Surveillance strategies using routine microbiology for antimicrobial resistance in low- and middle-income countries

BackgroundRoutine microbiology results are a valuable source of antimicrobial resistance (AMR) surveillance data in low- and middle-income countries (LMICs) as well as in high-income countries. Different approaches and strategies are used to generate AMR surveillance data.ObjectivesWe aimed to review strategies for AMR surveillance using routine microbiology results in LMICs and to highlight areas that need support to generate high-quality AMR data.SourcesWe searched PubMed for papers that used routine microbiology to describe the epidemiology of AMR and drug-resistant infections in LMICs. We also included papers that, from our perspective, were critical in highlighting the biases and challenges or employed specific strategies to overcome these in reporting AMR surveillance in LMICs.ContentTopics covered included strategies of identifying AMR cases (including case-finding based on isolates from routine diagnostic specimens and case-based surveillance of clinical syndromes), of collecting data (including cohort, point-prevalence survey, and case–control), of sampling AMR cases (including lot quality assurance surveys), and of processing and analysing data for AMR surveillance in LMICs.ImplicationsThe various AMR surveillance strategies warrant a thorough understanding of their limitations and potential biases to ensure maximum utilization and interpretation of local routine microbiology data across time and space. For instance, surveillance using case-finding based on results from clinical diagnostic specimens is relatively easy to implement and sustain in LMIC settings, but the estimates of incidence and proportion of AMR is at risk of biases due to underuse of microbiology. Case-based surveillance of clinical syndromes generates informative statistics that can be translated to clinical practices but needs financial and technical support as well as locally tailored trainings to sustain. Innovative AMR surveillance strategies that can easily be implemented and sustained with minimal costs will be useful for improving AMR data availability and quality in LMICs.     

Setting up laboratory-based antimicrobial resistance surveillance in low- and middle-income countries: lessons learned from Georgia

BackgroundAntimicrobial resistance (AMR) is a growing problem worldwide, with an estimated high burden in low- and middle-income countries (LMICs). In these settings, tackling the problem of AMR is often constrained by a lack of reliable surveillance data due to limited use of microbiological diagnostics in clinical practice.ObjectivesThe aim of this article is to present an overview of essential elements for setting up an AMR surveillance system in LMICs, to summarize the steps taken to develop such a system in the country of Georgia, and to describe its impact on microbiology laboratories.SourcesA literature review of published papers using PubMed and experiences of experts involved in setting up AMR surveillance in Georgia.ContentBasic requirements for implementing a laboratory-based surveillance system in LMICs can be captured under four pillars: (a) governmental support, (b) laboratory capacity and quality management, (c) materials and supplies, and (d) sample collection, data management, analysis and reporting. In Georgia, the World Health Organization Proof-of-Principle project helped to start the collection of AMR surveillance data on a small scale by promoting the use of microbiological diagnostics in clinics, and by providing training and materials for laboratories. Thanks to governmental support and a strong lead by the national reference laboratory, the AMR surveillance network was sustained and expanded after the project ended.ImplicationsThis review describes the Georgian approach in building and expanding a functional AMR surveillance system, considering the elements identified from the literature. The introduction of quality management systems, standardization of guidelines and training paired with targeted capacity building led to improved laboratory standards and management of patients with bloodstream infections. Reliable AMR surveillance data may inform and facilitate policy-making on AMR control. The Georgian experience can guide other countries in the process of building up their national AMR surveillance system.     

