Update on Susceptibility Testing: Genotypic and Phenotypic Methods

Navigating the network: a narrative overview of AMR surveillance and data flow in the United States

The antimicrobial resistance (AMR) surveillance landscape in the United States consists of a data flow that starts in the clinical setting and is maintained by a network of national and state public health laboratories. These organizations are well established, with robust methodologies to test and confirm antimicrobial susceptibility. Still, the bridge that guides the flow of data is often one directional and caught in a constant state of rush hour that can only be refined with improvements to infrastructure and automation in the data flow. Moreover, there is an absence of information in the literature explaining the processes clinical laboratories use to coalesce and share susceptibility test data for AMR surveillance, further complicated by variability in testing procedures. This knowledge gap limits our understanding of what is needed to improve and streamline data sharing from clinical to public health laboratories. Successful models of AMR surveillance display attributes like 2-way communication between clinical and public health laboratories, centralized databases, standardized data, and the use of electronic health records or data systems, highlighting areas of opportunity and improvement. This article explores the roles and processes of the organizations involved in AMR surveillance in the United States and identifies current knowledge gaps and opportunities to improve communication between them through standardization, communication, and modernization of data flow.

Metagenomic next-generation sequencing for the identification of infections caused by Gram-negative pathogens and the prediction of antimicrobial resistance

OBJECTIVE

The aim of this study was to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) for the identification of Gram-negative bacteria (GNB) infections and the prediction of antimicrobial resistance.

METHODS

A retrospective analysis was conducted on 182 patients with diagnosis of GNB infections who underwent mNGS and conventional microbiological tests (CMTs).

RESULTS

The detection rate of mNGS was 96.15%, higher than CMTs (45.05%) with a significant difference (χ 2 = 114.46, P < .01). The pathogen spectrum identified by mNGS was significantly wider than CMTs. Interestingly, the detection rate of mNGS was substantially higher than that of CMTs (70.33% vs 23.08%, P < .01) in patients with but not without antibiotic exposure. There was a significant positive correlation between mapped reads and pro-inflammatory cytokines (interleukin-6 and interleukin-8). However, mNGS failed to predict antimicrobial resistance in 5 of 12 patients compared to phenotype antimicrobial susceptibility testing results.

CONCLUSIONS

Metagenomic next-generation sequencing has a higher detection rate, a wider pathogen spectrum, and is less affected by prior antibiotic exposure than CMTs in identifying Gram-negative pathogens. The mapped reads may reflect a pro-inflammatory state in GNB-infected patients. Inferring actual resistance phenotypes from metagenomic data remains a great challenge.

Microwell-enhanced optical rapid antibiotic susceptibility testing of single bacteria

Bacteria that are resistant to antibiotics present an increasing burden on healthcare. To address this emerging crisis, novel rapid antibiotic susceptibility testing (AST) methods are eagerly needed. Here, we present an optical AST technique that can determine the bacterial viability within 1 h down to a resolution of single bacteria. The method is based on measuring intensity fluctuations of a reflected laser focused on a bacterium in reflective microwells. Using numerical simulations, we show that both refraction and absorption of light by the bacterium contribute to the observed signal. By administering antibiotics that kill the bacteria, we show that the variance of the detected fluctuations vanishes within 1 h, indicating the potential of this technique for rapid sensing of bacterial antibiotic susceptibility. We envisage the use of this method for massively parallelizable AST tests and fast detection of drug-resistant pathogens.

The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance in Enterobacterales

Carbapenem-resistant Enterobacterales (CRE) are important pathogens that can develop resistance via multiple molecular mechanisms, including hydrolysis or reduced antibiotic influx. Identifying these mechanisms can improve pathogen surveillance, infection control, and patient care. We investigated how resistance mechanisms influence the carbapenem inoculum effect (IE), a phenomenon where inoculum size affects antimicrobial susceptibility testing (AST). We demonstrated that seven different carbapenemases impart a meropenem IE in Escherichia coli. Across 110 clinical CRE isolates, the carbapenem IE strictly depended on resistance mechanism: all carbapenemase-producing CRE (CP-CRE) exhibited a strong IE, whereas porin-deficient CRE displayed none. Concerningly, 50% and 24% of CP-CRE isolates changed susceptibility classification to meropenem and ertapenem, respectively, across the allowable inoculum range in clinical guidelines. The meropenem IE, and the ratio of ertapenem to meropenem minimal inhibitory concentration (MIC) at standard inoculum, reliably identified CP-CRE. Understanding how resistance mechanisms affect AST could improve diagnosis and guide therapies for CRE infections.

Tick-tock, beat the clock: comparative analysis of disc diffusion testing with 6-, 10-, and 24-h growth for accelerated antimicrobial susceptibility testing and antimicrobial stewardship

Disc diffusion testing by Kirby-Bauer technique is the most used method for determining antimicrobial susceptibility in microbiological laboratories. The current guidelines by The Clinical and Laboratory Standards Institute (CLSI) 2022 specify using an 18- to 24-h growth for testing by disc diffusion. We aim to determine if using an early growth (6 h and 10 h) would produce comparable results, thus ultimately leading to reduced turnaround time. Six-hour, 10-h, and 24-h growths of 20 quality control strains and 6-h and 24-h growths of 48 clinical samples were used to perform disc diffusion testing using a panel of appropriate antimicrobial agents. Disc diffusion zone sizes were interpreted for all and comparative analyses were performed to determine categorical agreement, minor errors (mE), major errors (ME), and very major errors (VME) according to CLSI guidelines. On comparing with the standard 24 h of incubation, disc diffusion from 6-h and 10-h growths of quality control strains showed 94.38% categorical agreement, 5.10% mE, 0.69% MEs, and no VMEs. Disc diffusion testing for the additional 40 clinical samples yielded a similarly high level of categorical agreement (98.15%) and mE, ME, and VME of 1.29%, 1.22%, and 0% respectively. Disc diffusion testing using early growth is a simple and accurate method for susceptibility testing that can reduce turnaround time and may prove to be critical for timely patient management.

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.

Staphylococcus aureus infections in children

PURPOSE OF REVIEW

Staphylococcus aureus is the most common invasive bacterial pathogen infecting children in the U.S. and many parts of the world. This major human pathogen continues to evolve, and recognition of recent trends in epidemiology, therapeutics and future horizons is of high importance.

RECENT FINDINGS

Over the past decade, a relative rise of methicillin-susceptible S. aureus (MSSA) has occurred, such that methicillin-resistant S. aureus (MRSA) no longer dominates the landscape of invasive disease. Antimicrobial resistance continues to develop, however, and novel therapeutics or preventive modalities are urgently needed. Unfortunately, several recent vaccine attempts proved unsuccessful in humans.

SUMMARY

Recent scientific breakthroughs highlight the opportunity for novel interventions against S. aureus by interfering with virulence rather than by traditional antimicrobial mechanisms. A S. aureus vaccine remains elusive; the reasons for this are multifactorial, and lessons learned from prior unsuccessful attempts may create a path toward an effective preventive. Finally, new diagnostic modalities have the potential to greatly enhance clinical care for invasive S. aureus disease in children.

Rapid Antimicrobial Susceptibility Testing Methods for Blood Cultures and Their Clinical Impact

Antimicrobial susceptibility testing (AST) of bacteria isolated in blood cultures is critical for optimal management of patients with sepsis. This review describes new and emerging phenotypic and genotypic AST methods and summarizes the evidence that implementation of these methods can impact clinical outcomes of patients with bloodstream infections.