Expert systems in clinical microbiology

β-lactam resistant phenotypes reported by VITEK®2 advanced expert systemTM (AES) compared to whole genome sequencing in Enterobacterales from North and Latin America

The VITEK®2 AES β-lactam phenotypes of 488 Enterobacterales from North and Latin America generated by the VITEK®2 were compared to the resistance genotypes provided by whole genome sequencing (WGS). The AES provided phenotypic reports for 447 (91.6 %) isolates, including isolates harbouring carbapenemases (195; 43.6 %), ESBLs (103; 23.0 %) and transferable AmpCs (tAmpC; 28; 6.3 %) genes, as well as wildtype isolates (WT; 121; 27.1 %). Overall, the AES report was accurate for 433/447 (96.9 %) isolates. The AES accurately reported carbapenemase, ESBL, and tAmpC phenotypes for 93.7 %, 93.7 %, and 98.4 % of isolates, respectively, and sensitivity/specificity rates were 96.4 %/91.7 %, 98.1 %/92.4 %, 82.1 %/99.5 %, and 100 %/98.8 %. 14 isolates carrying carbapenemase (7 total; 3 KPC, 2 MBL, 2 OXA-48-like), ESBL (2), and tAmpC-encoding genes (5) were not correctly identified by AES. The AES phenotypic report detected resistance mechanisms among Enterobacterales rapidly and could significantly aid future antimicrobial stewardship initiatives and patient care.

Comparative Analysis of Two Commercial Automated Systems with Agar Dilution for Oxacillin Susceptibility and Their Association with Genotypes of Invasive Staphylococcus aureus Isolates (2011-2021)

Background

Determining oxacillin susceptibility using reference methods and automated systems is crucial for treating invasive infections caused by Staphylococcus aureus. This study compares the oxacillin susceptibility results from the two automated systems with agar dilution and correlates them with genotypes of invasive S. aureus.

Methods

Non-duplicate S. aureus invasive isolates were collected over an 11-year period. The oxacillin susceptibility was determined with Phoenix 100 (Jan 2011 to Aug 2018) or Vitek 2 (Sep 2018 to Dec 2021), and susceptibility for oxacillin and cefoxitin was determined with agar dilution. Methicillin-resistant S. aureus (MRSA) was confirmed with mecA existence, and the genotype was determined using SCCmec. The association between genotype and antibiotic susceptibility using two automated systems and agar dilution was evaluated.

Results

A total of 842 invasive S. aureus, including 443 mecA+ MRSA and 399 mecA- MSSA, were collected. The susceptibility rates of oxacillin determined by two automated systems and agar dilution were 68.8% (76.8% for Phoenix 100 and 57.6% for Vitek 2) and 54.0%, respectively. When compared with the oxacillin susceptibility using agar dilution, the categorical agreement for Phoenix 100 and Vitek 2 were 0.46% and 0.88%, respectively (p < 0.001). One hundred and forty-three isolates were misinterpreted as oxacillin-susceptible S. aureus (OSSA) using automated systems while comparing with agar dilution, among which molecularly community-associated MRSA (CA-MRSA) outnumbered healthcare-associated MRSA (HA-MRSA) (99 vs 34, p < 0.001). There were 70 mecA+ OSSA (OS-MRSA) using agar dilution, among which 42 harbored SCCmec types were predominantly categorized as CA-MRSA (38, p < 0.001).

Conclusion

The categorical agreement of Vitek 2 in determining oxacillin susceptibility and predicting mecA existence is comparable with agar dilution, whereas Phoenix 100 is not. Most of those ORSA determined by agar dilution but misinterpreted as OSSA by automated systems and OS-MRSA are categorized as CA-MRSA.

Microbiological Survey and Evaluation of Antimicrobial Susceptibility Patterns of Microorganisms Obtained from Suspect Cases of Canine Otitis Externa in Gran Canaria, Spain

A retrospective study of microbiological laboratory results from 2020 to 2022, obtained from a veterinary diagnostic laboratory of the island of Gran Canaria, Spain, focused on canine otitis cases, was performed. The objective of this study was to analyze the pathogen distribution, antimicrobial susceptibility, prevalence of multidrug resistant phenotypes and the role of coinfections in otitis cases in order to provide up-to-date evidence that could support effective control strategies for this prevalent pathology. A total of 604 submissions were processed for the diagnosis of canine external otitis. Of the samples analyzed, 472 were positive for bacterial or fungal growth (78.1%; 95% CI: 74.8-81.4%). A total of 558 microbiological diagnoses were obtained, divided in 421 bacterial (75.4%; 95% CI: 71.8-79.0%) and 137 fungal (24.6%; 95% CI: 20.9-28.1%) identifications. Staphylococcus pseudintermedius, Malassezia pachydermatis and Pseudomonas aeruginosa were the most prevalent microorganisms detected in clinical cases of otitis. High level antimicrobial resistance was found for Pseudomonas aeruginosa (30.7%), Proteus mirabilis (29.4%), Staphylococcus pseudintermedius (25.1%) and Escherichia coli (19%). Multidrug-resistant phenotypes were observed in 47% of the bacteria isolated. In addition, a 26.4% prevalence of methicillin-resistant Staphylococcus pseudintermedius was detected. The high prevalence of antimicrobial resistant phenotypes in these bacteria highlights the current necessity for constant up-to-date prevalence and antimicrobial susceptibility data that can support evidence-based strategies to effectively tackle this animal and public health concern.

Rapid Drug Susceptibility Testing to Preserve Antibiotics

Antibiotic resistance is a global challenge likely to cost trillions of dollars in excess costs in the health system and more importantly, millions of lives every year. A major driver of resistance is the absence of susceptibility testing at the time a healthcare worker needs to prescribe an antimicrobial. The effect is that many prescriptions are unintentionally wasted and expose mutable organisms to antibiotics increasing the risk of resistance emerging. Often simplistic solutions are applied to this growing issue, such as a naïve drive to increase the speed of drug susceptibility testing. This puts a spotlight on a technological solution and there is a multiplicity of such candidate DST tests in development. Yet, if we do not define the necessary information and the speed at which it needs to be available in the clinical decision-making progress as well as the necessary integration into clinical pathways, then little progress will be made. In this chapter, we place the technological challenge in a clinical and systems context. Further, we will review the landscape of some promising technologies that are emerging and attempt to place them in the clinic where they will have to succeed.

The Use of Machine Learning for Image Analysis Artificial Intelligence in Clinical Microbiology

The growing transition to digital microbiology in clinical laboratories creates the opportunity to interpret images using software. Software analysis tools can be designed to use human-curated knowledge and expert rules, but more novel artificial intelligence (AI) approaches such as machine learning (ML) are being integrated into clinical microbiology practice. These image analysis AI (IAAI) tools are beginning to penetrate routine clinical microbiology practice, and their scope and impact on routine clinical microbiology practice will continue to grow. This review separates the IAAI applications into 2 broad classification categories: (i) rare event detection/classification or (ii) score-based/categorical classification. Rare event detection can be used for screening purposes or for final identification of a microbe including microscopic detection of mycobacteria in a primary specimen, detection of bacterial colonies growing on nutrient agar, or detection of parasites in a stool preparation or blood smear. Score-based image analysis can be applied to a scoring system that classifies images in toto as its output interpretation and examples include application of the Nugent score for diagnosing bacterial vaginosis and interpretation of urine cultures. The benefits, challenges, development, and implementation strategies of IAAI tools are explored. In conclusion, IAAI is beginning to impact the routine practice of clinical microbiology, and its use can enhance the efficiency and quality of clinical microbiology practice. Although the future of IAAI is promising, currently IAAI only augments human effort and is not a replacement for human expertise.