Operational models and criteria for incorporating microbial whole genome sequencing in hospital microbiology – A systematic literature review

BackgroundMicrobial whole genome sequencing (WGS) has many advantages over standard microbiological methods. However, it is not yet widely implemented in routine hospital diagnostics due to notable challenges.ObjectivesThe aim was to extract managerial, financial and clinical criteria supporting the decision to implement WGS in routine diagnostic microbiology, across different operational models of implementation in the hospital setting.MethodsThis was a systematic review of literature identified through PubMed and Web of Science. English literature studies discussing the applications of microbial WGS without limitation on publication date were eligible. A narrative approach for categorization and synthesis of the sources identified was adopted.ResultsA total of 98 sources were included. Four main alternative operational models for incorporating WGS in clinical microbiology laboratories were identified: full in-house sequencing and analysis, full outsourcing of sequencing and analysis and two hybrid models combining in-house/outsourcing of the sequencing and analysis components. Six main criteria (and multiple related sub-criteria) for WGS implementation emerged from our review and included cost (e.g. the availability of resources for capital and operational investment); manpower (e.g. the ability to provide training programmes or recruit trained personnel), laboratory infrastructure (e.g. the availability of supplies and consumables or sequencing platforms), bioinformatics requirements (e.g. the availability of valid analysis tools); computational infrastructure (e.g. the availability of storage space or data safety arrangements); and quality control (e.g. the existence of standardized procedures).ConclusionsThe decision to incorporate WGS in routine diagnostics involves multiple, sometimes competing, criteria and sub-criteria. Mapping these criteria systematically is an essential stage in developing policies for adoption of this technology, e.g. using a multicriteria decision tool. Future research that will prioritize criteria and sub-criteria that were identified in our review in the context of operational models will inform decision-making at clinical and managerial levels with respect to effective implementation of WGS for routine use. Beyond WGS, similar decision-making challenges are expected with respect to future integration of clinical metagenomics.     

The unintended contribution of clinical microbiology laboratories to climate change and mitigation strategies: a combination of descriptive study,short survey,literature review and opinion

ObjectiveClimate change poses a significant threat to humanity and human activity is largely responsible for it. Clinical microbiology laboratories have their unintended shares in carbon dioxide (CO₂) emissions. The aim of this study is to estimate CO₂ emission of a clinical microbiology laboratory and to propose initiatives to reduce the emissions.MethodsCO₂ emission of instruments was estimated based on their electricity consumption. CO₂ emitted in producing consumables was estimated by weighing the consumables needed to perform major tests in a large academic hospital. A systematic literature review was performed to identify studies on the impact of clinical microbiology laboratories on the environment. A short survey was sent to four major manufacturers of agar plates on initiatives to reduce the environmental impact of their products. Opinion was given on activities that can reduce CO₂ emission in laboratories.ResultsThe study shows that the largest amount of CO₂ emission in the microbiological laboratories comes from consumables and personnel commuting. For example, the production and transportation of agar plates needed to culture samples for a year in a hospital with 1320 beds result in 16 590 kg CO₂ is emitted. All survey participants mentioned that they were committed to reduce environmental impact of their products. The initiatives to reduce CO₂ emission can be performed at the laboratory and at policy level, such as reducing the number of tests to only the necessary amount to reduce consumables.DiscussionThe calculations contribute to map CO₂-related emissions in clinical microbiology laboratory activities, and the proposed initiatives to reduce the CO₂ may serve as starting point for further discussions.     

Practical issues in implementing whole-genome-sequencing in routine diagnostic microbiology

BackgroundNext generation sequencing (NGS) is increasingly being used in clinical microbiology. Like every new technology adopted in microbiology, the integration of NGS into clinical and routine workflows must be carefully managed.AimTo review the practical aspects of implementing bacterial whole genome sequencing (WGS) in routine diagnostic laboratories.SourcesReview of the literature and expert opinion.ContentIn this review, we discuss when and how to integrate whole genome sequencing (WGS) in the routine workflow of the clinical laboratory. In addition, as the microbiology laboratories have to adhere to various national and international regulations and criteria for their accreditation, we deliberate on quality control issues for using WGS in microbiology, including the importance of proficiency testing. Furthermore, the current and future place of this technology in the diagnostic hierarchy of microbiology is described as well as the necessity of maintaining backwards compatibility with already established methods. Finally, we speculate on the question of whether WGS can entirely replace routine microbiology in the future and the tension between the fact that most sequencers are designed to process multiple samples in parallel whereas for optimal diagnosis a one-by-one processing of the samples is preferred. Special reference is made to the cost and turnaround time of WGS in diagnostic laboratories.ImplicationsFurther development is required to improve the workflow for WGS, in particular to shorten the turnaround time, reduce costs, and streamline downstream data analyses. Only when these processes reach maturity will reliance on WGS for routine patient management and infection control management become feasible, enabling the transformation of clinical microbiology into a genome-based and personalized diagnostic field.     

