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The recent progress made in developing laser-induced breakdown spectroscopy (LIBS) has transformed LIBS from an elemental analysis technique to one that can be applied for the reagentless analysis of molecularly complex biological materials or clinical specimens. Rapid advances in the LIBS technology have spawned a growing number of recently published articles in peer-reviewed journals which have consistently demonstrated the capability of LIBS to rapidly detect, biochemically characterize and analyse, and/or accurately identify various biological, biomedical or clinical samples. These analyses are inherently real-time, require no sample preparation, and offer high sensitivity and specificity. This overview of the biomedical applications of LIBS is meant to summarize the research that has been performed to date, as well as to suggest to health care providers several possible specific future applications which, if successfully implemented, would be significantly beneficial to humankind. [ABSTRACT FROM AUTHOR]

Although silver is known for its antibacterial activity, its exact mode of action remains unclear. In our previous work, we described AgNbO 3 nanoparticles (AgNbO 3 NPs) prepared using a ceramic method, followed by high-energy and low-energy ball-milling processes, which exhibited antimicrobial activity with negligible release of Ag + in deionized water. Here, we investigated thoroughly the mode of action of these AgNbO 3 NPs against Escherichia coli . Drastic morphological changes in E. coli were observed after their exposure to AgNbO 3 NPs. In addition to cellular damage, AgNbO 3 NPs induced the production of reactive oxygen species and lipid peroxidation, likely following the release of small amounts of Ag + . This was concluded from the characterization of mutants resistant to AgNbO 3 NPs that showed cross-resistance to AgNO 3 , impaired reactive oxygen species production and lipid peroxidation, and harbored a key mutation in a two-component regulatory system regulating an Ag + efflux pump. We calculated, however, that the quantity of Ag + released from AgNbO 3 NPs is not sufficient by itself to lead to bacterial death. We propose that bacterial contact with the AgNbO 3 NPs in combination with Ag + release is necessary for the mode of action of AgNbO 3 NPs.IMPORTANCESilver is known for its antibacterial activity, but its exact mode of action remains unclear. Here, we investigated thoroughly the mode of action of AgNbO 3 nanoparticles against Escherichia coli . Our data suggest that AgNbO 3 nanoparticles have dual effects on the cell and that both are required for its lethal action.

The morphological dynamics of microbial cell proliferation on an antimicrobial surface at an early growth stage was studied with Escherichia coli on the surface of a gel supplied with AgNbO3 antimicrobial particles. We demonstrated an inhibitory surface concentration, analogous to minimum inhibitory concentration, beyond which the growth of colonies and formation of biofilm are inhibited. In contrast, at lower concentrations of particles, after a lag time the cells circumvent the antimicrobial activity of the particles and grow with a rate similar to the case in the absence of particles. The lag time depends on the surface concentration of the particles and amounts to 2 h at a concentration of ½ minimum inhibitory concentration. The applicability of these findings, in terms of estimating inhibitory surface concentration, was tested in the case of antimicrobial polymethyl methacrylate (PMMA) bone cement., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Talebpour et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

We investigated the possibility of loading PMMA bone cement with antimicrobial nanostructured AgNbO 3 particles to counter biofilm formation at the cement-tissue interface. We found that a formulation containing (1-4)% AgNbO 3 showed high antibacterial activity against Gram-positive Staphylococcus aureus and Gram-negative Pseudomonas aeruginosa while not showing any toxicity against THP1 human cell lines. In addition, loading the particles did not impact the mechanical properties of the cement. The results thus obtained illustrate the potential of the approach to replace the current technique of mixing cement with conventional antibiotics, which is associated with shortcomings such as efficacy loss from antibiotic depletion.

Chimeric antigen receptor (CAR) T-cell therapy has emerged as a novel therapeutic option for hematologic malignancies. Human immunodeficiency virus (HIV) nucleic acid amplification tests (NAATs) amplifying 5' long terminal repeat and gag genes cross-react with lentiviral vector-based CAR T-cell products. Cross-reactivity between CAR T-cell products and HIV NAATs may lead to false-positive test results., Competing Interests: Potential conflicts of interest. All authors: No reported conflicts., (© The Author(s) 2023. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Background: Restrictive lung disease leading to abnormal lung function in kidney transplant recipients is commonly associated with noninfectious complications or medications used for post-transplant immunosuppression. Herein, we report an interesting case of pediatric kidney transplant recipient with weight loss and abnormal spirometry who was diagnosed to have late-onset Pneumocystis pneumonia., Case Report: A 17-year-old male patient with a history of allergic rhinitis, mild persistent asthma, and deceased donor kidney transplant, performed 18 months prior, presented for routine evaluation of his asthma to the pulmonology clinic. He was clinically asymptomatic except for a weight loss of 8 kg over 6-month period prior to presentation. Patient's spirometry was suggestive of a restrictive pattern and further investigation using a high-resolution computed tomography (HRCT) of the chest showed bilateral diffuse ground-glass reticulonodular opacities with subpleural sparing suggestive of interstitial pneumonitis. A bronchoscopy with bronchoalveolar lavage revealed organisms consistent with Pneumocystis jirovecii on gomori-methenamine-silver (GMS) staining. Beta-d-glucan testing in serum revealed a level of >500 pg/mL (normal 0-59 pg/mL) further supportive of Pneumocystis jirovecii infection. Patient was treated with a 6-week course of trimethoprim-sulfamethoxazole. His weight loss and beta-d-glucan levels improved over a course of 6 months, and he continues to be on trimethoprim-sulfamethoxazole prophylaxis., Conclusion: Late-onset Pneumocystis jirovecii infection in kidney transplant recipients can have an atypical presentation. Treating physicians should consider PJP in the differential diagnosis of unexplained weight loss in pediatric kidney transplant recipients, especially those receiving a large cumulative burden of immunosuppression., (© 2023 Wiley Periodicals LLC.)

