Clinical Relevance of Pathogens Detected by Multiplex PCR in Blood of Very-Low-Birth Weight Infants with Suspected Sepsis - Multicentre Study of the German Neonatal Network

Use of Rapid Molecular Polymerase Chain Reaction in Early Detection of Bacteremia in Neonates Prior to Blood Culture Positivity: A Pilot Study

OBJECTIVE

 There has been national strive to decrease the time needed to identify microorganisms in blood culture samples to reduce antibiotic use. This study evaluated rapid molecular polymerase chain reaction (PCR) use in identifying microorganisms in negative culture bottles from neonates with suspected bacterial blood stream infection at 20 to 24 hours of incubation.

STUDY DESIGN

 All blood specimens from neonates with suspected blood stream infection were included. Specimens were incubated using a standard blood culturing instrument that would flag positive if bacterial growth was detected. If the specimen was flagged positive at <20 hours, it was tested by PCR and plated for identification as per standard protocol. In our design, if specimen was not flagged at 20 hours of incubation, the bottle was sterilely accessed and a sample was obtained for PCR testing. The bottle would be returned for incubation for 120 hours or until flagged positive.

RESULTS

 A total of 192 blood specimens were included. Four specimens flagged positive at <20 hours and were all found to be positive by PCR. All other samples did not flag positive by 20 hours of incubation and were tested by PCR between 20 and 24 hours. One sample tested positive via PCR at 21.6 hours then flagged positive on the culturing instrument at 23.5 hours. All other specimens were negative by PCR and remained culture negative at 120 hours. The positive and negative predictive value of PCR verified by blood culture were both equal to 1.0.

CONCLUSION

 Using rapid molecular PCR on blood culture specimens at 20 to 24 hours of incubation provides 100% true negative results possibly allowing providers to discontinue antibiotics at 24 hours.

KEY POINTS

· Antibiotic overuse leads to adverse neonatal outcomes.. · Molecular PCR may have true negative results.. · Larger study is needed to discontinue antibiotics earlier..

Diagnostic Accuracy of Multiplex Polymerase Chain Reaction in Early Onset Neonatal Sepsis

Early onset neonatal sepsis is a significant contributor to neonatal morbidity and mortality. Although blood cultures remain the diagnostic gold standard, they detect pathogens in only a minority of suspected cases. This study compared the accuracy of blood cultures with a rapid multiplex PCR test. Newborns at risk of neonatal sepsis were prospectively screened as recommended per national guidelines. Evaluations included laboratory parameters (CrP, IL6, differential blood count), blood culture, and a molecular multiplex PCR test (ROCHE LightCycler SeptiFast®) identifying 20 common microbial agents. Blood samples were taken simultaneously from umbilical cord or venous sources on the first day of life. Of 229 infants included, 69% were born preterm. Blood culture and multiplex PCR sensitivity were 7.4% and 14.8%, respectively. Specificity, negative and positive predictive values between methods showed no significant variance, although multiplex PCR had more false positives due to contamination. The limited sensitivity of blood cultures for early onset neonatal sepsis is concerning. Despite quicker results, multiplex PCR does not enhance diagnostic accuracy or antibiotic therapy guidance, thus it cannot be recommended for this indication.

Clinical Utility of the FilmArray® Blood Culture Identification (BCID) Panel for the Diagnosis of Neonatal Sepsis

This prospective single-center study was designed to assess the clinical utility of the FilmArray® blood culture identification (BCID) panel for improving the diagnostic accuracy in neonatal sepsis. Results obtained using the FilmArray® BCID panel were correlated with results of blood culture in all consecutive neonates with suspicion of early-onset (EOS) and late-onset sepsis (LOS) attended in our service over a two-year period. A total of 102 blood cultures from 92 neonates were included, 69 (67.5%) in cases of EOS and 33 (32.3%) in LOS. The FilmArray® BCID panel was performed in negative culture bottles at a median of 10 h of blood culture incubation (IQR 8–20), without differences by the type of sepsis. The FilmArray® BCID panel showed a 66.7% sensitivity, 100% specificity, 100% positive predictive value, and 95.7% negative predictive value. There were four false-negative cases, three of which were Streptococcus epidermidis in neonates with LOS, and there was one case of Granulicatella adiacens in one neonate with EOS. We conclude that the use of the FilmArray® BCID panel in negative blood cultures from neonates with clinical suspicion of sepsis is useful in decision-making of starting or early withdrawal of empirical antimicrobials because of the high specificity and negative predictive values of this assay.

