Molecular antimicrobial susceptibility testing in sepsis

Rapidly detecting and identifying pathogens is crucial for appropriate antimicrobial therapy in patients with sepsis. Conventional diagnostic methods have been a great asset to medicine, though they are time consuming and labor intensive. This work will enable healthcare professionals to understand the bacterial community better and enhance their diagnostic capacity by using novel molecular methods that make obtaining quicker, more precise results possible. The authors discuss and critically assess the merits and drawbacks of molecular testing and the added value of these tests, including the shift turnaround time, the implication for clinicians' decisions, gaps in knowledge, future research directions and novel insights or innovations. The field of antimicrobial molecular testing has seen several novel insights and innovations to improve the diagnosis and management of infectious diseases.

The contribution of human conflict to the development of antimicrobial resistance

Pallet et al. discuss the impact of human conflict on development of antimicrobial resistance. They overview approaches to limit the spread of antimicrobial resistance, using the ongoing conflict in Ukraine as an example of the challenges and opportunities.

A multicentre evaluation and expert recommendations of use of the newly developed BioFire Joint Infection polymerase chain reaction panel

Septic arthritis is a serious condition with significant morbidity and mortality, routinely diagnosed using culture. The FDA has recently approved the rapid molecular BioFire® Joint Infection Panel (BJIP) for synovial fluid. We aimed to evaluate the BJIP compared to culture and its potential use in patient management. A multicentre retrospective evaluation of BJIP was conducted in the UK and Ireland. Positive percent agreement (PPA) and negative percent agreement (NPA) were calculated between the BJIP and routine culture. A multidisciplinary team (MDT) discussion addressing the optimal or potential case use of the assay practice was facilitated. Three hundred ninety-nine surplus synovial fluid samples (~ 70% from native joints) from eight centres were processed using BJIP in addition to routine culture. An increased yield of positive results was detected using BJIP compared to routine culture (98 vs 83), giving an overall PPA of 91.6% and overall NPA of 93% for the BJIP compared to culture results. The BJIP detected resistant markers and additional organisms that could influence antibiotic choices including Neisseria gonorrhoeae and Kingella kingae. The MDT agreed that the assay could be used, in addition to standard methods, in adult and children patients with specialist advice use based on local needs. Rapid results from BJIP were assessed as having potential clinical impact on patient management. Organisms not included in the panel may be clinically significant and may limit the value of this test for PJI.

Evaluating the potential for respiratory metagenomics to improve treatment of secondary infection and detection of nosocomial transmission on expanded COVID-19 intensive care units

BACKGROUND

Clinical metagenomics (CMg) has the potential to be translated from a research tool into routine service to improve antimicrobial treatment and infection control decisions. The SARS-CoV-2 pandemic provides added impetus to realise these benefits, given the increased risk of secondary infection and nosocomial transmission of multi-drug-resistant (MDR) pathogens linked with the expansion of critical care capacity.

METHODS

CMg using nanopore sequencing was evaluated in a proof-of-concept study on 43 respiratory samples from 34 intubated patients across seven intensive care units (ICUs) over a 9-week period during the first COVID-19 pandemic wave.

RESULTS

An 8-h CMg workflow was 92% sensitive (95% CI, 75-99%) and 82% specific (95% CI, 57-96%) for bacterial identification based on culture-positive and culture-negative samples, respectively. CMg sequencing reported the presence or absence of β-lactam-resistant genes carried by Enterobacterales that would modify the initial guideline-recommended antibiotics in every case. CMg was also 100% concordant with quantitative PCR for detecting Aspergillus fumigatus from 4 positive and 39 negative samples. Molecular typing using 24-h sequencing data identified an MDR-K. pneumoniae ST307 outbreak involving 4 patients and an MDR-C. striatum outbreak involving 14 patients across three ICUs.

CONCLUSION

CMg testing provides accurate pathogen detection and antibiotic resistance prediction in a same-day laboratory workflow, with assembled genomes available the next day for genomic surveillance. The provision of this technology in a service setting could fundamentally change the multi-disciplinary team approach to managing ICU infections. The potential to improve the initial targeted treatment and rapidly detect unsuspected outbreaks of MDR-pathogens justifies further expedited clinical assessment of CMg.

Validating a prediction tool to determine the risk of nosocomial multidrug-resistant Gram-negative bacilli infection in critically ill patients: A retrospective case-control study

BACKGROUND

The Singapore GSDCS score was developed to enable clinicians predict the risk of nosocomial multidrug-resistant Gram-negative bacilli (RGNB) infection in critically ill patients. We aimed to validate this score in a UK setting.

METHOD

A retrospective case-control study was conducted including patients who stayed for more than 24h in intensive care units (ICUs) across two tertiary National Health Service hospitals in London, UK (April 2011-April 2016). Cases with RGNB and controls with sensitive Gram-negative bacilli (SGNB) infection were identified.