This study describes the clinical features, severity, and outcomes in children <5 years of age with respiratory syncytial virus (RSV) infection during an atypical summer surge during the coronavirus disease 2019 (COVID-19) pandemic. Although timing was uncharacteristic, clinical features and illness severity were representative of a typical RSV season. Co-infection with SARS-CoV-2 was low.

Objective: To assess the incidence rate of S. aureus colonization at baseline along with the mupirocin susceptibility (or resistance) rate in patients in a neonatal intensive care unit (NICU) and a pediatric intensive care unit (PICU) in conjunction with the implementation of universal decolonization as the standard of care., Design: Prospective cohort study., Setting: Children's Hospital of Michigan (CHM) inpatient intensive care units (ICUs)., Participants: Newly admitted pediatric patients to the CHM NICU or PICU aged between 1 day and ≤21 years., Interventions: Baseline and follow-up S. aureus screening cultures were obtained before patients underwent universal decolonization with mupirocin 2% antibiotic ointment (intranasal and umbilical) and chlorhexidine baths as standard of care to reduce CLABSI rates., Results: Baseline S. aureus colonization rates of new admissions to the CHM NICU and PICU were high at 32% and 29%, respectively. Baseline mupirocin susceptibility to any S. aureus growth was 98.4%. All baseline culture isolates whether positive for MRSA or MSSA, with one exception, had minimum inhibitory concentrations (MICs) of ≤0.19 µg/mL. All follow-up study cultures after universal decolonization at 7 days or beyond with any S. aureus growth had mupirocin MICs of ≤0.125 µg/mL., Conclusions: Baseline S. aureus colonization rates of new admissions to the CHM ICUs were high as was baseline mupirocin susceptibility. Follow-up cultures, albeit limited in number, did not detect increasing mupirocin MICs over 1 year, despite broad mupirocin exposure due to the implementation of universal decolonization.

Central line associated blood stream infections (CLABSIs) in infants and children with intestinal failure due to short bowel syndrome may be caused by different organisms due to intestinal translocation and skin contamination. We report what we believe the first case of candidemia in an infant with short bowel syndrome caused by the environmental yeast Candida sojae that was initially misidentified as Candida tropicalis . We discuss its possible sources including a central venous catheter (CVC) and gut translocation and the differences between the two Candida species., Competing Interests: The authors report no conflict of interest., (© 2022 The Authors.)

We report our clinical and laboratory experience treating a 50-year-old patient who was critically ill with extensively drug-resistant Acinetobacter baumannii necrotizing pneumonia complicated by empyema in Detroit, Michigan. A precision medicine approach using whole-genome sequencing, susceptibility testing, and synergy analysis guided the selection of rational combination antimicrobial therapy., (© The Author(s) 2022. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Campylobacter commonly causes foodborne infections and antibiotic resistance is an imminent concern. It is not clear, however, if the human gut 'resistome' is affected by Campylobacter during infection. Application of shotgun metagenomics on stools from 26 cases with Campylobacter infections and 44 healthy family members (controls) identified 406 unique antibiotic resistance genes (ARGs) representing 153 genes/operons, 40 mechanisms, and 18 classes. Cases had greater ARG richness (p < 0.0001) and Shannon diversity (p < 0.0001) than controls with distinct compositions (p = 0.000999; PERMANOVA). Cases were defined by multidrug resistance genes and were dominated by Proteobacteria (40.8%), specifically those representing Escherichia (20.9%). Tetracycline resistance genes were most abundant in controls, which were dominated by Bacteroidetes (45.3%) and Firmicutes (44.4%). Hierarchical clustering of cases identified three clusters with distinct resistomes. Case clusters 1 and 3 differed from controls containing more urban and hospitalized patients. Relative to family members of the same household, ARG composition among matched cases was mostly distinct, though some familial controls had similar profiles that could be explained by a shorter time since exposure to the case. Together, these data indicate that Campylobacter infection is associated with an altered resistome composition and increased ARG diversity, raising concerns about the role of infection in the spread of resistance determinants., (© 2021. The Author(s).)

Background: Hospitalization of patients infected with the severe acute respiratory syndrome virus 2 (SARS-CoV-2) have remained considerable worldwide. Patients often develop severe complications and have high mortality rates. The cycle threshold (Ct) value derived from nasopharyngeal swab samples using real time polymerase chain reaction (RT-PCR) may be a useful prognostic marker in hospitalized patients with SARS-CoV-2 infection, however, its role in predicting the course of the pandemic has not been evaluated thus far., Methods: We conducted a retrospective cohort study which included all patients who had a nasopharyngeal sample positive for SARS-CoV-2 between April 4 -June 5, 2020. The Ct value was used to estimate the number of viral particles in a patient sample. The trend in initial viral load on admission on a population level was evaluated. Moreover, patient characteristics and outcomes stratified by viral load categories were compared and initial viral load was assessed as an independent predictor of intubation and in-hospital mortality., Results: A total of 461 hospitalized patients met the inclusion criteria. This study consisted predominantly of acutely infected patients with a median of 4 days since symptom onset to PCR. As the severity of the pandemic eased, there was an increase in the percentage of samples in the low initial viral load category, coinciding with a decrease in deaths. Compared to an initial low viral load, a high initial viral load was an independent predictor of in-hospital mortality (OR 5.5, CI 3.1-9.7, p < 0.001) and intubation (OR 1.82 CI 1.07-3.11, p = 0.03), while an initial intermediate viral load was associated with increased risk of inpatient mortality (OR 1.9, CI 1.14-3.21, p = 0.015) but not with increased risk for intubation., Conclusion: The Ct value obtained from nasopharyngeal samples of hospitalized patients on admission may serve as a prognostic marker at an individual level and may help predict the course of the pandemic when evaluated at a population level., Competing Interests: The authors have declared that no competing interests exist.

