Syndromic diagnostic testing: a new way to approach patient care in the treatment of infectious diseases

A capillary-driven microfluidic device for performing spatial multiplex PCR

Multiplex polymerase chain reaction (PCR) tests multiple biomarkers or pathogens that cause overlapping symptoms, making it an essential tool in syndromic testing. To achieve a multiplex PCR on chip, a design based on capillary-driven fluidic actuation is proposed. Our silicon chip features 22 reaction chambers and allows primers and probes to be pre-spotted in the reaction chambers prior to use. The design facilitates rapid sample loading through a common inlet channel, delivering reagents to all reaction chambers in less than 10 s. A custom clamping mechanism combined with a double depth cavity design ensures proper sealing during temperature cycling without the need for extra reagents like oil. Temperature cycling and fluorescence imaging were performed using custom-made hardware. As a proof of concept, two single nucleotide polymorphisms (SNPs), CyP2C19*2 and PCSK9 were detected. These results demonstrate the feasibility of on-chip multiplex PCR, compatible with different assays in parallel and requiring only a single pipetting step for reagent loading, without active fluidic actuation like pumping.

Elucidating Infectious Causes of Fever of Unknown Origin: A Laboratory-Based Observational Study of Patients with Suspected Ebola Virus Disease, Guinea, 2014

BACKGROUND

The etiology of fever of unknown origin (FUO) in sub-Saharan Africa often remains unexplained.

METHODS

We performed a retrospective laboratory-based observational study of 550 Guinean patients with FUO testing negative for Ebola virus from March to December 2014. Blood-borne pathogens were diagnosed by polymerase chain reaction (PCR) or reverse transcription-PCR (RT-PCR), serologic tests, and targeted and unbiased high-throughput sequencing (HTS).

RESULTS

In 275 of 550 individuals, we found evidence of ≥1 pathogen by molecular methods. We identified Plasmodium in 35.6% of patients via PCR, with P falciparum constituting 96.4% of these cases. Pathogenic bacteria, including Salmonella and Klebsiella, were detected in 18.4% of patients through PCR and HTS. Resistance determinants against first-line antibiotics were found in 26.9% of pooled sera by HTS. Yellow fever, Lassa, and Ebola viruses were detected in 5.8% of patients by RT-PCR; HTS-guided RT-PCR confirmed Orungo virus infection in 1 patient. Phylogenetic analyses revealed that the viral genomes matched the available genomic data in terms of location and time. Indirect immunofluorescence assays revealed immunoglobulin M antibodies against yellow fever, Ebola, dengue, West Nile, and Crimean Congo hemorrhagic fever viruses in 11 of 100 patients who were PCR or RT-PCR negative. One in 5 patients who were infected presented coinfections, predominantly malaria associated with sepsis-causing bacteria, in adults (12.1%) and children (12.5%), whereas viral coinfections were rare. Patients presented fever (74.7%), asthenia (67.7%), emesis (38.2%), diarrhea (28.3%), and hemorrhage (11.8%), without clear etiology associations.

CONCLUSIONS

An exhaustive laboratory investigation elucidated infectious causes of FUO in 52.3% of patients. Quality control and strengthening laboratory capacities in sub-Saharan Africa are essential for patient care, outbreak response, and regionally appropriate diagnostics.

Targeted syndromic next-generation sequencing panel for simultaneous detection of pathogens associated with bovine reproductive failure

Bovine reproductive failure, which includes infertility, abortion, and stillbirth in cattle, leads to significant economic losses for beef and milk producers. Diagnosing the infectious causes of bovine reproductive failure is challenging as there are multiple pathogens associated with it. The traditional stepwise approach to diagnostic testing is time-consuming and can cause significant delays. In this study, we have developed a syndromic next-generation sequencing panel (BovReproSeq) for the simultaneous detection of 17 pathogens (bacteria, virus, and protozoa) associated with bovine reproductive failure. This targeted approach involves amplifying multiple pathogen-specific targets using ultra-multiplex PCR, followed by sequencing with the Oxford Nanopore platform and subsequent analysis of the data using a custom bioinformatic pipeline to determine the presence or absence of pathogens. We tested 116 clinical samples and found that BovReproSeq results matched with current diagnostic methods for 93% of the samples, and most of the disagreements occurring in samples with very low pathogen loads (Ct >35). At the optimal read-count threshold of 10 reads (minimum number of reads to classify the sample as positive), the clinical sensitivity of the assay was approximately 82%, while clinical specificity was 100%. The overall accuracy of the assay was 98.8%. Matthews correlation coefficient (correlation coefficient of binary classification) was approximately 0.90 and F1 score (harmonic mean of precision and recall) was 0.90, indicating excellent overall performance. Our study presents a significant advancement in detecting the infectious agents associated with bovine reproductive failure and the BovReproSeq panel's ability to detect 17 pathogens makes it a promising tool for veterinary diagnostics.IMPORTANCEBovine reproductive failure causes substantial economic losses to beef and milk producers, and infectious disease contributes significantly to this syndrome. Etiologic diagnosis is complicated since multiple pathogens can be involved and infections with some pathogens are asymptomatic or cause similar clinical signs. A stepwise approach to diagnostic testing is time-consuming and increases the risk of missing the correct diagnosis. BovReproSeq is a next-generation sequencing-based diagnostic panel that allows detection of 17 reproductive failure pathogens simultaneously.

