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Medical microbiologists, defined as doctoral-level laboratory directors with subspecialty training in medical microbiology, lead the clinical laboratory operations through activities such as clinical consultations, oversight of diagnostic testing menu, institutional leadership, education, and scholastic activities. However, unlike their clinical colleagues, medical microbiologists are largely unable to bill for clinical consultations performed within the hospital and, therefore, unable to generate relative value units or a similar quantifiable metric. As hospital budgets tighten and justification of staffing becomes a necessity, this may present a challenge to the medical microbiologist attempting to prove their value to the organization. To aid in providing tangible data, the Personnel Standards and Workforce subcommittee of the American Society for Microbiology conducted a multi-center study across seven medical centers to document clinical consultations and their impact. Consults were generated equally from internal (laboratory-based) and external (hospital-based) parties, with the majority directly impacting patient management. Near universal acceptance of the medical microbiologist's recommendation highlights the worth derived from their expertise. External consults required more time commitment from the medical microbiologist than internal consults, although both presented ample opportunity for secondary value, including impact through stewardship, education, clinical guidance, and cost reduction. This study is a description of the content and impact of consultations that underscore the importance of the medical microbiologist as a key member of the healthcare team. IMPORTANCE: Medical microbiologists are invaluable to the clinical microbiology laboratory and the healthcare system as a whole. However, as medical microbiologists do not regularly generate relative value units, capturing and quantifying the value provided is challenging. As hospital budgets tighten, justification of staffing becomes a necessity. To aid in providing tangible data, the Personnel Standards and Workforce subcommittee of the American Society for Microbiology conducted a multi-center study across seven medical centers to document clinical consultations and their impact. To our knowledge, this is the first study to provide detailed evaluation of the consultative value provided by medical microbiologists.
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Invasive fungal infections are increasing worldwide due to factors such as climate change and immunomodulating therapies. Unfortunately, the detection of these infections is limited due to the low sensitivity and long periods required for laboratory testing. Point-of-care testing could lead to more rapid diagnosis of these often devasting infections. However, there are currently no true point-of-care tests on the market for the detection of fungi. In this article, the current state of fungal antigen and molecular testing is reviewed, with commentary on the potential for development and use in the point-of-care setting.
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Micoses , Humanos , Micoses/diagnóstico , Testes Imediatos , Antígenos de Fungos , Sistemas Automatizados de Assistência Junto ao Leito , Técnicas de Diagnóstico Molecular , Sensibilidade e Especificidade , MananasRESUMO
The Streptococcus bovis group (previously group D streptococci) consists of seven distinct species and subspecies. Definitive identification within the group is important, as certain organisms have been associated with gastrointestinal carcinoma, bacteremia, infective endocarditis, meningitis, biliary tract disease, and carcinoma, among others. Definitive identification, however, remains elusive due to limitations and inconsistencies across commonly used identification platforms in the United States. Here, we compared the performance of standard biochemical (Trek Gram-positive identification [GPID] plate, Vitek 2 GPID), sequencing (16S rDNA, sodA) databases (NCBI, RDP, CDC MicrobeNet), and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) platforms (Vitek MS, Bruker Biotyper MS) using a set of eight type strains representing all seven strains within the S. bovis group. Despite the evaluation of contemporary methods, no single platform was able to definitively identify all type strains within the S. bovis group. Vitek MS (85.7%, 7/8) provided the most accurate definitive identifications, followed by sodA sequencing (75%, 6/8). Vitek 2 and Bruker Biotyper RUO platforms performed the next best (62.5%, 5/8). All remaining platforms failed to adequately differentiate type strains within the S. bovis group (range, 0 to 37.5%). Laboratorians and clinicians should be aware of the identification limitations of routine testing algorithms and incorporate reflex testing, when appropriate, to platforms such as Vitek MS and/or sodA sequencing that are more able to definitively identify S. bovis group organisms. Further clinical evaluation was conducted using 65 clinical isolates from three geographically distinct U.S. institutions. Future improvements in identification platforms may reveal new clinical and epidemiological trends for members of the S. bovis group.