Bacteremia can progress to septic shock and death without appropriate medical intervention. Increasing evidence supports the role of molecular diagnostic panels in reducing the clinical impact of these infections through rapid identification of the infecting organism and associated antimicrobial resistance genes. We report the results of a multicenter clinical study assessing the performance of the GenMark Dx ePlex investigational-use-only blood culture identification Gram-negative panel (BCID-GN), a rapid diagnostic assay for detection of bloodstream pathogens in positive blood culture (PBC) bottles. Prospective, retrospective, and contrived samples were tested. Results from the BCID-GN were compared to standard-of-care bacterial identification methods. Antimicrobial resistance genes (ARGs) were identified using PCR and sequence analysis. The final BCID-GN analysis included 2,444 PBC samples, of which 926 were clinical samples with negative Gram stain results. Of these, 109 samples had false-negative and/or -positive results, resulting in an overall sample accuracy of 88.2% (817/926). After discordant resolution, overall sample accuracy increased to 92.9% (860/926). Pre- and postdiscordant resolution sample accuracy excludes 37 Gram-negative organisms representing 20 uncommon genera, 10 Gram-positive organisms, and 1 Candida species present in 5% of samples that are not targeted by the BCID-GN. The overall weighted positive percent agreement (PPA), which averages the individual PPAs from the 27 targets (Gram-negative and ARG), was 94.9%. The limit of detection ranged from 10 4 to 10 7 CFU/ml, except for one strain of Fusobacterium necrophorum at 10 8 CFU/ml.

Campylobacter jejuni is the leading cause of bacterial gastroenteritis and antibiotic resistant C. jejuni are a serious threat to public health. Herein, we sought to evaluate trends in C. jejuni infections, quantify resistance frequencies, and identify epidemiological factors associated with infection. Campylobacter jejuni isolates ( n = 214) were collected from patients via an active surveillance system at four metropolitan hospitals in Michigan between 2011 and 2014. The minimum inhibitory concentration for nine antibiotics was determined using microbroth dilution, while demographic and clinical data were used for the univariate and multivariate analyses. Over the 4-year period, a significant increase in the recovery of C. jejuni was observed ( p ≤ 0.0001). Differences in infection rates were observed by hospital and several factors were linked to more severe disease. Patients residing in urban areas, for instance, were significantly more likely to be hospitalized than rural residents as were patients over 40 years of age and those self-identifying as non-White, highlighting potential disparities in disease outcomes. Among the 214 C. jejuni isolates, 135 (63.1%) were resistant to at least one antibiotic. Resistance was observed for all nine antibiotics tested yielding 11 distinct resistance phenotypes. Tetracycline resistance predominated ( n = 120; 56.1%) followed by resistance to ciprofloxacin ( n = 49; 22.9%), which increased from 15.6% in 2011 to 25.0% in 2014. Resistance to two antibiotic classes was observed in 38 (17.8%) isolates, while multidrug resistance, or resistance to three or more classes, was observed in four (1.9%). Notably, patients with ciprofloxacin resistant infections were more likely to report traveling in the past month (Odds Ratio (OR): 3.0; 95% confidence interval (CI): 1.37, 6.68) and international travel (OR: 9.8; 95% CI: 3.69, 26.09). Relative to patients with only tetracycline resistant infections, those with ciprofloxacin resistance were more likely to travel internationally, be hospitalized and have an infection during the fall or summer. Together, these findings show increasing rates of infection and resistance and highlight specific factors that impact both outcomes. Enhancing understanding of factors linked to C. jejuni resistance and more severe infections is critical for disease prevention, particularly since many clinical laboratories have switched to the use of culture-independent tests for the detection of Campylobacter ., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Rodrigues, Cha, Mosci, Mukherjee, Newton, Lephart, Salimnia, Khalife, Rudrik and Manning.)

Background . The COVID-19 pandemic has shed light on communities of racial/ethnic minority groups in the US where long-standing health issues and structural inequities are now known to have resulted in increased risk for infection, severe illness, and death from the virus. The objective of our study was to describe demographic characteristics, clinical presentations, medical interventions and outcomes of pediatric patients with COVID-19 treated at Children's Hospital of Michigan (CHM), a tertiary care center in urban Detroit, an early hotspot during the initial surge of the SARS-CoV-2 pandemic. Methods. A retrospective chart review was performed of children ≤18 years of age who had polymerase chain reaction (RT-PCR) testing via NP swab or serum IgG antibody testing for SARS-CoV-2 during March 1, 2020-June 30, 2020. Results. Seventy-eight COVID-19 infected children were identified of whom 85.8% (67/78) were from minority populations (African American, Hispanic). Hospitalization rate was 82% (64/78). About 44% (34/78) had an associated comorbidity with asthma and obesity being most common. Although all ages were affected, infants <1 year of age had the highest hospitalization rate (19/64, 30%). In all disease severity categories, dichotomized non-whites had more severe disease by percentage within race/ethnicity than Whites, and also within percent disease severity ( P -value = .197). Overall, 37% of hospitalized patients required intensive care. Conclusions. Extremely high rates of COVID-19 hospitalization and requirement of ICU care were identified in our patient population. Further studies are needed to better understand the contributing factors to this health disparity in disadvantaged communities., Competing Interests: Declaration of Conflicting Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article., (© The Author(s) 2021.)