The role of rapid multiplex molecular syndromic panels in the clinical management of infections in critically ill patients: an experts-opinion document

Rapid multiplex molecular syndromic panels (RMMSP) (3 or more pathogens and time-to-results < 6 h) allow simultaneous detection of multiple pathogens and genotypic resistance markers. Their implementation has revolutionized the clinical landscape by significantly enhancing diagnostic accuracy and reducing time-to-results in different critical conditions. The current revision is a comprehensive but not systematic review of the literature. We conducted electronic searches of the PubMed, Medline, Embase, and Google Scholar databases to identify studies assessing the clinical performance of RMMSP in critically ill patients until July 30, 2024. A multidisciplinary group of 11 Spanish specialists developed clinical questions pertaining to the indications and limitations of these diagnostic tools in daily practice in different clinical scenarios. The topics covered included pneumonia, sepsis/septic shock, candidemia, meningitis/encephalitis, and off-label uses of these RMMSP. These tools reduced the time-to-diagnosis (and therefore the time-to-appropriate treatment), reduced inappropriate empiric treatment and the length of antibiotic therapy (which has a positive impact on antimicrobial stewardship and might be associated with lower in-hospital mortality), may reduce the length of hospital stay, which could potentially lead to cost savings. Despite their advantages, these RMMSP have limitations that should be known, including limited availability, missed diagnoses if the causative agent or resistance determinants are not included in the panel, false positives, and codetections. Overall, the implementation of RMMSP represents a significant advancement in infectious disease diagnostics, enabling more precise and timely interventions. This document addresses relevant issues related to the use of RMMSP on different critically ill patient profiles, to standardize procedures, assist in making management decisions and help specialists to obtain optimal outcomes.

Advantages of Syndromic Diagnostics: Detection of the Pathogens Causing Urethritis/Cervicitis with the STI CNM Real-Time PCR Kit from Vitro S.A

The STI CNM Real-Time PCR Kit from Vitro S.A. (Spain) demonstrates high sensitivity and specificity, is cost-effective, and can detect the three main etiological agents of urethritis/cervicitis in a single multiplex PCR. Sexually transmitted infections (STIs) are a significant public health problem and a significant burden of morbidity and mortality in hospitals. The World Health Organization (WHO) estimates the number of daily infections to be 1 million. Currently, the number of infections and antimicrobial-resistant strains is rising. A rapid and accurate etiologic diagnosis is critical to solving this problem. In this study, we compared the STI CNM Real-Time PCR Kit using the Xpert® CT/NG technique (Cepheid®, USA) as Gold Standard for the diagnosis of Chlamydia trachomatis and Neisseria gonorrhoeae and EasyNAT® MG (Ustar Biotechnologies (Hangzhou) Ltd., China) as Gold Standard for the diagnosis of Mycoplasma genitalium infection. Regarding C. trachomatis and N. gonorrhoeae, out of 200 samples, there was a match in 199 cases, with only one positive sample not being detected by the STI CNM Real-Time PCR Kit. This results in a sensitivity of 96% and a specificity of 100% for this kit. Diagnosing M. genitalium infection, out of 200 samples, the STI CNM Real-Time PCR Kit correctly detected all negative and positive samples, with 100% agreement compared to the reference technique. In summary, the STI assay has a very high sensitivity and specificity, comparable to other commercial diagnostic kits. Furthermore, it has the advantage of bundling the detection of the three main bacterial agents of urethritis/cervicitis, resulting in better cost efficiency.

