Evaluation of BacLite Rapid MRSA, a rapid culture based screening test for the detection of ciprofloxacin and methicillin resistant S. aureus (MRSA) from screening swabs

Emerging strategies and therapeutic innovations for combating drug resistance in Staphylococcus aureus strains: A comprehensive review

In recent years, antibiotic therapy has encountered significant challenges due to the rapid emergence of multidrug resistance among bacteria responsible for life-threatening illnesses, creating uncertainty about the future management of infectious diseases. The escalation of antimicrobial resistance in the post-COVID era compared to the pre-COVID era has raised global concern. The prevalence of nosocomial-related infections, especially outbreaks of drug-resistant strains of Staphylococcus aureus, have been reported worldwide, with India being a notable hotspot for such occurrences. Various virulence factors and mutations characterize nosocomial infections involving S. aureus. The lack of proper alternative treatments leading to increased drug resistance emphasizes the need to investigate and examine recent research to combat future pandemics. In the current genomics era, the application of advanced technologies such as next-generation sequencing (NGS), machine learning (ML), and quantum computing (QC) for genomic analysis and resistance prediction has significantly increased the pace of diagnosing drug-resistant pathogens and insights into genetic intricacies. Despite prompt diagnosis, the elimination of drug-resistant infections remains unattainable in the absence of effective alternative therapies. Researchers are exploring various alternative therapeutic approaches, including phage therapy, antimicrobial peptides, photodynamic therapy, vaccines, host-directed therapies, and more. The proposed review mainly focuses on the resistance journey of S. aureus over the past decade, detailing its resistance mechanisms, prevalence in the subcontinent, innovations in rapid diagnosis of the drug-resistant strains, including the applicants of NGS and ML application along with QC, it helps to design alternative novel therapeutics approaches against S. aureus infection.

Cas12a/Guide RNA-Based Platforms for Rapidly and Accurately Identifying Staphylococcus aureus and Methicillin-Resistant S. aureus

In order to ensure the prevention and control of methicillin-resistant Staphylococcus aureus (MRSA) infection, rapid and accurate detection of pathogens and their resistance phenotypes is a must. Therefore, this study aimed to develop a fast and precise nucleic acid detection platform for identifying S. aureus and MRSA. We initially constructed a CRISPR-Cas12a detection system by designing single guide RNAs (sgRNAs) specifically targeting the thermonuclease (nuc) and mecA genes. To increase the sensitivity of the CRISPR-Cas12a system, we incorporated PCR, loop-mediated isothermal amplification (LAMP), and recombinase polymerase amplification (RPA). Subsequently, we compared the sensitivity and specificity of the three amplification methods paired with the CRISPR-Cas12a system. Finally, the clinical performance of the methods was tested by analyzing the fluorescence readout of 111 clinical isolates. In order to visualize the results, lateral-flow test strip technology, which enables point-of-care testing, was also utilized. After comparing the sensitivity and specificity of three different methods, we determined that the nuc-LAMP-Cas12a and mecA-LAMP-Cas12a methods were the optimal detection methods. The nuc-LAMP-Cas12a platform showed a limit of detection (LOD) of 10 aM (~6 copies μL-1), while the mecA-LAMP-Cas12a platform demonstrated a LOD of 1 aM (~1 copy μL-1). The LOD of both platforms reached 4 × 103 fg/μL of genomic DNA. Critical evaluation of their efficiencies on 111 clinical bacterial isolates showed that they were 100% specific and 100% sensitive with both the fluorescence readout and the lateral-flow readout. Total detection time for the present assay was approximately 80 min (based on fluorescence readout) or 85 min (based on strip readout). These results indicated that the nuc-LAMP-Cas12a and mecA-LAMP-Cas12a platforms are promising tools for the rapid and accurate identification of S. aureus and MRSA. IMPORTANCE The spread of methicillin-resistant Staphylococcus aureus (MRSA) poses a major threat to global health. Isothermal amplification combined with the trans-cleavage activity of Cas12a has been exploited to generate diagnostic platforms for pathogen detection. Here, we describe the design and clinical evaluation of two highly sensitive and specific platforms, nuc-LAMP-Cas12a and mecA-LAMP-Cas12a, for the detection of S. aureus and MRSA in 111 clinical bacterial isolates. With a limit of detection (LOD) of 4 × 103 fg/μL of genomic DNA and a turnaround time of 80 to 85 min, the present assay was 100% specific and 100% sensitive using either fluorescence or the lateral-flow readout. The present assay promises clinical application for rapid and accurate identification of S. aureus and MRSA in limited-resource settings or at the point of care. Beyond S. aureus and MRSA, similar CRISPR diagnostic platforms will find widespread use in the detection of various infectious diseases, malignancies, pharmacogenetics, food contamination, and gene mutations.

