Impact of improper sample handling on Cobas CT/NG testing platform with dual swab sample collection kit for detecting Chlamydia trachomatis and Neisseria gonorrhoeae

IMPORTANCE

The importance of this observation lies in its potential to directly impact testing outcomes and patient care. By identifying improper sample handling as a contributing factor to a substantial number of invalid results, we emphasize the need for meticulous adherence to recommended protocols during sample collection. Laboratories that overlook or are unaware of such deviations may inadvertently compromise the reliability and efficacy of their diagnostic processes, leading to misdiagnoses, delayed treatment, and patient dissatisfaction.

Diagnostic performance of DNA probe-based and PCR-based molecular vaginitis testing

Vaginitis is usually diagnosed empirically, microscopically, via cultures, or by molecular testing for the detection of bacterial vaginosis (BV), vulvovaginal candidiasis (VVC), or Trichomonas vaginalis (TV). The DNA probe-based technique detects BV by identifying Gardnerella vaginalis, VVC by identifying Candida spp., while real-time PCR-based detection methods identify BV by algorithmic analysis of the absence or presence of known vaginal flora. We examined 8,878 total orders placed for DNA probe-based identification (ID) and 10,464 total orders placed for molecular panel ID. We found that PCR-based BV test positivity reduced from 30% to 23% compared with the population tested with DNA probe-based testing. We also found that PCR-based testing VVC positivity increased from 6.3% and 11.6% when compared with DNA probe-based testing. Bayesian generalized linear analysis estimated a lower mean proportion of positive tests for BV in PCR-based molecular panels than DNA probe testing suggesting an under-call of BV. The same models estimated a higher mean proportion of positive tests for molecular vaginal panels than DNA probe testing suggesting an increased detection of candidal vaginitis. In addition, the mean (SD) age for patients with Candida albicans was 40.5 (40.0-41.1) years. Patients with Candida glabrata (now N. glabrata) were 5.2-8.1 (mean 6.7) years older than patients with Candida albicans. Our retrospective data analysis found that BD Max MVP's ability to discriminate between vaginal candidiasis versus other yeast will help to implement CDC (Centers for Disease Control and Prevention)-recommended treatment options. We also believe that providers' inattention to non-albicans treatment could be an issue nationwide. IMPORTANCE Using retrospective data from U.S. Food and Drug Administration-approved/cleared molecular vaginal panels, molecular methods were found to have higher detection for Candida vaginitis and lower detection for bacterial vaginitis when compared to probe-based methods. In addition, the differentiation of Candida and non-Candida yeast has not reached the physician community as we observed noncompliance in recommended therapy. Furthermore, the pros and cons of migrating to molecular testing from conventional microscopy for identifying bacterial vaginitis and fungal vaginitis have been examined and reported in this paper. Interestingly, the mean (SD) age for patients with Candida albicans was 40.5 (40.0-41.1) years. Patients with N. glabrata were 5.2-8.1 (mean 6.7) years older than patients with Candida albicans.

Case of Extensively Drug-Resistant Shigella sonnei Infection, United States

We report extensively drug-resistant (XDR) Shigella sonnei infection in an immunocompromised patient in Texas, USA. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry failed to identify XDR Shigella, but whole-genome sequencing accurately characterized the strain. First-line antimicrobials are not effective against emerging XDR Shigella. Fosfomycin, carbapenems, and tigecycline are potential alternatives.

Campylobacter coli bacteremia associated with diarrhea

Campylobacter coli (C. coli) is a gram negative, non-spore forming, mobile, curved, or spiral-shaped rod organisms and one of the most common gastrointestinal human pathogens. Campylobacter very rarely causes bacteremia. However, there are reports of bloodstream infection of C. coli and most of the Campylobacterbacteremia have been found among immunocompromised patients. In this study, a case of C. coli blood stream infection that was associated with diarrhea in an immunocompetent patient.

Presumptive positive with the Cepheid Xpert Xpress SARS-CoV-2 Assay due to N mutations in the Delta variant

The Cepheid Xpert® Xpress SARS-CoV-2 assay is 1 of the several real-time reverse transcription polymerase chain reaction (RT-PCR) assays that received Emergency Use Authorization from the United States Food and Drug Administration (FDA) for detection of SARS-CoV-2. Here we report 4 SARS-CoV-2 samples that were reported as presumptive positives on the Cepheid platform while reported as positives on alternative RT-PCR platforms. Whole genome sequencing indicated that the samples were Delta variants and had point mutations in the N gene which potentially interfered with SARS-CoV-2 detection. Two types of point mutations were found in these samples in the US CDC 2019-nCoV Real time PCR N2 Probe region: C29203T and C29200T. C29203T is a novel point mutation, and C29200T has not been previously reported in the Delta variants. This underlines the fact that mutations in the real-time RT-PCR assay target region could hinder accurate detection of SARS-CoV-2.

Rare Lelliottia nimipressuralis from a wound infection case report using whole genome sequencing-based bacterial identification

Identification of clinical bacterial isolates is an essential first step to provide guidelines for treatment of pathogenic bacterial infection. Infection occurred in a laceration along the medial aspect of left upper arm of a 71-year-old female. Conventional biochemical testing and MALDI-TOF MS identification failed to correctly identify a bacterial isolate. Using whole genome sequencing, the isolate was identified as Lelliottia nimipressuralis. WGS can overcome the limitations of conventional phenotypic and molecular identification methods and successfully identified a rare pathogen. This case is the first report of a human infection of L. nimipressuralis.