Background: The protection against aerosol transmission provided by masks vs face shields or in combination when speaking indoors is not well understood., Methods: To simulate a human source, an aerosol generating system was made using a bacterial suspension in a nebulizer attached to an oxygen cylinder. A fan connected to the nebulizer created aerosols. Transmitted aerosols were detected using blood agar plates at 0.1524 and 1.8288 meters from source, simulating exposed person. The study was performed under controlled conditions at room temperature in a biohazard hood with high-efficiency particulate air (HEPA) filter and UV light., Results: When face shields were used alone, significant numbers of bacterial colonies grew on blood agar plates. When a mask used alone for both the subjects (source and exposed), the blood agar yielded minimal colony forming units at both distances. When face shields were used in combination with masks, no significant improvement was observed as compared to masks alone., Discussion: Our results were similar to what have been observed in related studies., Conclusions: Surgical masks alone provided good protection, surpassing the protection provided by face shields alone. Both used together provided the best protection, although the combined protection was similar to surgical masks use alone., (Copyright © 2021 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.)

Staphylococcus pettenkoferi (S.pettenkoferi), originally described in Germany in 2002 by Trülzsch et al, is a coagulase negative staphylococcus whose clinical relevance is yet to be determined. With about 10 case reports in the literature from several parts of the world, there is no data on S. pettenkoferi infection from the United States. This is a retrospective cohort study of 80 patients ≥ 18 years of age who had at least 1 S. pettenkoferi-positive blood culture, identified by matrix-assisted laser desorption/ionization time-of-flight at a tertiary academic center in Detroit, Michigan. We describe the features of S. pettenkoferi-positive blood cultures in order to identify cases of true bacteremia. The mean age of the cohort was 66 ± 16 years and 1 out of 3 had immunosuppressing conditions. No case of true S.pettenkoferi bacteremia was identified. More studies are needed to determine its role as a pathogen in the United States., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Pooling of 1 positive sample with up to 5 negative samples prior to testing with the Cepheid GenXpert SARS-CoV-2 assay did not adversely impact detection of positive samples. At our current prevalence of 2%, it could save up to 70% of the test kits., (Copyright © 2020. Published by Elsevier Inc.)

Background: Bloodstream infections (BSIs) due to ceftriaxone (CRO)-resistant Enterobacteriaceae are associated with delays in time to appropriate therapy and worse outcomes compared with infections due to susceptible isolates. However, treating all at-risk patients with empiric carbapenem therapy risks overexposure. Strategies are needed to appropriately balance these competing interests. The purpose of this study was to compare 4 methods for achieving this balance., Methods: This was a retrospective hypothetical observational study of patients at the Detroit Medical Center with monomicrobial BSIs due to E. coli, K. oxytoca, K. pneumoniae, or P. mirabilis . This study compared the effectiveness of 4 methods to predict CRO resistance at the time of organism isolation. Three methods were based on applying published extended-spectrum beta-lactamase (ESBL) scoring tools. The fourth method was based on the presence or absence of the CTX-M marker from Verigene., Results: Four hundred fifty-one Enterobacteriaceae BSIs were included, 73 (16%) of which were CRO-resistant. Verigene accurately predicted ceftriaxone susceptibility for 97% of isolates, compared with 70%-81% using the scoring tools ( P  < .001). Verigene was associated with fewer cases of treatment with CRO when the isolate was CRO-resistant (15% vs 63%-71% with scoring tools) and fewer cases of overtreatment with a carbapenem for CRO-susceptible strains (0.3% vs 10%-12%)., Conclusions: Verigene significantly outperformed published ESBL scoring tools for identifying CRO-resistant Enterobacteriaceae BSI. Institutions should validate scoring tools before implementation. Stewardship programs should consider adoption of rapid diagnostic tests to optimize early therapy., (© The Author(s) 2020. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

Group A streptococcus (GAS) species cause bacterial pharyngitis in both adults and children. Early and accurate diagnosis of GAS is important for appropriate antibiotic therapy to prevent GAS sequalae. The Revogene Strep A molecular assay (Meridian Bioscience Canada Inc, Quebec City, QC, Canada) is an automated real-time PCR assay for GAS detection from throat swab specimens within approximately 70 min. This multicenter prospective study evaluated the performance of the Revogene Strep A molecular assay compared to that of bacterial culture. Dual throat swab specimens in either liquid Amies or Stuart medium were collected from eligible subjects (pediatric population and adults) enrolled across 7 sites (USA and Canada). Revogene Strep A and reference testing was performed within 7 days and 48 h of sample collection, respectively. Of the 604 evaluable specimens, GAS was detected in 154 (25.5%) samples by the reference method and in 175 (29%) samples by the Revogene Strep A assay. Revogene Strep A assay sensitivity and specificity were reported to be 98.1% (95% confidence interval [CI], 94.4 to 99.3) and 94.7% (95% CI, 92.2 to 96.4), respectively. The positive predictive value was 86.3% (95% CI, 80.4 to 90.6), negative predictive value was 99.3% (95% CI, 98.0 to 99.8) with a 1.0% invalid rate. Discrepant analysis with alternative PCR/bidirectional sequencing was performed for 24 false-positive (FP) and 3 false-negative (FN) specimens. Concordant results were reported for 17 (FP only) of 27 discordant specimens. The Revogene Strep A assay had high sensitivity and specificity for GAS detection and provides a faster alternative for GAS diagnosis., (Copyright © 2020 Banerjee et al.)

