A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology

Compliance of clinical microbiology laboratories with recommendations for the diagnosis of bloodstream infections: Data from a nationwide survey in Italy

In 2014, the Italian Working Group for Infections in Critically Ill Patient of the Italian Association of Clinical Microbiologists updated the recommendations for the diagnostic workflow for bloodstream infections (BSI). Two years after publication, a nationwide survey was conducted to assess the compliance with the updated recommendations by clinical microbiology laboratories. A total of 168 microbiologists from 168 laboratories, serving 204 acute care hospitals and postacute care facilities, were interviewed during the period January–October 2016 using a questionnaire consisting of nineteen questions which assessed the level of adherence to various recommendations. The most critical issues were as follows: (a) The number of sets of blood cultures (BC) per 1,000 hospitalization days was acceptable in only 11% of laboratories; (b) the minority of laboratories (42%) was able to monitor whether BCs were over or under‐inoculated; (c) among the laboratories monitoring BC contamination (80%), the rate of contaminated samples was acceptable in only 12% of cases;(d) the Gram‐staining results were reported within 1 hr since BC positivity in less than 50% of laboratories. By contrast, most laboratories received vials within 2–4 hr from withdrawal (65%) and incubated vials as soon as they were received in the laboratory (95%). The study revealed that compliance with the recommendations is still partial. Further surveys will be needed to monitor the situation in the future.

Understanding and interpreting community sequencing measurements of the vaginal microbiome

Community-wide high-throughput sequencing has transformed the study of the vaginal microbiome, and clinical applications are on the horizon. Here we outline the three main community sequencing methods: (1) amplicon sequencing, (2) shotgun metagenomic sequencing, and (3) metatranscriptomic sequencing. We discuss the advantages and limitations of community sequencing generally, and the unique strengths and weaknesses of each method. We briefly review the contributions of community sequencing to vaginal microbiome research and practice. We develop suggestions for critically interpreting research results and potential clinical applications based on community sequencing of the vaginal microbiome. TWEETABLE ABSTRACT: We review the advantages and limitations of amplicon sequencing, metagenomics, and metatranscriptomics methods for the study of the vaginal microbiome.

Clinical microbiology

The clinical microbiology laboratory relies on traditional diagnostic methods such as culturing, Gram stains, and biochemical testing. Receipt of a high-quality specimen with an appropriate test order is integral to accurate testing. Recent technological advancements have led to decreased time to results and improved diagnostic accuracy. Examples of advancements discussed in this chapter include automation of bacterial culture processing and incubation, as well as introduction of mass spectrometry for the proteomic identification of microorganisms. In addition, molecular testing is increasingly common in the clinical laboratory. Commercially available multiplex molecular assays simultaneously test for a broad array of syndromic-related pathogens, providing rapid and sensitive diagnostic results. Molecular advancements have also transformed point-of-care (POC) microbiology testing, and molecular POC assays may largely supplant traditional rapid antigen testing in the future. Integration of new technologies with traditional testing methods has led to improved quality and value in the clinical microbiology laboratory.

After reviewing this chapter, the reader will be able to:•

List key considerations for specimen collection for microbiology testing.

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Discuss the advantages and limitations of automation in the clinical microbiology laboratory.

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Describe the evolution of microorganism identification methods.

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Discuss the benefits and limitations of molecular microbiology point-of-care testing.

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Summarize currently available multiplex molecular microbiology testing options.

Intermittent Negative Blood Cultures in Staphylococcus aureus Bacteremia; a Retrospective Study of 1071 Episodes

Background

Recommended management of Staphylococcus aureus bacteremia (SAB) includes follow-up blood culture sets (BCs) to determine the duration of bacteremia. Duration of bacteremia is an important prognostic factor in SAB, and follow-up BCs have a critical role in differentiation of uncomplicated and complicated SAB. However, intermittent negative BCs occur in SAB. Clinical guidelines for SAB management do not specify an approach to follow-up BCs' collection or define the number of negative BCs required to demonstrate resolution of bacteremia. This study assessed the frequency of intermittent negative BCs in SAB and used these findings to formulate a recommendation for collection of follow-up BCs.

Methods

This retrospective study reviewed 1071 episodes of SAB. Clinical and microbiological data including the duration of bacteremia and the occurrence of intermittent negative BCs (those preceded and followed by positive cultures) were considered.

Results

Intermittent bacteremia occurred in 13% (140/1071) of episodes. A single negative BC on days 1-3 had a predictive value of 87%-93% for resolution of bacteremia, although this was improved if all BCs collected within the same day were considered.

Conclusions

Intermittent negative BCs are common in SAB. Given this, we would not recommend accepting a single negative BC as demonstrating resolution of the bacteremia. This is particularly important if a patient is to be classified as having uncomplicated SAB.

Printculture of Surgical Pathology and Autopsy Specimens

OBJECTIVES

Printculture is a method of microbiologic assessment previously described for use in the autopsy setting. We sought to compare printculture of surgical and autopsy pathology specimens to standard microbiology culture using matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF)-based colony identification.