RESULTS

The derived GSDCS score was calculated from when there was a step change in antimicrobial therapy in response to clinical suspicion of infection as follows: prior Gram-negative organism, Surgery, Dialysis with end-stage renal disease, prior Carbapenem use and intensive care Stay of more than 5 days. A total of 110 patients with RGNB infection (cases) were matched 1:1 to 110 geotemporally chosen patients with SGNB infection (controls). The discriminatory ability of the prediction tool by receiver operating characteristic curve analysis in our validation cohort was 0.75 (95% confidence interval 0.65-0.81), which is comparable with the area under the curve of the derivation cohort (0.77). The GSDCS score differentiated between low- (0-1.3), medium- (1.4-2.3) and high-risk (2.4-4.3) patients for RGNB infection (P<0.001) in a UK setting.

CONCLUSION

A simple bedside clinical prediction tool may be used to identify and differentiate patients at low, medium and high risk of RGNB infection prior to initiation of prompt empirical antimicrobial therapy in the intensive care setting.

Quantifying drivers of antibiotic resistance in humans: a systematic review

Mitigating the risks of antibiotic resistance requires a horizon scan linking the quality with the quantity of data reported on drivers of antibiotic resistance in humans, arising from the human, animal, and environmental reservoirs. We did a systematic review using a One Health approach to survey the key drivers of antibiotic resistance in humans. Two sets of reviewers selected 565 studies from a total of 2819 titles and abstracts identified in Embase, MEDLINE, and Scopus (2005-18), and the European Centre for Disease Prevention and Control, the US Centers for Disease Control and Prevention, and WHO (One Health data). Study quality was assessed in accordance with Cochrane recommendations. Previous antibiotic exposure, underlying disease, and invasive procedures were the risk factors with most supporting evidence identified from the 88 risk factors retrieved. The odds ratios of antibiotic resistance were primarily reported to be between 2 and 4 for these risk factors when compared with their respective controls or baseline risk groups. Food-related transmission from the animal reservoir and water-related transmission from the environmental reservoir were frequently quantified. Uniformly quantifying relationships between risk factors will help researchers to better understand the process by which antibiotic resistance arises in human infections.

Considerations for effect site pharmacokinetics to estimate drug exposure: concentrations of antibiotics in the lung

Bronchoalveolar lavage (BAL) and microdialysis have become the most reliable and relevant methods for measuring lung concentrations of antibiotics, with the majority of BAL studies involving either healthy adult subjects or patients undergoing diagnostic bronchoscopy. Emphasis on the amount of drug that reaches the site of infection is increasingly recognized as necessary to determine whether a dose selection will translate to good clinical outcomes in the treatment of patients with pneumonia. Observed concentrations and/or parameters of exposure (e.g. area-under-the-curve) need to be incorporated with pharmacokinetic-pharmacodynamic indices so that rational dose selection can be identified for specific pathogens and types of pneumonic infection (community-acquired vs hospital-acquired bacterial pneumonia, including ventilator-associated bacterial pneumonia). Although having measured plasma or lung concentration-time data from critically ill patients to incorporate into pharmacokinetic-pharmacodynamic models is very unlikely during drug development, it is essential that altered distribution, augmented renal clearance, and renal or hepatic dysfunction should be considered. Notably, the number of published studies involving microdialysis and intrapulmonary penetration of antibiotics has been limited and mainly involve beta-lactam agents, levofloxacin, and fosfomycin. Opportunities to measure in high-resolution effect site spatial pharmacokinetics (e.g. with MALDI-MSI or PET imaging) and in vivo continuous drug concentrations (e.g. with aptamer-based probes) now exist. Going forward these studies could be incorporated into antibiotic development programs for pneumonia in order to further increase the probability of candidate success.

Molecular composition of recycled organic wastes, as determined by solid-state 13C NMR and elemental analyses

Using solid state (13)C NMR data and elemental composition in a molecular mixing model, we estimated the molecular components of the organic matter in 16 recycled organic (RO) wastes representative of the major materials generated in the Sydney basin area. Close correspondence was found between the measured NMR signal intensities and those predicted by the model for all RO wastes except for poultry manure char. Molecular nature of the organic matter differed widely between the RO wastes. As a proportion of organic C, carbohydrate C ranged from 0.07 to 0.63, protein C from <0.01 to 0.66, lignin C from <0.01 to 0.31, aliphatic C from 0.09 to 0.73, carbonyl C from 0.02 to 0.23, and char C from 0 to 0.45. This method is considered preferable to techniques involving imprecise extraction methods for RO wastes. Molecular composition data has great potential as a predictor of RO waste soil carbon and nutrient outcomes.

Substance abuse treatment counselors and tobacco use: a comparison of comprehensive and indoor-only workplace smoking bans

INTRODUCTION

While indoor smoking bans reduce employee tobacco use, less is known about whether comprehensive bans, which prohibit smoking in both indoor and outdoor areas, are associated with lower rates of tobacco use than indoor-only bans.