Predicting treatment response to vancomycin using bacterial DNA load as a pharmacodynamic marker in premature and very low birth weight neonates: A population PKPD study

Background: While positive blood cultures are the gold standard for late-onset sepsis (LOS) diagnosis in premature and very low birth weight (VLBW) newborns, these results can take days, and early markers of possible treatment efficacy are lacking. The objective of the present study was to investigate whether the response to vancomycin could be quantified using bacterial DNA loads (BDLs) determined by real-time quantitative polymerase chain reaction (RT-qPCR). Methods: VLBW and premature neonates with suspected LOS were included in a prospective observational study. Serial blood samples were collected to measure BDL and vancomycin concentrations. BDLs were measured with RT-qPCR, whereas vancomycin concentrations were measured by LC-MS/MS. Population pharmacokinetic-pharmacodynamic modeling was performed with NONMEM. Results: Twenty-eight patients with LOS treated with vancomycin were included. A one-compartment model with post-menstrual age (PMA) and weight as covariates was used to describe the time PK profile of vancomycin concentrations. In 16 of these patients, time profiles of BDL could be described with a pharmacodynamic turnover model. The relationship between vancomycin concentration and first-order BDL elimination was described with a linear-effect model. Slope S increased with increasing PMA. In 12 patients, no decrease in BDL over time was observed, which corresponded with clinical non-response. Discussion: BDLs determined through RT-qPCR were adequately described with the developed population PKPD model, and treatment response to vancomycin using BDL in LOS can be assessed as early as 8 h after treatment initiation.

Transcriptome profiles discriminate between Gram-positive and Gram-negative sepsis in preterm neonates

BACKGROUND

Genome-wide expression profiles have been previously employed as clinical research diagnostic tools for newborn sepsis. We aimed to determine if transcriptomic profiles could discriminate between Gram-positive and Gram-negative bacterial sepsis in preterm infants.

METHODS

Prospective, observational, double-cohort study was conducted in very low birth weight infants with clinical signs and culture-positive sepsis. Blood samples were collected when clinical signs became apparent. Total RNA was processed for transcriptomic analysis. Results were validated by both reverse-transcription polymerase chain reaction and a mathematical model.

RESULTS

We included 25 septic preterm infants, 17 with Gram-positive and 8 with Gram-negative bacteria. The principal component analysis identified these two clusters of patients. We performed a predictive model based on 21 genes that showed an area under the receiver-operating characteristic curve of 1. Eight genes were overexpressed in Gram-positive septic infants: CD37, CSK, MAN2B2, MGAT1, MOB3A, MYO9B, SH2D3C, and TEP1. The most significantly overexpressed pathways were related to metabolic and immunomodulating responses that translated into an equilibrium between pro- and anti-inflammatory responses.

CONCLUSIONS

The transcriptomic profile allowed identification of whether the causative agent was Gram-positive or Gram-negative bacteria. The overexpression of genes such as CD37 and CSK, which control cytokine production and cell survival, could explain the better clinical outcome in sepsis caused by Gram-positive bacteria.

IMPACT

Transcriptomic profiles not only enable an early diagnosis of sepsis in very low birth weight infants but also discriminate between Gram-positive and Gram-negative bacteria as causative agents. The overexpression of some genes related to cytokine production and cell survival could explain the better clinical outcome in sepsis caused by Gram-positive bacteria, and could lead us to a future, targeted therapy.

Antibiotics in critically ill children-a narrative review on different aspects of a rational approach

Especially critically ill children are exposed to antibiotic overtreatment, mainly caused by the fear of missing out a severe bacterial infection. Potential adverse effects and selection of multi-drug resistant bacteria play minor roles in decision making. This narrative review first describes harm from antibiotics and second focuses on different aspects that could help to reduce antibiotic overtreatment without harming the patient: harm from antibiotic treatment, diagnostic approaches, role of biomarkers, timing of antibiotic therapy, empiric therapy, targeted therapy, and therapeutic drug monitoring. Wherever possible, we linked the described evidence to the current Surviving Sepsis Campaign guidelines. Antibiotic stewardship programs should help guiding antibiotic therapy for critically ill children. IMPACT: Critically ill children can be harmed by inadequate or overuse of antibiotics. Hemodynamically unstable children with a suspicion of infection should be immediately treated with broad-spectrum antibiotics. In contrast, in hemodynamically stable children with sepsis and organ dysfunction, a time frame of 3 h for proper diagnostics may be adequate before starting antibiotics if necessary. Less and more targeted antibiotic treatment can be achieved via antibiotic stewardship programs.