Misattributed parentage as an unanticipated finding during exome/genome sequencing: current clinical laboratory practices and an opportunity for standardization

PurposeClinical laboratories performing exome or genome sequencing (ES/GS) are familiar with the challenges associated with proper consenting for and reporting of medically actionable secondary findings based on recommendations from the American College of Medical Genetics and Genomics (ACMG). Misattributed parentage is another type of unanticipated finding a laboratory may encounter during family-based ES/GS; however, there are currently no professional recommendations related to the proper consenting for and reporting of misattributed parentage encountered during ES/GS.MethodsWe surveyed 10 clinical laboratories offering family-based ES/GS regarding their consent language, discovery, and reporting of misattributed parentage.ResultsMany laboratories have already developed their own practices/policies for these issues, which do not necessarily agree with those from other labs.ConclusionThere are several other possibilities besides true misattributed parentage that could result in similar laboratory findings, and laboratories often feel they lack sufficient information to make formal conclusions on a report regarding the true genetic relatedness of the submitted samples. However, understanding the genetic relatedness (or lack thereof) of the samples submitted for family-based ES/GS has medical relevance. Therefore, professional recommendations for the appropriate handling of suspected misattributed parentage encountered during ES/GS are needed to help standardize current clinical laboratory practices.     

How to isolate,identify and determine antimicrobial susceptibility of anaerobic bacteria in routine laboratories

BackgroundThere has been increased interest in the study of anaerobic bacteria that cause human infection during the past decade. Many new genera and species have been described using 16S rRNA gene sequencing of clinical isolates obtained from different infection sites with commercially available special culture media to support the growth of anaerobes. Several systems, such as anaerobic pouches, boxes, jars and chambers provide suitable anaerobic culture conditions to isolate even strict anaerobic bacteria successfully from clinical specimens. Beside the classical, time-consuming identification methods and automated biochemical tests, the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry has revolutionized identification of even unusual and slow-growing anaerobes directly from culture plates, providing the possibility of providing timely information about anaerobic infections.AimsThe aim of this review article is to present methods for routine laboratories, which carry out anaerobic diagnostics on different levels.SourcesRelevant data from the literature mostly published during the last 7 years are encompassed and discussed.ContentThe review involves topics on the anaerobes that are members of the commensal microbiota and their role causing infection, the key requirements for collection and transport of specimens, processing of specimens in the laboratory, incubation techniques, identification and antimicrobial susceptibility testing of anaerobic bacteria. Advantages, drawbacks and specific benefits of the methods are highlighted.ImplicationsThe present review aims to update and improve anaerobic microbiology in laboratories with optimal conditions as well as encourage its routine implementation in laboratories with restricted resources.     

Surge capacity for response to bioterrorism in hospital clinical microbiology laboratories