METHODS

Printculture was performed on 18 frozen samples with corresponding standard culture results. The results of MALDI-TOF identification of colonies recovered by printculture were compared with standard cultures, and percent concordance was calculated.

RESULTS

There was 95.8% concordance to standard culture methods for cases with infections and 100% concordance for cases without infection. The pattern of growth was found to aid in the distinction between contamination and true infection.

CONCLUSIONS

Printculture allows the identification of microorganisms from routinely frozen tissues and provides a bridge between microbiology and histomorphology through the identification of associated histologic features of infection. This technique can be successfully integrated into autopsy and surgical pathology workup of potentially infected tissues.

Two cases of fungal cyst infection in ADPKD: is this really a rare complication?

Background

Cyst infection is a prevalent complication in autosomal dominant polycystic kidney disease (ADPKD) patients, however therapeutic and diagnostic approaches towards this condition remain unclear. The confirmation of a likely episode of cyst infection by isolating the pathogenic microorganism in a clinical scenario is possible only in the minority of cases. The available antimicrobial treatment guidelines, therefore, might not be appropriate to some patients.

Case presentation

We describe two unique cases of kidney cyst infection by Candida albicans, a condition that has not been previously described in literature. Both cases presented clear risk factors for Candida spp. infection. However, since there was no initial indication of cyst aspiration and culture, antifungal therapy was not immediately started and empirical treatment was initiated as recommended by the current guidelines. Antifungal treatment was instituted in both cases along the clinical course, according to their specificities.

Conclusion

Our report highlights the possibility of Candida spp. cyst infection. Failure of clinical improvement with antibiotics should raise the suspicion of a fungal infection. Identification of infected cysts should be pursued in such cases, particularly with PET-CT, and when technically possible followed by cyst aspiration and culture to guide treatment. Risk factors for this condition, such as Candida spp. colonization, previous antimicrobial therapy, hemodialysis, necrotizing pancreatitis, gastrointestinal/hepatobiliary surgical procedure, central venous catheter, total parenteral nutrition, diabetes mellitus and immunodeficiency (neutropenia < 500 neutrophils/mL, hematologic malignancy, chemotherapy, immunosuppressant drugs), should be also considered accepted criteria for empirical antifungal therapy.

The correct blood volume for paediatric blood cultures: a conundrum?

BACKGROUND

Bloodstream infections (BSIs) are a major cause of morbidity and mortality in paediatric patients. For fast and accurate diagnosis, blood culture (BC) is the reference standard. However, the procedure for blood sampling in paediatric patients, particularly the optimal blood volume, is the subject of controversy stemming from a lack of knowledge of the bacterial load and because of several obstacles such as low intravascular volume and the risk of causing anaemia.

AIMS

The aim of this narrative review is to summarize current knowledge on blood sampling in paediatric patients for BC purposes, in particular blood volume and number and type of BC bottles needed for reasonable future guidelines/recommendations.

SOURCES

A comprehensive literature search of PubMed, including all publications in English, was performed in June 2019 using the search terms 'blood culture', 'blood volume', 'bloodstream infection', 'diagnostic', 'paediatric' and/or 'sepsis'.

CONTENT

The amount of inoculated blood determines the sensitivity, specificity and time to positivity of a BC, and low-level bacteraemia (≤10 cfu/mL) in paediatric patients is presumed to be more common than reported. Current approaches for 'adequate' blood volume for paediatric BC are mainly weight- or age-dependent. Of these recommendations, the scheme devised by Gaur and colleagues seems most appropriate and calls for a sample of 1-1.5 mL for children weighing <11 kg and 7.5 mL for a patient weight of 11-17 kg to be drawn into one BC bottle. Inclusion of a more detailed grading in the weight range 4-14 kg, as published by Gonsalves and colleagues, might be useful.

IMPLICATIONS

This review could be important for future guidelines on paediatric BC collection and thus could contribute to improving patient management and lowering the economic and global health burden associated with BSI. Furthermore, upcoming molecular-based approaches with low sample volumes might be an interesting alternative.

Treatment outcomes in patients with pyogenic vertebral osteomyelitis who have cirrhosis

Early diagnosis and proper treatment of pyogenic vertebral osteomyelitis (PVO) in patients with cirrhosis is challenging to clinicians, and the mortality rate is expected to be high. A retrospective study was conducted to investigate the treatment outcome in PVO patients with cirrhosis and to identify the predictors of their mortality. Mortality was divided into two categories, 30-day and 90-day mortality. A stepwise multivariate logistic regression model was used to identify predictors of mortality. Eighty-five patients were identified after initial exclusion. The patients’ mean age was 60.5 years, and 50 patients were male. The early mortality rates within 30 and 90 days were 17.6% and 36.5%, respectively. Multivariate analysis revealed that increased age, CTP class C, and bacteremia at the time of PVO diagnosis were predictors of 30-day mortality, while higher MELD score, presence of combined infection, and multiple spinal lesions were predictors of 90-day mortality. Attention should be paid to the high mortality between 30 and 90 days after PVO diagnosis (18.8%), which was higher than the 30-day mortality. Liver function was consistently a strong predictor of mortality in PVO patients with cirrhosis. The high-risk patients should be targeted for an aggressive diagnostic approach, using spinal MRI and intensive monitoring and treatment strategies.