#AMRrounds: a systematic educational approach for navigating bench to bedside antimicrobial resistance

Antimicrobial resistance (AMR) continues to serve as a major global health crisis. Clinicians practising in this modern era are faced with ongoing challenges in the therapeutic management of patients suffering from antimicrobial-resistant infections. A strong educational understanding and synergistic application of clinical microbiology, infectious disease and pharmacological concepts can assist the adventuring clinician in the navigation of such cases. Important items include mobilizing laboratory testing for pathogen identification and susceptibility data, harnessing an understanding of intrinsic pathogen resistance, acknowledging epidemiological resistance trends, recognizing acquired AMR mechanisms, and consolidating these considerations when constructing an ideal pharmacological plan. In this article, we outline a novel framework by which to systematically approach clinical AMR, encourage AMR-related education and optimize therapeutic decision-making in AMR-related illnesses.

Performance of the Vitek 2 Advanced Expert System (AES) as a Rapid Tool for Reporting Antimicrobial Susceptibility Testing (AST) in Enterobacterales from North and Latin America

This study evaluated the performance of the Vitek 2 Advanced Expert System (AES) confidence level report as a rapid tool for reporting antimicrobial susceptibility testing (AST) results for a challenging set of Enterobacterales isolates from North and Latin America. Enterobacterales isolates (n = 513) were tested by CLSI broth microdilution (BMD) and Vitek 2 (N802 and XN15 AST cards). Wild-type isolates and isolates harboring acquired β-lactamases by whole-genome sequencing were included. The AES assessment of confidence level (green, yellow, and red reports) was compared to BMD results and known genotypes and reviewed by a microbiologist for accuracy. Totals of 148 (28.8%) wild-type isolates and 365 (71.2%) Enterobacterales isolates harboring carbapenemase (211 [41.1%]), extended-spectrum β-lactamase (ESBL) (122 [23.8%]), and/or transferrable AmpC (tAmpC) (32 [6.2%]) genes were evaluated. The AES confidence level was assessed for 488 isolates, and a phenotype was recognized for 447 (91.6%) isolates. Green, yellow, and red AES reports were noted for 382 (78.3%), 65 (13.3%), and 41 (8.4%) isolates, respectively. Compared to BMD, 96.3% of green AES reports could be confidently and rapidly auto-released, enabling rapid adjustments to antimicrobial therapy. In addition, 69.2% of yellow reports were acceptable, and recommendations to address current AES limitations were made. IMPORTANCE Antimicrobial susceptibility testing (AST) reports are one of the most important clinical microbiology laboratory tasks. AST reports are essential to drive antimicrobial therapy, provide information to monitor antimicrobial resistance rates, and trigger further tests to detect outbreaks or confirm new mechanisms of resistance. Commercial AST devices are frequently used to generate AST reports, and an advanced expert system (AES), such as the Vitek 2 AES, incorporates extensive knowledge to recognize certain susceptibility patterns as indicative of specific phenotypes. Moreover, the Vitek 2 AES also provides a level of confidence for auto-releasing the reports. In this study, the performance of the Vitek 2 AES was compared to state-of-the-art methodologies for AST, broth microdilution and β-lactamase gene detection, whole-genome sequencing, against a collection of 513 Enterobacterales clinical isolates harboring various β-lactamase genes, including carbapenemase, ESBL, and transferrable AmpC genes, from 73 medical centers in 7 countries in North and Latin America.

Salmonella Subpopulations Identified from Human Specimens Express Heterogenous Phenotypes That Are Relevant to Clinical Diagnosis

Clonal bacterial cells can give rise to functionally heterogeneous subpopulations. This diversification is considered an adaptation strategy that has been demonstrated for several bacterial species, including Salmonella enterica serovar Typhimurium. In previous studies on mouse models infected orally with pure Salmonella cultures, derived bacterial cells collected from animal tissues were found to express heterogenous phenotypes. Here, we show mixed Salmonella populations, apparently derived from the same progenitor, present in human specimens collected at a single disease time point, and in a long-term-infected patient, these Salmonella were no longer expressing surface-exposed antigen epitopes by isolates collected at earlier days of the disease. The subpopulations express different phenotypes related to cell surface antigen expression, motility, biofilm formation, biochemical metabolism, and antibiotic resistance, which can all contribute to pathogenicity. Some of the phenotypes correlate with single nucleotide polymorphisms or other sequence changes in bacterial genomes. These genetic variations can alter synthesis of cell membrane-associated molecules such as lipopolysaccharides and lipoproteins, leading to changes in bacterial surface structure and function. This study demonstrates the limitation of Salmonella diagnostic methods that are based on a single-cell population which may not represent the heterogenous bacterial community in infected humans. IMPORTANCE In animal model systems, heterogenous Salmonella phenotypes were found previously to regulate bacterial infections. We describe in this communication that different Salmonella phenotypes also exist in infected humans at a single disease time point and that their phenotypic and molecular traits are associated with different aspects of pathogenicity. Notably, variation in genes encoding antibiotic resistance and two-component systems were observed from the subpopulations of a patient suffering from persistent salmonellosis. Therefore, clinical and public health interventions of the disease that are based on diagnosis of a single-cell population may miss other subpopulations that can cause residual human infections.

Development of a Real-Time Recombinase-Aided Amplification Method to Rapidly Detect Methicillin-Resistant Staphylococcus aureus

Methicillin-resistant staphylococcus aureus (MRSA) is a major pathogen responsible for human hospital and community-onset diseases and severe invasive livestock infections. Rapid detection of MRSA is essential to control the spread of MRSA. Conventional identification methods and antibacterial susceptibility tests of MRSA are time-consuming. The commonly used qPCR assay also has the disadvantages of being complicated and expensive, restricting its application in resource-limited clinical laboratories. Here, a real-time fluorescent recombinase-assisted amplification (RAA) assay targeting the most conserved regions within the mecA gene of MRSA was developed and evaluated to detect MRSA. The detection limit of this assay was determined to be 10 copies/reaction of positive plasmids. The established RAA assay showed high specificity for MRSA detection without cross-reactivities with other clinically relevant bacteria. The diagnostic performance of real-time RAA was evaluated using 67 clinical S. aureus isolates from dairy farms, which were detected in parallel using the TaqMan probe qPCR assay. The results showed that 56 and 54 samples tested positive for MRSA by RAA and qPCR, respectively. The overall agreement between both assays was 97.01% (65/67), with a kappa value of 0.9517 (p < 0.001). Further linear regression analysis demonstrated that the detection results between the two assays were significantly correlated (R2 = 0.9012, p < 0.0001), indicating that this RAA assay possesses similar detection performance to the qPCR assay. In conclusion, our newly established RAA assay is a time-saving and convenient diagnostic tool suitable for MRSA detection and screening.

Overprediction of Carbapenemase-Containing Isolates by an Automated AST Instrument's Computer Algorithm

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.

Direct MALDI-TOF MS and Antimicrobial Susceptibility Testing of Positive Blood Cultures Using the FASTTM System and FAST-PBC Prep Cartridges—Performance Evaluation in a Clinical Microbiology Laboratory Serving High-Risk Patients

Bloodstream infections are a leading cause of morbidity and mortality. The rapid diagnostic testing of positive blood cultures (PBCs) shortens times to effective therapy and the de-escalation of broad-spectrum empiric therapy. This is the first study examining the Qvella FAST^TM System for the rapid (~20 min) purification of microorganisms directly from PBCs using BacT/Alert^® FA/FAN bottles in the bioMérieux Virtuo instrument. We compared the performance of the FAST^TM System Liquid Colony^TM (LC), for immediate downstream ID and phenotypic AST, to standard workflow involving colonies obtained by overnight subculture. The LC yielded a concordant species ID by VITEK MS in 121/138 (87.7%) samples, identifying 32 different Gram-positive and Gram-negative species with 3/123 (2.6%) discordances. Compared to standard workflow, direct AST of the LC using VITEK^® 2 yielded 98.4% categorical agreement and 98.0% essential agreement. Very major error, major error, and minor error rates were 1.0%, 0.0%, and 1.8%, respectively, for Gram-negative organisms; and 1.9%, 0.2%, and 1.2%, respectively, for Gram-positive organisms. The median times from positive blood culture flag to results by FAST^TM System for ID and AST were 7.8 h and 15.7 h, respectively, versus 22.4 h and 36.6 h for standard workflow, respectively. In conclusion, the FAST^TM System provides reliable results for direct ID and AST from PBCs with significantly decreased turnaround times.