Surge capacity is the ability to rapidly mobilize to meet an increased demand. While large amounts of federal funding have been allocated to public health laboratories, little federal funding has been allocated to hospital microbiology laboratories. There are concerns that hospital laboratories may have inadequate surge capacities to deal with a significant bioterrorism incident. A workflow analysis of a clinical microbiology laboratory that serves an urban medical center was performed to identify barriers to surge capacity in the setting of a bioterrorism event and to identify solutions to these problems. Barriers include a national shortage of trained medical technologists, the inability of clinical laboratories to deal with a dramatic increase in the number of blood cultures, a delay while manufacturers increase production of critical products and then transport and deliver these products to clinical laboratories, and a shortage of class II biological safety cabinets. Federal funding could remedy staffing shortages by making the salaries of medical technologists comparable to those of similarly educated health care professionals and by providing financial incentives for students to enroll in clinical laboratory science programs. Blood culture bottles, and possibly continuous-monitoring blood culture instruments, should be added to the national antibiotic stockpile. Federal support must ensure that companies that manufacture essential laboratory supplies are capable of rapidly scaling up production. Hospitals must provide increased numbers of biological safety cabinets and amounts of space dedicated to clinical microbiology laboratories. Laboratories should undertake limited cross-training of technologists, ensure that adequate packaging supplies are available, and be able to move to a 4-day blood culture protocol.     

A Side-by-Side Comparison of Clinical versus Current Good Manufacturing Practices (cGMP) Microbiology Laboratory Requirements for Sterility Testing of Cellular and Gene Therapy Products

Over the last few years, there have been numerous discussions on the American Society for Microbiology’s clinical listservs (DivC, and ClinMicroNet) regarding sterility testing of cell and gene therapy products and environmental monitoring and gloved fingertip testing for hospital pharmacies. Clinical microbiology laboratories have often been asked to assist with testing due to the on-site proximity of laboratory equipment and microbiological expertise within the hospital environment. The role of the clinical microbiology laboratory in this setting, however, is questionable due to major differences in test requirements and regulatory oversight. Here, we provide a side-by-side comparison of clinical versus current good manufacturing practices microbiology laboratories to provide guidance to those that are currently assisting with or have been asked to assist with sterility testing of manufactured biopharmaceutical products that have become common frontline treatments in modern medicine.     

Digital microbiology

BackgroundDigitalization and artificial intelligence have an important impact on the way microbiology laboratories will work in the near future. Opportunities and challenges lie ahead to digitalize the microbiological workflows. Making efficient use of big data, machine learning, and artificial intelligence in clinical microbiology requires a profound understanding of data handling aspects.ObjectiveThis review article summarizes the most important concepts of digital microbiology. The article gives microbiologists, clinicians and data scientists a viewpoint and practical examples along the diagnostic process.SourcesWe used peer-reviewed literature identified by a PubMed search for digitalization, machine learning, artificial intelligence and microbiology.ContentWe describe the opportunities and challenges of digitalization in microbiological diagnostic processes with various examples. We also provide in this context key aspects of data structure and interoperability, as well as legal aspects. Finally, we outline the way for applications in a modern microbiology laboratory.ImplicationsWe predict that digitalization and the usage of machine learning will have a profound impact on the daily routine of laboratory staff. Along the analytical process, the most important steps should be identified, where digital technologies can be applied and provide a benefit. The education of all staff involved should be adapted to prepare for the advances in digital microbiology.     

Brucella abortus RB51 Strain Sent in a Proficiency Testing Panel to Clinical and Public Health Laboratories

In early 2017, a laboratory proficiency testing panel, designed to assess laboratory competency for culture and identification of bacterial organisms, was distributed to clinical and public health microbiology laboratories. The panel included a Brucella abortus RB51 isolate. Although B. abortus RB51 is an attenuated Brucella species strain, it still poses some risk to laboratory personnel, particularly if safety precautions and personal protective equipment are not adequately deployed. The PT event highlighted the challenges that clinical and public health microbiology laboratories face when handling samples that can contain highly transmissible organisms that can lead to laboratory-acquired infections. This review describes the B. abortus RB51 PT event, its associated exposures, and subsequent medical interventions. General considerations for handling Brucella species, including RB51, in the clinical microbiology laboratory are also discussed. Finally, we describe lessons learned from this event, including improving a “culture of safety” in the clinical laboratory.     