Diagnostic Challenges and Laboratory Considerations for Pediatric Sepsis

Background

Sepsis is a leading cause of death for children in the US and worldwide. There is a lack of consensus how sepsis is clinically defined, and sepsis definitions and diagnostic guidelines for the pediatric population have remained unchanged for more than a decade now. Current pediatric definitions are largely based on adult guidelines and expert opinion rather than evidence based on outcomes in the pediatric populations. Without a clear definition of sepsis, it is challenging to evaluate the performance of new laboratory tests on the diagnosis and management of sepsis.

Content

This review provides an overview of common etiologies of sepsis in pediatric populations, challenges in defining and diagnosing pediatric sepsis, and current laboratory tests used to identify and monitor sepsis. Strengths and limitations of emerging diagnostic strategies will also be discussed.

Summary

Currently there is no single biomarker that can accurately diagnose or predict sepsis. Current biomarkers such as C-reactive protein and lactate are neither sensitive nor specific for diagnosing sepsis. New biomarkers and rapid pathogen identification assays are much needed. Procalcitonin, although having some limitations, has emerged as a biomarker with demonstrated utility in management of sepsis in adults. Parallel studies analyzing the utility of procalcitonin in pediatric populations are lagging but have shown potential to affect sepsis care in pediatric populations. Multibiomarker approaches and stepwise algorithms show promise in the management of pediatric sepsis. However, a major hurdle is the lack of validated clinical criteria for classification of pediatric sepsis, which is necessary for the development of well-designed studies that can assess the clinical impact of these emerging biomarkers.

Strategies for increasing diagnostic yield of community-onset bacteraemia within the emergency department: A retrospective study

Bloodstream infections (BSI) are associated with high mortality. Therefore, reliable methods of detection are of paramount importance. Efficient strategies to improve diagnostic yield of bacteraemia within the emergency department (ED) are needed. We conducted a retrospective analysis of all ED encounters in a high-volume, city-centre university hospital within Germany during a five-year study period from October 2013 to September 2018. A time-series analysis was conducted for all ED encounters in which blood cultures (BCs) were collected. BC detection rates and diagnostic yield of community-onset bacteraemia were compared during the study period (which included 45 months prior to the start of a new diagnostic Antibiotic Stewardship (ABS) bundle and 15 months following its implementation). BCs were obtained from 5,191 out of 66,879 ED admissions (7.8%). Bacteraemia was detected in 1,013 encounters (19.5% of encounters where BCs were obtained). The overall yield of true bacteraemia (defined as yielding clinically relevant pathogens) was 14.4%. The new ABS-related diagnostic protocol resulted in an increased number of hospitalised patients with BCs collected in the ED (18% compared to 12.3%) and a significant increase in patients with two or more BC sets taken (59% compared to 25.4%), which resulted in an improved detection rate of true bacteraemia (2.5% versus 1.8% of hospital admissions) without any decrease in diagnostic yield. This simultaneous increase in BC rates without degradation of yield was a valuable finding that indicated success of this strategy. Thus, implementation of the new diagnostic ABS bundle within the ED, which included the presence of a skilled infectious disease (ID) team focused on obtaining BCs, appeared to be a valuable tool for the accurate and timely detection of community-onset bacteraemia.

Fungal Diagnostic Stewardship in Bronchoscopy Specimens for Immunocompetent Patients in the Intensive Care Unit

OBJECTIVE

To evaluate the diagnostic yield of fungal smears and cultures from bronchial lavage and wash specimens obtained from immunocompetent patients in the intensive care unit (ICU) because respiratory tract samples from patients in the ICU often undergo extensive microbiological testing.

PATIENTS AND METHODS

In total, we enrolled 112 immunocompetent adult patients treated in the medical and surgical ICU between July 1, 2016, and June 30, 2017. We evaluated whether the results of fungal smears and cultures of specimens obtained from bronchoscopy and bronchoalveolar lavage changed patient care.

RESULTS

In total, 131 bronchoscopic specimens and 31 bronchoalveolar lavage specimens were tested for fungi. Cultures were held for an estimated 4680 culture-days. Two results changed patient therapy. In both cases, other routine tests provided the same information as fungal culture before these results were returned.

CONCLUSION

In immunocompetent, critically ill patients, fungal culture of respiratory tract specimens does not add diagnostic value. Routine fungal culture of respiratory tract specimens should be discouraged in this population.