Evaluation of three different methods for susceptibility testing of gentamicin in carbapenem resistant Enterobacterales

Carbapenem-resistant Enterobacterales (CRE) have become a growing problem worldwide in recent years. Options for the treatment of CRE are limited and one of these options is gentamicin. For this reason, gentamicin susceptibility should be properly determined. In a recently reported study, it is recommended to review the results of automated systems for assessing gentamicin susceptibility in carbapenem-resistant isolates. In this study, we aimed to determine gentamicin susceptibility using three different methods and compare the methods. The study included 107 CRE isolates from different samples. Gentamicin susceptibility was determined using Vitek 2 Compact (bioMérieux, France), Microscan Walkaway Plus (Beckman Coulter, USA) automatic systems, and disk diffusion (DD) method. The broth microdilution method (BMD) was used as reference method. Minor, major, and very major errors and categorical agreement rates were determined for each method. Aminoglycoside-modifying enzymes (aac(6')Ib and aph(2″)Ia) were assayed in discrepant isolates. According to BMD results, 90.7%, 1,8 %, and 7.5 % of the isolates were determined as susceptible, intermediate, and resistant to gentamicin, respectively. Compared to the results of the BMD for detecting gentamicin susceptibility, disk diffusion method showed the highest categorical agreement (98.1%), and Vitek 2 Compact showed the lowest categorical agreement (90.6%). The very major error rates were determined 7.5%, 0.9%, and 0.9% for Vitek 2 Compact, Microscan Walkaway Plus, and DD method, respectively. In addition, aac(6')Ib and aph(2″)Ia genes were detected in 8 discrepant isolates. For gentamicin susceptibility, the DD showed the most compatible results. The DD can be used as a reliable method for determining gentamicin susceptibility. Compatibility of automated systems with BMD was acceptable, although lower than DD. The discrepancies detected in the Vitek 2 Compact results could be due to the presence of aac(6')Ib and/or aph(2″)Ia aminoglycoside-modifying enzymes.

Low back pain expert systems: Clinical resolution through probabilistic considerations and poset

OBJECTIVE

Proper diagnosis of Low Back Pain (LBP) is quite challenging in especially the developing countries like India. Though some developed countries prepared guidelines for evaluation of LBP with tests to detect psychological overlay, implementation of the recommendations becomes quite difficult in regular clinical practice, and different specialties of medicine offer different modes of management. Aiming at offering an expert-level diagnosis for the patients having LBP, this paper uses Artificial Intelligence (AI) to derive a clinically justified and highly sensitive LBP resolution technique.

MATERIALS AND METHODS

The paper considers exhaustive knowledge for different LBP disorders (classified based on different pain generators), which have been represented using lattice structures to ensure completeness, non-redundancy, and optimality in the design of knowledge base. Further the representational enhancement of the knowledge has been done through construction of a hierarchical network, called RuleNet, using the concept of partially-ordered set (poset) with respect to the subset equality (⊆) relation. With implicit incorporation of probability within the knowledge, the RuleNet is used to derive reliable resolution logic along with effective resolution of uncertainties during clinical decision making.

RESULTS

The proposed methodology has been validated with clinical records of seventy seven LBP patients accessed from the database of ESI Hospital Sealdah, India over a period of one year from 2018 to 2019. Achieving 83% sensitivity of the proposed technique, the pain experts at the hospital find the design clinically satisfactory. The inferred outcomes have also been found to be homogeneous with the actual or original diagnosis.

DISCUSSIONS

The proposed approach achieves the clinical and computational efficiency by limiting the shortcomings of the existing methodologies for AI-based LBP diagnosis. While computational efficiency (with respect to both time and space complexity) is ensured by inferring clinical decisions through optimal processing of the knowledge items using poset, the clinical acceptability has been ascertained reaching to the most-likely diagnostic outcomes through probabilistic resolution of clinical uncertainties.

CONCLUSION

The derived resolution technique, when embedded in LBP medical expert systems, would provide a fast, reliable, and affordable healthcare solution for this ailment to a wider range of general population suffering from LBP. The proposed scheme would significantly reduce the controversies and confusion in LBP treatment, and cut down the cost of unnecessary or inappropriate treatment and referral.

Surveillance of antimicrobial resistant bacteria in flies (Diptera) in Rio de Janeiro city

Antimicrobial-resistant bacteria were isolated from muscoid dipterans collected at five different areas of Rio de Janeiro city, in proximity to hospitals. Extracts obtained by maceration of flies were diluted and used as inocula for different culture media, with or without antibiotic (ceftriaxone 1 mg/L) supplementation. Purified isolates were submitted to antimicrobial susceptibility testing (AST). Bacterial identification was performed by MALDI TOF Microflex LT (Bruker Daltonics). A total of 197 bacterial strains were obtained from 117 dipterous muscoids. Forty-two flies (35.9%) carried bacteria resistant to at least one antimicrobial, while 7 insects (5.9%) carried multidrug-resistant bacteria (MDR), which were all members of the family Enterobacteriaceae. Among 10 MDR bacteria (5%), 5 strains (2,5%) were positive by PCR for one or more of the following antibiotic resistance genes: aac(6')-Ib, bla_TEM-1, bla_CTX-M-15, bla_KPC-2 and bla_NDM-1. Analysis of variance (ANOVA) and cluster analysis compared the number of resistant isolates per collection point and showed that a single location was statistically different from the others with regard to resistance. Although there are still no criteria to determine the environmental contamination by resistant bacteria the fact that they have been isolated from flies is an indication of a disseminated contamination. As such, these insects may be useful in monitoring programs of antibiotic resistance in non-hospital environments, where they could function as sentinels.

Nanomotion Detection-Based Rapid Antibiotic Susceptibility Testing

Rapid antibiotic susceptibility testing (AST) could play a major role in fighting multidrug-resistant bacteria. Recently, it was discovered that all living organisms oscillate in the range of nanometers and that these oscillations, referred to as nanomotion, stop as soon the organism dies. This finding led to the development of rapid AST techniques based on the monitoring of these oscillations upon exposure to antibiotics. In this review, we explain the working principle of this novel technique, compare the method with current ASTs, explore its application and give some advice about its implementation. As an illustrative example, we present the application of the technique to the slowly growing and pathogenic Bordetella pertussis bacteria.

AI-based mobile application to fight antibiotic resistance

Antimicrobial resistance is a major global health threat and its development is promoted by antibiotic misuse. While disk diffusion antibiotic susceptibility testing (AST, also called antibiogram) is broadly used to test for antibiotic resistance in bacterial infections, it faces strong criticism because of inter-operator variability and the complexity of interpretative reading. Automatic reading systems address these issues, but are not always adapted or available to resource-limited settings. We present an artificial intelligence (AI)-based, offline smartphone application for antibiogram analysis. The application captures images with the phone’s camera, and the user is guided throughout the analysis on the same device by a user-friendly graphical interface. An embedded expert system validates the coherence of the antibiogram data and provides interpreted results. The fully automatic measurement procedure of our application’s reading system achieves an overall agreement of 90% on susceptibility categorization against a hospital-standard automatic system and 98% against manual measurement (gold standard), with reduced inter-operator variability. The application’s performance showed that the automatic reading of antibiotic resistance testing is entirely feasible on a smartphone. Moreover our application is suited for resource-limited settings, and therefore has the potential to significantly increase patients’ access to AST worldwide.