Background : Clostridium difficile (CD) is often classified as a healthcare-associated infection (HAI) and a hospital-acquired condition (HAC) in the hospital setting. However, pediatric oncology patients comprise a significant portion of Clostridium difficile infections (CDI), with hematopoietic stem cell transplant (HSCT) recipients constituting a major subset of this group due to unique, non-modifiable risk factors. We evaluated patterns of clostridium difficile infections at our institution to provide an accurate evaluation of the vulnerability of pediatric oncology and HSCT patients to clostridium difficile infections in comparison to the general pediatric population and underscore the non-tenability of classifying clostridium difficile infections as a hospital-acquired condition in HSCT patients. Methods : Single-center retrospective review of all clostridium difficile stool tests performed over an 11-year period; data analyzed and statistical comparisons performed between patient groups. Results : 5271 total samples were obtained during the study time period from 3127 patients. At least one positive test result was found in 18.6% of patients. Oncology and HSCT patients (38.2%) were more likely to have a positive test result than hematology (17.5%) and other patients (16.8%) ( p  < 0.001). Sixty-percent of patients who underwent HSCT were tested during this time frame. Of those, 39.3% had a positive test result and 48.5% of those patients went on to have a subsequent infection that met the criteria to be defined as recurrent. Conclusions : The high incidence rate and frequency of recurrence underscores the current near-inevitable nature of clostridium difficile infections in oncology and HSCT patients. We conclude that a blanket designation of clostridium difficile infections as an hospital-acquired condition is therefore questionable in this population.

Clostridioides difficile is the leading cause of diarrhea in hospitalized U.S. patients and results in over 400,000 cases of C. difficile infection per year. C. difficile infections have mortality rates of 6 to 30% and significantly increase health care costs, because of increased length of stay and increased frequency of readmissions due to recurrences. Efforts to reduce the spread of C. difficile in hospitals have led to the development of rapid sensitive diagnostic methods. A multicenter study was performed to establish the performance characteristics of the Revogene C. difficile test (Meridian Bioscience, Cincinnati, OH, USA) for use in detection of the toxin B ( tcdB ) gene from toxigenic C. difficile The Revogene instrument is a new molecular platform that uses real-time PCR to detect nucleic acids in up to 8 specimens at a time. A total of 2,461 specimens from symptomatic patients that had been submitted for C. difficile testing were enrolled at 7 sites throughout the United States and Canada for evaluation of the assay. Each stool specimen was tested for the presence of the tcdB gene using the Revogene C. difficile test, and results were compared with those of the reference method, a combination of direct and enriched culture methods. Overall, the Revogene C. difficile test demonstrated a sensitivity of 85.0% (95% confidence interval, 80% to 88%) and a specificity of 97.2% (95% confidence interval, 96% to 98%). The Revogene C. difficile test, using clinical stool specimens for detection of tcdB in C. difficile , demonstrated acceptable sensitivity and specificity, with a short turnaround time., (Copyright © 2020 Mashock et al.)

Non-typhoidal Salmonella (NTS) are important enteric pathogens causing over 1 million foodborne illnesses in the U.S. annually. The widespread emergence of antibiotic resistance in NTS isolates has limited the availability of antibiotics that can be used for therapy. Since Michigan is not part of the FoodNet surveillance system, few studies have quantified antibiotic resistance frequencies and identified risk factors for NTS infections in the state. We obtained 198 clinical NTS isolates via active surveillance at four Michigan hospitals from 2011 to 2014 for classification of serovars and susceptibility to 24 antibiotics using broth microdilution. The 198 isolates belonged to 35 different serovars with Enteritidis (36.9%) predominating followed by Typhimurium (19.5%) and Newport (9.7%), though the proportion of each varied by year, residence, and season. The number of Enteritidis and Typhimurium cases was higher in the summer, while Enteritidis cases were significantly more common among urban vs. rural residents. A total of 30 (15.2%) NTS isolates were resistant to ≥1 antibiotic and 15 (7.5%) were resistant to ≥3 antimicrobial classes; a significantly greater proportion of Typhimurium isolates were resistant compared to Enteritidis isolates and an increasing trend in the frequency of tetracycline resistance and multidrug resistance was observed over the 4-year period. Resistant infections were associated with longer hospital stays as the mean stay was 5.9 days for patients with resistant isolates relative to 4.0 days for patients infected with susceptible isolates. Multinomial logistic regression indicated that infection with serovars other than Enteritidis [Odds ratio (OR): 3.8, 95% confidence interval (CI): 1.23-11.82] as well as infection during the fall (OR: 3.0; 95% CI: 1.22-7.60) were independently associated with resistance. Together, these findings demonstrate the importance of surveillance, monitoring resistance frequencies, and identifying risk factors that can aid in the development of new prevention strategies., (Copyright © 2019 Mukherjee, Anderson, Mosci, Newton, Lephart, Salimnia, Khalife, Rudrik and Manning.)

Background: We noted a recent increase in cases of urinary tract infection due to community-acquired ESBL-producing Escherichia coli in children treated at our institution. Risk factors of urinary tract infection due to ESBL-producing E. coli in children in the USA remain unclear. Methods: A single center retrospective case control study of UTI due to CA-ESBL-producing E. coli during a 5-year period (2012-2016). Control cases with non-ESBL-producing E. coli urinary tract infection were matched by age, gender and year of infection. Results: A total of 111 patients with ESBL-producing E coli urinary tract infection and 103 controls were included. The proportion of ESBL-producing E coli urinary tract infection ranged from 7% to 15% of all UTI cases. The distribution of ESBL cases per year: 27 in 2012; 18 in 2013; 22 in 2014; 15 in 2015 and 29 in 2016. Median age was 4 years with female predominance (84%). The ESBL group was predominantly African American (32%) followed by individuals of Middle Eastern ethnic background (31%). Risk factors by univariate analysis were vesicoureteral reflux: (20.9 ESBL group vs 6% controls; p  = .002), prior antibiotic usage in the last 3 months (including β-lactams), prior UTI (last 3 months), recent hospitalization (last 3 months) and Middle Eastern ethnic background. However, multivariate analysis showed that only prior antibiotic usage ( p  = .001) and Middle Eastern ethnic background ( p  < .001) were independent risk factors. ESBL-producing strains were more frequently resistant to trimethoprim-sulfamethoxazole (72% vs 25%) and ciprofloxacin (73% vs 5%) than strains not producing ESBL. Conclusion: Risk factors for community-acquired ESBL-producing E coli urinary tract in our pediatric patient population were antibiotic usage within the previous 3 months and Middle Eastern ethnic background. This may be related to increased risk of intestinal colonization with resistant bacterial strains.

