Journal of Clinical Microbiology最新文献

Rapid antimicrobial susceptibility testing (rAST) performed directly from blood cultures is essential to influencing the selection of appropriate antibiotics, preferably targeted therapy, for the treatment of bloodstream infections. Affinity Biosensors has developed the LifeScale, a phenotypic rAST system based on microfluidic sensors with a mechanical resonator that measures the mass of individual microbes. The combination of replication, biomass, and population profiling of individual microbes is analyzed to produce rAST results. The performance of the LifeScale was evaluated and compared to our current standard of care (SOC) antimicrobial susceptibility testing (AST) system under clinical conditions. The results indicated that the LifeScale is easy to use and provides rapid, reliable, and accurate AST results in less than 5 h directly from from positive blood cultures containing Gram-negative organisms listed in the current database. For all organism-antibiotic combinations involving polymicrobial cultures, LifeScale showed a resistant result when either mixed isolate was resistant. If these results prove to be robust on further testing, this may justify the reporting of rapid LifeScale results without the need for additional confirmatory testing.

Importance: This is the first clinical-based study of a unique technology using microfluidic sensors to generate rapid antimicrobial susceptibility test results directly from blood cultures containing Gram-negative rods. The issue of polymicrobial cultures was also addressed in this study, which, to our knowledge, has not been addressed in publications of other rapid phenotypic AST systems. Overall, LifeScale results compared favorably with the SOC in terms of overall agreement, especially categorical agreement.

Taxonomy is a systematic practice in which microorganisms are granted names to facilitate and standardize multi-disciplinary communication. We summarize novel bacterial taxa derived from human clinical material that were published in peer-reviewed literature and/or included by the International Journal of Systematic and Evolutionary Microbiology during calendar year 2023, as well as taxonomic revisions that have been published/included by the same entity. While the majority of newly discovered facultative and anaerobic organisms were derived from microbiome surveillance, noteworthy novel taxa in the realm of pathogenicity potential include those related to Aerococcus spp., several Corynebacterium spp., Exercitatus varius gen. nov., sp. nov., and Mycoplasma phocimorsus sp. nov. With respect to nomenclature revision, the Bacillus and Clostridium genera continue to be visited annually. Creation of novel anaerobic Gram-negative bacillus genera Hallella, Hoylesella, Leyella, Segatella, and Xylanibacter impacted several Bacteroides spp. and Prevotella spp. Additional studies are necessary to ascertain the clinical significance of several of these microbes.

Rapid multiplex PCR kits have been used for rapid identification of blood culture isolates and prediction of antimicrobial resistance. We performed an evaluation of the QIAstat-Dx BCID GN and GPF research use only (RUO) kits on positive blood culture bottles using routine laboratory testing as the reference standard. Positive blood culture bottles between November 2023 and January 2024 were tested with QIAstat-Dx BCID GN and GPF kits based on initial Gram stain results and compared against routine identification and phenotypic susceptibility testing. A total of 174 monomicrobial blood cultures were included in the final analysis. The 174 monomicrobial blood cultures composed of 129 BCID GN tests and 45 BCID GPF tests. The majority of on-target Gram-negative organisms in monomicrobial cultures were identified. One Escherichia coli isolate was not identified as such, although the pan-Enterobacterales target was positive. All on-target Gram-positive organisms in monomicrobial cultures were identified. Overall sensitivity and specificity of tem/shv for detection of aminopenicillin resistance in E. coli was 94.7% (18/19) and 95.8% (23/24). The presence/absence of ctx-m and ampC had 100% sensitivity and specificity for identification of third-generation cephalosporin resistance in E. coli and Klebsiella pneumoniae. The combination of blaZ and mecA gene detection was fully predictive of phenotypic susceptibility results to penicillin and cloxacillin for Staphylococcus aureus. Overall, the QIAstat-Dx BCID GN and GPF kits were able to identify on-target pathogens. Detected resistance mechanisms were highly predictive of β-lactam resistance. Prediction of resistance for non-β-lactam antimicrobial was more variable.

Importance: This is one of the first evaluations of the QIAstat BCID kit and demonstrates high levels of correlation for both identification and antimicrobial resistance prediction.