Antimicrobial resistance is a major global health threat and its development is promoted by antibiotic misuse. Here, the authors present an offline smartphone application for automated and standardized antibiotic susceptibility testing, to be deployed in resource-limited settings.

Performance of the VITEK®2 advanced expert system™ for the validation of antimicrobial susceptibility testing results

Time to reporting antimicrobial susceptibility testing (AST) results to physicians plays an essential role in antibiotic stewardship programs. Expert software has been developed for facilitating the microbiologists' AST review process. The reliability of the VITEK®2 Advanced Expert™ software to effectively alert the microbiologist in detection of atypical and inconsistent AST results was assessed at the Labor Berlin-Charité Vivantes services. The results demonstrated a confidence rate of 99.3% in reporting fully consistent AST results to physicians.

Potentiation of imipenem by relebactam for Pseudomonas aeruginosa from bacteraemia and respiratory infections

BACKGROUND

Imipenem resistance in Pseudomonas aeruginosa most often entails loss of the 'carbapenem-specific' porin OprD; more rarely it reflects acquired carbapenemases. Loss of OprD only confers resistance to imipenem if AmpC β-lactamase is expressed, and we investigated whether this mechanism was overcome by relebactam, a developmental diazabicyclooctane β-lactamase inhibitor.

METHODS

Consecutive P. aeruginosa isolates causing bacteraemia or hospital-onset lower respiratory tract infections were collected between 2014 and 2016 under the aegis of the BSAC Resistance Surveillance Programme. Imipenem MICs were determined centrally by BSAC agar dilution, with relebactam at a fixed concentration (4 mg/L).

RESULTS

For most imipenem-susceptible P. aeruginosa (726/759, 95.7%), the MICs of imipenem alone were 0.5-2 mg/L and were decreased 3- to 4-fold by addition of relebactam, as based on geometric means or modes. For most imipenem-resistant P. aeruginosa (82/92, 89%), imipenem MICs were 8-16 mg/L, and were reduced to 1-2 mg/L by relebactam. These patterns applied regardless of whether the isolates were susceptible to penicillins and cephalosporins or had phenotypes suggesting derepressed AmpC or up-regulated efflux. Imipenem MICs for five P. aeruginosa with MBLs remained high (≥16 mg/L) regardless of relebactam.

CONCLUSIONS

Potentiation of imipenem by relebactam was almost universal, in accordance with the view that endogenous pseudomonal AmpC ordinarily protects against this carbapenem to a small degree. Imipenem MICs were reduced to the current breakpoint, or lower, except for MBL producers. Potentiation was not compromised by derepression of AmpC or up-regulation of efflux.

Digital microbiology

BACKGROUND

Digitalization 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.

OBJECTIVE

This 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.

SOURCES

We used peer-reviewed literature identified by a PubMed search for digitalization, machine learning, artificial intelligence and microbiology.

CONTENT

We 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.

IMPLICATIONS

We 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.

Recommendations of the Spanish Antibiogram Committee (COESANT) for selecting antimicrobial agents and concentrations for in vitro susceptibility studies using automated systems

Automated antimicrobial susceptibility testing devices are widely implemented in clinical microbiology laboratories in Spain, mainly using EUCAST (European Committee on Antimicrobial Susceptibility Testing) breakpoints. In 2007, a group of experts published recommendations for including antimicrobial agents and selecting concentrations in these systems. Under the patronage of the Spanish Antibiogram Committee (Comité Español del Antibiograma, COESANT) and the Study Group on Mechanisms of Action and Resistance to Antimicrobial Agents (GEMARA) from the Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), and aligned with the Spanish National Plan against Antimicrobial Resistance (PRAN), a group of experts have updated this document. The main modifications from the previous version comprise the inclusion of new antimicrobial agents, adaptation of the ranges of concentrations to cover the EUCAST breakpoints and epidemiological cut-off values (ECOFFs), and the inference of new resistance mechanisms. This proposal should be considered by different manufacturers and users when designing new panels or cards. In addition, recommendations for selective reporting are also included. With this approach, the implementation of EUCAST breakpoints will be easier, increasing the quality of antimicrobial susceptibility testing data and their microbiological interpretation. It will also benefit epidemiological surveillance studies as well as the clinical use of antimicrobials aligned with antimicrobial stewardship programs.

Impact of an Antimicrobial Stewardship Program on Resistance to Fluoroquinolones of Urinary Enterobacteriaceae Isolated From Nursing Home Residents: A Retrospective Cohort Study

OBJECTIVES

This study investigated the impact of an antimicrobial stewardship program on fluoroquinolone (FLQ) resistance in urinary Enterobacteriaceae isolated from residents of 3 French nursing homes.

DESIGN

A multicentric retrospective before-and-after study was conducted.

SETTING AND PARTICIPANTS

All the first urinary Enterobacteriaceae isolates obtained from nursing home residents were included. Two time frames were analyzed: 2013-2015 and 2016-2017.

METHODS

The antimicrobial stewardship program started in 2015 and was based on (1) 1-day training for use of an "antimicrobial stewardship kit for nursing homes;" and (2) daily support and training of the coordinating physician by an antibiotic mobile team (AMT) in 2 of 3 nursing homes.

RESULTS

Overall, 338 urinary isolates were analyzed. Escherichia coli was the most frequent species (212/338, 63%). A significant reduction of resistance to ofloxacin was observed between 2013-2015 and 2016-2017 in general (Δ = -16%, P = .004) and among isolates obtained from patients hospitalized in the county nursing home with AMT support (Δ = -28%, P < .01). A nonstatistically significant reduction in ofloxacin resistance was also observed in the hospital nursing home with AMT support (Δ = -18%, P = .06).

CONCLUSIONS AND IMPLICATIONS

Our antimicrobial stewardship program resulted in a decrease in resistance to FLQ among urinary Enterobacteriaceae isolated from nursing home residents. The support of an AMT along with continuous training of the coordinating physician seems to be an important component to ensure efficacy of the intervention.

Coevolution of Resistance Against Antimicrobial Peptides

Antimicrobial peptides (AMPs) are produced by all forms of life, ranging from eukaryotes to prokaryotes, and they are a crucial component of innate immunity, involved in clearing infection by inhibiting pathogen colonization. In the recent past, AMPs received high attention due to the increase of extensive antibiotic resistance by these pathogens. AMPs exhibit a diverse spectrum of activity against bacteria, fungi, parasites, and various types of cancer. AMPs are active against various bacterial pathogens that cause disease in animals and plants. However, because of the coevolution of host and pathogen interaction, bacteria have developed the mechanisms to sense and exhibit an adaptive response against AMPs. These resistance mechanisms are playing an important role in bacterial virulence within the host. Here, we have discussed the different resistance mechanisms used by gram-positive and gram-negative bacteria to sense and combat AMP actions. Understanding the mechanism of AMP resistance may provide directions toward the development of novel therapeutic strategies to control multidrug-resistant pathogens.

Carbapenem-Resistant Klebsiella pneumoniae: Microbiology Key Points for Clinical Practice

Carbapenemase–producing Klebsiella pneumoniae strains (Cp-Kpn) represent a challenge for clinical practitioners due to their increasing prevalence in hospital settings and antibiotic resistance. Clinical practitioners are often overwhelmed by the extensive list of publications regarding Cp-Kpn infections, treatment, characteristics, identification, and diagnosis. In this perspective article, we provide key points for clinical practitioners to consider for improved patient management including identification of risk factors and strategies for treatment. Additionally, we also discuss genetic underpinnings of antibiotic resistance, implementation of an antimicrobial stewardship program (ASP), and use of automated systems for detection of Cp-Kpn. Collectively, implementation of such key points would enhance clinical practices through providing practical knowledge to health professionals worldwide.