Detection of Klebsiella pneumonia DNA and ESBL positive strains by PCR-based CRISPR-LbCas12a system

INTRODUCTION

Klebsiella pneumonia (K. pneumonia) is a Gram-negative bacterium that opportunistically causes nosocomial infections in the lung, bloodstream, and urinary tract. Extended-spectrum β-Lactamases (ESBLs)-expressed K. pneumonia strains are widely reported to cause antibiotic resistance and therapy failure. Therefore, early identification of K. pneumonia, especially ESBL-positive strains, is essential in preventing severe infections. However, clinical detection of K. pneumonia requires a time-consuming process in agar disk diffusion. Nucleic acid detection, like qPCR, is precise but requires expensive equipment. Recent research reveals that collateral cleavage activity of CRISPR-LbCas12a has been applied in nucleic acid detection, and the unique testing model can accommodate various testing models.

METHODS

This study established a system that combined PCR with CRISPR-LbCas12a targeting the K. pneumoniae system. Additionally, this study summarized the antibiotic-resistant information of the past five years' K. pneumoniae clinic cases in Luohu Hospital and found that the ESBL-positive strains were growing. This study then designs a crRNA that targets SHV to detect ESBL-resistant K. pneumoniae. This work is to detect K. pneumoniae and ESBL-positive strains' nucleic acid using CRISPR-Cas12 technology. We compared PCR-LbCas12 workflow with PCR and qPCR techniques.

RESULTS AND DISCUSSION

This system showed excellent detection specificity and sensitivity in both bench work and clinical samples. Due to its advantages, its application can meet different detection requirements in health centers where qPCR is not accessible. The antibiotic-resistant information is valuable for further research.

A passive monitoring tool using hospital administrative data enables earlier specific detection of healthcare-acquired infections

BACKGROUND

Healthcare-associated infections impose a significant burden on the healthcare system. Current methods for detecting these infections are constrained by combinations of high cost, long processing times and imperfect accuracy, reducing their effectiveness.

METHODS

This study examined whether the amount of time a patient spends on a ward with other patients clinically suspected of infection, termed 'co-presence', can be used as a tool to predict subsequent healthcare-associated infection. Compared with contact tracing, this leverages passively collected electronic data rather than manually collected data, allowing for improved monitoring. All 133,304 inpatient records between 2011 and 2015 were abstracted from a healthcare system in the UK. The area under the receiver-operator curve (AUROC) for each of five pathogens was calculated based on co-presence time, sensitivity and specificity of the test, and how much earlier co-presence would have predicted infection for the true-positive cases.

FINDINGS

For the five pathogens, AUROC ranged from 0.92 to 0.99, and was 0.52 for the negative control. Optimal cut-points of co-presence ranged from 25 to 59 h, and would have led to detection of true-positive cases up to an average of 1 day earlier.