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Bacteriemia , Endocardite , Streptococcus bovis , Humanos , Streptococcus bovis/genética , Proteômica , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodosRESUMO
OBJECTIVES: We evaluated the clinical characteristics and outcomes of patients with COVID-19 who received three-drug combination regimens for treatment of carbapenem-resistant Acinetobacter baumannii (CRAB) infections during a single-centre outbreak. Our objective was to describe the clinical outcomes and molecular characteristics and in vitro synergy of antibiotics against CRAB isolates. MATERIALS AND METHODS: Patients with severe COVID-19 admitted between April and July 2020 with CRAB infections were retrospectively evaluated. Clinical success was defined as resolution of signs/symptoms of infection without need for additional antibiotics. Representative isolates underwent whole-genome sequencing (WGS) and in vitro synergy of two- or three-drug combinations was assessed by checkerboard and time-kill assays, respectively. RESULTS: Eighteen patients with CRAB pneumonia or bacteraemia were included. Treatment regimens included high-dose ampicillin-sulbactam, meropenem, plus polymyxin B (SUL/MEM/PMB; 72%), SUL/PMB plus minocycline (MIN; 17%) or other combinations (12%). Clinical resolution was achieved in 50% of patients and 30-day mortality was 22% (4/18). Seven patients had recurrent infections, during which further antimicrobial resistance to SUL or PMB was not evident. PMB/SUL was the most active two-drug combination by checkerboard. Paired isolates collected before and after treatment with SUL/MEM/PMB did not demonstrate new gene mutations or differences in the activity of two- or three-drug combinations. CONCLUSIONS: Use of three-drug regimens for severe CRAB infections among COVID-19 resulted in high rates of clinical response and low mortality relative to previous studies. The emergence of further antibiotic resistance was not detected phenotypically or through WGS analysis. Additional studies are needed to elucidate preferred antibiotic combinations linked to the molecular characteristics of infecting strains.
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Infecções por Acinetobacter , Acinetobacter baumannii , COVID-19 , Humanos , Carbapenêmicos/farmacologia , Carbapenêmicos/uso terapêutico , Estudos Retrospectivos , Infecções por Acinetobacter/tratamento farmacológico , Sinergismo Farmacológico , Antibacterianos/uso terapêutico , Combinação de Medicamentos , Acinetobacter baumannii/genética , Testes de Sensibilidade MicrobianaRESUMO
BACKGROUND: The VITEK® 2 is generally accepted as a reliable method for predicting antibiotic resistance mechanisms including aminoglycoside phenotypes, beta lactam phenotypes, impermeability, and penicillinases. However, when it comes to predicting carbapenemases, the research that has been done is inconsistent in both methods and results. METHODS: We compared the predictions of the VITEK 2 and Advanced Expert System™ (AES) with the results of the modified carbapenemase inactivation method in an academic medical center lab to evaluate the clinical reliability of the VITEK 2 and AES in routine workflow for the detection of carbapenemases. RESULTS: Our findings show that the positive predictive value of carbapenemase detection on the VITEK2 and AES is 30.3% (91/300) in our patient population. CONCLUSIONS: In light of these results, we propose that the VITEK 2 and AES be used as a screening tool for carbapenemase-containing organisms rather than as a definitive test.
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Computadores , beta-Lactamases , Humanos , Reprodutibilidade dos Testes , Testes de Sensibilidade Microbiana , beta-Lactamases/genéticaRESUMO
Invasive fungal diseases cause significant morbidity and mortality, in particular affecting immunocompromised patients. Resistant organisms are of increasing importance, yet there are many notable differences in the ability to both perform and interpret antifungal susceptibility testing compared with bacteria. In this review, we will highlight the strengths and limitations of resistance data of pathogenic yeasts and moulds that may be used to guide treatment and predict clinical outcomes.