Infants Younger Than 90 Days Admitted for Late-Onset Sepsis Display a Reduced Abundance of Regulatory T Cells

Objective

To provide epidemiological data of infants < 90 days of age with suspected late-onset sepsis (LOS) and evaluate distinct immunological specificities. We hypothesized that previously healthy infants < 3 months of age with sepsis have a yet undefined immunological predisposition; e.g. differences in lymphocyte subsets including regulatory T cells.

Methods

We performed an exploratory, single center study between January 1^st, 2019 and June 1^st, 2021. Routine diagnostics included conventional culture (blood, cerebrospinal fluid, urine), PCR and inflammatory markers in infants < 90 days of age with suspected sepsis. We additionally analyzed lymphocyte subsets and CD4+ CD25+ forkhead box protein (FoxP3)⁺ Tregs at admission for sepsis workup as compared to age-matched controls.

Results

A convenience sample cohort of n= 51 infants with sepsis workup was enrolled. Invasive bacterial infection (IBI) was diagnosed in 25 (49.0%) patients including two infants with a rhinovirus co-infection and viral infection in 14 (27.5%) neonates. No infectious cause was found in 12 cases. Infants with suspected LOS displayed a decreased abundance of CD4+ FoxP3+ T cells as compared to controls, which was most pronounced in the subgroup of infants with IBI. We also noticed elevated HLA-DR-positive CD3+ cells in infants with LOS and a higher CD4/CD8-ratio in infants with viral infection as compared to healthy controls. Infants with viral infections had a higher number of natural killer cells as compared to infants with IBI.

Conclusion

Our exploratory data support the concept of a potential immaturity state and failed immune tolerance development for young infants with LOS. Future large-scale studies are needed to elucidate pre-sepsis conditions and to target the microbiome-immunity interplay as a potential risk pattern.

Role of microbiological tests and biomarkers in antibiotic stewardship

Laboratory tests are critical in the detection and timely treatment of infection. Two categories of tests are commonly used in neonatal sepsis management: those that identify the pathogen and those that detect host response to a potential pathogen. Decision-making around antibiotic choice is related to the performance of tests that directly identify pathogens. Advances in these tests hold the key to progress in antibiotic stewardship. Tests measuring host response, on the other hand, are an indirect marker of potential infection. While an important measure of the patient's clinical state, in the absence of pathogen detection these tests cannot confirm the appropriateness of antibiotic selection. The overall impact these tests then have on antibiotic utilization depends the test's specificity for bacterial infection, clinical scenario where it is being used and the decision-rule it is being integrated into for use. In this review we discuss common and emerging laboratory tests available for assisting management of neonatal infection and specifically focus on the role they play in optimizing antibiotic utilization.

Fast I(n)dentification of Pathogens in Neonates (FINDPATH-N): protocol for a prospective pilot cohort study of next-generation sequencing for pathogen identification in neonates with suspected sepsis

INTRODUCTION

Sepsis is a major source of morbidity and mortality in neonates; however, identification of the causative pathogens is challenging. Many neonates have negative blood cultures despite clinical evidence of sepsis. Next-generation sequencing (NGS) is a high-throughput, parallel sequencing technique for DNA. Pathogen-targeted enrichment followed by NGS has the potential to be more sensitive and faster than current gold-standard blood culture. In this pilot study, we will test the feasibility and pathogen detection patterns of pathogen-targeted NGS in neonates with suspected sepsis. Additionally, the distribution and diagnostic accuracy of biomarkers cell-free DNA and protein C levels at two time points will be explored.

METHODS AND ANALYSIS

We will conduct a prospective, pilot observational study. Neonates over 1 kg with suspected sepsis from a single tertiary care children's hospital will be recruited for the study. Recruitment will be censored at 200 events or 6 months' duration. Two blood study samples will be taken: the first simultaneous to the blood culture (time=0 hour, for NGS and biomarkers) via an exception to consent (deferred consent) and another 24 hours later after prospective consent (biomarkers only). Neonates will be adjudicated into those with clinical sepsis, culture-proven sepsis and without sepsis based on clinical criteria. Feasibility parameters (eg, recruitment) and NGS process time will be reported.For analysis, NGS results will be described in aggregate, compared with the simultaneous blood culture (sensitivity and specificity) and reviewed via expert panel for plausibility. Pilot data for biomarker distribution and diagnostic accuracy (sensitivity and specificity) for distinguishing between septic and non-septic neonates will be reported.