Retrospective validation study of a machine learning-based software for empirical and organism-targeted antibiotic therapy selection

Errors in antibiotic prescriptions are frequent, often resulting from the inadequate coverage of the infection-causative microorganism. The efficacy of iAST, a machine-learning-based software offering empirical and organism-targeted antibiotic recommendations, was assessed. The study was conducted in a 12-hospital Spanish institution. After model fine-tuning with 27,531 historical antibiograms, 325 consecutive patients with acute infections were selected for retrospective validation. The primary endpoint was comparing each of the top three of iAST's antibiotic recommendations' success rates (confirmed by antibiogram results) with the antibiotic prescribed by the physicians. Secondary endpoints included examining the same hypothesis within specific study population subgroups and assessing antibiotic stewardship by comparing the percentage of antibiotics recommended that belonged to different World Health Organization AWaRe groups within each arm of the study. All of iAST first three recommendations were non-inferior to doctor prescription in the primary endpoint analysis population as well as the secondary endpoint. The overall success rate of doctors' empirical treatment was 68.93%, while that of the first three iAST options was 91.06% (P < 0.001), 90.63% (P < 0.001), and 91.06% (P < 001), respectively. For organism-targeted therapy, the doctor's overall success rate was 84.16%, and that of the first three ranked iAST options was 97.83% (P < 0.001), 94.09% (P < 0.001), and 91.30% (P < 0.001), respectively. In empirical therapy, compared to physician prescriptions, iAST demonstrated a greater propensity to recommend access antibiotics, fewer watch antibiotics, and higher reserve antibiotics. In organism-targeted therapy, iAST advised a higher utilization of access antibiotics. The present study demonstrates iAST accuracy in predicting antibiotic susceptibility, showcasing its potential to promote effective antibiotic stewardship.

CLINICAL TRIALS

This study is registered with ClinicalTrials.gov as NCT06174519.

Respiratory viral infections in children with cancer and febrile neutropenia and children undergoing hematopoietic stem cell transplantation

PURPOSE OF REVIEW

The scope of this review is to understand the epidemiology and potential role of respiratory viral infections in children with cancer and febrile neutropenia, as well as in children, undergoing hematopoietic stem cell transplantation. Early detection of respiratory viral infections through molecular diagnostic techniques has allowed recent randomized clinical studies to advance the possibility of more rational use of antimicrobials in this susceptible population.

RECENT FINDINGS

Progress has been made in the early detection of respiratory viruses in episodes of fever and neutropenia in children with cancer. In selected patients who meet specific clinical safety criteria and have negative bacterial cultures, it has been possible to safely and effectively discontinue antimicrobials. This has been validated in recent randomized clinical studies. However, more evidence is still needed for a similar indication in children, undergoing hematopoietic stem cell transplantation with viral respiratory infection episodes.

SUMMARY

Understanding the role of respiratory viral infections in populations of immunocompromised children may contribute to a more rational use of antimicrobials and, in the near future, may help to decrease antimicrobial resistance in this susceptible population.

A multicenter randomized control trial: Point-of-care syndromic assessment versus standard testing in urgent care center patients with acute respiratory illness

Objective

Syndromic assessment with multiplex polymerase chain reaction (mPCR) testing in patients with acute respiratory illness (ARI) allows for simultaneous identification of multiple possible infectious etiologies. Point-of-care (POC) syndromic assessment can be conducted in a clinical setting, such as an urgent care center (UCC), without requiring certified laboratories. The primary objective of this study was to determine whether POC syndromic assessment improved patient satisfaction for patients seen at an UCC with ARI; secondary objectives included whether syndromic assessment reduced self-isolation time, increased diagnostic confidence, and reduced overall antibiotic utilization.

Methods

We conducted an unblinded multicenter randomized controlled trial on UCC patients with an ARI. Patients were randomized to either SC (defined as standard UCC testing for ARI) or syndromic assessment with POC mPCR. Patients were surveyed for patient satisfaction, self-isolation plans, diagnostic confidence, and overall antibiotic utilization.

Results

Among the 360 patients enrolled, those in the syndromic assessment group were more satisfied with the time required to communicate the results (98.4% vs. 42.4%, p < 0.001) on day of treatment, more likely to resume normal activities sooner (83.3% vs. 69.4%, p = 0.039), and more confident in their illness cause (60.7% vs. 29.6%, p < 0.001); however, the rate of antibiotic utilization did not differ (33.5% vs. 26%, p = 1.0).

Conclusion

In conclusion, our study provides evidence supporting the use of syndromic assessment in UCCs for ARI diagnosis, including patient-centered outcomes such as greater confidence in diagnosis and more efficient isolation strategies. This study did not show a difference in more clinically oriented outcomes, such as a change in antibiotic utilization. Future studies should identify clinical care pathways to improve antibiotic stewardship for likely viral syndromes and whether the increased initial cost of syndromic assessment is offset by the clinical benefits and subsequent cost savings.