Medically important pathogenic fungi invade vertebrate tissue and are considered primary when part of their nature life cycle is associated with an animal host and are usually able to infect immunocompetent hosts. Opportunistic fungal pathogens complete their life cycle in environmental habitats or occur as commensals within or on the vertebrate body, but under certain conditions can thrive upon infecting humans. The extent of host damage in opportunistic infections largely depends on the portal and modality of entry as well as on the host's immune and metabolic status. Diseases caused by primary pathogens and common opportunists, causing the top approximately 80% of fungal diseases [D. W. Denning, Lancet Infect Dis, 24:e428-e438, 2024, https://doi.org/10.1016/S1473-3099(23)00692-8], tend to follow a predictive pattern, while those by occasional opportunists are more variable. For this reason, it is recommended that diseases caused by primary pathogens and the common opportunists are named after the etiologic agent, for example, histoplasmosis and aspergillosis, while this should not be done for occasional opportunists that should be named as [causative fungus] [clinical syndrome], for example, Alternaria alternata cutaneous infection. The addition of a descriptor that identifies the location or clinical type of infection is required, as the general name alone may cover widely different clinical syndromes, for example, "rhinocerebral mucormycosis." A list of major recommended human and animal disease entities (nomenclature) is provided in alignment with their causative agents. Fungal disease names may encompass several genera of etiologic agents, consequently being less susceptible to taxonomic changes of the causative species, for example, mucormycosis covers numerous mucormycetous molds.

Shiga toxin-producing Escherichia coli (STEC) are the main etiological agents of hemolytic uremic syndrome (HUS). Good clinical management of STEC infections and HUS depends on early, rapid, and accurate diagnosis. Here, we have developed and evaluated the first multiplex and glycoprotein-based immunochromatographic test for the detection of IgM antibodies against the O-polysaccharide of the lipopolysaccharide of E. coli O157 and O145 in human serum samples. A retrospective study was carried out resulting in a diagnostic sensitivity of the E. coli O157/O145 LFIA (lateral flow immunoassay) of 97.1% and 98.9% for O157 and O145, respectively, and 97.9% for both serogroups. The diagnostic specificity was 98.7% for O157 and O145, and the overall specificity 97.4%. In samples obtained before 3 days after the onset of diarrhea, the detection percentage was 83%, increasing to 100% from 3 days onward. Finally, the association of bloody diarrhea (BD) or HUS cases to an STEC infection increased from 22.8% to 77.2% when stool culture and stx/Stx detection were combined with serology by LFIA. Our results demonstrate that the E. coli O157/O145 LFIA is a highly accurate and serospecific test for the early and rapid diagnosis of E. coli O157 and O145 infections in BD or HUS cases. This test allows the detection of specific IgM antibodies very early in the course of the infection, making it an ideal diagnostic tool to be implemented in pediatric emergencies and, thus, avoid delays in the application of the correct supportive or specific treatment and prevent complications associated with HUS.

A total of 1,925 Corynebacterium isolates were tested for antimicrobial susceptibility at the Mayo Clinic Microbiology laboratory (Rochester, Minnesota) from January 2012 to March 2023, with C. striatum (35.6%) and C. amycolatum (24.4%) identified as the predominant species. Species known to potentially carry diphtheria toxin were excluded. Common sources of isolation included skin and soft tissue (56.8%), bone and/or native joint synovial fluid (14.2%), urine (13.1%), sputum (6.1%), and blood (5.9%). For penicillin, susceptibility decreased from 47.5% (58 of 122) in 2012 to 20.6% (14 of 68) in 2023. Isolates also showed a decrease in susceptibility to erythromycin from 22.4% (26 of 116) in 2012 to 13.2% (9 of 68) in 2023. Susceptibility to trimethoprim-sulfamethoxazole averaged around 50% throughout the period. Notably, linezolid and vancomycin were universally effective in vitro against all species. The highest susceptibility rates among tested oral agents were to linezolid and doxycycline for non-C. striatum species. Daptomycin minimal inhibitory concentrations (MICs) of >256 µg/mL were observed for one C. amycolatum isolate, one C. tuberculostearicum isolate, and for seven C. striatum isolates, all from patients with prior daptomycin exposure. Daptomycin MICs of 2 µg/mL (nonsusceptible) were observed in one C. striatum isolate recovered from a daptomycin-naïve patient and in six C. jeikeium isolates, from both daptomycin-exposed and non-exposed patients. Significant variation in susceptibility profiles across different Corynebacterium species underscores the importance of performing antimicrobial susceptibility testing to guide effective treatment. Moreover, multidrug resistance observed in C. striatum poses substantial therapeutic challenges especially in patients requiring prolonged or chronic antibiotic suppression.