INTERPRETATION

These findings show that co-presence time would help to predict healthcare-acquired infection, and would do so earlier than the current standard of care. Using this measure prospectively in hospitals based on real-time data could limit the consequences of infection, both by being able to treat individual infected patients earlier, and by preventing potential secondary infections stemming from the original infected patient.

Current state of the art in rapid diagnostics for antimicrobial resistance

Antimicrobial resistance (AMR) is a fundamental global concern analogous to climate change threatening both public health and global development progress. Infections caused by antimicrobial-resistant pathogens pose serious threats to healthcare and human capital. If the increasing rate of AMR is left uncontrolled, it is estimated that it will lead to 10 million deaths annually by 2050. This global epidemic of AMR necessitates radical interdisciplinary solutions to better detect antimicrobial susceptibility and manage infections. Rapid diagnostics that can identify antimicrobial-resistant pathogens to assist clinicians and health workers in initiating appropriate treatment are critical for antimicrobial stewardship. In this review, we summarize different technologies applied for the development of rapid diagnostics for AMR and antimicrobial susceptibility testing (AST). We briefly describe the single-cell technologies that were developed to hasten the AST of infectious pathogens. Then, the different types of genotypic and phenotypic techniques and the commercially available rapid diagnostics for AMR are discussed in detail. We conclude by addressing the potential of current rapid diagnostic systems being developed as point-of-care (POC) diagnostic tools and the challenges to adapt them at the POC level. Overall, this review provides an insight into the current status of rapid and POC diagnostic systems for AMR.

High-throughput screening of colonization samples for methicillin-resistant Staphylococcus aureus

BACKGROUND

We present here the first application of 2-photon excited fluorescence detection (TPX) technology for the direct screening of clinical colonization samples for methicillin-resistant Staphylococcus aureus (MRSA).

METHODS

A total of 125 samples from 14 patients with previously identified MRSA carriage and 16 controls from low-prevalence settings were examined.

RESULTS

The results were compared to those obtained by both standard phenotypic and molecular methods. In identifying MRSA carriers, i.e. persons with at least 1 MRSA positive colonization sample by standard methods, the sensitivity of the TPX technique was 100%, the specificity 78%, the positive predictive value 75%, and the negative predictive value 100%. The TPX assay sensitivity per colonization sample was 89%, the specificity 93%, the positive predictive value 84%, and the negative predictive value 95%. The median time for a true-positive test result was 3 h and 26 min; negative test results are available after 13 h. The assay capacity was 48 samples per test run.

CONCLUSIONS

The TPX MRSA technique could provide early preliminary results for clinicians, while simultaneously functioning as a selective enrichment step for further conventional testing. Costs and workload associated with hospital infection control can be reduced using this high-throughput, point-of-care compatible methodology.

Detection of epidemic USA300 community-associated methicillin-resistant Staphylococcus aureus strains by use of a single allele-specific PCR assay targeting a novel polymorphism of Staphylococcus aureus pbp3

In recent years, the dramatic increase in community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections has become a significant health care challenge. Early detection of CA-MRSA is important because of its increased virulence associated with the arginine catabolic mobile element (ACME), Panton-Valentine leukocidin (PVL), and other toxins that may contribute to disease severity. In particular, the USA300 epidemic clone has emerged and now represents the cause of as much as 98% of CA-MRSA skin and soft tissue infections in the United States. Current diagnostic assays used to identify CA-MRSA strains are based on complex multiplex PCRs targeting the staphylococcal cassette chromosome mec (SCCmec) DNA junction, a multitude of genes, and noncoding DNA fragments or on a number of lengthy sequence-typing methods. Here, two nucleotide polymorphisms, G88A and G2047A, that were found to be in strict linkage disequilibrium in the S. aureus penicillin-binding protein 3 (pbp3) gene were also found to be highly associated with the USA300 clone of CA-MRSA. Clinical isolates that contained this pbp3 allele were also positive for the presence of SCCmec type IV, the ACME, and the PVL toxin gene and matched the t008 or t121 molecular spa types, which are associated specifically with the USA300 CA-MRSA clone. A single allele-specific PCR targeting the G88A polymorphism was developed and was found to be 100% sensitive and specific for the detection of USA300 CA-MRSA and 91.5% sensitive and 100% specific for the detection of all CA-MRSA isolates in this study.