Advancing quantitative PCR with color cycle multiplex amplification

Quantitative PCR (qPCR) is the gold standard for detection and quantitation of known DNA targets, but the scarcity of spectrally distinct fluorophores and filter sets limits the number of detectable targets. Here, we introduce color cycle multiplex amplification (CCMA) to significantly increase the number of detectable DNA targets in a single qPCR reaction using standard instrumentation. In CCMA, presence of one DNA target species results in a pre-programmed pattern of fluorescence increases. This pattern is distinguished by cycle thresholds (Cts) through rationally designed delays in amplification. For example, we design an assay wherein Staphylococcus aureus sequentially induces FAM, then Cy5.5, then ROX fluorescence increases with more than 3 cycles between each signal. CCMA offers notably higher potential for multiplexing because it uses fluorescence permutation rather than combination. With 4 distinct fluorescence colors, CCMA theoretically allows the detection of up to 136 distinct DNA target sequences using fluorescence permutation. Experimentally, we demonstrated a single-tube qPCR assay screening 21 sepsis-related bacterial DNA targets in samples of blood, sputum, pleural effusion and bronchoalveolar lavage fluid, with 89% clinical sensitivity and 100% clinical specificity, showing its potential as a powerful tool for advanced quantitative screening in molecular diagnostics.

Efficacy and safety of withholding antimicrobial therapy in children with cancer, fever, and neutropenia, with a demonstrated viral respiratory infection: a randomized clinical trial

OBJECTIVES

To validate the efficacy and safety of withholding antimicrobial therapy in a new cohort of children with cancer and febrile neutropenia (FN) having a demonstrated viral respiratory tract infection.

METHODS

Prospective, multicenter, noninferiority, randomized study, approved by the ethical committee, in children presenting with FN at seven hospitals in Chile, evaluated at admission for diagnosis of bacterial and viral pathogens. Children who were positive for a respiratory virus, negative for a bacterial pathogen, and had a favourable evolution after 48-72 hours of antimicrobial therapy were randomized to either maintain or withhold antimicrobial therapy. The primary endpoint was the percentage of episodes with an uneventful resolution, whereas the secondary endpoints were days of fever, days of hospitalization, requirement of antimicrobial treatment readministration, sepsis, paediatric intensive care unit admission, and death.

RESULTS

A total of 301 of 939 children with FN episodes recruited between March 2021 and December 2023 had a respiratory virus as a unique identified microorganism, of which 139 had a favourable evolution at 48-72 hours and were randomized, 70 to maintain and 69 to withdraw antimicrobial therapy. The median days of antimicrobial therapy was 5 (IQR 3-6) versus 3 (IQR 3-6) days (p < 0.001), with similar frequency of uneventful resolution 66/70 (94%) and 66/69 (96%); relative risk, 1.01; (95% CI, 0.93 to 1.09), absolute risk difference 0.01; (95% CI, -0.05 to 0.08) and similar number of days of fever and days of hospitalization. No cases of sepsis, paediatric intensive care unit admission, or death were reported.

DISCUSSION

We validated the strategy of withdrawal antimicrobial therapy in children with FN and viral respiratory tract infection based on clinical and microbiological/molecular diagnostic criteria. This will enable advances in antimicrobial stewardship strategies with a possible future impact on antimicrobial resistance.

The epidemiology of intestinal protozoa in the Israeli population based on molecular stool test: a nationwide study

Stool examination using microscopy was the traditional method for the diagnosis of intestinal parasites. Recently, the use of molecular tests to identify stool protozoa has become the main tool used in most clinical laboratories in Israel. This study aimed to evaluate the prevalence of intestinal parasites in Israel and to compare this prevalence in laboratories that use molecular tests vs a laboratory that uses microscopy. Samples collected from January to October 2021 at seven laboratories were analyzed by real-time PCR (RT-PCR) or by microscopy. The multiplex panel included the following pathogens: Giardia lamblia, Entamoeba histolytica, Cryptosporidium spp., Cyclospora, Dientamoeba fragilis, and Blastocystis spp. Overall, 138,415 stool samples were tested by RT-PCR and 6,444 by microscopy. At least one protozoa species was identified in 28.4% of the PCR-tested samples compared to 4.6% of the microscopy-tested samples. D. fragilis was the most common PCR-identified species (29%). D. fragilis, G. lamblia, and Cryptosporidium spp. were mainly found in pediatric population, while Blastocystis spp. was most prevalent among adults (P < 0.001). In a sub-cohort of 21,480 samples, co-infection was found in 4,113 (19.15%) samples, with Blastocystis spp. and D. fragilis being the most common (14.9%) pair. Molecular stool testing proved more sensitive compared to microscopy. D. fragilis was the most commonly detected pathogen. The above profile was identified during the COVID pandemic when traveling was highly restricted and most likely represents the locally circulating protozoa.