Activity of ceftazidime/avibactam against problem Enterobacteriaceae and Pseudomonas aeruginosa in the UK, 2015-16

Background

Ceftazidime/avibactam combines an established oxyimino-cephalosporin with the first diazabicyclooctane β-lactamase inhibitor to enter clinical use. We reviewed its activity against Gram-negative isolates, predominantly from the UK, referred for resistance investigation in the first year of routine testing, beginning in July 2015.

Methods

Isolates were as received from referring laboratories; there is a bias to submit those with suspected carbapenem resistance. Identification was by MALDI-TOF mass spectroscopy, and susceptibility testing by BSAC agar dilution. Carbapenemase genes were sought by PCR; other resistance mechanisms were inferred using genetic data and interpretive reading.

Results

Susceptibility rates to ceftazidime/avibactam exceeded 95% for: (i) Enterobacteriaceae with KPC, GES or other Class A carbapenemases; (ii) Enterobacteriaceae with OXA-48-like enzymes; and (iii) for ESBL or AmpC producers, even when these had impermeability-mediated ertapenem resistance. Almost all isolates with metallo-carbapenemases were resistant. Potentiation of ceftazidime by avibactam was seen for 87% of ceftazidime-resistant Enterobacteriaceae with 'unassigned' ceftazidime resistance mechanisms, including two widely referred groups of Klebsiella pneumoniae where no synergy was seen between cephalosporins and established β-lactamase inhibitors. Potentiation here may be a diazabicyclooctane/cephalosporin enhancer effect. Activity was seen against Pseudomonas aeruginosa with derepressed AmpC, but not for those with efflux-mediated resistance.

Conclusions

Of the available β-lactams or inhibitor combinations, ceftazidime/avibactam has the widest activity spectrum against problem Enterobacteriaceae, covering all major types except metallo-carbapenemase producers; against P. aeruginosa it has a slightly narrower spectrum than ceftolozane/tazobactam, which also covers efflux-type resistance.

Semantic data interoperability, digital medicine, and e-health in infectious disease management: a review

Disease management requires the use of mixed languages when discussing etiology, diagnosis, treatment, and follow-up. All phases require data management, and, in the optimal case, such data are interdisciplinary and uniform and clear to all those involved. Such semantic data interoperability is one of the technical building blocks that support emerging digital medicine, e-health, and P4-medicine (predictive, preventive, personalized, and participatory). In a world where infectious diseases are on a trend to become hard-to-treat threats due to antimicrobial resistance, semantic data interoperability is part of the toolbox to fight more efficiently against those threats. In this review, we will introduce semantic data interoperability, summarize its added value, and analyze the technical foundation supporting the standardized healthcare system interoperability that will allow moving forward to e-health. We will also review current usage of those foundational standards and advocate for their uptake by all infectious disease-related actors.

Identification and Antibiotic-Susceptibility Profiling of Infectious Bacterial Agents: A Review of Current and Future Trends

Antimicrobial resistance is one of the most worrying threats to humankind with extremely high healthcare costs associated. The current technologies used in clinical microbiology to identify the bacterial agent and profile antimicrobial susceptibility are time-consuming and frequently expensive. As a result, physicians prescribe empirical antimicrobial therapies. This scenario is often the cause of therapeutic failures, causing higher mortality rates and healthcare costs, as well as the emergence and spread of antibiotic resistant bacteria. As such, new technologies for rapid identification of the pathogen and antimicrobial susceptibility testing are needed. This review summarizes the current technologies, and the promising emerging and future alternatives for the identification and profiling of antimicrobial resistance bacterial agents, which are expected to revolutionize the field of clinical diagnostics.

Methicillin-resistant Staphylococcus aureus

Since the 1960s, methicillin-resistant Staphylococcus aureus (MRSA) has emerged, disseminated globally and become a leading cause of bacterial infections in both health-care and community settings. However, there is marked geographical variation in MRSA burden owing to several factors, including differences in local infection control practices and pathogen-specific characteristics of the circulating clones. Different MRSA clones have resulted from the independent acquisition of staphylococcal cassette chromosome mec (SCCmec), which contains genes encoding proteins that render the bacterium resistant to most β-lactam antibiotics (such as methicillin), by several S. aureus clones. The success of MRSA is a consequence of the extensive arsenal of virulence factors produced by S. aureus combined with β-lactam resistance and, for most clones, resistance to other antibiotic classes. Clinical manifestations of MRSA range from asymptomatic colonization of the nasal mucosa to mild skin and soft tissue infections to fulminant invasive disease with high mortality. Although treatment options for MRSA are limited, several new antimicrobials are under development. An understanding of colonization dynamics, routes of transmission, risk factors for progression to infection and conditions that promote the emergence of resistance will enable optimization of strategies to effectively control MRSA. Vaccine candidates are also under development and could become an effective prevention measure.

Incidence and Determinants of Health Care-Associated Blood Stream Infection at a Neonatal Intensive Care Unit in Ujjain, India: A Prospective Cohort Study

Very little is known about laboratory-confirmed blood stream infections (LCBIs) in neonatal intensive care units (NICUs) in resource-limited settings. The aim of this cohort study was to determine the incidence, risk factors, and causative agents of LCBIs in a level-2 NICU in India. The diagnosis of LCBIs was established using the Centre for Disease Control, USA criteria. A predesigned questionnaire containing risk factors associated with LCBIs was filled-in. A total of 150 neonates (43% preterm) were included in the study. The overall incidence of LCBIs was 31%. The independent risk factors for LCBIs were: preterm neonates (relative risk (RR) 2.23), duration of NICU stay more than 14 days (RR 1.75), chorioamnionitis in the mother (RR 3.18), premature rupture of membrane in mothers (RR 2.32), neonate born through meconium-stained amniotic fluid (RR 2.32), malpresentation (RR 3.05), endotracheal intubation (RR 3.41), umbilical catheterization (RR 4.18), and ventilator-associated pneumonia (RR 3.17). The initiation of minimal enteral nutrition was protective from LCBIs (RR 0.22). The predominant causative organisms were gram-negative pathogens (58%). The results of the present study can be used to design and implement antibiotic stewardship policy and introduce interventions to reduce LCBIs in resource-limited settings.

Discrepant susceptibility to gentamicin despite amikacin resistance in Klebsiella pneumoniae by VITEK 2 represents false susceptibility associated with the armA 16S rRNA methylase gene

Because we experienced gentamicin failure in Klebsiella pneumoniae bacteraemia that was susceptible to gentamicin despite amikacin resistance, as determined by VITEK 2, we evaluated the true susceptibility and mechanism of resistance. We screened 2818 K. pneumoniae isolates during a 1-year period at a university hospital and reviewed anti-microbial susceptibility reports using the VITEK 2 system. The minimum inhibitory concentration was substantiated by broth microdilution (BMD), and the presence of 16S rRNA methylase genes and aminoglycoside-modifying enzymes was also investigated. A total of 131 amikacin-resistant isolates from 19 patients were gentamicin non-resistant according to the VITEK 2 system. Among these, we were able to collect isolates from 12 patients (63.2 %), and a single isolate from each patient was tested. Eleven of the gentamicin non-resistant isolates (91.7 %) showed high-level resistance to both amikacin and gentamicin by BMD in association with the armA gene. Gentamicin is not an adequate treatment option for amikacin-resistant K. pneumoniae, even if VITEK 2 reports susceptibility.