Diagnostic accuracy of culture-based and PCR-based detection tests for methicillin-resistant Staphylococcus aureus: a meta-analysis

A systematic review and meta-analysis were performed to determine and compare the sensitivity and specificity of PCR-based and culture-based diagnostic tests for methicillin-resistant Staphylococcus aureus (MRSA). Our analysis included 74 accuracy measurements from 29 publications. Nine tests were evaluated: the PCR-based Genotype MRSA Direct and IDI-MRSA, the chromogenic media CHROMagar, Chromogenic MRSA Medium, MRSA ID, MRSA Select and ORSAB, and the nonchromogenic culture media MSA-Cefoxitin and MSA-Oxacillin. For four chromogenic media, incubation periods of 18-24 and 48 h were evaluated. Considerable heterogeneity was detected in most analyses. A significantly higher sensitivity was found for the overall PCR pooled estimate (92.5; 95% CI 87.4-95.9) and the chromogenic media after 48 h of incubation (87.6; 95% CI 82.1-91.6) compared to the overall sensitivity of chromogenic media after 18-24 h (78.3; 95% CI 71.0-84.1). The specificity of chromogenic media after 18-24 h (98.6; 95% CI 97.7-99.1) was higher than the specificity of PCR (97.0; 95% CI 94.5-98.4) but declined after 48 h of incubation (94.7; 95% CI 91.6-96.8).The most sensitive chromogenic medium after 18-24 h of incubation was Chromogenic MRSA Medium (sensitivity: 89.3; 95% CI 72.8-96.3), whereas the most specific chromogenic medium after 18-24 h of incubation was MRSA Select (specificity: 99.4; 95% CI 98.6-99.7). After 48 h of incubation, MRSA Select had the highest sensitivity (93.2; 95% CI 83.5-97.0), whereas CHROMagar had the highest specificity (96.4; 95% CI 91.3-98.5). This meta-analysis showed statistically significant differences in diagnostic accuracy between several of the tests and the test methods evaluated. A reduction of the incubation time of chromogenic media (from 48 to 18-24 h) increases specificity but reduces sensitivity.

Staphylococcus aureus: An old pathogen with new weapons

Staphylococcus aureus has been recognized as an important human pathogen for more than 100 years. S aureus has been able to adapt and evolve in terms of its resistance traits and virulence factors; it is among the most important causes of human infections in the twenty-first century. Rapid molecular identification in the clinical microbiology laboratory of these resistance and virulence factors expressed by S aureus will play an important role in the future in decreasing the morbidity and mortality of infections. This article addresses the emerging aspects of infections caused by S aureus, including microbiology, epidemiology, clinical presentation, pathogenesis, diagnosis, treatment and prognosis, and immunity.

Current diagnostic tools for methicillin-resistant Staphylococcus aureus infections

Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen responsible for a wide spectrum of healthcare-associated and community-acquired infections. Infections with MRSA strains that are resistant to beta-lactams and other types of antibiotics are a serious therapeutic problem - first, because in such cases only a limited spectrum of antibiotics can be used; and second, because such infections require prolonged hospitalization and result in economic losses. Therefore, in order to limit the overspread of pathogens, the development of diagnostic tools enabling rapid identification of carriers and infected patients, as well as proper identification of drug-resistance mechanisms to enable development of more targeted clinical treatment, are vital. This article reviews the current knowledge concerning prospective diagnostics of MRSA infections.