IMPORTANCE

This study sheds light on the prevalence of stool parasites in Israel. Additionally, this study indicates that the shift from microscope analysis to molecular tests improved protozoa diagnosis.

Comparison of three cartridge-based platforms for syndromic testing for respiratory viruses

Syndromic testing, the simultaneous testing for multiple pathogens causing similar symptoms, has recently gained ground in clinical diagnostics. This approach can significantly shorten time to diagnosis and speed up decision-making, leading to an improved outcome for the patient. Here, we compared three automated multiplex PCR platforms for syndromic testing of respiratory samples in a retrospective study, and assessed their relative sensitivities. The PPA between BioFire and QIAstat compared to ePlex was 98.4 % and 93.8 %, respectively, and 6 discrepant results were observed. The BioFire was identified as the platform with the highest relative sensitivity. Overall, the platforms performed similarly and are all suitable for syndromic testing of respiratory samples.

Multicenter evaluation of BioCode GPP for syndromic molecular detection of gastrointestinal pathogens from stool specimens

Acute gastroenteritis (AGE) is a leading cause of morbidity and mortality worldwide across all age groups that disproportionally affects young children in low- and middle-income countries and immunocompromised patients in high-income countries. Regional outbreaks of AGE are typically detected by traditional microbiological detection methods that target limited organisms and are associated with low sensitivity and lengthy time-to-results. Combined, these may result in repeat testing, imprecise or delayed treatment, and delayed recognition of outbreaks. We conducted a multi-site prospective study comparing the BioCode Gastrointestinal Pathogen Panel (BioCode GPP) for the detection of 17 common bacterial, viral, and protozoan causes of gastroenteritis with reference methods, including stool culture, enzyme immunoassays, pathogen-specific PCR assays, and sequencing. One thousand five hundred fifty-eight residual, de-identified stool samples (unpreserved stool and stool in Cary-Blair transport medium) were enrolled and tested for 11 bacterial, 3 viral, and 3 protozoan pathogens. BioCode GPP and reference methods were positive for 392 (25.2%) and 283 (18.2%) samples, respectively (P < 0.0001). In this study, the BioCode GPP and reference methods detected 69 and 65 specimens positive for Clostridioides difficile, 51 and 48 for enteroaggregative Escherichia coli, 33 and 27 for enterotoxigenic E. coli, 50 and 47 for norovirus GI/GII, and 30 and 22 for rotavirus A, respectively. The BioCode GPP showed good positive and negative agreements for each pathogen ranging from 89.5% to 100%, with overall sensitivity and specificity of 96.1% and 99.7%, post adjudication. The BioCode GPP detected >1 pathogens in 49 samples, representing 12.5% of the total 392 positive specimens.

IMPORTANCE

This study highlights performance of a novel technology for timely and accurate detection and differentiation of 17 common bacterial, viral, and protozoan causes of gastroenteritis. Utilizing molecular tests such as the BioCode Gastrointestinal Pathogen Panel may improve the detection of gastrointestinal pathogens and provide actionable results, particularly for patient populations at most risk.

Tackling Infectious Diseases with Rapid Molecular Diagnosis and Innovative Prevention

Infectious diseases (IDs) are a leading cause of death. The diversity and adaptability of microbes represent a continuing risk to health. Combining vision with passion, our transdisciplinary medical research team has been focussing its work on the better management of infectious diseases for saving human lives over the past five decades through medical discoveries and innovations that helped change the practice of medicine. The team used a multiple-faceted and integrated approach to control infectious diseases through fundamental discoveries and by developing innovative prevention tools and rapid molecular diagnostic tests to fulfill the various unmet needs of patients and health professionals in the field of ID. In this article, as objectives, we put in context two main research areas of ID management: innovative infection prevention that is woman-controlled, and the rapid molecular diagnosis of infection and resistance. We also explain how our transdisciplinary approach encompassing specialists from diverse fields ranging from biology to engineering was instrumental in achieving success. Furthermore, we discuss our vision of the future for translational research to better tackle IDs.