Optimization of Turnaround Time for Group A Streptococcus PCR

The use of some nucleic acid amplification tests (NAATs) for the diagnosis of group A Streptococcus (GAS) pharyngitis allows laboratories to adopt single-tiered testing without reflex culture. However, centralization may delay the delivery of actionable information to the bedside, particularly in the outpatient setting. We describe two novel workflows at our institution and their effect on in-lab turnaround time (TAT) at a tertiary care microbiology lab. Laboratory records were extracted, and relevant data were analyzed after the implementation of qualitative in vitro diagnostic testing for GAS with the Xpert Xpress Strep A assay, performed using the GeneXpert Infinity-48s. Workflow optimization steps studied included: (i) direct specimen submission to the microbiology laboratory via the pneumatic tube system and (ii) autoverification of GAS NAAT results in the laboratory information system. Between April 2018 and October 2018, 2,595 unique specimens were tested for GAS by PCR. Of these, 2,523 were included in the final analysis. Linear regression established that the total in-lab TAT was significantly reduced by direct specimen submission to the microbiology laboratory, autoverification, and processing during the night shift. We describe two workflow optimization methods that reduced the in-lab TAT for GAS NAAT. Although microbiology labs historically use manual processes, the advent of total laboratory automation and the adoption of on-demand NAATs will allow for more streamlined processing of microbiology specimens. It may be beneficial to consider instrument interfacing and specimen processing optimization during the early phases of implementation planning for NAATs in the microbiology laboratory.

Challenges and research priorities to progress the impact of antimicrobial stewardship

Antimicrobial stewardship programmes have been playing an important role in patient care and hospital policies. These programmes are now recognised as formal strategies for curbing the upward trend in antibiotic resistance and for improving the appropriate antimicrobial and antifungal use. The role of such programs in the era of antimicrobial resistance presents several unique challenges and opportunities, most notably in the diagnostic and therapeutic setting. Controversies remain regarding the most effective interventions and the appropriate design to evaluate their impact. In this review, based on rounds of discussion, we explain the most important challenges faced by antibiotic stewardship and antifungal stewardship programmes. We also try to suggest areas for further research.

Infections in patients with multiple myeloma treated with conventional chemotherapy: a single-center, 10-year experience in Pakistan

Introduction

Multiple myeloma (MM) is a common hematologic malignancy with variable degrees of immunodeficiency. Disease- and treatment-related compromise of the immune system predisposes patients to infections, which are a major cause of morbidity and mortality.

Objective

We aimed to establish the incidence and main characteristics of infections in MM patients treated at our center over a 10-year period.

Method and results

Of the 412 patients retrospectively analyzed, 154 (37.4%) were documented to have at least one episode of infection and were included in this study. A total of 244 infectious episodes were documented. The most common site of infection was the lung, followed by the genitourinary system. The most common infections were bacterial, followed by viral. Escherichia coli were the most common organism. In 160 (65.5%) episodes, the organism was not isolated. Thalidomide with dexamethasone was the most common treatment regimen, followed by melphalan with dexamethasone. Infection was the main cause of death in 26 (6.3%) out of all 412 patients.

Conclusion

Infections are a notable cause of morbidity and mortality in the clinical course of MM patients. By considering patient and disease characteristics, a risk-adapted selection of the MM treatment should be employed, with special attention toward patient age and disease-associated organ dysfunction. Patient education, access to healthcare and physician vigilance are also essential. Vaccination and antimicrobial prophylaxis may be considered prior to or during therapy.

Highly Sensitive Molecular Assay for Group A Streptococci Over-identifies Carriers and May Impact Outpatient Antimicrobial Stewardship

BACKGROUND

Timely, accurate diagnosis of group A streptococci (GAS) pharyngitis prevents acute rheumatic fever and limits antibiotic overuse. The illumigene group A Streptococcus assay (Meridian Bioscience, Cincinnati, OH) is a molecular test for GAS pharyngitis with high sensitivity and specificity. We sought to determine whether the illumigene test is more likely than throat culture to be positive in patients without pharyngeal symptoms and explore the limits of detection of the test.

METHODS

Patients 3-17 years of age were eligible if they had no history of pharyngitis or use of antibiotics within the previous 2 weeks; there were no upper respiratory infection symptoms, sore throat or fever and no signs of infection. Culture and illumigene were performed on duplicate throat swabs. Excess lysate from a subset of illumigene tests was evaluated by real-time polymerase chain reaction. Institutional Review Board approval was obtained.

RESULTS

We enrolled 385 patients from February 2016 to October 2017; mean age was 10 yr; 51% were male. Most visits were for health supervision (69%). Significantly more illumigene tests (78/385, 20.3%) than throat cultures (48/385, 12.5%) were positive (χ; P =0.0035). Illumigene was "indeterminate" for 3 patients, leaving 382 pairs of swabs for analysis. Results were discordant for 32 of 382 pairs (8.4%); 31 of 32 (97%) were illumigene-positive/culture-negative (McNemar test; P < 0.000001). Real-time polymerase chain reaction was negative in 4 of 13 (31%) tested illumigene-positive lysates; the paired culture had been negative in all four. The limit of detection for the illumigene test was 55 colony forming units/mL.