Methicillin-resistant Staphylococcus aureus screening by online immunometric monitoring of bacterial growth under selective pressure

Rapid, high-throughput screening tools are needed to contain the spread of hospital-acquired methicillin (meticillin)-resistant Staphylococcus aureus (MRSA) strains. Most techniques used in current clinical practice still require time-consuming culture for primary isolation of the microbe. We present a new phenotypic assay for MRSA screening. The technique employs a two-photon excited fluorescence (TPX) detection technology with S. aureus-specific antibodies that allows the online monitoring of bacterial growth in a single separation-free process. Different progressions of fluorescence signals are recorded for methicillin-susceptible and -resistant strains when the growth of S. aureus is monitored in the presence of cefoxitin. The performance of the new technique was evaluated with 20 MRSA strains, 6 methicillin-susceptible S. aureus strains, and 7 coagulase-negative staphylococcal strains and two different monoclonal S. aureus-specific antibodies. When either of these antibodies was used, the sensitivity and the specificity of the TPX assay were 100%. All strains were correctly classified within 8 to 12 h, and up to 70 samples were simultaneously analyzed on a single 96-well microtiter plate. As a phenotypic method, the TPX assay is suited for screening purposes. The final definition of methicillin resistance in any S. aureus strain should be based on the presence of the mecA gene. The main benefit afforded by the initial use of the TPX methodology lies in its low cost and applicability to high-throughput analysis.

Rapid diagnostics for methicillin-resistant Staphylococcus aureus: current status

Methicillin-resistant Staphylococcus aureus (MRSA) is a significant cause of healthcare- and community-associated infections, and its prevalence continues to increase. These infections are associated with morbidity and excessive mortality compared with infections caused by methicillin-susceptible S. aureus (MSSA). Numerous studies have cited the increased healthcare costs associated with MRSA infections. Infection control guidelines that combine active surveillance with aggressive patient management, such as patient isolation, decontamination, and other strategies, have been shown to reduce transmission and subsequent infections. The availability of rapid molecular diagnostics has strengthened infection control programs by providing results in hours rather than days, as the time required for culture-based methods. This review summarizes the current status of rapid diagnostic methods available for MRSA detection from nasal surveillance specimens, and assays available for rapid identification of MRSA from positive blood cultures containing Gram-positive cocci in clusters. Both amplification- and probe-based assays are highlighted and discussed in detail. Future technological advances are likely to see real-time assays that combine multiple gene targets for assessment of microbial identification, virulence detection, and mechanisms of resistance beyond mecA.

Rapid differentiation of methicillin-susceptible Staphylococcus aureus from methicillin-resistant S. aureus and MIC determinations by isothermal microcalorimetry

In this study, the use of isothermal microcalorimetry (IMC) for differentiation between methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) and MIC determination was evaluated. It was possible to differentiate between MRSA and MSSA within 4 h, whereas the standard method required 24 h. The MICs of cefoxitin were successfully determined for MRSA and MSSA by using IMC.

Microbiological evaluation of a new growth-based approach for rapid detection of methicillin-resistant Staphylococcus aureus

Objectives

Recently, a rapid screening tool for methicillin-resistant Staphylococcus aureus (MRSA) has been introduced that applies a novel detection technology allowing the rapid presence or absence of MRSA to be determined from an enrichment broth after only a few hours of incubation. To evaluate the reliability of this new assay to successfully detect MRSA strains of different origin and clonality, well-characterized S. aureus strains were tested in this study.

Methods

More than 700 methicillin-susceptible and methicillin-resistant strains covering >90% of all registered European MRSA spa types within the SeqNet network were studied.

Results

All 513 MRSA strains tested were recognized as methicillin-resistant: among these, 96 MRSA strains were from an institutional collection, each presenting a unique spa type. None of the 211 methicillin-susceptible strains were detected as positive.

Conclusions

The new growth-based rapid MRSA assay was shown to detect without exception all MRSA strains of large collections of strains comprising highly diverse genetic backgrounds, indicating that such a phenotypic test might be potentially more likely to cope with new strains.