Identification of Emerging Human Mastitis Pathogens by MALDI-TOF and Assessment of Their Antibiotic Resistance Patterns

Lactational mastitis constitutes one of the main causes of undesired weaning, depriving the mother–infant pair from the benefits of breastfeeding; therefore, this condition should be considered a relevant public health issue. The role of specific microorganisms remains unclear since human milk cultures and antibiotic susceptibility testing (AST) are not routinely performed, despite the fact that this would be key to ensure an early and effective diagnosis and treatment. The objective of this study was to describe the culturable microbial diversity in 647 milk samples from breastfeeding women with clinical symptoms of mastitis by Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF) VITEK MS technology and to analyze the antimicrobial susceptibility profiles of a collection of isolates from these samples by the VITEK 2 AST system. Staphylococcus epidermidis was the most common species isolated from mastitis samples (87.6%), while Staphylococcus aureus was detected in 22.1%. Streptococci constituted the second (68.6%) most prevalent bacterial group, with Streptococcus mitis/oralis, Streptococcus salivarius, and Streptococcus parasanguinis detected with frequencies of 40.8, 36.8, and 14.4%, respectively. The antibiotic susceptibility profiles of 642 staphylococcal isolates indicated a remarkable resistance to benzylpenicillin (88.3%) and erythromycin (67.3%) with differences between species. A high percentage of Staphylococcus isolates were resistant to at least one antibiotic (Staphylococcus hominis, 100%; S. epidermidis, 98.2%; S. aureus, 92.9%; Staphylococcus lugdunensis, 90.5%) and the percentage of multidrug-resistance (MDR) isolates was noticeable (S. hominis, 81%; S. epidermidis, 64.4%; S. aureus, 11.5%; S. lugdunensis, 10.5%). In relation to streptococcal isolates (n = 524), AST revealed high or moderate percentages of resistance to erythromycin (68.7%), benzylpenicillin (63.7%), ampicillin (51.5%), and tetracycline (30.8%). Antibiotic resistance to at least one antibiotic was detected in 97.6% of S. parasanguinis, 92.6% of S. salivarius, 83.3% of S. mitis/oralis, and 72.4% of Streptococcus vestibularis isolates. A significant number of MDR streptococcal isolates was also found (S. parasanguinis, 51.2%; S. salivarius, 39.3%; S. mitis/oralis, 34.6%; and S. vestibularis, 19%). The results highlight the important role of coagulase-negative staphylococci and streptococci as human mastitis-causing agents. Moreover, the high rates of antimicrobial resistance among these microorganisms must be contemplated as an issue of clinical relevance in relation to treatment options.

Current and emerging techniques for antibiotic susceptibility tests

Infectious diseases caused by bacterial pathogens are a worldwide burden. Serious bacterial infection-related complications, such as sepsis, affect over a million people every year with mortality rates ranging from 30% to 50%. Crucial clinical microbiology laboratory responsibilities associated with patient management and treatment include isolating and identifying the causative bacterium and performing antibiotic susceptibility tests (ASTs), which are labor-intensive, complex, imprecise, and slow (taking days, depending on the growth rate of the pathogen). Considering the life-threatening condition of a septic patient and the increasing prevalence of antibiotic-resistant bacteria in hospitals, rapid and automated diagnostic tools are needed. This review summarizes the existing commercial AST methods and discusses some of the promising emerging AST tools that will empower humans to win the evolutionary war between microbial genes and human wits.

High Heterogeneity of Escherichia coli Sequence Types Harbouring ESBL/AmpC Genes on IncI1 Plasmids in the Colombian Poultry Chain

Background

Escherichia coli producing ESBL/AmpC enzymes are unwanted in animal production chains as they may pose a risk to human and animal health. Molecular characterization of plasmids and strains carrying genes that encode these enzymes is essential to understand their local and global spread.

Objectives

To investigate the diversity of genes, plasmids and strains in ESBL/AmpC-producing E. coli from the Colombian poultry chain isolated within the Colombian Integrated Program for Antimicrobial Resistance Surveillance (Coipars).

Methods

A total of 541 non-clinical E. coli strains from epidemiologically independent samples and randomly isolated between 2008 and 2013 within the Coipars program were tested for antimicrobial susceptibility. Poultry isolates resistant to cefotaxime (MIC ≥ 4 mg/L) were screened for ESBL/AmpC genes including bla_CTX-M, bla_SHV, bla_TEM, bla_CMY and bla_OXA. Plasmid and strain characterization was performed for a selection of the ESBL/AmpC-producing isolates. Plasmids were purified and transformed into E. coli DH10B cells or transferred by conjugation to E. coli W3110. When applicable, PCR Based Replicon Typing (PBRT), plasmid Multi Locus Sequence Typing (pMLST), plasmid Double Locus Sequence Typing (pDLST) and/or plasmid Replicon Sequence Typing (pRST) was performed on resulting transformants and conjugants. Multi Locus Sequence Typing (MLST) was used for strain characterization.

Results

In total, 132 of 541 isolates were resistant to cefotaxime and 122 were found to carry ESBL/AmpC genes. Ninety-two harboured bla_CMY-2 (75%), fourteen bla_SHV-12 (11%), three bla_SHV-5 (2%), five bla_CTX-M-2 (4%), one bla_CTX-M-15 (1%), one bla_CTX-M-8 (1%), four a combination of bla_CMY-2 and bla_SHV-12 (4%) and two a combination of bla_CMY-2 and bla_SHV-5 (2%). A selection of 39 ESBL/AmpC-producing isolates was characterized at the plasmid and strain level. ESBL/AmpC genes from 36 isolates were transferable by transformation or conjugation of which 22 were located on IncI1 plasmids. These IncI1 plasmids harboured predominantly bla_CMY-2 (16/22), and to a lesser extend bla_SHV-12 (5/22) and bla_CTX-M-8 (1/22). Other plasmid families associated with ESBL/AmpC-genes were IncK (4/33), IncHI2 (3/33), IncA/C (2/33), IncΒ/O (1/33) and a non-typeable replicon (1/33). Subtyping of IncI1 and IncHI2 demonstrated IncI1/ST12 was predominantly associated with bla_CMY-2 (12/16) and IncHI2/ST7 with bla_CTX-M-2 (2/3). Finally, 31 different STs were detected among the 39 selected isolates.

Conclusions

Resistance to extended spectrum cephalosporins in E. coli from Colombian poultry is mainly caused by bla_CMY-2 and bla_SHV-12. The high diversity of strain Sequence Types and the dissemination of homogeneous IncI1/ST12 plasmids suggest that spread of the resistance is mainly mediated by horizontal gene transfer.

Personalized Weight Management Interventions for Cardiovascular Risk Reduction: A Viable Option for African-American Women

Obesity is an independent contributor to cardiovascular disease (CVD) and a major driving force behind racial/ethnic and gender disparities in risk. Due to a multitude of interrelating factors (i.e., personal, social, cultural, economic and environmental), African-American (AA) women are disproportionately obese and twice as likely to succumb to CVD, yet they are significantly underrepresented in behavioral weight management interventions. In this selective review we highlight components of the limited interventions shown to enhance weight loss outcomes in this population and make a case for leveraging Web-based technology and artificial intelligence techniques to deliver personalized programs aimed at obesity treatment and CVD risk reduction. Although many of the approaches discussed are generally applicable across populations burdened by disparate rates of obesity and CVD, we specifically focus on AA women due to the disproportionate impact of these non-communicable diseases and the general paucity of interventions targeted to this high-risk group.

Why is antibiotic resistance a deadly emerging disease?

Evolution of bacteria towards resistance to antimicrobial agents, including multidrug resistance, is unavoidable because it represents a particular aspect of the general evolution of bacteria that is unstoppable. Therefore, the only means of dealing with this situation is to delay the emergence and subsequent dissemination of resistant bacteria or resistance genes. In this review, we will consider the biochemical mechanisms and the genetics that bacteria use to offset antibiotic selective pressure. The data provided are mainly, if not exclusively, taken from the work carried out in the laboratory, although there are numerous other examples in the literature.

