Klebsiella pneumoniae and the closely related species K. variicola and K. quasipneumoniae are common causes of health care-associated infections, and patients frequently become infected with their ...intestinal colonizing strain. To assess the association between Klebsiella colonization density and subsequent infections, a case-control study was performed. A multiplex quantitative PCR (qPCR) assay was developed and validated to quantify Klebsiella (K. pneumoniae, K. variicola, and K. quasipneumoniae combined) relative to total bacterial DNA copies in rectal swabs. Cases of Klebsiella infection were identified based on clinical definitions and having a clinical culture isolate and a preceding or coincident colonization isolate with the same wzi capsular sequence type. Controls were colonized patients without subsequent infection and were matched 2:1 to cases based on age, sex, and rectal swab collection date. qPCR from rectal swab samples was used to measure the association between the relative abundance of Klebsiella and subsequent infections. The Klebsiella relative abundance by qPCR was highly correlated with 16S sequencing (ρ = 0.79; P < 0.001). The median Klebsiella relative abundance was higher in cases (15.7% interquartile range {IQR}, 0.93 to 52.6%) (n = 83) than in controls (1.01% IQR, 0.02 to 12.8%) (n = 155) (P < 0.0001). Adjusting for multiple clinical covariates using inverse probability of treatment weighting, a Klebsiella relative abundance of >22% was associated with infection overall (odds ratio OR, 2.87 95% confidence interval {CI}, 1.64 to 5.03) (P = 0.0003) and with bacteremia in a secondary analysis (OR, 4.137 95% CI, 1.448 to 11.818) (P = 0.0084). Measurement of colonization density by qPCR could represent a novel approach to identify hospitalized patients at risk for Klebsiella infection. IMPORTANCE Colonization by bacterial pathogens often precedes infection and offers a window of opportunity to prevent these infections in the first place. Klebsiella colonization is significantly and reproducibly associated with subsequent infection; however, factors that enhance or mitigate this risk in individual patients are unclear. This study developed an assay to measure the density of Klebsiella colonization, relative to total fecal bacteria, in rectal swabs from hospitalized patients. Applying this assay to 238 colonized patients, a high Klebsiella density, defined as >22% of total bacteria, was significantly associated with subsequent infection. Based on widely available PCR technology, this type of assay could be deployed in clinical laboratories to identify patients at an increased risk of Klebsiella infections. As novel therapeutics are developed to eliminate pathogens from the gut microbiome, a rapid Klebsiella colonization density assay could identify patients who would benefit from this type of infection prevention intervention.
Reported here are the sequences for 11 Escherichia coli and four Enterococcus strains isolated from post-menopausal women with a recurrent urinary tract infection. Each of the Enterococcus strains ...were isolated along with an E. coli strain. This provides a resource of high-quality complete genomes from polymicrobial infections.
Epitopes from the Candida cell surface proteins Fba and Met6 are putative vaccine targets for invasive candidiasis. Here, we describe a Candida vaccine approach in which short peptides derived from ...Fba and Met6 are used in spontaneous nanoliposome antigen particle (SNAP) format. SNAP was enabled by the interaction of cobalt porphyrin phospholipid in liposomes with three histidine residues on the N-terminus of synthetic short peptide immunogens from Fba (F-SNAP), Met6 (M-SNAP), or bivalent Fba and Met6 (FM-SNAP). Liposomes were adjuvanted with synthetic monophosphoryl lipid and QS-21. In mice, immunization with F-SNAP, M-SNAP, or FM-SNAP induced antigen-specific IgG responses and mixed Th1/Th2 immunity. The duplex FM-SNAP vaccine elicited stronger antibody responses against each peptide, even at order-of-magnitude lower peptide dosing than a comparable adjuvanted, conjugate vaccine. Enzyme-linked immunosorbent spot analysis revealed the induction of antigen-specific, cytokine-producing T cells. Compared to F-SNAP or M-SNAP, higher production of TNFα, IL-2, and IFNγ was observed with re-stimulation of splenocytes from bivalent FM-SNAP-immunized mice. When vaccinated BALB/c mice were challenged with Candida auris, analysis of the fungal burden in the kidneys showed that SNAP vaccination protected from disseminated candidiasis. In a lethal fungal exposure model in A/J mice, F-SNAP, M-SNAP, and FM-SNAP vaccination protected mice from candidiasis challenge. Together, these results show that further investigation into the SNAP adjuvant platform is warranted using Fba and Met6 epitopes for a pan-Candida peptide vaccine that provides multifaceted protective immune responses.IMPORTANCEThis study introduces a promising vaccine strategy against invasive candidiasis, a severe fungal infection, by targeting specific peptides on the surface of Candida. Using a novel approach called spontaneous nanoliposome antigen particle (SNAP), we combined peptides from two key Candida proteins, Fba and Met6, into a vaccine. This vaccine induced robust immune responses in mice, including the production of protective antibodies and the activation of immune cells. Importantly, mice vaccinated with SNAP were shielded from disseminated candidiasis in experiments. These findings highlight a potential avenue for developing a broad-spectrum vaccine against Candida infections, which could significantly improve outcomes for patients at risk of these often deadly fungal diseases.
Since the beginning of the COVID-19 pandemic, molecular methods (e.g., real-time PCR) have been the primary means of diagnosing the disease. It is now well established that molecular tests can ...continue to detect SARS-CoV-2 genomic RNA for weeks or months following the resolution of clinical illness. This has prompted public health agencies to recommend a symptom- and/or time-based strategy for discontinuation of isolation precautions, which, for hospitalized patients, results in significant use of personal protective equipment. Due to the inability of current molecular diagnostic assays to differentiate between the presence of remnant viral RNA (i.e., noninfectious) and replication-competent (i.e., infectious) virus, there has been interest in determining whether laboratory tests can be used to predict an individual’s likelihood of transmitting the virus to others. This review will highlight what is currently known about the potential for existing assays, such as real-time PCR and antigen tests, to predict active viral infection. In addition, data on the performance of new methods, such as molecular tests targeting viral RNA intermediates (e.g., subgenomic RNA), will be discussed.