Treatment and diagnosis of severe KPC-producing Klebsiella pneumoniae infections: a perspective on what has changed over last decades

Antimicrobial resistance is a global health threat. Among Gram-negative bacteria, resistance to carbapenems, a class of β-lactam antibiotics, is usually a proxy for difficult-to-treat resistance, since carbapenem-resistant organisms are often resistant to many classes of antibiotics. Carbapenem resistance in the Gram-negative pathogen Klebsiella pneumoniae is mostly due to the production of carbapenemases, enzymes able to hydrolyze carbapenems, and K. pneumoniae carbapenemase (KPC)-type enzymes are overall the most prevalent carbapenemases in K. pneumoniae. In the last decade, the management of severe infections due to KPC-producing K. pneumoniae (KPC-Kp) in humans has presented many peculiar challenges to clinicians worldwide. In this perspective, we discuss how the treatment of severe KPC-Kp infections has evolved over the last decades, guided by the accumulating evidence from clinical studies, and how recent advances in diagnostics have allowed to anticipate identification of KPC-Kp in infected patients.KEY MESSAGESIn the last decade, the management of severe infections due to KPC-Kp has presented many peculiar challenges to clinicians worldwideFollowing the introduction in clinical practice of novel β-lactam/β-lactamase inhibitor combinations and novel β-lactams active against KPC-producing bacteria, the management of severe KPC-Kp infections has witnessed a remarkable evolutionTreatment of severe KPC-Kp infections is a highly dynamic process, in which the wise use of novel antimicrobials should be accompanied by a continuous refinement based on evolving clinical evidence and laboratory diagnostics.

A cooperativity between virus and bacteria during respiratory infections

Respiratory tract infections remain the leading cause of morbidity and mortality worldwide. The burden is further increased by polymicrobial infection or viral and bacterial co-infection, often exacerbating the existing condition. Way back in 1918, high morbidity due to secondary pneumonia caused by bacterial infection was known, and a similar phenomenon was observed during the recent COVID-19 pandemic in which secondary bacterial infection worsens the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) condition. It has been observed that viruses paved the way for subsequent bacterial infection; similarly, bacteria have also been found to aid in viral infection. Viruses elevate bacterial infection by impairing the host's immune response, disrupting epithelial barrier integrity, expression of surface receptors and adhesion proteins, direct binding of virus to bacteria, altering nutritional immunity, and effecting the bacterial biofilm. Similarly, the bacteria enhance viral infection by altering the host's immune response, up-regulation of adhesion proteins, and activation of viral proteins. During co-infection, respiratory bacterial and viral pathogens were found to adapt and co-exist in the airways of their survival and to benefit from each other, i.e., there is a cooperative existence between the two. This review comprehensively reviews the mechanisms involved in the synergistic/cooperativity relationship between viruses and bacteria and their interaction in clinically relevant respiratory infections.

Respiratory virus infections after allogeneic stem cell transplantation: Current understanding, knowledge gaps, and recent advances

Before the COVID-19 pandemic, common community-acquired seasonal respiratory viruses (CARVs) were a significant threat to the health and well-being of allogeneic hematopoietic cell transplant (allo-HCT) recipients, often resulting in severe illness and even death. The pandemic has further highlighted the significant risk that immunosuppressed patients, including allo-HCT recipients, face when infected with SARS-CoV-2. As preventive transmission measures are relaxed and CARVs circulate again among the community, including in allo-HSCT recipients, it is crucial to understand the current state of knowledge, gaps, and recent advances regarding CARV infection in allo-HCT recipients. Urgent research is needed to identify seasonal respiratory viruses as potential drivers for future pandemics.

Old and new aspects of influenza

Influenza is a classic infectious disease that, through the continuous variation of the viruses that produce it, imposes new challenges that we must solve as quickly as possible. The COVID-19 pandemic has substantially modified the behavior of influenza and other respiratory viruses, and in the coming years we will have to coexist with a new pathogen that will probably interact with existing pathogens in a way that we cannot yet glimpse. However, knowledge prior to the pandemic allows us to focus on the aspects that must be modified to make influenza an acceptable challenge for the future. In this review, emphasis is placed on the most relevant aspects of epidemiology, disease burden, diagnosis, and vaccine prevention, and how scientific and clinical trends in these aspects flow from the previously known to future challenges.