ETHICS AND DISSEMINATION

Ethics approval has been granted by the Hamilton Integrated Research Ethics Board. We will seek publication of study results in peer-reviewed journals.

[A clinical analysis of late-onset sepsis in very low birth weight and extremely low birth weight infants]

OBJECTIVE

To study the clinical features and pathogenic bacteria of late-onset sepsis (LOS) in very low birth weight (VLBW) and extremely low birth weight (ELBW) infants.

METHODS

Among the VLBW/ELBW infants with a gestational age of <32 weeks who were admitted to the hospital between January 2012 and December 2016, those with LOS were enrolled as the LOS group, and those without sepsis were matched for the infant with LOS in gestational age were enrolled as the control group. According to the presence or absence of in-hospital death, the LOS group was further divided into a death subgroup and a survival subgroup. Risk factors for LOS, clinical features, distribution of pathogenic bacteria, drug resistance, and high-risk factors for LOS-related death were analyzed.

RESULTS

A total of 513 VLBW/ELBW infants were enrolled, and there were 65 infants in the LOS group and 130 in the control group. The incidence rate of LOS was 12.7%. In the LOS group, 6 infants died and 59 survived. Compared with the control group, the LOS group had a significantly lower birth weight (P<0.05) and significantly longer indwelling time of peripherally inserted central catheter (PICC), duration of mechanical ventilation, and length of hospital stay (P<0.05). Compared with the control group, the LOS group had a significantly higher proportion of small-for-gestational-age infants, infants undergoing mechanical ventilation, infants with neonatal necrotizing enterocolitis, or infants who died (P<0.05). Low birth weight, small-for-gestational-age infant, and long indwelling time of PICC were independent risk factors for LOS in VLBW/ELBW infants (OR=1.396, 2.550, and 1.068 respectively, P<0.05). Purulent meningitis was an independent risk factor for LOS-related death in VLBW/ELBWIs infants (OR=13.443, P<0.05). A total of 65 strains of pathogenic bacteria were cultured in the LOS group, among which there were 39 strains (60%) of Gram-negative bacteria, including 15 strains producing extended spectrum beta-lactamases (ESBLs), and antibiotics were applied for 67% (10/15) of the ESBL strains within 2 weeks before the onset of LOS. The rate of antibiotic use for ESBL strains was significantly higher than that for non-resistant strains [67% (10/15) vs 29% (7/24); P<0.05].

CONCLUSIONS

Low birth weight, SGA infant, and long indwelling time of PICC are independent risk factors for LOS in VLBW/ELBW infants, and death tends to occur in LOS infants with purulent meningitis. Most pathogenic bacteria of LOS are Gram-negative bacteria, and use of antibiotics within 2 weeks before disease onset may increase the risk of ESBL strain infection.

[A clinical analysis of late-onset sepsis in very low birth weight and extremely low birth weight infants]

OBJECTIVE

To study the clinical features and pathogenic bacteria of late-onset sepsis (LOS) in very low birth weight (VLBW) and extremely low birth weight (ELBW) infants.

METHODS

Among the VLBW/ELBW infants with a gestational age of <32 weeks who were admitted to the hospital between January 2012 and December 2016, those with LOS were enrolled as the LOS group, and those without sepsis were matched for the infant with LOS in gestational age were enrolled as the control group. According to the presence or absence of in-hospital death, the LOS group was further divided into a death subgroup and a survival subgroup. Risk factors for LOS, clinical features, distribution of pathogenic bacteria, drug resistance, and high-risk factors for LOS-related death were analyzed.