The collaborative African genomics network training program: a trainee perspective on training the next generation of African scientists

PurposeThe Collaborative African Genomics Network (CAfGEN) aims to establish sustainable genomics research programs in Botswana and Uganda through long-term training of PhD students from these countries at Baylor College of Medicine. Here, we present an overview of the CAfGEN PhD training program alongside trainees’ perspectives on their involvement.BackgroundHistorically, collaborations between high-income countries (HICs) and low- and middle-income countries (LMICs), or North–South collaborations, have been criticized for the lack of a mutually beneficial distribution of resources and research findings, often undermining LMICs. CAfGEN plans to address this imbalance in the genomics field through a program of technology and expertise transfer to the participating LMICs.MethodsAn overview of the training program is presented. Trainees from the CAfGEN project summarized their experiences, looking specifically at the training model, benefits of the program, challenges encountered relating to the cultural transition, and program outcomes after the first 2 years.ConclusionCollaborative training programs like CAfGEN will not only help establish sustainable long-term research initiatives in LMICs but also foster stronger North–South and South–South networks. The CAfGEN model offers a framework for the development of training programs aimed at genomics education for those for whom genomics is not their “first language.”Genet Med advance online publication 06 April 2017     

Evaluation of six commercial products for colistin susceptibility testing in Enterobacterales

ObjectivesThe recommended technique for colistin susceptibility testing by both EUCAST and CLSI is broth microdilution (BMD). However, many routine laboratories still use other methods such as gradient strips or semi-automated systems. The objective of this study was to compare six of the most widespread commercial products for colistin susceptibility testing in Europe with in-house prepared BMD.MethodsA collection of 325 carbapenemase-producing Enterobacterales was tested for colistin susceptibility with three semi-automated systems (Vitek 2, BD Phoenix, MicroScan WalkAway), one gradient-strip test (Etest®) and two commercial BMD products (MICRONAUT-S, TREK Sensititre). BMD, in-house prepared according to ISO standard 20776-1, served as reference.ResultsThe MICRONAUT-S BMD performed best with only one false-resistant (major error, ME) and four false-susceptible (very major error, VME) results while the TREK BMD performed poorer with 16 ME and seven VME. The semi-automated systems Vitek 2 and Phoenix performed poorly with 31 and 26 VME, respectively. The WalkAway semi-automated system showed 16 and 13 false results, depending on the inoculation method. The Etest® showed six ME and 10 VME.ConclusionsThis study shows that colistin susceptibility testing remains a challenging task for laboratories. It emphasizes the need for selecting the most reliable test method to advocate proper treatment and shows that critical evaluation and precautious usage of colistin susceptibility testing results is constantly required.     

How to: accreditation of blood cultures' proceedings. A clinical microbiology approach for adding value to patient care

BackgroundQuality assurance and quality management are driving forces for controlling blood culture best practices but should not be disconnected from the end-point target, i.e. patient value.AimsThis article is intended to help microbiologists implement blood culture accreditation that is actually beneficial to patient management.SourcesExperience from a nationwide taskforce for promoting quality assurance and competence in clinical microbiology laboratories, guidelines on blood culture.ContentExperience in blood culture accreditation according to International standard ISO 15189 standards is provided in this review, with a particular focus on critical points that are specific to blood culture (e.g. excluding strain identification or antimicrobial susceptibility testing). Blood culture test method verification is based on risk analysis, and evaluation of the test method's performance is based on the literature review and suppliers' data. In addition, blood culture performance relies largely on the quality of its pre-analytical phase, and the test method should be monitored based on key performance indicators such as the volume of blood cultured, the contamination rate and time to transportation. Other critical key indicators include the rate of false-positive signals, the rate of positive blood cultures, the ecology associated with positive results, and the timely communication of the results to the ward during the post-analytical phase. Finally, a critical analysis of quality controls and of the tools needed to improve blood culture monitoring in the future is provided.ImplicationAppropriate quality assurance should focus on patient value rather than technical details to provide an appropriate clinical service.     