The Interventions and Challenges of Antimicrobial Stewardship in the Emergency Department

Over the last decades, we have witnessed a constant increase in infections caused by multi-drug-resistant strains in emergency departments. Despite the demonstrated effectiveness of antimicrobial stewardship programs in antibiotic consumption and minimizing multi-drug-resistant bacterium development, the characteristics of emergency departments pose a challenge to their implementation. The inclusion of rapid diagnostic tests, tracking microbiological results upon discharge, conducting audits with feedback, and implementing multimodal educational interventions have proven to be effective tools for optimizing antibiotic use in these units. Nevertheless, future multicenter studies are essential to determine the best way to proceed and measure outcomes in this scenario.

Impact of multiplex polymerase chain reaction syndromic panel on antibiotic use among hospitalized children with respiratory tract illness during COVID-19 pandemic

BACKGROUND/PURPOSE

Precise detection of respiratory pathogens by molecular method potentially may shorten the time to diagnose and reduce unnecessary antibiotic use.

METHODS

Medical records of hospitalized children from January 2020 to June 2021 with acute respiratory illness who received a FilmArray RP for respiratory pathogens were reviewed and compared with data from diagnosis-matched patients without receiving the test.

RESULTS

In total, 283 patients and 150 diagnosis-matched controls were included. Single pathogen was detected in 84.3% (193/229) of the patients. The most common pathogen was human rhinovirus/enterovirus (31.6%, 84/266), followed by respiratory syncytial virus (18.8%, 50/266) and adenovirus (15%, 40/266). Although antimicrobial days of therapy (DOT) was significantly longer in FilmArray group than the control [7.1 ± 4.9 days vs 5.7 ± 2.7 days, P = 0.002], the former showed a higher intensive care unit (ICU) admission rate (3.9% vs 0%; P = 0.010). All ICU admissions were in FilmArray RP-positive group. There was no difference in antimicrobial DOT between FilmArray RP-positive and the negative groups, in all admissions, even after excluding ICU admissions. Antimicrobial DOT was shorter in the positive than negative group in patients with lower respiratory tract infections without admission to ICU [median (IQR): 6 (4-9) days vs 9 (4-12) days, P = 0.047].

CONCLUSIONS

Shorter antimicrobial DOTs were identified in children with lower respiratory tract infection admitted to general pediatric ward and with an identifiable respiratory pathogen, indicating a role of the multiplex PCR in reducing antimicrobial use for children with respiratory tract infection.

Evaluation of the Liquid Colony™ Produced by the FAST System for Shortening the Time of Bacterial Identification and Phenotypic Antimicrobial Susceptibility Testing and Detection of Resistance Mechanisms from Positive Blood Cultures

BACKGROUND

the aim of this study was to evaluate the performance of the Liquid Colony™ (LC) generated directly from positive blood cultures (PBCs) by the FAST System (Qvella, Richmond Hill, ON, Canada) for rapid identification (ID) and antimicrobial susceptibility testing (AST) compared with the standard of care (SOC) workflow.

METHODS

Anonymized PBCs were processed in parallel by the FAST System and FAST PBC Prep cartridge (35 min runtime) and SOC. ID was performed by MALDI-ToF mass spectrometry (Bruker, Billerica, MA, USA). AST was performed by reference broth microdilution (Merlin Diagnostika, Bornheim, Germany). Carbapenemase detection was carried out with the lateral flow immunochromatographic assay (LFIA) RESIST-5 O.O.K.N.V. (Coris, Gembloux, Belgium). Polymicrobial PBCs and samples containing yeast were excluded.

RESULTS

241 PBCs were evaluated. ID results showed 100% genus-level concordance and 97.8% species-level concordance between LC and SOC. The AST results for Gram-negative bacteria showed a categorical agreement (CA) of 99.1% (1578/1593), with minor error (mE), major error (ME), and very major error (VME) rates of 0.6% (10/1593), 0.3% (3/1122), and 0.4% (2/471), respectively. The results from Gram-positive bacteria showed a CA of 99.6% (1655/1662), with mE, ME, and VME rates of 0.3% (5/1662), 0.2% (2/1279), and 0.0% (0/378), respectively. Bias evaluation revealed acceptable results for both Gram-negatives and Gram-positives (-12.4% and -6.5%, respectively). The LC yielded the detection of 14/18 carbapenemase producers by LFIA. In terms of turnaround time, the ID, AST, and carbapenemase detection results were generally obtained one day earlier with the FAST System compared with the SOC workflow.

CONCLUSIONS

The ID, AST, and carbapenemase detection results generated with the FAST System LC were highly concordant with the conventional workflow. The LC allowed species ID and carbapenemase detection within around 1 h after blood culture positivity and AST results within approximately 24 h, which is a significant reduction in the turnaround time of the PBC workflow.