RESULTS

A total of 513 VLBW/ELBW infants were enrolled, and there were 65 infants in the LOS group and 130 in the control group. The incidence rate of LOS was 12.7%. In the LOS group, 6 infants died and 59 survived. Compared with the control group, the LOS group had a significantly lower birth weight (P<0.05) and significantly longer indwelling time of peripherally inserted central catheter (PICC), duration of mechanical ventilation, and length of hospital stay (P<0.05). Compared with the control group, the LOS group had a significantly higher proportion of small-for-gestational-age infants, infants undergoing mechanical ventilation, infants with neonatal necrotizing enterocolitis, or infants who died (P<0.05). Low birth weight, small-for-gestational-age infant, and long indwelling time of PICC were independent risk factors for LOS in VLBW/ELBW infants (OR=1.396, 2.550, and 1.068 respectively, P<0.05). Purulent meningitis was an independent risk factor for LOS-related death in VLBW/ELBWIs infants (OR=13.443, P<0.05). A total of 65 strains of pathogenic bacteria were cultured in the LOS group, among which there were 39 strains (60%) of Gram-negative bacteria, including 15 strains producing extended spectrum beta-lactamases (ESBLs), and antibiotics were applied for 67% (10/15) of the ESBL strains within 2 weeks before the onset of LOS. The rate of antibiotic use for ESBL strains was significantly higher than that for non-resistant strains [67% (10/15) vs 29% (7/24); P<0.05].

CONCLUSIONS

Low birth weight, SGA infant, and long indwelling time of PICC are independent risk factors for LOS in VLBW/ELBW infants, and death tends to occur in LOS infants with purulent meningitis. Most pathogenic bacteria of LOS are Gram-negative bacteria, and use of antibiotics within 2 weeks before disease onset may increase the risk of ESBL strain infection.

Multiplex PCR of bronchoalveolar lavage fluid in children enhances the rate of pathogen detection

Background

Culturing of bronchoalveolar lavage (BAL) fluid is a commonly used method for pathogen detection in pneumonia. However, the sensitivity is low, especially in patients pre-treated with anti-infective agents. The early detection of a pathogen is crucial for the outcome of respiratory tract infections. For bloodstream infections, a multiplex polymerase chain reaction (PCR) assay (SeptiFast®, SF) is available for improved pathogen detection from blood.

Objective

The aim of the present study was to determine whether the SF assay is applicable to the BAL of children with pulmonary infections and whether the frequency of pathogen detection is enhanced by the use of this multiplex PCR method.

Methods

We investigated 70 BAL samples of 70 children simultaneously by culture and multiplex PCR. The frequency of pathogen detection was compared.

Results

Pathogens were detected more frequently by SF than by culture (83% vs. 31%; p < 0.001). This advantage was shown for immunocompetent patients (p = 0.001) as well as for immunocompromised patients (p = 0.003). The majority (38/44; 86%) of the Gram positive cocci were only detected by SF. Fungal organisms were detected in 7/70 patients (10%) by SF and in 2/70 (3%) by culture (p = 0.125).

Conclusion

Compared to conventional culture, the use of the SF assay on the BAL of children with pneumonia increases pathogen detection rates and therefore adds important information to guide anti-infective therapy.

Beyond sepsis: Staphylococcus epidermidis is an underestimated but significant contributor to neonatal morbidity

Staphylococcus epidermidis accounts for the majority of cases of neonatal sepsis. Moreover, it has been demonstrated to be associated with neonatal morbidities, such as bronchopulmonary dysplasia (BPD), white matter injury (WMI), necrotizing enterocolitis (NEC) and retinopathy of prematurity (ROP), which affect short-term and long-term neonatal outcome. Imbalanced inflammation has been considered to be a major underlying mechanism of each entity. Conventionally regarded as a harmless commensal on human skin, S. epidermidis has received less attention than its more virulent relative Staphylococcus aureus. Particularities of neonatal innate immunity and nosocomial environmental factors, however, may contribute to the emergence of S. epidermidis as a significant nosocomial pathogen. Neonatal host response to S. epidermidis sepsis has not been fully elucidated. Evidence is emerging regarding the implication of S. epidermidis sepsis in the pathogenesis of neonatal inflammatory diseases. This review focuses on the interplay among S. epidermidis, neonatal innate immunity and inflammation-driven organ injury.

Using anaerobic blood cultures for infants younger than 90 days rarely showed anaerobic infections but increased yields of bacterial growth

AIM

The use of anaerobic blood cultures in infants suspected of bacteraemia is controversial. Our children's hospital uses both aerobic and anaerobic media, regardless of the risk of anaerobic infection, and the aim of this study was to re-evaluate the use of anaerobic cultures in infants.

METHODS

We collected retrospective data from 2002 to 2016 on all blood cultures taken from infants younger than 90 days in the Hadassah-Hebrew University Medical Centre, Jerusalem, Israel. The incidence and characteristics of infants with positive anaerobic blood cultures were assessed.