Rapid antimicrobial susceptibility testing of clinical isolates by digital time-lapse microscopy

Rapid antimicrobial susceptibility testing (AST) is essential for early and appropriate therapy. Methods with short detection time enabling same-day treatment optimisation are highly favourable. In this study, we evaluated the potential of a digital time-lapse microscope system, the oCelloScope system, to perform rapid AST. The oCelloScope system demonstrated a very high accuracy (96 % overall agreement) when determining the resistance profiles of four reference strains, nine clinical isolates, including multi-drug-resistant isolates, and three positive blood cultures. AST of clinical isolates (168 antimicrobial agent–organism combinations) demonstrated 3.6 % minor, no major and 1.2 % very major errors of the oCelloScope system compared to conventional susceptibility testing, as well as a rapid and correct phenotypic detection of strains with methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL) profiles. The net average time-to-result was 108 min, with 95 % of the results being available within 180 min. In conclusion, this study strongly indicates that the oCelloScope system holds considerable potential as an accurate and sensitive AST method with short time-to-result, enabling same-day targeted antimicrobial therapy, facilitating antibiotic stewardship and better patient management. A full-scale validation of the oCelloScope system including more isolates is necessary to assess the impact of using it for AST.

Evaluation of the PREVI® Isola automated seeder system compared to reference manual inoculation for antibiotic susceptibility testing by the disk diffusion method

The disk diffusion (DD) method remains the most popular manual technique for antibiotic susceptibility testing (AST) in clinical microbiology laboratories. This is because of its simplicity, reproducibility, and limited cost compared to (automated) microdilution systems, which are usually less sensitive at detecting certain important mechanisms of resistance. Here, we evaluate the PREVI® Isola automated seeder system using a new protocol for spreading bacterial suspensions (eight deposits of calibrated inocula of bacteria, followed by two rounds of rotation) in comparison with manual DD reference testing on a large series of clinical and reference strains. The average time required for seeding one agar plate for DD with this new protocol was 51 s per plate, i.e., 70 agar plates/h. Reproducibility and repeatability was assessed on three reference and three randomly chosen clinical strains, as usually requested by the European Committee on Antimicrobial Susceptibility Testing (EUCAST), and was excellent compared to the manual method. The standard deviations of zones of growth inhibition showed no statistical discrimination. The correlation between the two methods, assessed using 294 clinical isolates and a panel of six antibiotics (n = 3,528 zones of growth inhibition measured), was excellent, with a correlation coefficient of 0.977. The new PREVI® Isola protocol adapted for DD had a sensitivity of 99 % and a specificity of 100 % compared to the manual technique for interpreting DD as recommended by the EUCAST.

The Resistant-Population Cutoff (RCOFF): a New Concept for Improved Characterization of Antimicrobial Susceptibility Patterns of Non-Wild-Type Bacterial Populations

This study aimed to determine resistant-population cutoffs (RCOFFs) to allow for improved characterization of antimicrobial susceptibility patterns in bacterial populations. RCOFFs can complement epidemiological cutoff (ECOFF)-based settings of clinical breakpoints (CBPs) by systematically describing the correlation between non-wild-type and wild-type populations. We illustrate this concept by describing three paradigmatic examples of wild-type and non-wild-type Escherichia coli populations from our clinical strain database of disk diffusion diameters. The statistical determination of RCOFFs and ECOFFs and their standardized applications in antimicrobial susceptibility testing (AST) facilitates the assignment of isolates to wild-type or non-wild-type populations. This should improve the correlation of in vitro AST data and distinct antibiotic resistance mechanisms with clinical outcome facilitating the setting and validation of CBPs.

Understanding bacterial resistance to antimicrobial peptides: From the surface to deep inside

Resistant bacterial infections are a major health problem in many parts of the world. The major commercial antibiotic classes often fail to combat common bacteria. Although antimicrobial peptides are able to control bacterial infections by interfering with microbial metabolism and physiological processes in several ways, a large number of cases of resistance to antibiotic peptide classes have also been reported. To gain a better understanding of the resistance process various technologies have been applied. Here we discuss multiple strategies by which bacteria could develop enhanced antimicrobial peptide resistance, focusing on sub-cellular regions from the surface to deep inside, evaluating bacterial membranes, cell walls and cytoplasmic metabolism. Moreover, some high-throughput methods for antimicrobial resistance detection and discrimination are also examined. This article is part of a Special Issue entitled: Bacterial Resistance to Antimicrobial Peptides.

Quality of water and antibiotic resistance of Escherichia coli from water sources of hilly tribal villages with and without integrated watershed management-a one year prospective study

In many hilly tribal areas of the world, water scarcity is a major problem and diarrhoea is common. Poor quality of water also affects the environment. An integrated watershed management programme (IWMP) aims to increase availability of water and to improve life conditions. Globally, there is a lack of information on water contamination, occurrence of diarrhoea and antibiotic resistance, a serious global concern, in relation to IWMP in hilly tribal areas. Therefore, a prospective observational study was conducted during 2011–2012 in six villages in a hilly tribal belt of India, three with and three without implementation of an IWMP, to explore quality of water, diarrhoeal cases in the community and antibiotic resistance of Escherichia coli from water sources. The results showed that physico-chemical quality of water was within limits of safe consumption in all samples. The odds of coliform contamination in water samples was 2.3 times higher in non-watershed management villages (NWMV) compared to integrated watershed management villages (IWMV) (95% CI 0.8–6.45, p = 0.081). The number of diarrhoeal cases (18/663 vs. 42/639, p < 0.05) was lower in IWMV as compared to NWMV. Overall E. coli isolates showed high susceptibility to antibiotics. Resistance to a wider range of antibiotics was observed in NWMV.

Low prevalence of methicillin resistant Staphylococcus aureus as determined by an automated identification system in two private hospitals in Nairobi, Kenya: a cross sectional study

Background

Staphylococcus aureus (S.aureus) is a major cause of both healthcare and community acquired infections. In developing countries, manual phenotypic tests are the mainstay for the identification of staphylococci with the tube and slide coagulase tests being relied upon as confirmatory tests for S. aureus. The subjectivity associated with interpretation of these tests may result in misidentification of coagulase negative staphylococci as S.aureus. Given that antibiotic resistance is more prevalent in CONS, this may result in over estimation of methicillin resistant S.aureus (MRSA) prevalence.

Methods

A review of susceptibility data from all non-duplicate S.aureus isolates generated between March 2011 and May 2013 by the Vitek-2 (bioMérieux) automated system was performed by the authors. The data was generated routinely from processed clinical specimens submitted to the microbiology laboratories for culture and sensitivity at the Aga Khan University Hospital and Gertrude’s children’s hospital both situated in Nairobi.

Results

Antimicrobial susceptibility data from a total of 731 non-duplicate S.aureus isolates was reviewed. Majority (79.2%) of the isolates were from pus swabs. Only 24 isolates were both cefoxitin and oxacillin resistant while 3 were resistant to oxacillin but susceptible to cefoxitin giving an overall MRSA prevalence of 3.7% (27/731). None of the isolates were resistant to mupirocin, linezolid, tigecycline, teicoplanin or vancomycin.

Conclusion

The prevalence of MRSA in this study is much lower than what has been reported in most African countries. The significant change in antibiotic susceptibility compared to what has previously been reported in our hospital is most likely a consequence of the transition to an automated platform rather than a trend towards lower resistance rates.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-014-0669-y) contains supplementary material, which is available to authorized users.