CONCLUSIONS

The illumigene test is significantly more likely than throat culture to yield positive results in patients without GAS pharyngitis. Failure to appropriately select patients for testing may negatively impact antimicrobial stewardship efforts without benefit to patients.

Disease severity and clinical outcomes of community-acquired pneumonia caused by non-influenza respiratory viruses in adults: a multicentre prospective registry study from the CAP-China Network

Although broad knowledge of influenza viral pneumonia has been established, the significance of non-influenza respiratory viruses in community-acquired pneumonia (CAP) and their impact on clinical outcomes remains unclear, especially in the non-immunocompromised adult population.Hospitalised immunocompetent patients with CAP were prospectively recruited from 34 hospitals in mainland China. Respiratory viruses were detected by molecular methods. Comparisons were conducted between influenza and non-influenza viral infection groups.In total, 915 out of 2336 adult patients with viral infection were enrolled in the analysis, with influenza virus (28.4%) the most frequently detected virus, followed by respiratory syncytial virus (3.6%), adenovirus (3.3%), human coronavirus (3.0%), parainfluenza virus (2.2%), human rhinovirus (1.8%) and human metapneumovirus (1.5%). Non-influenza viral infections accounted for 27.4% of viral pneumonia. Consolidation was more frequently observed in patients with adenovirus infection. The occurrence of complications such as sepsis (40.1% versus 39.6%; p=0.890) and hypoxaemia (40.1% versus 37.2%; p=0.449) during hospitalisation in the influenza viral infection group did not differ from that of the non-influenza viral infection group. Compared with influenza virus infection, the multivariable adjusted odds ratios of CURB-65 (confusion, urea >7 mmol·L^-1, respiratory rate ≥30 breaths·min^-1, blood pressure <90 mmHg (systolic) or ≤60 mmHg (diastolic), age ≥65 years) ≥3, arterial oxygen tension/inspiratory oxygen fraction <200 mmHg, and occurrence of sepsis and hypoxaemia for non-influenza respiratory virus infection were 0.87 (95% CI 0.26-2.84), 0.72 (95% CI 0.26-1.98), 1.00 (95% CI 0.63-1.58) and 1.05 (95% CI 0.66-1.65), respectively. The hazard ratio of 90-day mortality was 0.51 (95% CI 0.13-1.91).The high incidence of complications in non-influenza viral pneumonia and similar impact of non-influenza respiratory viruses relative to influenza virus on disease severity and outcomes suggest more attention should be given to CAP caused by non-influenza respiratory viruses.

Detailed Analysis of the Characteristics of Sample Volume in Blood Culture Bottles

Blood volume is the most important variable for the detection of microorganisms in blood cultures (BCs). Most standards recommend 40 to 60 ml blood, collected in several BC bottles filled up to 10 ml. We measured blood volume in individual BC bottles and analyzed the associations of hospital, bottle type, day of the week, daily sampling time, and age and sex of the patient with sampling volume and BC result. The variation in blood volume per BC bottle was analyzed in a mixed linear model using hospital, bottle type, weekday, sampling time, age, and sex as fixed factors and patient identification (ID) and episode as random factors to control for repetitive sampling of individual patients. Only 18% of all bottles were filled with the recommended 8 to 10 ml, and 47% were filled with less than 8 ml. The mean (± standard error) volume was larger in positive bottles (9.09 ± 0.15) than in negative bottles (8.47 ± 0.07) (P < 0.001). Blood volume was larger in BacT/Alert-FA Plus bottles than in -FN Plus BC bottles (P < 0.001). There were significantly lower volumes collected during the night (P < 0.001). The volume of blood collected decreased significantly with increasing patient age (P < 0.001). Larger volumes were collected from male patients than from female patients: 8.78 (± 0.06) versus 8.36 (± 0.06) ml (mean ± standard error [SE]), respectively (P < 0.001). The odds of detecting a positive patient increases by 13% for each additional milliliter of blood drawn. Our results show that we need to work actively with the development of blood sampling routines to overcome age and sex effects and to optimize blood sampling volumes.

Approach to Positive Blood Cultures in the Hospitalized Patient: A Review

The use of blood cultures as a diagnostic tool has increased over the years along with improvements in techniques and results. The diagnostic dilemma arises when blood cultures are positive and there is possibility of contamination. Hence obtaining blood cultures in the appropriate setting and the interpretation of blood cultures by the hospitalist is imperative to the management of the hospitalized patient.

The role of patients and healthcare workers Staphylococcus aureus nasal colonization in occurrence of surgical site infection among patients admitted in two centers in Tanzania

Background

Colonization with Staphylococcus aureus has been identified as a risk for subsequent occurrence of infection. This study investigated the relationship between S. aureus colonization of patients and healthcare workers (HCWs), and subsequent surgical site infections (SSI).