Large-Scale Clinical Evaluation of Rapid Blood Culture Identification Panels for Bloodstream Infections at a Tertiary Hospital

The prompt implementation of optimal antibacterial therapy through the rapid identification of the causative organisms is essential for improving outcomes for critically ill patients with bloodstream infections. We evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel for rapidly identifying causative pathogens in the bloodstream using large-scale clinical samples. We analyzed the results of identification using a BCID panel performed on 2005 positive blood culture bottles from September 2019 to June 2022. Pathogen detection efficiency and interval from Gram staining to identification using the BCID panel were compared to those of conventional identification systems—VITEK MS MALDI-TOF Mass Spectrometer and Vitek2—and antibiotic susceptibility testing—Vitek2. We detected 2167 isolates from 2005 positive blood culture bottles. In these isolates, the BCID panel showed 93% full agreement—both organisms and antimicrobial resistance genes were matched, and no off-target organisms were detected. Species-level discordance was found in 0.6% of tests. Sixty-five isolates (3.0%) were only detected by BCID, whereas 22 isolates (1.0%) from the on-target panel were not detected by BCID. This large-scale study demonstrated that the BCID panel was a reliable and rapid identification method for directly identifying bloodstream pathogens in a positive blood culture.

The Impact of a Positive Biofire® FilmArray® Gastrointestinal Panel Result on Clinical Management and Outcomes

The gold standard diagnostic method for gastrointestinal infections is stool culture, which has limited sensitivity and long turnaround time. Infection diagnosis recently shifted to syndrome-based panel assays. This study employed the FilmArray® Gastrointestinal Panel, which detects 22 pathogens simultaneously, to investigate gastrointestinal infection and pathogen distribution in 91 stool samples of patients hospitalized at the Tzafon Medical Center, Israel, during 2020, and to compare the clinical and demographic data of negative vs. positive samples. Among the 61 positive samples (67%), the most common pathogen was Campylobacter (34.4%). Positive test results were associated with a slightly younger patient age (p = 0.012), significantly higher post-diagnosis use of antibiotics (63.9% vs. 36.7%; p = 0.014), and shorter length of stay and time to discharge (p = 0.035, p = 0.003, respectively) than negative test results. To conclude, the FilmArray® Gastrointestinal Panel enabled the early identification of causative infectious agents and enhanced clinical management and outcomes.

Respiratory Tract Infections and Laboratory Diagnostic Methods: A Review with A Focus on Syndromic Panel-Based Assays

Respiratory tract infections (RTIs) are the focus of developments in public health, given their widespread distribution and the high morbidity and mortality rates reported worldwide. The clinical spectrum ranges from asymptomatic or mild infection to severe or fatal disease. Rapidity is required in diagnostics to provide adequate and prompt management of patients. The current algorithm for the laboratory diagnosis of RTIs relies on multiple approaches including gold-standard conventional methods, among which the traditional culture is the most used, and innovative ones such as molecular methods, mostly used to detect viruses and atypical bacteria. The implementation of molecular methods with syndromic panels has the potential to be a powerful decision-making tool for patient management despite requiring appropriate use of the test in different patient populations. Their use radically reduces time-to-results and increases the detection of clinically relevant pathogens compared to conventional methods. Moreover, if implemented wisely and interpreted cautiously, syndromic panels can improve antimicrobial use and patient outcomes, and optimize laboratory workflow. In this review, a narrative overview of the main etiological, clinical, and epidemiological features of RTI is reported, focusing on the laboratory diagnosis and the potentialities of syndromic panels.

Molecular Pathology Education: A Suggested Framework for Primary Care Resident Training in Genomic Medicine: A Report of the Association for Molecular Pathology Training and Education Committee

Developments in genomics are profoundly influencing medical practice. With increasing use of genetic and genomic testing across every aspect of the health care continuum, patients and their families are increasingly turning to primary care physicians (PCPs) for discussion and advice regarding tests, implications, and results. Yet, with the rapid growth of information, technology, and applications, PCPs are finding it challenging to fill the gaps in knowledge and support the growing needs of their patients. A critical component in expanding PCP genomic literacy lies in the education of physicians in training and in practice. Although a framework for developing physician competencies in genomics has already been developed, the Association for Molecular Pathology is uniquely situated to actively utilize the skills of its members to engage and support PCPs in this effort. This report provides an overview and a suggested basic teaching framework, which can be used by molecular professionals in their individual institutions as a starting point for educational outreach.