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We report a case of septic shock attributable to monomicrobial bloodstream infection secondary to Wohlfahrtiimonas chitiniclastica infection. This case suggests that W. chitiniclastica likely possesses the virulence to cause severe disease. Culture-independent techniques were essential in the identification of this organism, which enabled selection of appropriate therapy.
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Bacteriemia , Gammaproteobacteria , Infecções por Bactérias Gram-Negativas , Xanthomonadaceae , Bacteriemia/diagnóstico , Bacteriemia/tratamento farmacológico , Infecções por Bactérias Gram-Negativas/diagnóstico , Infecções por Bactérias Gram-Negativas/tratamento farmacológico , Humanos , MasculinoRESUMO
BACKGROUND: Streptococcus pyogenes, or Group A Streptococcus (GAS), is not considered a typical cause of infective endocarditis (IE), but has anecdotally been observed in unexpectedly high rates in people who inject drugs (PWID) at our institution. METHODS: All cases of possible or definite GAS IE per Modified Duke Criteria in adults at an academic hospital between 11/15/2015 and 11/15/2020 were identified. Medical records were reviewed for demographics, comorbidities, treatment, and outcomes related to GAS IE. The literature on cases of GAS IE was reviewed. RESULTS: Eighteen cases of probable (11) or definite (7) GAS IE were identified; the mean age was 38 years, and the population was predominantly female (56%) and Caucasian (67%), which is inconsistent with local population demographics. Sixteen cases were in people who inject drugs (PWID; 89%); 14 were also homeless, 6 also had HIV (33%), and 2 were also pregnant. Antibiotic regimens were variable due to polymicrobial bacteremia (39%). One patient underwent surgical valve replacement. Four patients (22%) died due to complications of infection. The literature review revealed 42 adult cases of GAS IE, only 17 of which were in PWID (24%). CONCLUSIONS: The 16 cases of possible and definite GAS IE in PWID over a 5-year period in a single institution reported nearly doubles the number of cases in PWID from all previous reports. This suggests a potential increase in GAS IE particularly in PWID and PWH, which warrants further epidemiologic investigation.
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BACKGROUND: The COVID-19 pandemic has strained clinical microbiology laboratories due to testing supply allocations. As a result, laboratories have had to invest in multiple COVID-19 assays performed on different testing instruments. Comparing the results achieved by testing positive samples between in-use assays can provide insights into which platforms may be interchangeable for testing in times of supply chain emergencies. METHODS: Nasopharyngeal and nasal swab specimens collected in viral transport media that tested positive on the Xpert® Xpress SARS-CoV-2 assay were tested on the ePlex® SARS-CoV-2 and BD SARS-CoV-2 Reagents for BD Max™ assays. Positive percent agreement was calculated using the Xpert Xpress SARS-CoV-2 assay as the reference method. RESULTS: We tested 78 positive swabs, resulting in a positive percentage agreement (PPA) of 92% (CI 84-97%) for the BD SARS-CoV-2 assay and 58% (CI 47-70%) for the ePlex assay. Following development of a new workflow for the ePlex, we detected SARS-CoV-2 in 7 additional samples, resulting in a new PPA of 68% (CI 56-78). CONCLUSIONS: During times of supply allocation and shortage of the Xpert Xpress SARS-CoV-2 assay, the BD SARS-CoV-2 assay is well suited to test substitutions due to its high PPA.