RESULTS

During the study period, 51 035 blood cultures were drawn from 44 304 infants. Of these, 1496 (2.9%) were clinically significant positive cultures. Pathogenic obligatory anaerobic bacteraemia was extremely rare, with only 37 positive cultures (0.07%) from all of the cultures drawn. No specific risk factors for obligatory anaerobic bacteraemia could be defined, but as many as 174 (11.6%) clinically significant isolates were only detected in the anaerobic culture bottle.

CONCLUSION

True anaerobic bacteraemia was extremely rare in neonates. Nevertheless, using anaerobic culture media may increase the overall yield of bacterial culture growth by isolating anaerobic-facultative bacteria. This should be weighed up against increasing the volume of blood used for the aerobic culture.

Evaluation of a real-time PCR assay for detection and quantification of bacterial DNA directly in blood of preterm neonates with suspected late-onset sepsis

Background

Rapid and accurate diagnosis of neonatal sepsis is highly warranted because of high associated morbidity and mortality. The aim of this study was to evaluate the performance of a novel multiplex PCR assay for diagnosis of late-onset sepsis and to investigate the value of bacterial DNA load (BDL) determination as a measure of infection severity.

Methods

This cross-sectional study was conducted in a neonatal intensive care unit. Preterm and/or very low birth weight infants suspected for late-onset sepsis were included. Upon suspicion of sepsis, a whole blood sample was drawn for multiplex PCR to detect the eight most common bacteria causing neonatal sepsis, as well as for blood culture. BDL was determined in episodes with a positive multiplex PCR.

Results

In total, 91 episodes of suspected sepsis were investigated, and PCR was positive in 53 (58%) and blood culture in 60 (66%) episodes, yielding no significant difference in detection rate (p = 0.17). Multiplex PCR showed a sensitivity of 77%, specificity of 81%, positive predictive value of 87%, and negative predictive value of 68% compared with blood culture. Episodes with discordant results of PCR and blood culture included mainly detection of coagulase-negative staphylococci (CoNS). C-reactive protein (CRP) level and immature to total neutrophil (I/T) ratio were lower in these episodes, indicating less severe disease or even contamination. Median BDL was high (4.1 log₁₀ cfu Eq/ml) with a wide range, and was it higher in episodes with a positive blood culture than in those with a negative blood culture (4.5 versus 2.5 log₁₀ cfu Eq/ml; p < 0.0001). For CoNS infection episodes BDL and CRP were positively associated (p = 0.004), and for Staphylococcus aureus infection episodes there was a positive association between BDL and I/T ratio (p = 0.049).

Conclusions

Multiplex PCR provides a powerful assay to enhance rapid identification of the causative pathogen in late-onset sepsis. BDL measurement may be a useful indicator of severity of infection.

Electronic supplementary material

The online version of this article (10.1186/s13054-018-2010-4) contains supplementary material, which is available to authorized users.

Emerging Technologies for Molecular Diagnosis of Sepsis

Rapid and accurate profiling of infection-causing pathogens remains a significant challenge in modern health care. Despite advances in molecular diagnostic techniques, blood culture analysis remains the gold standard for diagnosing sepsis. However, this method is too slow and cumbersome to significantly influence the initial management of patients. The swift initiation of precise and targeted antibiotic therapies depends on the ability of a sepsis diagnostic test to capture clinically relevant organisms along with antimicrobial resistance within 1 to 3 h. The administration of appropriate, narrow-spectrum antibiotics demands that such a test be extremely sensitive with a high negative predictive value. In addition, it should utilize small sample volumes and detect polymicrobial infections and contaminants. All of this must be accomplished with a platform that is easily integrated into the clinical workflow. In this review, we outline the limitations of routine blood culture testing and discuss how emerging sepsis technologies are converging on the characteristics of the ideal sepsis diagnostic test. We include seven molecular technologies that have been validated on clinical blood specimens or mock samples using human blood. In addition, we discuss advances in machine learning technologies that use electronic medical record data to provide contextual evaluation support for clinical decision-making.

Evaluation of updated sepsis scoring systems and systemic inflammatory response syndrome criteria and their association with sepsis in equine neonates

Background

The original equine sepsis score provided a method of identifying foals with sepsis. New variables associated with sepsis have been evaluated, but the sepsis score has not been updated.

Objectives

To evaluate the sensitivity and specificity of 2 updated sepsis scores and the systemic inflammatory response syndrome (SIRS) criteria in regard to detecting sepsis in foals.