Non-O1, non-O139 Vibrio cholerae (NOVC) are genetically diverse strains that are generally non-pathogenic in healthy hosts. In immunocompromised patients or those with liver disease, NOVC have been shown to cause gastroenteritis, wound infections or sepsis and are often associated with high mortality rates. We report a case of a patient with liver cirrhosis and chronic venous insufficiency who was found to have NOVC bacteremia. The patient had recently visited Florida, USA but had no seafood consumption or exposure to aquatic environments. The patient was managed with antimicrobials, with a favorable outcome.

Strategies are needed to improve time to optimal therapy in patients with bloodstream infections (BSI) due to resistant Gram-negative (GN) pathogens. Accelerate Pheno (ACC) can provide antimicrobial susceptibility results within 7 h of a positive culture and may more rapidly optimize therapy. The primary objective of this study was to evaluate the hypothetical impact of ACC on time to effective therapy (TTET) and time to definitive therapy (TTDT) among patients with BSI due to resistant GN pathogens. ACC was performed on resistant GN BSI isolates, and results were not available to clinicians in real time. A potential benefit of having ACC on TTET or TTDT was determined if modifications to antimicrobial regimens could have been made sooner with ACC. Comparisons on the impact of ACC in the presence or absence of testing by the Verigene Gram-negative blood culture test (Verigene GN-BC) were performed. Sixty-one patients with resistant GN BSI were evaluated. The median actual TTET and TTDT in the cohort were 25.9 h (interquartile range [IQR], 18.5, 42.1) and 47.6 h (IQR, 24.9, 79.6), respectively. Almost half of the patients had potential improvement in TTET and/or TTDT with ACC. In patients who would have had a benefit the median potential decreases in TTET and TTDT were 16.6 h (IQR, 5.5 to 30.6) and 29.8 h (IQR, 13.6 to 43), respectively. The largest potential improvements were seen in patients for whom Verigene results were not available. In conclusion, among patients with resistant GN BSI in a setting where other rapid diagnostic technologies are utilized, ACC results could have further improved TTET and TTDT., (Copyright © 2019 American Society for Microbiology.)

Background: Rapid organism identification and antimicrobial susceptibility testing (AST) can optimize antimicrobial therapy in patients with bacteraemia. The Accelerate Pheno™ system (ACC) can provide identification and AST results within 7 h of a positive culture., Objectives: To assess the hypothetical impact of ACC on time to effective therapy (TTET), time to definitive therapy (TTDT) and antimicrobial usage at the Detroit Medical Center (DMC)., Methods: Patients with positive blood cultures from 29 March to 24 June 2016 were included. ACC was performed in parallel with normal laboratory procedures, but results were not made available to the clinicians. The potential benefit of having ACC results was determined if clinicians modified therapy based on actual AST results. Potential changes in TTET, TTDT and antibiotic usage were calculated., Results: One hundred and sixty-seven patients were included. The median TTET was 2.4 h (IQR 0.5, 15.1). Had ACC results been available, TTET could have been improved in four patients (2.4%), by a median decrease of 18.9 h (IQR 11.3, 20.4). The median TTDT was 41.4 h (IQR 21.7, 73.3) and ACC results could have improved TTDT among 51 patients (30.5%), by a median decrease of 25.4 h (IQR 18.7, 37.5). ACC implementation could have led to decreases in usage of cefepime (16% reduction), aminoglycosides (23%), piperacillin/tazobactam (8%) and vancomycin (4%)., Conclusions: ACC results could potentially improve time to de-escalation and reduce use of antimicrobials. The impact of ACC on TTET was small, likely related to the availability of other rapid diagnostic tests at DMC.

Background: Health care and public health professionals rely on accurate, real-time monitoring of infectious diseases for outbreak preparedness and response. Early detection of outbreaks is improved by systems that are comprehensive and specific with respect to the pathogen but are rapid in reporting the data. It has proven difficult to implement these requirements on a large scale while maintaining patient privacy., Objective: The aim of this study was to demonstrate the automated export, aggregation, and analysis of infectious disease diagnostic test results from clinical laboratories across the United States in a manner that protects patient confidentiality. We hypothesized that such a system could aid in monitoring the seasonal occurrence of respiratory pathogens and may have advantages with regard to scope and ease of reporting compared with existing surveillance systems., Methods: We describe a system, BioFire Syndromic Trends, for rapid disease reporting that is syndrome-based but pathogen-specific. Deidentified patient test results from the BioFire FilmArray multiplex molecular diagnostic system are sent directly to a cloud database. Summaries of these data are displayed in near real time on the Syndromic Trends public website. We studied this dataset for the prevalence, seasonality, and coinfections of the 20 respiratory pathogens detected in over 362,000 patient samples acquired as a standard-of-care testing over the last 4 years from 20 clinical laboratories in the United States., Results: The majority of pathogens show influenza-like seasonality, rhinovirus has fall and spring peaks, and adenovirus and the bacterial pathogens show constant detection over the year. The dataset can also be considered in an ecological framework; the viruses and bacteria detected by this test are parasites of a host (the human patient). Interestingly, the rate of pathogen codetections, on average 7.94% (28,741/362,101), matches predictions based on the relative abundance of organisms present., Conclusions: Syndromic Trends preserves patient privacy by removing or obfuscating patient identifiers while still collecting much useful information about the bacterial and viral pathogens that they harbor. Test results are uploaded to the database within a few hours of completion compared with delays of up to 10 days for other diagnostic-based reporting systems. This work shows that the barriers to establishing epidemiology systems are no longer scientific and technical but rather administrative, involving questions of patient privacy and data ownership. We have demonstrated here that these barriers can be overcome. This first look at the resulting data stream suggests that Syndromic Trends will be able to provide high-resolution analysis of circulating respiratory pathogens and may aid in the detection of new outbreaks., (©Lindsay Meyers, Christine C Ginocchio, Aimie N Faucett, Frederick S Nolte, Per H Gesteland, Amy Leber, Diane Janowiak, Virginia Donovan, Jennifer Dien Bard, Silvia Spitzer, Kathleen A Stellrecht, Hossein Salimnia, Rangaraj Selvarangan, Stefan Juretschko, Judy A Daly, Jeremy C Wallentine, Kristy Lindsey, Franklin Moore, Sharon L Reed, Maria Aguero-Rosenfeld, Paul D Fey, Gregory A Storch, Steve J Melnick, Christine C Robinson, Jennifer F Meredith, Camille V Cook, Robert K Nelson, Jay D Jones, Samuel V Scarpino, Benjamin M Althouse, Kirk M Ririe, Bradley A Malin, Mark A Poritz. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 06.07.2018.)

