canis in 112 (7.4%). Babesia gibsoni was detected in 408 dogs while B. vogeli was detected in 27 dogs. Babesia canis was not detected in any dog. Co-infections of different combinations of B. gibsoni, B. vogeli and E. canis were present in 25 dogs. In multivariable logistic regression, mixed breed dogs were more likely to be infected with B. gibsoni than purebreds (P=0.005), while dogs >10 years of age were less likely to be infected than younger dogs (P=0.019). Hematological abnormalities significantly associated with B. gibsoni infection included thrombocytopenia, neutropenia, or pancytopenia. Babesiosis caused by B. gibsoni is a common infection in owned dogs suspected of tick-borne infection in Hong Kong. The risk factors reported should be considered in diagnosing dogs suspected of infection with this agent. Furthermore, consideration for testing for B. gibsoni infection should be given if the results of a complete blood count show thrombocytopenia even in the absence of anemia, neutropenia or pancytopenia.

Beta-lactam-resistant Staphylococcus aureus in spinal osteomyelitis and spondylodiscitis: current landscape in antibiotic resistance, treatment, and complications.

Spinal osteomyelitis and spondylodiscitis (SD) are infections of the vertebral body and disc, respectively, with more than 50% associated with Staphylococcus aureus. Methicillin-resistant S. aureus (MRSA) has become a pathogen of interest in cases of SD due to increasing prevalence. The purpose of this investigation was to characterize the current epidemiological and microbiological landscape in SD cases, in addition to medical and surgical challenges in treating these infections. The PearlDiver Mariner database was queried for ICD-10 codes to identify cases of SD from 2015 to 2021. The initial cohort was stratified by offending pathogens, including methicillin-sensitive S. aureus (MSSA) and MRSA. Primary outcome measures included epidemiological trends, demographics, and rates of surgical management. Secondary outcomes included length of hospital stay, rate of reoperation, and complications associated with surgical cases. Multivariable logistic regression was used to control for age, gender, region, and Charlson Comorbidity Index (CCI). Nine thousand nine hundred eighty-three patients met the inclusion criteria and were retained for this study. Approximately half (45.5%) of SD cases resulting from S. aureus infections each year were resistant to beta-lactam antibiotics. The proportion of cases that were managed surgically was 31.02%. Among the cases that involved surgical intervention, 21.83% underwent revision operations within 30 days of the original procedure and 37.29% of cases returned to the operating room within 1 year. Substance abuse, specifically alcohol, tobacco, and drug use, were strong predictors for surgical intervention in cases of SD (all p < 0.001), in addition to obesity (p = 0.002), liver disease (p < 0.001), and valvular disease (p = 0.025). After adjusting for age, gender, region, and CCI, cases of MRSA were more likely to undergo surgical management (OR 1.19, p = 0.003). MRSA SD also exhibited higher rates of reoperation within 6 months (OR 1.29, p = 0.001) and 1 year (OR 1.36, p < 0.001). Surgical cases resulting from MRSA infections also exhibited higher morbidity and significant rates of transfusion (OR 1.47, p = 0.030), acute kidney injury (OR 1.35, p = 0.001), pulmonary embolism (OR 1.44, p = 0.030), pneumonia (OR 1.49, p = 0.002), and urinary tract infection (OR 1.45, p = 0.002) compared with MSSA SD infections. More than 45% of cases of S. aureus SD in the US are resistant to beta-lactam antibiotics, presenting obstacles in treatment. Cases of MRSA SD are more likely to be managed surgically and have higher rates of complications and reoperations. Early detection and prompt operative management are imperative to reduce the risk of complications.