Ethical,social, and cultural issues related to clinical genetic testing and counseling in low- and middle-income countries: a systematic review

PurposeWe performed a systematic review of the ethical, social, and cultural issues associated with delivery of genetic services in low- and middle-income countries (LMICs).MethodsWe searched 11 databases for studies addressing ethical, social, and/or cultural issues associated with clinical genetic testing and/or counselling performed in LMICs. Narrative synthesis was employed to analyze findings, and resultant themes were mapped onto the social ecological model (PROSPERO #CRD42016042894).ResultsAfter reviewing 13,308 articles, 192 met inclusion criteria. Nine themes emerged: (1) genetic counseling has a tendency of being directive, (2) genetic services have psychosocial consequences that require improved support, (3) medical genetics training is inadequate, (4) genetic services are difficult to access, (5) social determinants affect uptake and understanding of genetic services, (6) social stigma is often associated with genetic disease, (7) family values are at risk of disruption by genetic services, (8) religious principles pose barriers to acceptability and utilization of genetic services, and (9) cultural beliefs and practices influence uptake of information and understanding of genetic disease.ConclusionWe identified a number of complex and interrelated ethical, cultural, and social issues with implications implications for further development of genetic services in LMICs.     

Evaluation of ten brands of pre-poured Mueller-Hinton agar plates for EUCAST disc diffusion testing

ObjectivesMueller-Hinton agar (MHA) is recommended by EUCAST and CLSI for disc diffusion antimicrobial susceptibility testing (AST). We have previously investigated the quality of dehydrated MHA from several manufacturers. In this study, we evaluated the performance of ten commercial brands of pre-poured MHA plates.MethodsAST was performed according to EUCAST methodology and results analyzed against targets and ranges in EUCAST quality control (QC) tables. MHA plates from different brands were tested in triplicate against four non-fastidious QC strains. The agar depth and pH were measured for all products.ResultsThe best performance was observed for MHA from Becton Dickinson (BBL MHA II), bioMérieux (MHE agar) and Hardy Diagnostics, for which >97% of zone diameters were within QC ranges and >60% on target ±1 mm. The poorest performance was seen for plates from HiMedia (MHA and MHA no. 2), where 20% and 18% of readings were outside the QC ranges, respectively. The differences in pH and agar depth of the products were small and mostly within EUCAST specifications.DiscussionThe accuracy and reproducibility of disc diffusion AST depends on standardised procedures and high-quality discs and media. The performance among ten brands of pre-poured MHA plates differed significantly. The results indicate a poorer performance for pre-poured commercial plates as compared to in-house prepared plates from dehydrated powder of corresponding brands in our previous study. Manufacturers and clinical laboratories have a shared responsibility for the quality of AST. EUCAST provides QC criteria to be used both by manufacturers and laboratories.     

Microbiological diagnostics of bloodstream infections in Europe—an ESGBIES survey

ObjectivesHigh-quality diagnosis of bloodstream infections (BSI) is important for successful patient management. As knowledge on current practices of microbiological BSI diagnostics is limited, this project aimed to assess its current state in European microbiological laboratories.MethodsWe performed an online questionnaire-based cross-sectional survey comprising 34 questions on practices of microbiological BSI diagnostics. The ESCMID Study Group for Bloodstream Infections, Endocarditis and Sepsis (ESGBIES) was the primary platform to engage national coordinators who recruited laboratories within their countries.ResultsResponses were received from 209 laboratories in 25 European countries. Although 32.5% (68/209) of laboratories only used the classical processing of positive blood cultures (BC), two-thirds applied rapid technologies. Of laboratories that provided data, 42.2% (78/185) were able to start incubating BC in automated BC incubators around-the-clock, and only 13% (25/192) had established a 24-h service to start immediate processing of positive BC. Only 4.7% (9/190) of laboratories validated and transmitted the results of identification and antimicrobial susceptibility testing (AST) of BC pathogens to clinicians 24 h/day. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry from briefly incubated sub-cultures on solid media was the most commonly used approach to rapid pathogen identification from positive BC, and direct disc diffusion was the most common rapid AST method from positive BC.ConclusionsLaboratories have started to implement novel technologies for rapid identification and AST for positive BC. However, progress is severely compromised by limited operating hours such that current practice of BC diagnostics in Europe complies only partly with the requirements for optimal BSI management.     