The number of days until pharyngeal Neisseria gonorrhoeae nucleic acid amplification test (NAAT) results become negative after treatment remains unknown. Between March 2019 and April 2021, we ...enrolled men who have sex with men (MSM) who had a clinical positive pharyngeal N. gonorrhoeae Aptima Combo 2 test result but had not yet been treated in a prospective longitudinal cohort study. MSM were enrolled on their day of treatment and self-collected daily pharyngeal specimens for 21 days at home. We used Kaplan-Meier estimates to determine the median time to clearance and the >95% time to clearance and the log rank test for equality to evaluate factors associated with time to clearance. Sixty-four men were enrolled in the study. Analyses excluded 8 men (12.5%) who were N. gonorrhoeae negative by NAAT at enrollment and 11 (17%) who failed to return any home-collected specimens. Among the 45 men included in the analysis, the median time to N. gonorrhoeae NAAT clearance was 3 days (95% confidence interval CI, 2 to 5 days). Time to clearance for >95% of the cohort was 12 days (95% CI, 10 days to an undefined time). Men with a history of N. gonorrhoeae infection cleared faster than men without such history (8 days versus 17 days for >95% time to clearance;
= 0.03). In the absence of reexposure, positive N. gonorrhoeae Aptima Combo 2 assay results obtained prior to 12 days after treatment are likely false-positive results.
Antibiotic-resistant infections are an urgent problem in clinical settings because they sharply increase mortality risk in critically ill patients. The horizontal spread of antibiotic resistance ...genes among bacteria is driven by bacterial plasmids, promoting the evolution of resistance. Crucially, particular associations exist between resistance plasmids and bacterial clones that become especially successful in clinical settings. However, the factors underlying the success of these associations remain unknown. Recent in vitro evidence reveals (i) that plasmids produce fitness costs in bacteria, and (ii) that these costs are alleviated over time through compensatory mutations. I argue that plasmid-imposed costs and subsequent compensatory adaptation may determine the success of associations between plasmids and bacteria in clinical settings, shaping the in vivo evolution of antibiotic resistance.
Antibiotic resistance (AR) in bacteria is one of the biggest threats currently facing humanity, and plasmids play an essential role in the dissemination of AR among clinically important pathogens.
Certain associations between AR plasmids and pathogenic bacterial clones are extremely prevalent.
In the absence of selection for plasmid-encoded traits, most plasmids reduce bacterial fitness. Recent in vitro findings demonstrate that this cost is alleviated by compensatory evolution. These evolutionary dynamics (cost versus compensation) determine the fate of the plasmid-carrying clone in the bacterial population.
The involvement of plasmid costs and compensatory evolution in the rise and spread of successful plasmid–bacterium associations in clinical contexts remains unexplored.
The rapid identification of blood culture isolates and antimicrobial susceptibility test (AST) results play critical roles for the optimal treatment of patients with bloodstream infections. Whereas ...others have looked at the time to detection in automated culture systems, we examined the overall time from specimen collection to actionable test results. We examined four points of time, namely, blood specimen collection, Gram stain, organism identification (ID), and AST reports, from electronic data from 13 U.S. hospitals for the 11 most common, clinically significant organisms in septic patients. We compared the differences in turnaround times and the times from when specimens were collected and the results were reported in the 24-h spectrum. From January 2015 to June 2016, 165,593 blood specimens were collected, of which, 9.5% gave positive cultures. No matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry was used during the study period. Across the 10 common bacterial isolates (
= 6,412), the overall median (interquartile range) turnaround times were 0.80 (0.64 to 1.08), 1.81 (1.34 to 2.46), and 2.71 (2.46 to 2.99) days for Gram stain, organism ID, and AST, respectively. For all positive cultures, approximately 25% of the specimens were collected between 6:00 a.m. and 11:59 a.m. In contrast, more of the laboratory reporting times were concentrated between 6:00 a.m. and 11:59 a.m. for Gram stain (43%), organism ID (78%), and AST (82%), respectively (
< 0.001). The overall average turnaround times from specimen collection for Gram stain, organism ID, and AST were approximately 1, 2, and 3 days, respectively. The laboratory results were reported predominantly in the morning hours. Laboratory automation and work flow optimization may play important roles in reducing the microbiology result turnaround time.
Preexisting immunity to Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) was nonexistent in humans, which coupled with high transmission rates of certain SARS-CoV-2 variants and limited ...vaccine uptake or availability, has collectively resulted in an ongoing global pandemic. The identification and establishment of one or multiple correlates of protection (CoP) against infectious pathogens is challenging, but beneficial from both the patient care and public health perspectives. Multiple studies have shown that neutralizing antibodies, whether generated following SARS-CoV-2 infection, vaccination, or a combination of both (
hybrid immunity), as well as adaptive cellular immune responses, serve as CoPs for COVID-19. However, the diverse number and type of serologic assays, alongside the lack of cross-assay standardization and emergence of new SARS-CoV-2 variants with immune evasive characteristics, have collectively posed challenges to determining a robust CoP 'threshold' and for the routine utilization of these assays to document 'immunity,' as is commonly done for other vaccine preventable diseases. Here, we discuss what CoPs are, review our current understanding of infection-induced, vaccine-elicited and hybrid immunity to COVID-19 and summarize the current and potential future utility of SARS-CoV-2 serologic testing.
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