Monitoring phage-induced lysis of gram-negatives in real time using a fluorescent DNA dye

Bacteriophages (phages) are viruses that specifically attack bacteria. Their use as therapeutics, which constitutes a promising alternative to antibiotics, heavily relies on selecting effective lytic phages against the pathogen of interest. Current selection techniques are laborious and do not allow for direct visualization of phage infection dynamics. Here, we present a method that circumvents these limitations. It can be scaled for high-throughput and permits monitoring of the phage infection in real time via a fluorescence signal readout. This is achieved through the use of a membrane-impermeant nucleic acid dye that stains the DNA of damaged or lysed bacteria and new phage progeny. We have tested the method on Pseudomonas aeruginosa and Klebsiella pneumoniae and show that an increase in fluorescence reflects phage-mediated killing. This is confirmed by other techniques including spot tests, colony plating, flow cytometry and metabolic activity measurements. Furthermore, we illustrate how our method may be used to compare the activity of different phages and to screen the susceptibility of clinical isolates to phage. Altogether, we present a fast, reliable way of selecting phages against Gram-negative bacteria, which may be valuable in optimizing the process of selecting phages for therapeutic use.

Use of fluorescence imaging to optimize location of tissue sampling in hard-to-heal wounds.

Wound microflora in hard-to-heal wounds is invariably complex and diverse. Determining the interfering organisms(s) is therefore challenging. Tissue sampling, particularly in large wounds, is subjective and, when performed, might involve swabbing or biopsy of several locations. Fluorescence (FL) imaging of bacterial loads is a rapid, non-invasive method to objectively locate microbial hotspots (loads >104 CFU/gr). When sampling is deemed clinically necessary, imaging may indicate an optimal site for tissue biopsy. This study aimed to investigate the microbiology of wound tissue incisional biopsies taken from sites identified by FL imaging compared with sites selected by clinical judgment. A post hoc analysis of the 350-patient FLAAG wound trial was conducted; 78 wounds were included in the present study. All 78 wounds were biopsied at two sites: one at the center of the wound per standard of care (SoC) and one site guided by FL-imaging findings, allowing for comparison of total bacterial load (TBL) and species present. The comparison between the two biopsy sites revealed that clinical uncertainty was higher as wound surface area increased. The sensitivity of a FL-informed biopsy was 98.7% for accurately finding any bacterial loads >104 CFU/g, compared to 87.2% for SoC (p=0.0059; McNemar test). Regarding species detected, FL-informed biopsies detected an average of 3 bacterial species per biopsy versus 2.2 species with SoC (p < 0.001; t-test). Microbial hotspots with a higher number of pathogens also included the CDC's pathogens of interest. FL imaging provides a more accurate and relevant microbiological profile that guides optimal wound sampling compared to clinical judgment. This is particularly interesting in large, complex wounds, as evidenced in the wounds studied in this post hoc analysis. In addition, fluorescence imaging enables earlier bacterial detection and intervention, guiding early and appropriate wound hygiene and potentially reducing the need for antibiotic use. When indicated, this diagnostic partnership with antibiotic stewardship initiatives is key to ameliorating the continuing threat of antibiotic resistance.

Promise and perils of paper-based point-of-care nucleic acid detection for endemic and pandemic pathogens.

From HIV and influenza to emerging pathogens like COVID-19, each new infectious disease outbreak has highlighted the need for massively-scalable testing that can be performed outside centralized laboratory settings at the point-of-care (POC) in order to prevent, track, and monitor endemic and pandemic threats. Nucleic acid amplification tests (NAATs) are highly sensitive and can be developed and scaled within weeks while protein-based rapid tests require months for production. Combining NAATs with paper-based detection platforms are promising due to the manufacturability, scalability, and simplicity of each of these components. Typically, paper-based NAATs consist of three sequential steps: sample collection and preparation, amplification of DNA or RNA from pathogens of interest, and detection. However, these exist within a larger ecosystem of sample collection and interpretation workflow, usability, and manufacturability which can be vastly perturbed during a pandemic emergence. This review aims to explore the challenges of paper-based NAATs covering sample-to-answer procedures along with three main types of clinical samples; blood, urine, and saliva, as well as broader operational, scale up, and regulatory aspects of device development and implementation. To fill the technological gaps in paper-based NAATs, a sample-in-result-out system that incorporates the integrated sample collection, sample preparation, and integrated internal amplification control while also balancing needs of users and manufacturability upfront in the early design process is required.