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COVID-19 , Pandemias , Humanos , RNA Viral/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , SARS-CoV-2 , Sensibilidade e EspecificidadeRESUMO
BACKGROUND: An evolving COVID-19 testing landscape and issues with test supply allocation, especially in the current pandemic, has made it challenging for ordering providers. We audited orders of the Xpert® Xpress SARS-CoV-2 PCR with reverse transcription (RT-PCR) platform-the fastest of several other testing modalities available-to illuminate these challenges utilizing a multidisciplinary laboratory professional team consisting of a pathology resident and microbiology laboratory director. METHODS: Retrospective review of the first 5 hundred Xpert Xpress SARS-CoV-2 RT-PCR test orders from a 2-week period to determine test appropriateness based on the following indications: emergency surgery, emergent obstetric procedures, initial behavioral health admission, and later including discharge to skilled care facilities and pediatric admissions. Our hypothesis was that a significant proportion of orders for this testing platform were inappropriate. RESULTS: On review, a significant proportion of orders were incorrect, with 69.8% (n = 349, P < 0.0001) not meeting indications for rapid testing. Of all orders, 249 designated as emergency surgery were inappropriate, with 49.0% of those orders never proceeding with any surgical intervention; most of these were trauma related (64.6% were orders associated with a trauma unit). CONCLUSIONS: Significant, pervasive inappropriate ordering practices were identified at this center. A laboratory professional team can be key to identifying problems in testing and play a significant role in combating inappropriate test utilization.
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COVID-19 , Centros Médicos Acadêmicos , Teste para COVID-19 , Criança , Feminino , Humanos , Gravidez , Estudos Retrospectivos , Reação em Cadeia da Polimerase Via Transcriptase Reversa , SARS-CoV-2RESUMO
Fungal infections are a rising threat to our immunocompromised patient population, as well as other nonimmunocompromised patients with various medical conditions. However, little progress has been made in the past decade to improve fungal diagnostics. To jointly address this diagnostic challenge, the Fungal Diagnostics Laboratory Consortium (FDLC) was recently created. The FDLC consists of 26 laboratories from the United States and Canada that routinely provide fungal diagnostic services for patient care. A survey of fungal diagnostic capacity among the 26 members of the FDLC was recently completed, identifying the following diagnostic gaps: lack of molecular detection of mucormycosis; lack of an optimal diagnostic algorithm incorporating fungal biomarkers and molecular tools for early and accurate diagnosis of Pneumocystis pneumonia, aspergillosis, candidemia, and endemic mycoses; lack of a standardized molecular approach to identify fungal pathogens directly in formalin-fixed paraffin-embedded tissues; lack of robust databases to enhance mold identification with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry; suboptimal diagnostic approaches for mold blood cultures, tissue culture processing for Mucorales, and fungal respiratory cultures for cystic fibrosis patients; inadequate capacity for fungal point-of-care testing to detect and identify new, emerging or underrecognized, rare, or uncommon fungal pathogens; and performance of antifungal susceptibility testing. In this commentary, the FDLC delineates the most pressing unmet diagnostic needs and provides expert opinion on how to fulfill them. Most importantly, the FDLC provides a robust laboratory network to tackle these diagnostic gaps and ultimately to improve and enhance the clinical laboratory's capability to rapidly and accurately diagnose fungal infections.
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Laboratórios , Mucorales , Canadá , Técnicas de Laboratório Clínico , Prova Pericial , HumanosAssuntos
Meningite por Listeria/complicações , Debilidade Muscular/etiologia , Hemocultura/métodos , Serviço Hospitalar de Emergência/organização & administração , Feminino , Humanos , Listeria monocytogenes/efeitos dos fármacos , Listeria monocytogenes/patogenicidade , Pessoa de Meia-Idade , Mieloma Múltiplo/complicações , Mieloma Múltiplo/fisiopatologiaRESUMO
BACKGROUND: Staphylococcus lugdunensis is a coagulase negative Staphylococcus species and frequent human skin commensal with the potential for aggressive infection. Guidance surrounding S. lugdunensis bacteremia (SLB) from a single set of blood cultures is lacking. METHODS: A multicenter, retrospective cohort of patients with SLB from at least one blood culture set within the University of Maryland Medical System from 2015 to 2019 is presented. Objectives are to describe baseline characteristics, compare the clinical status and treatment course, and to evaluate the clinical outcomes among patients with SLB in single versus multiple sets. RESULTS: Thirty-six patients were included, 24 with one set of blood cultures positive for S lugdunensis and 12 with multiple sets. Baseline characteristics were similar between the groups, though patients with SLB in multiple sets were more commonly on hemodialysis (Pâ¯=â¯0.029). Central lines were the most common source (17%). Most (97%) fulfilled systemic inflammatory response syndrome or Souvenir criteria, had an infectious focus on imaging, or had a second positive culture site. Most (78%) were treated as clinically significant. Patients with multiple positive sets were more commonly treated with antibiotics for >2 weeks (Pâ¯=â¯0.02). CONCLUSIONS: SLB was rare and occurred more frequently as a single set of positive cultures. Patient characteristics and clinical courses were similar between single and multiple set groups. Given the potential severity of S. lugdunensis bacteremia it seems prudent to treat S. lugdunensis in a single blood culture as true bacteremia, pending larger studies and guidelines.