Molecular biological techniques have evolved expeditiously and in turn have been applied to the detection of infectious disease. Maturation of these technologies and their coupling with related technological advancement in fluorescence, electronics, digitization, nanodynamics, and sensors among others have afforded clinical medicine additional tools toward expedient identification of infectious organisms at concentrations and sensitivities previously unattainable. These advancements have been adapted in select settings toward addressing clinical demands for more timely and effective patient management., (Copyright © 2018 Elsevier Inc. All rights reserved.)

Rapid diagnostic tests (RDTs) have revolutionized the management of Gram-negative bacteremia by allowing antimicrobial stewardship teams the ability to escalate therapy and improve patient outcomes through timely organism identification and detection of certain resistance determinants. However, given the complex nature of Gram-negative resistance, stewardship teams are left without clear direction for how to respond when resistance determinants are absent, as the safety of de-escalation in this setting is unknown. The primary purpose of this analysis was to determine the negative predictive values (NPVs) of resistance marker absence for predicting susceptibility in target bug-drug scenarios at two geographically distinct institutions. A total of 1,046 Gram-negative bloodstream isolates that were analyzed with the Verigene BC-GN platform were assessed. Except for Pseudomonas aeruginosa , the absence of resistance determinants as reported by the RDT largely predicted susceptibility to target antibiotics at both institutions. NPVs for ceftriaxone susceptibility in Escherichia coli and Klebsiella pneumoniae in the absence of either CTX-M or a carbapenemase gene were 98% and 93 to 94%, respectively. Similar results were seen with other target bug-drug scenarios, with NPVs of 94 to 100% demonstrated at both institutions, with the exception of P. aeruginosa , for which NPVs were poor, likely due to the more complex nature of resistance in this pathogen. The results of this study show that clinicians at both institutions should have confidence in de-escalation in the absence of resistance determinant detection by Verigene BC-GN testing, and the methodology described within this article can serve as a blueprint for other stewardship programs to employ at their institutions to optimize management of Gram-negative bacteremia., (Copyright © 2018 American Society for Microbiology.)

FilmArray Meningitis/Encephalitis (ME) polymerase chain reaction (PCR) panel was tested on 62 cerebrospinal fluid (CSF) samples from young infants (0-3 months) with suspected meningitis and compared with CSF cultures. Twelve CSF samples from 9 infants were positive by ME PCR panel (10 Group B Streptococcus (GBS) and 2 Escherichia coli) of which only 5 were positive by culture. The 7 CSF samples that were positive only by ME PCR panel were obtained from infants who had received prior antibiotic treatment. The ME PCR panel can be a useful tool in the rapid diagnosis of bacterial meningitis in pretreated young infants.

Rapid diagnosis and treatment of infectious meningitis and encephalitis are critical to minimize morbidity and mortality. Comprehensive testing of cerebrospinal fluid (CSF) often includes Gram stain, culture, antigen detection, and molecular methods, paired with chemical and cellular analyses. These methods may lack sensitivity or specificity, can take several days, and require significant volume for complete analysis. The FilmArray Meningitis/Encephalitis (ME) Panel is a multiplexed in vitro diagnostic test for the simultaneous, rapid (∼1-h) detection of 14 pathogens directly from CSF specimens: Escherichia coli K1, Haemophilus influenzae, Listeria monocytogenes, Neisseria meningitidis, Streptococcus pneumoniae, Streptococcus agalactiae, cytomegalovirus, enterovirus, herpes simplex virus 1 and 2, human herpesvirus 6, human parechovirus, varicella-zoster virus, and Cryptococcus neoformans/Cryptococcus gattii We describe a multicenter evaluation of 1,560 prospectively collected CSF specimens with performance compared to culture (bacterial analytes) and PCR (all other analytes). The FilmArray ME Panel demonstrated a sensitivity or positive percentage of agreement of 100% for 9 of 14 analytes. Enterovirus and human herpesvirus type 6 had agreements of 95.7% and 85.7%, and L. monocytogenes and N. meningitidis were not observed in the study. For S. agalactiae, there was a single false-positive and false-negative result each, for a sensitivity and specificity of 0 and 99.9%, respectively. The specificity or negative percentage of agreement was 99.2% or greater for all other analytes. The FilmArray ME Panel is a sensitive and specific test to aid in diagnosis of ME. With use of this comprehensive and rapid test, improved patient outcomes and antimicrobial stewardship are anticipated., (Copyright © 2016, American Society for Microbiology. All Rights Reserved.)