Systematic review of time lag between antibiotic use and rise of resistant pathogens among hospitalized adults in Europe.

Antimicrobial resistance (AMR) causes substantial health and economic burden to individuals, healthcare systems and societies globally. Understanding the temporal relationship between antibiotic consumption and antibiotic resistance in hospitalized patients can better inform antibiotic stewardship activities and the time frame for their evaluation. This systematic review examined the temporal relationship between antibiotic use and development of antibiotic resistance for 42 pre-defined antibiotic and pathogen combinations in hospitalized adults in Europe. Searches in MEDLINE, Embase, Cochrane Library and NIHR Centre for Reviews and Dissemination were undertaken from 2000 to August 2021. Pathogens of interest were Escherichia coli, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Enterococcus faecium, CoNS, Pseudomonas aeruginosa and Acinetobacter baumannii complex. Twenty-eight ecological studies and one individual-level study were included. Ecological studies were predominantly retrospective in design (19 studies) and of reasonable (20 studies) to high (8 studies) methodological quality. Of the eight pathogens of interest, no relevant data were identified for S. pneumoniae and CoNS. Across all pathogens, the time-lag data from the 28 ecological studies showed a similar pattern, with the majority of studies reporting lags ranging from 0 to 6 months. Development of antibiotic resistance for the investigated antibiotic/pathogen combinations tends to occur over 0 to 6 months following exposure within European hospitals. This information could inform planning of antibiotic stewardship activities in hospital settings.

Current status of silica-based nanoparticles as therapeutics and its potential as therapies against viruses

In the past decade, interest in nanoparticles for clinical indications has been steadily gaining traction. Most recently, Lipid Nanoparticles (LNP) have been used successfully to construct the SARS-CoV-2 mRNA vaccines for rapid pandemic response. Similarly, silica is another nanomaterial which holds much potential to create nanomedicines against pathogens of interest. One major advantage of silica-based nanoparticles is its crystalline and highly ordered structure, which can be specifically tuned to achieve the desired properties needed for clinical applications. Increasingly, clinical research has shown the potential of silica nanoparticles not only as an antiviral, but also its ability as a delivery system for antiviral small molecules and vaccines against viruses. Silica has an excellent biosafety profile and has been tested in several early phase clinical trials since 2012, demonstrating good tolerability and minimal reported side effects. In this review, we discuss the clinical development of silica nanoparticles to date and identify the gaps and potential pitfalls in its path to clinical translation.

A Practical Bioinformatics Workflow for Routine Analysis of Bacterial WGS Data.

The use of whole-genome sequencing (WGS) for bacterial characterisation has increased substantially in the last decade. Its high throughput and decreasing cost have led to significant changes in outbreak investigations and surveillance of a wide variety of microbial pathogens. Despite the innumerable advantages of WGS, several drawbacks concerning data analysis and management, as well as a general lack of standardisation, hinder its integration in routine use. In this work, a bioinformatics workflow for (Illumina) WGS data is presented for bacterial characterisation including genome annotation, species identification, serotype prediction, antimicrobial resistance prediction, virulence-related genes and plasmid replicon detection, core-genome-based or single nucleotide polymorphism (SNP)-based phylogenetic clustering and sequence typing. Workflow was tested using a collection of 22 in-house sequences of Salmonella enterica isolates belonging to a local outbreak, coupled with a collection of 182 Salmonella genomes publicly available. No errors were reported during the execution period, and all genomes were analysed. The bioinformatics workflow can be tailored to other pathogens of interest and is freely available for academic and non-profit use as an uploadable file to the Galaxy platform.