Animals

Two‐hundred and seventy‐three ill foals and 25 healthy control foals.

Methods

Historical, physical examination, and clinicopathologic findings were used to calculate the original sepsis score and 2 updated sepsis scores. SIRS criteria were also evaluated. Sepsis scores and positive SIRS scores were statistically compared to foals with sepsis.

Results

One‐hundred and twenty‐six foals were septic and 147 sick‐nonseptic. The original and updated sepsis scores were significantly higher in septic foals as compared to sick‐nonseptic and healthy foals. The sensitivity and specificity of the updated sepsis scores to predict sepsis were not significantly better than those of the original sepsis score. One‐hundred and twenty‐seven of 273 (46.5%) foals met the original SIRS criteria and 88/273 (32%) foals met the equine neonatal SIRS criteria. The original SIRS criteria had similar sensitivity and specificity for predicting sepsis as did the 3 sepsis scores in our study.

Conclusions and Clinical Importance

The updated sepsis scores did not provide improved ability in predicting sepsis. Fulfilling the original SIRS criteria provided similar sensitivity and specificity in predicting sepsis as the modified sepsis score and might serve as a diagnostic aid in identifying foals at risk for sepsis.

Profile of GenMark's ePlex® blood culture identification fungal pathogen panel

INTRODUCTION

Fungemia presents high morbi-mortality and thus rapid microbiological diagnosis may contribute to appropriate patient management. In the last decade, kits based on molecular technologies have become available and health care institutes are increasingly facing critical investment choices. Although all these tools aim to achieve rapid fungal detection and species identification, they display different inherent characteristics. Areas covered: Considering technologies allowing detection and identification of fungal species in a sepsis context, the market proposes either tests on positive blood culture or tests on patient's whole blood. In this review, the authors describe and compare the ePlex® Blood Culture Identification Fungal Pathogen (BCID-FP) test, a fully automated one-step single-use cartridge assay that has been designed to detect identify frequent or rare but emerging, fungal species, from positive blood culture. A comparison with the competing kits is provided. Expert commentaries: The ePlex BCID-FP test provides a diversified and rather relevant panel. Its easy-to-use cartridges allow flexible use around the clock. Nevertheless, prospective clinical studies assessing the time-to-result benefit on antifungal stewardship and on hospital length of stay are not available yet. New tools aim to benefit clinicians and patients, but they should be accompanied by supervision of result interpretation and adaptation of antifungal stewardship.

High Amounts of S100-Alarmins Confer Antimicrobial Activity on Human Breast Milk Targeting Pathogens Relevant in Neonatal Sepsis

Sepsis is a leading cause of perinatal mortality worldwide. Breast milk (BM) feeding is protective against neonatal sepsis, but the molecular mechanisms remain unexplained. Despite various supplementations with potential bioactive components from BM formula feeding cannot protect from sepsis. S100-alarmins are important immunoregulators in newborns preventing excessive inflammation. At high concentrations, the S100A8/A9 protein complex also has antimicrobial properties due to its metal ion chelation capacity. To assess whether BM contains S100-alarmins that might mediate the sepsis-protective effect of BM 97 human BM samples stratified for gestational age, mode of delivery and sampling after birth were collected and analyzed. S100A8/A9 levels were massively elevated after birth (p < 0.0005). They slowly decreased during the first month of life, then reaching levels comparable to normal values in adult serum. The concentration of S100A8/A9 in BM was significantly higher after term compared with preterm birth (extremely preterm, p < 0.005; moderate preterm, p < 0.05) and after vaginal delivery compared with cesarean section (p < 0.0005). In newborn s100a9^−/− mice, enterally supplied S100-alarmins could be retrieved systemically in the plasma. To explore the antimicrobial activity against common causal pathogens of neonatal sepsis, purified S100-alarmins and unmodified as well as S100A8/A9-depleted BM were used in growth inhibition tests. The high amount of S100A8/A9 proved to be an important mediator of the antimicrobial activity of BM, especially inhibiting the growth of manganese (Mn) sensitive bacteria such as Staphylococcus aureus (p < 0.00005) and group B streptococci (p < 0.005). Depletion of S100A8/A9 significantly reduced this effect (p < 0.05, respectively). The growth of Escherichia coli was also inhibited by BM (p < 0.00005) as well as by S100A8/A9 in culture assays (p < 0.05). But its growth in BM remained unaffected by the removal of S100A8/A9 and was neither dependent on Mn suggesting that the antimicrobial effects of S100A8/A9 in BM are primarily mediated by its Mn chelating capacity. In summary, the enteral supply of bioavailable, antimicrobially active amounts of S100-alarmins might be a promising option to protect newborns at high risk from infections and sepsis.