Understanding false positives and the detection of SARS-CoV-2 using the Cepheid Xpert Xpress SARS-CoV-2 and BD MAX SARS-CoV-2 assays

Several real-time RT-PCR assays have received Emergency Use Authorization from the United States Food and Drug Administration. The BD MAX™ SARS-CoV-2 assay, run by the BD MAX™ system, is a qualitative test that detects the SARS-CoV-2 specific nucleocapsid phosphoprotein gene regions, N1 and N2. The human RNase P gene is used as the endogenous nucleic acid extraction control. The Cepheid Xpert® Xpress SARS-CoV-2 assay, run by the GeneXpert system, detects the pan-sarbecovirus E gene and the N2 region of the N gene. We evaluated the performance characteristics of the BD and Cepheid assays using matched patient samples. We also analyzed comparative Ct values for both assays using 183 positive samples tested at this facility. In addition, we mitigated reporting false positive results without relying on interpretive software. We found that both systems showed comparable sensitivity. We found an approximately 3.5% false positive rate from the BD MAX™ system results.

Asynchronous Testing of 2 Specimen-Diversion Devices to Reduce Blood Culture Contamination: A Single-Site Product Supply Quality Improvement Project

OBJECTIVE

Blood culture contamination above the national threshold has been a consistent clinical issue in the ED setting. Two commercially available devices were examined that divert an initial small volume of the specimen before the collection of blood culture to reduce skin contamination.

METHODS

Prospectively, 2 different blood culture-diversion devices were made available in the unit supplies to ED clinicians at a single site during 2 different periods of time as a follow-up strategy to an ongoing quality improvement project. Blood samples were collected in the emergency department over a period of 16 months. A retrospective record review study was conducted comparing the use of the 2 specimen-diversion devices with no device (control group) for blood culture contamination rates. The main outcome of monthly blood culture contamination per device was tested using a Bayesian Poisson multilevel regression model.

RESULTS

A total of 4030 blood samples were collected and analyzed from November 2017 to February 2019. The model estimated that the mean incidence of contaminated blood draws in the device A group was 0.29 (0.14-0.55) times the incidence of contaminated draws in the control group. The mean incidence of contaminated blood draws in the device B group was 0.23 (0.13-0.37) times the incidence of contaminated draws in the control group, suggesting that initial-diversion methods reduced blood culture contamination.

CONCLUSION

Initial specimen-diversion devices supplement present standard phlebotomy protocols to bring down the blood culture contamination rate.

Disseminated Invasive Candidiasis in an Immunocompetent Host

Health care providers should consider a nonbacterial source as the causative agent for invasive candidiasis infection in immunocompetent patients.

Endothelial nitric oxide synthase limits host immunity to control disseminated Candida albicans infections in mice

Three isoforms of nitric oxide synthase (NOS) occur in mammals. High levels of NO produced by NOS2/iNOS can protect against bacterial and parasitic infections, but the role of NOS in fungal innate immunity is less clear. Compared to wild type mice, Nos3-/- mice showed significantly higher survival of candidemia caused by Candida albicans SC5314. NOS3/eNOS is expressed by endothelial cells in the kidney, and colonization of this organ was decreased during the sub-acute stage of disseminated candidiasis. Nos3-/- mice more rapidly eliminated Candida from the renal cortex and exhibited more balanced local inflammatory reactions, with similar macrophage but less neutrophil infiltration than in infected wild type. Levels of the serum cytokines IL-9, IL-12, IL-17 and chemokines GM-CSF, MIP1α, and MIP1β were significantly elevated, and IL-15 was significantly lower in infected Nos3-/- mice. Spleens of infected Nos3-/- mice had significantly more Th2 and Th9 but not other CD4+ T cells compared with wild type. Inflammatory genes associated with leukocyte chemotaxis, IL-1 signaling, TLR signaling and Th1 and Th2 cell differentiation pathways were significantly overexpressed in infected Nos3-/- kidneys, with Nos2 being the most strongly induced. Conversely, the general NOS inhibitor NG-nitro-L-arginine methyl ester increased virulence in the mouse candidemia model, suggesting that iNOS contributes to the protective mechanism in infected Nos3-/- mice. By moderating neutrophil infiltration, the absence of eNOS may reduce the collateral damage to kidney cortex, and Th-9 CD4+ cells may enhance clearance of the infection. These data suggest that selective eNOS inhibition could mitigate candidemia by a combination of systemic and local responses that promote a more effective host immune response.

Imaging Candida Infections in the Host

Disseminated fungal infections caused by Candida species are associated with homing of the pathogen to specific organs in human and murine hosts. Kidneys are a primary target organ of Candida albicans, and invasion into the kidney medulla can lead to loss of renal function and death. Therefore, development of noninvasive methods to assess kidney infections could aid in the management of disseminated candidemia. We describe a magnetic resonance imaging method utilizing iron oxide-based contrast agents to noninvasively assess recruitment of phagocytes and kidney inflammation. C. albicans also colonizes the brain and can cause meningoencephalitis. We describe additional imaging methods to assess loss of the blood-brain barrier function that initiates brain infections.