Methods

Between December 2014 and September 2015, a total of 930 patients and 143 HCWs were enrolled from the Bugando Medical Centre and Sekou Toure hospital in Mwanza, Tanzania. On admission and discharge nasal swabs, with an additional of wound swab for those who developed SSI were collected from patients whereas HCWs were swabbed once. Identification and antimicrobial susceptibility testing were done by VITEK-MS and VITEK-2, respectively. Detection of Panton Valentine leukocidin (PVL) and mecA genes was done by PCR. S. aureus isolates were further characterized by spa typing and Multi-Locus Sequence Typing (MLST).

Results

Among 930 patients screened for S. aureus on admission, 129 (13.9%) were positive of which 5.4% (7/129) were methicillin-resistant S. aureus (MRSA). Amongst 363 patients rescreened on discharge, 301 patients had been tested negative on admission of whom 29 (9.6%) turned positive after their hospital stay. Three (10.3%) of the 29 acquired S. aureus were MRSA. Inducible Clindamycin resistance occurred more often among acquired S. aureus isolates than among isolates from admission [34.5% (10/29) vs. 17.1% (22/129), P = 0.018]. S. aureus contributed to 21.1% (n = 12) of the 57 cases of investigated SSIs among 536 patients followed. Seven out of eight S. aureus carriage/infection pairs had the same spa and sequence types. The previously reported dominant PVL-positive ST88 MRSA strain with spa type t690 was detected in patients and HCW.

Conclusion

A significant proportion of patients acquired S. aureus during hospitalization. The finding of more than 90% of S. aureus SSI to be of endogenous source underscores the need of improving infection prevention and control measures including screening and decolonization of high risk patients.

Culture of Rectal Swab Specimens for Enteric Bacterial Pathogens Decreases Time to Test Result While Preserving Assay Sensitivity Compared to Bulk Fecal Specimens

Diarrheal illness is a major cause of morbidity and mortality throughout the world, yet the etiologic agent of many cases of gastrointestinal illness remains unspecified, often due to the lack of convenient, timely, and sensitive diagnostic testing. Although bulk fecal specimens remain the recommended specimen type for enteric culture, rectal swabs may be an option preferred by clinicians and patients due to the convenience and timing of collection. However, the lack of data evaluating the sensitivity of rectal swabs compared to fecal specimens for detection of enteric pathogens precludes this specimen type from being recommended by national guidelines. In this study, we retrospectively reviewed 480 paired rectal swab and fecal specimens submitted for enteric culture to the Barnes-Jewish Hospital and St. Louis Children's Hospital microbiology laboratories in St. Louis, MO, from 2002 to 2017. We report 32% positivity of paired specimens with an overall agreement of 93% and Cohen's κ of 0.84 (95% confidence interval, 0.78 to 0.89). Additionally, we evaluated the time to result from the time of patient presentation to the health care setting and demonstrate that rectal swabs have a significantly shorter time to an actionable result than bulk fecal specimens (median, 67.4 h versus 78.4 h, respectively; P < 0.001). These findings indicate that rectal swabs facilitate on-demand culture-based testing with a sensitivity comparable to that of fecal specimens and thus should be recommended for enteric bacterial culture when bulk fecal specimens are unavailable.

The Journey of Cultures Taken During Revision Joint Arthroplasty: Preanalytical Phase

Background: Microbiological culture has been considered the standard for pathogen identification for decades. However, culture is a laborious, time consuming, imperfect and outdated process. This study aims to inform the orthopedic community of the steps and timing of routine culture processing. Methods: We prospectively tracked 103 cultures from 33 revision hip and knee arthroplasty patients between September 2017-February 2018. Times were recorded at intraoperative collection; time of pick up from OR, transportation time; arrival at the laboratory; culture processing and plating time; and time to final result reporting. Results: Of the 103 cultures, 45.6% were processed and incubated in less than two hours, and 54.4% greater than or equal to two hours. The mean time spent in the OR, during transport, and within the laboratory prior to incubation was 0:53, 0:06 and 1:12. The range of time that samples remained at each stage varied considerably in the OR (0:03-3:33), in transit(0:04-0:16), and in the lab prior to incubation(0:26-3:01). The proportion of the total time to incubation attributed to idle time samples spent in the OR after initial sampling was 40.0%. In contrast, transport to the laboratory represented 5.1% of the total time. Idle time in the laboratory represented the greatest share at 54.9%. Conclusion: There is significant variability in the time to transport, process and incubate culture samples. Almost half of the specimens were processed outside the 2-hour recommended window. Surgeons should be aware of idle time during processing and seek to optimize their institutional pathways to maximize culture yield.

Outcome of Electronic Order Alert Intervention Relative to Toxigenic Clostridium difficile PCR Analysis and Hospital-Onset C difficile Infection in a Multihospital Health Care System

OBJECTIVES

Concern exists regarding overdiagnosis of Clostridium difficile infection (CDI) via molecular modalities. We determined effects of a preanalytic order intervention on laboratory and CDI prevention measures in a multihospital system.