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Bacteriemia/microbiologia , Infecções Estafilocócicas/sangue , Staphylococcus lugdunensis/isolamento & purificação , Adulto , Idoso , Idoso de 80 Anos ou mais , Hemocultura/métodos , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Estudos RetrospectivosAssuntos
Abscesso Encefálico/microbiologia , Nocardiose/diagnóstico , Nocardiose/microbiologia , Nocardia , Antibacterianos/uso terapêutico , Feminino , Humanos , Hospedeiro Imunocomprometido , Imunossupressores/farmacologia , Pessoa de Meia-Idade , Ácido Micofenólico/farmacologia , Nocardiose/patologia , Nocardiose/terapia , Prednisona/farmacologiaRESUMO
BACKGROUND: Sepsis is a life-threatening condition with high rates of morbidity and mortality; effective and appropriate antibiotic therapy is essential for ensuring patient improvement. To aid in the diagnosis of sepsis, blood cultures are drawn and sent to the microbiology laboratory for pathogen growth, identification, and susceptibility testing. The clinical microbiology laboratory can assist the medical team by providing timely identification of the pathogen(s) causing the bloodstream infection through the use of rapid diagnostic technology. One of these rapid diagnostic technologies, MALDI-TOF MS, has been proven to reduce the time required for appropriate antibiotic therapy when used to identify pathogens grown in culture. This technology has also been used to identify pathogens directly from the positive blood cultures with great success. CONTENT: In this minireview, we summarize the different methods that have been developed to directly identify pathogens from positive blood cultures by use of MALDI-TOF MS and the effect of this technology on patient outcomes. Additionally, we touch on current research in the field, including the identification of antimicrobial resistance directly from positive blood cultures by MALDI-TOF MS. SUMMARY: Rapid identification of pathogens is important in the survival of patients undergoing a septic event. MALDI-TOF MS technology has played an important role in rapid identification, which has led to a reduction in the time to appropriate antibiotic therapy and contributed to the improvement of patient outcomes. The high sensitivity and specificity of MALDI-TOF MS identification, in combination with MALDI-TOF's rapid function and reduced labor costs, make this technology an attractive choice for clinical laboratories.
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Bacteriemia/diagnóstico , Bactérias/isolamento & purificação , Hemocultura , Fungemia/diagnóstico , Fungos/isolamento & purificação , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz , Anti-Infecciosos/farmacologia , Anti-Infecciosos/uso terapêutico , Bacteriemia/tratamento farmacológico , Bacteriemia/microbiologia , Resistência Microbiana a Medicamentos , Fungemia/tratamento farmacológico , Fungemia/microbiologia , Humanos , Testes de Sensibilidade Microbiana/métodos , Sensibilidade e Especificidade , Fatores de Tempo , Tempo para o TratamentoRESUMO
The Mid-Atlantic Microbiome Meet-up (M3) organization brings together academic, government, and industry groups to share ideas and develop best practices for microbiome research. In January of 2018, M3 held its fourth meeting, which focused on recent advances in biodefense, specifically those relating to infectious disease, and the use of metagenomic methods for pathogen detection. Presentations highlighted the utility of next-generation sequencing technologies for identifying and tracking microbial community members across space and time. However, they also stressed the current limitations of genomic approaches for biodefense, including insufficient sensitivity to detect low-abundance pathogens and the inability to quantify viable organisms. Participants discussed ways in which the community can improve software usability and shared new computational tools for metagenomic processing, assembly, annotation, and visualization. Looking to the future, they identified the need for better bioinformatics toolkits for longitudinal analyses, improved sample processing approaches for characterizing viruses and fungi, and more consistent maintenance of database resources. Finally, they addressed the necessity of improving data standards to incentivize data sharing. Here, we summarize the presentations and discussions from the meeting, identifying the areas where microbiome analyses have improved our ability to detect and manage biological threats and infectious disease, as well as gaps of knowledge in the field that require future funding and focus.