Methods for isolation ofBordetella pertussis from patients with whooping cough

Culture remains the standard method for diagnosis of whooping cough. While in the past attempts at isolatingBordetella pertussis from patients with suspected whooping cough were often unsuccessful, new methods have recently been developed which are suitable for use in routine microbiology laboratories. Recent advances include the use of calcium alginate tipped swabs for taking nasopharyngeal swabs, use of charcoal horse blood agar for transport and culture, and the inclusion of cephalexin as a selective agent in agar media. Experience shows that careful application of these new methods often enablesBordetella pertussis to be isolated from clinical specimens, thereby permitting a diagnosis to be made at an early stage of the disease.     

Evaluation of CandiSelect4, a new chromogenic medium for isolation and presumptive identification of Candida species from clinical specimens

In clinical laboratories, isolation of Candida species is generally based on the culture of specimens on Sabouraud dextrose agar. This strategy does not allow species identification on primary culture and makes it difficult to detect mixed cultures. Chromogenic media contain substrates that react specifically with different Candida species, and partly overcome these difficulties.ObjectivesThe aim of this study was to compare two chromogenic media: (i) CandiSelect4 (C4), a new medium developed for direct identification of C. albicans and presumptive identification of C. krusei, C. tropicalis and C. glabrata (ii) CHROMagar Candida (CH), a medium licensed for direct identification of C. albicans, and presumptive identification of C. tropicalis and C. krusei, and employed in our laboratory since 2002.Materials and methodsAltogether, 533 clinical specimens were seeded on both media. Identification on C4 was compared to that achieved on CH, API 32 C test or an in-house C. glabrata rapid identification test.ResultsDiscrepant positive cultures occurred in 16 samples and were shared equally between C4 and CH. The ability of both media to detect associations was equivalent, with 34 associations identified with C4 and CH. No discrepancy was observed with respect to identification of C. albicans. C4 identified six of six C. krusei, but false-negative identification of C. tropicalis occurred in 2/11 cases and false-positive identification of C. glabrata occurred in 2/34 cases.ConclusionsThe overall performance of C4 and CH appeared almost identical during a two-month comparison in the clinical mycology setting.     

Rapid phenotypic methods to improve the diagnosis of bacterial bloodstream infections: meeting the challenge to reduce the time to result

BackgroundAdministration of appropriate antimicrobial therapy is one of the key factors in surviving bloodstream infections. Blood culture is currently the reference standard for diagnosis, but conventional practices have long turnaround times while diagnosis needs to be faster to improve patient care. Phenotypic methods offer an advantage over genotypic methods in that they can identify a wide range of taxa, detect the resistance currently expressed, and resist genetic variability in resistance detection.AimsWe aimed to discuss the wide array of phenotypic methods that have recently been developed to substantially reduce the time to result from identification to antibiotic susceptibility testing.SourcesA literature review focusing on rapid phenotypic methods for improving the diagnosis of bloodstream infection was the source.ContentRapid phenotypic bacterial identification corresponds to Matrix-assisted laser-desorption/ionization time of flight mass spectrometry (MALDI-TOF), and rapid antimicrobial susceptibility testing methods comprised of numerous different approaches, are considered and critically assessed. Particular attention is also paid to emerging technologies knocking at the door of routine microbiology laboratories. Finally, workflow integration of these methods is considered.ImplicationsThe broad panel of phenotypic methods currently available enables healthcare institutions to draw up their own individual approach to improve bloodstream infection diagnosis but requires a thorough evaluation of their workflow integration. Clinical microbiology will probably move towards faster methods while maintaining a complex multi-method approach as there is no all-in-one method.