METHODS

Intervals before and following implementation of a CDI electronic order alert (relative to appropriate testing scenario) were assessed for C difficile test volume and positivity rate, hospital-onset CDI frequency, and hospital-onset C difficile standardized infection ratio (SIR). C difficile detection occurred by PCR throughout the study.

RESULTS

During the first half of 2015, testing volume was 1,578, with 88 hospital-onset CDIs. Following implementation, 18.9% and 56.8% reductions in volume and hospital-onset CDIs were realized, respectively, in the first half of 2017. Regression analysis revealed decreasing trends in PCR volume, positivity rate, hospital-onset CDI frequency, and SIR in larger facilities.

CONCLUSIONS

Preanalytic considerations affect not only the microbiology laboratory but also hospital infection prevention in the context of CDI.

Risk Factors for Central Line-Associated Bloodstream Infection in Critically Ill Neonates

OBJECTIVE

To identify independent risk factors to develop a central line- associated bloodstream infection (CLABSI) in critically ill neonates with major underlying diseases.

METHODS

A nested case-control study was conducted in a neonatal intensive care unit (NICU). Patients with a central venous catheter (CVC) were included. Cases were neonates who developed a CLABSI and controls were patients without CLABSI. Variables included: perinatal history, characteristics of the catheter, installation and catheter use, surgical interventions, and hospital stay. Odds ratio (OR) and 95% confidence intervals (CI) were calculated. X², Fisher exact, and Mann-Whitney U tests were used when appropriate. Variables with a p value ≤0.10 in the univariate analysis were introduced in a non-conditional logistic regression model.

RESULTS

Seventy four cases and 105 controls were analyzed. Univariate risk factors were: any surgery, abdominal surgery, length of hospitalization (≥14 d), double-lumen CVC, surgical cut-down technique, complications, CVC placement in internal jugular vein, dressing type, blood transfusions, parenteral nutrition, and number of CVC manipulations (>200). In the logistic regression analysis, independent risk factors with a p value <0.05 were: double-lumen catheter (OR 5.8, 95% CI 1.2-30), length of hospitalization ≥14 d (OR 4.6, 95% CI 1.8-11.4), abdominal surgery (OR 2.7, 95% CI 1.2-6.2) and blood transfusions (OR 2.5, 95% CI 1.2-5.3).

CONCLUSIONS

One risk factor was related to the catheter itself. Management of underlying diseases in specialized NICU contributes to a greater extent to the development of a central line-associated bloodstream infection.

Diagnostic Stewardship: A Clinical Decision Rule for Blood Cultures in Community-Onset Methicillin-Resistant Staphylococcus aureus (MRSA) Skin and Soft Tissue Infections

Introduction

The emergence, spread and persistence of methicillin-resistant Staphylococcus aureus (MRSA) as a causative pathogen in community-onset (CO) skin and soft tissue infections (SSTIs) have resulted in substantial changes in the management of these infections. The indications for obtaining blood cultures in patients with CO-MRSA SSTIs remain poorly defined. The objectives of this study were to derive and validate a clinical decision rule that predicts the probability of MRSA bacteremia in CO-MRSA SSTIs and to identify a low-risk population for whom blood cultures may be safely omitted.

Methods

This was a retrospective, case-control study with an internal temporal validation cohort conducted at two large urban academic medical centers. Hospitalized adults with CO-MRSA SSTI between 2010 and 2018 were included. Independent predictors of MRSA bacteremia were identified through multivariable logistic regression. A decision rule was derived using weighted coefficient-based scoring. The decision rule was validated in an internal temporal validation cohort.

Results

A total of 307 patients (155 cases and 152 controls) were included in the derivation cohort. A decision rule was created with a “major criterion” defined as purulent cellulitis and “minor criteria” defined as abnormal temperature, intravenous drug use, leukocytosis, tachycardia, body mass index < 25 kg/m² and non-upper extremity infection site. A blood culture is indicated by this rule for patients with one major or at least two minor criteria. Otherwise patients are classified as low risk, and blood cultures may be omitted. The sensitivity of the decision rule in the derivation and validation cohorts was 98.71% (95% CI 95.42%, 99.84%) and 95.65% (78.05%, 99.89%), respectively. The specificity was 23.03% (95% CI 16.59%, 30.54%) and 30.77% (95% CI 24.15%, 38.02%), respectively.

Conclusion

The decision rule developed and validated in this study provides a standardized, evidenced-based approach to determine the need for blood cultures based on bacteremia risk.