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Armas Biológicas , Biologia Computacional/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Metagenômica/métodos , Humanos , Microbiota/fisiologia , Análise de Sequência de DNA/métodosRESUMO
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) has revolutionized fungal identification. Previously, we developed a MALDI-TOF MS mold extraction procedure and comprehensive database. While MALDI-TOF MS has become routine in a few laboratories, it has not yet become widespread. A major obstacle is the lack of a simple, reproducible and uniform protein extraction procedure. In this study, we developed and validated a rapid one-step protein extraction protocol for filamentous fungi. Excised molds were placed into tubes containing zirconia-silica beads and extraction solution without washing or ethanol inactivation steps. Extraction solutions containing different ratios of acetonitrile and formic acid were evaluated. Samples were then processed using a PowerLyzer high power bead based homogenizer and supernatants spotted for MALDI-TOF MS. The rapid method was evaluated prospectively and in parallel to our current mold extraction protocol for 3 months. Analysis of 106 clinical mold isolates resulted in an improved performance and a decrease in extraction time by 30 minutes to a total of 5 minutes of hands-on time. Acceptable identification scores (≥ 2.00) were achieved for up to 63.0% of mold isolates by the rapid method compared with 52.8% of isolates by the current routine protocol. Score comparisons between duplicate spots showed higher reproducibility of the rapid method as compared to the routine method. The rapid extraction method allows efficient analysis of clinical mold isolates both in scheduled batch runs and on an in-demand basis while providing a simple starting platform for laboratories adopting MALDI-TOF MS for mold identification.
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Fungos , Técnicas de Tipagem Micológica/métodos , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodos , Fungos/química , Fungos/classificação , Fungos/isolamento & purificação , Humanos , Micoses/microbiologia , Estudos Prospectivos , Reprodutibilidade dos TestesRESUMO
BACKGROUND: Autosplenectomy, as a result of sickle cell disease, is an important risk factor for severe malaria. While molecular methods are helpful in providing rapid and accurate infection detection and species identification, the effect of hyposplenism on result interpretation during the course of infection should be carefully considered. CASE PRESENTATION: A 32-year old autosplenectomized Nigerian male with severe sickle cell disease was referred to the National Institutes of Health for allogenic hematopoietic stem cell transplant. Despite testing negative for malaria by both smear and PCR 2 weeks after arrival in the USA, the patient developed fever and diffuse bilateral lower rib cage and upper abdominal pain 2 weeks later and subsequently tested positive for Plasmodium falciparum. Parasitaemia was tracked over time by microscopy and nucleic acid tests to evaluate the therapeutic response in the setting of hyposplenism. The patient showed prompt resolution of patent infection by microscopy but remained positive by molecular methods for > 30 days after treatment initiation. CONCLUSION: While molecular testing can provide sensitive Plasmodium nucleic acid detection, the persistence of Plasmodium nucleic acids following adequate treatment in functionally asplenic patients can lead to a diagnostic dilemma. In such patients, clinical response and peripheral blood smears should guide patient management following treatment. Nonetheless, in pre-transplant patients at high-risk for pre-existing Plasmodium infections, highly sensitive molecular assays can be useful to rule out infection prior to transplantation.