METHODS

This study integrated data collected via mailed surveys from 1,910 substance abuse treatment counselors and telephone interviews with 417 administrators of substance abuse treatment organizations. Multinomial logistic regression was used to estimate the associations between counselors' self-reported tobacco use and administrators' reports about organizational smoking bans while controlling for counselors' professional and demographic characteristics.

RESULTS

In this sample, 20.3% of counselors were current tobacco users, 47.7% identified as former users, and 32.0% reported never using tobacco products. Only 19.5% of counselors worked in a treatment organization that had a comprehensive smoking ban. The likelihood of being a current tobacco user, compared with being a former user or nonuser, was significantly lower for counselors in organizations with comprehensive bans even after controlling for professional and demographic characteristics.

CONCLUSIONS

Although relatively few substance abuse counselors worked in treatment organizations with comprehensive bans, such bans may represent a promising direction for tobacco control. Given recent research documenting how tobacco use is negatively associated with the delivery of smoking cessation services by health care workers, additional research on the impact of comprehensive environmental tobacco policies is needed.

Virtual patient instruction for dental students: can it improve dental care access for persons with special needs?

An interactive, virtual-patient module was produced on compact disc (CD-ROM) in response to the critical need to increase dental students' clinical exposure to patients with developmental disabilities. A content development team consisting of dental faculty members, parents of children with developmental disabilities, an individual with a developmental disability, and educational specialists developed the interactive, virtual-patient module. The module focused on a young man with congenital deafblindness presenting as a new patient with a painful molar. Students were required to make decisions regarding clinical interactions throughout the module. Differences in both comfort and knowledge level were measured pre- and post-module completion, as well as the dental students' overall satisfaction with the learning experience. Significant results were obtained in students' perceived comfort and knowledge base. Participants reported overall satisfaction using the modules. This study demonstrated that an interactive, multi-media (CD-ROM), virtual patient learning module for dental students could be an effective tool in providing students needed clinical exposure to patients with developmental disabilities.

Caring for children with intellectual and developmental disabilities: virtual patient instruction improves students' knowledge and comfort level

Nurses play a vital role in providing health care to children with developmental disability (DD) throughout the United States. Unfortunately, most nurses continue to report that they receive little or no clinical education in the area of DDs. In response to this need, a core development team consisting of nurse practitioners and nursing faculty from three universities, one physician assistant faculty, parents of children with DD, and educational specialists developed two multimedia (virtual patient) pediatric instructional modules in CD-ROM format--one involving a child with Down syndrome, and the other involving an infant born at 26 weeks' gestation. Participants were required to make clinical decisions throughout the cases. The modules on CD were piloted with nursing students from three universities. Results of the effectiveness study demonstrated significant gains in knowledge and comfort level regarding the care of children with DD.

The protease allergen Der p 1 cleaves cell surface DC-SIGN and DC-SIGNR: experimental analysis of in silico substrate identification and implications in allergic responses

BACKGROUND

The cysteine protease Der p 1 from the house dust mite Dermatophagoides pteronyssinus is one of the most potent allergens known. An attractive mechanism for a component of Der p 1 allergenicity lies in its ability to cleave key regulatory molecules from leucocyte surfaces, subverting cellular function and driving abnormal immunoglobulin E (IgE) responses.

OBJECTIVE

Although CD23, CD25 and CD40 have already been identified as major Der p 1 targets, other significant substrates may also exist.

METHODS

To investigate this, knowledge of the proteolytic properties of Der p 1 was used to perform in silico digestion of human dendritic cell surface proteins, using the prediction of protease specificity (PoPS) bioinformatics tool, in conjunction with cellular in vitro analysis and cleavage site determination.

RESULTS

Targets identified included DC-SIGN and DC-SIGNR, two C-type lectins implicated mostly in pathogen trafficking. Treatment of positively expressing cells with Der p 1 led to loss of detectable surface DC-SIGN and DC-SIGNR. Digestion of purified soluble recombinant DC-SIGN and DC-SIGNR, followed by N-terminal sequencing and MALDI mass spectrometry, indicated in each case one major cleavage site and several minor sites, the former correlating well with Der p 1 enzymology and the folded state of the substrate proteins. Loss of DC-SIGN from the cell surface led to reduced binding of intracellular adhesion molecule-3, an endogenous DC-SIGN ligand expressed on naïve T cells which is thought to be involved in T-helper type 1 cytokine signalling.

CONCLUSION

These data provide evidence of lectin involvement in the initiation of the allergic response and the value of using genome-wide in silico digestion tools.

Synthesis and Structure of Diacetato-[1-benzyloxy-1,1-bis(N-methylimdazol-2-yl)ethane]zinc(II)

The synthesis and single-crystal X-ray structure determination of the title compound are described. The crystals are monoclinic, P21/c, a 10.064(2), b 13.096(2), c 17.722(3) Ǻ, β 104.68(2)°; the structure was refined to a residual of 0.033 for 3138 independent observed reflections. The coordination about zinc is intermediate between four- and five-coordinate, and the angle between the planar imidazole groups is 14.9°.