Blood Smears Have Poor Sensitivity for Confirming Borrelia miyamotoi Disease

Borrelia miyamotoi disease (BMD) is a newly recognized borreliosis that is cotransmitted by ticks wherever Lyme disease is zoonotic. Unlike Borrelia burgdorferi sensu lato, the agent of Lyme disease, B. miyamotoi is closely related to relapsing fever spirochetes, such as Borrelia hermsi i Some authors have suggested that the disease caused by B. miyamotoi should be considered a hard-tick-transmitted relapsing fever, and thus, the main mode of confirming a diagnosis for that infection, microscopy to analyze a blood smear, may have clinical utility. To determine whether blood smears may detect B. miyamotoi in the blood of acute BMD patients, we made standard malariological thick smears from anticoagulated blood samples that were previously determined to contain this agent (by PCR) and analyzed them for morphological evidence of spirochetes. Spirochetes were not detected in the blood smears from 20 PCR positive patient blood samples after examination of 100 thick smear fields and only 2 of 20 demonstrated spirochetes when the examination was extended to 300 thick smear fields. Inoculation of severe combined immunodeficient (SCID) mice yielded isolates from 5 of 5 samples, but 0 of 3 BALB/c mice became infected. We conclude that in strong contrast to the diagnosis of typical relapsing fever, microscopy of blood smears is not sensitive enough for confirming a diagnosis of BMD but that SCID mouse inoculation could be a useful complement to PCR.

Respiratory Viral Infections in Children and Adolescents with Hematological Malignancies

Background

Despite the introduction of a polymerase chain reaction (PCR) test for the diagnosis of respiratory viral infection (RVI), guidance on the application of this test and the management of RVI in immunocompromised children is lacking. This study evaluated the clinical characteristics of RVI and established strategies for the PCR test in children and adolescents with hematological malignancies.

Methods

This study included children and adolescents with underlying hematological malignancies and respiratory symptoms, in whom a multiplex PCR test was performed. Patients in whom RVI was identified and not identified were categorized into Groups I and II, respectively. Group I was sub-divided into patients with upper and lower respiratory infections. The medical records of the enrolled patients were retrospectively reviewed.

Results

A total of 93 respiratory illnesses were included. Group I included 46 (49.5%) cases of RVI, including 31 (67.4%) upper and 15 (32.6%) lower respiratory infections. Rhinovirus (37.0%) was the most common viral pathogen. Significantly more patients in Group I had community-acquired respiratory illnesses (p=0.003) and complained of rhinorrhea (p<0.001) and sputum (p=0.008) than those in Group II. In Group I, significantly more patients with lower respiratory infections had uncontrolled underlying malignancies (p=0.038) and received re-induction or palliative chemotherapy (p=0.006) than those with upper respiratory infections.

Conclusions

A multiplex PCR test should be considered for RVI diagnosis in immunocompromised children and adolescents with respiratory symptoms, especially in those with rhinorrhea or sputum prominent over a cough. The early application of the PCR test in patients with uncontrolled underlying malignancies may improve outcomes.

Vaginosis. Vaginal microbiota

The latest advances in the vaginal microbiome and molecular diagnosis of bacterial vaginosis have allowed for a better knowledge of this entity, characterising aspects of its pathogenesis and the establishment of the vaginal biolayer, the models and new theories of its aetiology, how it is transmitted, with it being considered nowadays as a probable sexually transmitted infection, the separation of other entities such as aerobic vaginosis, its molecular diagnosis and treatment with new molecules to prevent frequent relapses. This entity and the study of the vaginal microbiome have made it possible to consider these infections as a polymicrobial syndrome, putting an end to the dogma: one microorganism, one disease. In addition, a lesser-known entity such as aerobic vaginosis and the methods for its detection are updated.

Metagenomics to Assist in the Diagnosis of Bloodstream Infection

BACKGROUND

Metagenomic next-generation sequencing (mNGS) has emerged as a promising technology that enables pan-pathogen detection from any source. However, clinical utility and practical integration into the clinical microbiology work flow and a bloodstream infection detection algorithm are currently uncharted. In the context of bloodstream infections, the challenges associated with blood culture, including sensitivity, postantibiotic treatment, attaining sufficient volumes sufficient volumes, and turnaround time, are well-known. Molecular assays have helped expedite turnaround time, especially when performed directly from positive culture media bottles. mNGS offers an unbiased but more complex version of molecular testing directly from sample, but it is unclear how and if it should be implemented in the clinical microbiology laboratory today.

CONTENT

Here we map out the potential utility and application of mNGS tests to infectious disease diagnostics from blood sources, including intrinsic limitations of the methodology in diagnosing bloodstream infections and sepsis vs DNAemia, current barriers to integration into routine workup, and milestones that may need to be met before implementation.

SUMMARY

Polymerases and pores move faster than bugs divide, so the thermodynamics of mNGS adoption for bloodstream infection is favorable. Nonetheless, considerable activation barriers exist that will slow this likely diagnostic transition. We eagerly await the manufacturer who designs an integrated sample-to-answer box to do for mNGS what has been done for other aspects of molecular detection.

Single Academic Center Experience of Unrestricted β-d-Glucan Implementation

We investigated serum β-d-glucan (BDG) testing among non-neutropenic adult inpatients at an academic center where the test is unrestricted. BDG orders were inappropriate in 49% of cases due to absence of predisposing host factors or clinical picture consistent with fungal infection. Providers' knowledge about BDG was insufficient.