After a sharp drop of rotavirus (RV) infections at Children's Hospital of Michigan, Detroit, USA in 2010 season, we noted an increase in the number of cases during the 2011 season including some RV vaccine (RVV) recipients. This study was conducted to determine the circulating genotypes during 2011 season and whether the increase in RV diarrhea was caused by replacement genotypes. G and P genotypes were determined by RT PCR and nucleotide sequencing of selected strains was performed. The vaccination rate among study patients was 24 %. RV strains from 68 stool samples were genotyped including 18 from vaccinated children and 50 from unvaccinated children. The predominant G genotype was G1 (58.8 %) followed by G9 (17.7 %) and G4 (15.5 %). P[8] was the predominant P genotype (68 %) followed by P[6] (17.6 %) and P[4] (3 %). All G9 strains were associated with P[6]. The most prevalent G-P combination was G1P[8] (56 %), followed by G9P[6] (17.6 %). Similar proportions of RV genotypes were found among vaccinated and unvaccinated children. Our local data suggest that 5 years after the introduction of RVV there has been no genotype replacement. Although a small increase in G9P[6] frequency was noted, G1P[8] remained the predominant strain of RV in our inner city community in the Midwestern USA.

Campylobacter jejuni is a zoonotic pathogen and the most common bacterial cause of human gastroenteritis worldwide. With the increase of antibiotic resistance to fluoroquinolones and macrolides, the drugs of choice for treatment, C. jejuni was recently classified as a serious antimicrobial resistant threat. Here, we characterized 94 C. jejuni isolates collected from patients at four Michigan hospitals in 2011 and 2012 to determine the frequency of resistance and association with phylogenetic lineages. The prevalence of resistance to fluoroquinolones (19.1%) and macrolides (2.1%) in this subset of C. jejuni isolates from Michigan was similar to national reports. High frequencies of fluoroquinolone-resistant C. jejuni isolates, however, were recovered from patients with a history of foreign travel. A high proportion of these resistant isolates were classified as multilocus sequence type (ST)-464, a fluoroquinolone-resistant lineage that recently emerged in Europe. A significantly higher prevalence of tetracycline-resistant C. jejuni was also found in Michigan and resistant isolates were more likely to represent ST-982, which has been previously recovered from ruminants and the environment in the U.S. Notably, patients with tetracycline-resistant C. jejuni infections were more likely to have contact with cattle. These outcomes prompt the need to monitor the dissemination and diversification of imported fluoroquinolone-resistant C. jejuni strains and to investigate the molecular epidemiology of C. jejuni recovered from cattle and farm environments to guide mitigation strategies.

Sepsis is a major cause of morbidity, mortality, and increased medical expense. Rapid diagnosis improves outcomes and reduces costs. The FilmArray blood culture identification panel (BioFire Diagnostics LLC, Salt Lake City, UT), a highly multiplexed PCR assay, can identify 24 etiologic agents of sepsis (8 Gram-positive, 11 Gram-negative, and 5 yeast species) and three antimicrobial resistance genes (mecA, vanA/B, and blaKPC) from positive blood culture bottles. It provides results in about 1 h with 2 min for assay setup. We present the results of an eight-center trial comparing the sensitivity and specificity of the panel with those of the laboratories' standard phenotypic identification techniques, as well as with molecular methods used to distinguish Acinetobacter baumannii from other members of the A. calcoaceticus-A. baumannii complex and to detect antimicrobial resistance genes. Testing included 2,207 positive aerobic blood culture samples, 1,568 clinical and 639 seeded. Samples were tested fresh or were frozen for later testing within 8 h after the bottles were flagged as positive by an automated blood culture system. At least one organism was detected by the panel in 1,382 (88.1%) of the positive clinical specimens. The others contained primarily off-panel organisms. The panel reported multiple organisms in 81 (5.86%) positive clinical specimens. The unresolved blood culture identification sensitivity for all target detections exceeded 96%, except for Klebsiella oxytoca (92.2%), which achieved 98.3% sensitivity after resolution of an unavoidable phenotypic error. The sensitivity and specificity for vanA/B and blaKPC were 100%; those for mecA were 98.4 and 98.3%, respectively., (Copyright © 2016 Salimnia et al.)

Clostridium difficile is a leading cause of infectious diarrhea in hematopoietic stem cell transplant (HSCT) recipients. Asymptomatic colonization of the gastrointestinal tract occurs before development of C. difficile infection (CDI). This prospective study examines the rates, risk factors, and outcomes of colonization with toxigenic and nontoxigenic strains of C. difficile in HSCT patients. This 18-month study was conducted in the HSCT unit at the Karmanos Cancer Center and Wayne State University in Detroit. Stool samples from the patients who consented for the study were taken at admission and weekly until discharge. Anaerobic culture for C. difficile and identification of toxigenic strains by PCR were performed on the stool samples. Demographic information and clinical and laboratory data were collected. Of the 150 patients included in the study, 29% were colonized with C. difficile at admission; 12% with a toxigenic strain and 17% with a nontoxigenic strain. Over a 90-day follow-up, 12 of 44 (26%) patients colonized with any C. difficile strain at admission developed CDI compared with 13 of 106 (12%) of patients not colonized (odds ratio [OR], 2.70; 95% confidence interval [95% CI], 1.11 to 6.48; P = .025). Eleven of 18 (61%) patients colonized with the toxigenic strain and 1 of 26 (4%) of those colonized with nontoxigenic strain developed CDI (OR, 39.30; 95% CI, 4.30 to 359.0; P < .001) at a median of 12 days. On univariate and multivariate analyses, none of the traditional factors associated with high risk for C. difficile colonization or CDI were found to be significant. Recurrent CDI occurred in 28% of cases. Asymptomatic colonization with C. difficile at admission was high in our HSCT population. Colonization with toxigenic C. difficile was predictive of CDI, whereas colonization with a nontoxigenic C. difficile appeared protective. These findings may have implications for infection control strategies and for novel approaches for the prevention and preemptive treatment of CDI in the HSCT patient population., (Copyright © 2016 American Society for Blood and Marrow Transplantation. Published by Elsevier Inc. All rights reserved.)