Diagnostic accuracy of the ROCHE Septifast PCR system for the rapid detection of blood pathogens in neonatal sepsis-A prospective clinical trial

Introduction

Diagnosis of neonatal sepsis remains a major challenge in neonatology. Most molecular-based methods are not customized for neonatal requirements. The aim of the present study was to assess the diagnostic accuracy of a modified multiplex PCR protocol for the detection of neonatal sepsis using small blood volumes.

Methods

212 episodes of suspected neonatal late onset sepsis were analyzed prospectively using the Roche SeptiFast^® MGRADE PCR with a modified DNA extraction protocol and software-handling tool. Results were compared to blood culture, laboratory biomarkers and clinical signs of sepsis.

Results

Of 212 episodes, 85 (40.1%) were categorized as “not infected”. Among these episodes, 1 was false positive by blood culture (1.2%) and 23 were false positive by PCR (27.1%). Of 51 (24.1%) episodes diagnosed as “culture proven sepsis”, the same pathogen was detected by blood culture and PCR in 39 episodes (76.5%). In 8 episodes, more pathogens were detected by PCR compared to blood culture, and in 4 episodes the pathogen detected by blood culture was not found by PCR. One of these episodes was caused by Bacillus cereus, a pathogen not included in the PCR panel. In 76/212 (35.8%) episodes, clinical sepsis was diagnosed. Among these, PCR yielded positive results in 39.5% of episodes (30/76 episodes). For culture-positive sepsis, PCR showed a sensitivity of 90.2% (95%CI 86.2–94.2%) and a specificity of 72.9% (95%CI 67.0–79.0%).

Conclusion

The Roche SeptiFast^® MGRADE PCR using a modified DNA extraction protocol showed acceptable results for rapid detection of neonatal sepsis in addition to conventional blood culture. The benefit of rapid pathogen detection has to be balanced against the considerable risk of contamination, loss of information on antibiotic sensitivity pattern and increased costs.

Advances in Rapid Identification and Susceptibility Testing of Bacteria in the Clinical Microbiology Laboratory: Implications for Patient Care and Antimicrobial Stewardship Programs

Early availability of information on bacterial pathogens and their antimicrobial susceptibility is of key importance for the management of infectious diseases patients. Currently, using traditional approaches, it usually takes at least 48 hours for identification and susceptibility testing of bacterial pathogens. Therefore, the slowness of diagnostic procedures drives prolongation of empiric, potentially inappropriate, antibacterial therapies. Over the last couple of years, the improvement of available techniques (e.g. for susceptibility testing, DNA amplification assays), and introduction of novel technologies (e.g. MALDI-TOF) has fundamentally changed approaches towards pathogen identification and characterization. Importantly, these techniques offer increased diagnostic resolution while at the same time shorten the time-to-result, and are thus of obvious importance for antimicrobial stewardship. In this review, we will discuss recent advances in medical microbiology with special emphasis on the impact of novel techniques on antimicrobial stewardship programs.

Contemporary approaches to the rapid molecular diagnosis of sepsis

INTRODUCTION

Although the administration of appropriate antimicrobials within the very first hour remains the mainstay of sepsis management, the correct selection of antimicrobials is hampered by the delay of conventional microbiology providing results after at least 48 hours. Methods of rapid detection of pathogens are an approach to overcome these difficulties. Areas covered: This review analyzes the advantages and the disadvantages of these approaches with major emphasis on technologies based on multiplex PCR for the rapid detection of pathogens using whole blood. The most broadly studied platform is SeptFast. Sensitivity ranges between 42% and 73% and specificity between 50% and 97%. The main disadvantages are high cost, the risk of contamination and the lack of information for the presence of resistance genes. A brief review of the use of PCR techniques for the diagnosis of endocarditis and of the recognition of the bacterial proteome for the rapid identification of grown colonies (MALDI-TOF) is also provided. Expert commentary: More randomized clinical trials are necessary to validate the use of molecular techniques for decision-making for patients' outcomes, taking into consideration the cost-benefit for the patient.