Clinical microbiology informatics

The clinical microbiology laboratory has responsibilities ranging from characterizing the causative agent in a patient's infection to helping detect global disease outbreaks. All of these processes are increasingly becoming partnered more intimately with informatics. Effective application of informatics tools can increase the accuracy, timeliness, and completeness of microbiology testing while decreasing the laboratory workload, which can lead to optimized laboratory workflow and decreased costs. Informatics is poised to be increasingly relevant in clinical microbiology, with the advent of total laboratory automation, complex instrument interfaces, electronic health records, clinical decision support tools, and the clinical implementation of microbial genome sequencing. This review discusses the diverse informatics aspects that are relevant to the clinical microbiology laboratory, including the following: the microbiology laboratory information system, decision support tools, expert systems, instrument interfaces, total laboratory automation, telemicrobiology, automated image analysis, nucleic acid sequence databases, electronic reporting of infectious agents to public health agencies, and disease outbreak surveillance. The breadth and utility of informatics tools used in clinical microbiology have made them indispensable to contemporary clinical and laboratory practice. Continued advances in technology and development of these informatics tools will further improve patient and public health care in the future.

Integrating forecast probabilities in antibiograms: a way to guide antimicrobial prescriptions more reliably?

Antimicrobial susceptibility testing (AST) assigns pathogens to "susceptible" or "resistant" clinical categories based on clinical breakpoints (CBPs) derived from MICs or inhibition zone diameters and indicates the likelihood for therapeutic success. AST reports do not provide quantitative measures for the reliability of such categorization. Thus, it is currently impossible for clinicians to estimate the technical forecast uncertainty of an AST result regarding clinical categorization. AST error rates depend on the localization of pathogen populations in relation to CBPs. Bacterial species are, however, not homogeneous, and subpopulations behave differently with respect to AST results. We addressed how AST reporting errors differ between isolates with and without acquired drug resistance determinants. Using as an example the beta-lactams and their most important resistance mechanisms, we analyzed different pathogen populations for their individual reporting error probabilities. Categorization error rates were significantly higher for bacterial populations harboring resistance mechanisms than for the wild-type population. Reporting errors for amoxicillin-clavulanic acid and piperacillin-tazobactam in Escherichia coli infection cases were almost exclusively due to the presence of broad-spectrum- and extended-spectrum-beta-lactamase (ESBL)-producing microorganisms (79% and 20% of all errors, respectively). Clinicians should be aware of the significantly increased risk of erroneous AST reports for isolates producing beta-lactamases, particularly ESBL and AmpC. Including probability indicators for interpretation would improve AST reports.

Transplantation of Human Fetal Tissue for Neurodegenerative Diseases: Validation of a New Protocol for Microbiological Analysis and Bacterial Decontamination

Restorative cell therapy concepts in neurodegenerative diseases are aimed at replacing lost neurons. Despite advances in research on pluripotent stem cells, fetal tissue from routine elective abortions is still regarded as the only safe cell source. Progenitor cells isolated from distinct first-trimester fetal CNS regions have already been used in clinical trials and will be used again in a new multicenter trial funded by the European Union (TRANSEURO). Bacterial contamination of human fetal tissue poses a potential risk of causing infections in the brain of the recipient. Thus, effective methods of microbial decontamination and validation of these methods are required prior to approval of a neurorestorative cell therapy trial. We have developed a protocol consisting of subsequent washing steps at different stages of tissue processing. Efficacy of microbial decontamination was assessed on rat embryonic tissue incubated with high concentrations of defined microbe solutions including representative bacterial and fungal species. Experimental microbial contamination was reduced by several log ranks. Subsequently, we have analyzed the spectrum of microbial contamination and the effect of subsequent washing steps on aborted human fetal tissue; 47.7% of the samples taken during human fetal tissue processing were positive for a microbial contamination, but after washing, no sample exhibited bacterial growth. Our data suggest that human fetal tissue for neural repair can carry microbes of various species, highlighting the need for decontamination procedures. The decontamination protocol described in this report has been shown to be effective as no microbes could be detected at the end of the procedure.

Validation of antibiotic susceptibility testing guidelines in a routine clinical microbiology laboratory exemplifies general key challenges in setting clinical breakpoints

This study critically evaluated the new European Committee for Antimicrobial Susceptibility Testing (EUCAST) antibiotic susceptibility testing guidelines on the basis of a large set of disk diffusion diameters determined for clinical isolates. We report several paradigmatic problems that illustrate key issues in the selection of clinical susceptibility breakpoints, which are of general importance not only for EUCAST but for all guidelines systems, i.e., (i) the need for species-specific determinations of clinical breakpoints/epidemiological cutoffs (ECOFFs), (ii) problems arising from pooling data from various sources, and (iii) the importance of the antibiotic disk content for separating non-wild-type and wild-type populations.

Multiresistant strains are as susceptible to photodynamic inactivation as their naïve counterparts: protoporphyrin IX-mediated photoinactivation reveals differences between methicillin-resistant and methicillin-sensitive Staphylococcus aureus strains

OBJECTIVE

The current study was aimed at the investigation of differences in response to photoinactivation between methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) isolates. Moreover, we aimed to elucidate if the observed variation resulted from antimicrobial resistance mechanisms and strains' susceptibility to antibiotic therapy.

BACKGROUND DATA

Because of the emergence of multidrug resistance, the development of alternative antimicrobial strategies seems to be required. The concept of photodynamic inactivation (PDI) involves cell exposure to appropriate wavelength light that leads to the excitation of photosensitizer molecules, resulting in the production of reactive oxygen species responsible for cell inactivation and death. Recently, we have demonstrated a strain-dependent response of S. aureus to photoinactivation, and observed elevated resistance to PDI among MRSA strains. Nevertheless, the mechanism underlying this phenomenon remains unexplained.

METHODS

S. aureus response to protoporphyrin IX (PPIX)-mediated photoinactivation was studied for 424 MRSA/MSSA isolates. VITEK 2 Advanced Expert System was used to detect antimicrobial resistance mechanisms and strains' susceptibility to antibiotictherapy.

RESULTS

Data obtained demonstrated that MRSA are significantly more resistant to photoinactivation than MSSA strains; however, the difference observed did not result from antimicrobial susceptibility or resistance mechanisms. Furthermore, regardless of the strains' origin, a similar effectiveness of PDI could be achieved. Moreover, it was determined that the ability to form biofilms in vitro, and the presence of mec element, does not explain the observed differences between MRSA and MSSA strains.

CONCLUSIONS

PDI could be highly effective against multidrug resistant pathogens as well as their naïve counterparts. Nevertheless, regardless of the antimicrobial resistance mechanism, the difference in response to PDI between MRSA and MSSA exists.

Developing the Serious Games potential in nursing education

Shortened hospital stays, high patient acuity and technological advances demand that nurses increasingly make decisions under conditions of uncertainty and risk (Ebright et al., 2003). With rising trends towards out-patient care, nurses will need to perform complex problem-solving within a dynamic and changing environment for which there is not one clear solution (Schofield et al., 2010; Wolff et al., 2009). The development of sharp clinical reasoning skills, as well as skills in detection, monitoring, investigation and evaluation are therefore essential (Aitken et al., 2002). Yet few nursing students have long-term exposure to home-care and community situations. This is primarily due to scarce human resources and the time-consuming requirements of student supervision (Duque et al., 2008). When students are given the opportunity to experience home-care or community visits these tend to be unstructured leading to wide variations in their competencies. New pedagogical tools are needed to adequately and consistently prepare nurses for the skills they will need to care for patients outside acute care settings. Advances in Information and Communications Technologies (ICT) offer an opportunity to explore innovative pedagogical solutions that could help students develop these skills in a safe environment. A three-phased project is underway that aims to create and test a Serious Game to improve nurses' clinical reasoning and detection skills in home-care and community settings. The first phase of this project involves the development of a scenario, the game engine and the graphic design and will be the focus of this paper. The second and third phases will test the Serious Game as an educational intervention and will be reported in subsequent papers.