PURPOSE:To report a case of isolated vitritis as the presenting feature of a disseminated infection with Mycobacterium chelonae subspecies gwanakae , a novel subspecies. METHODS:Case report. RESULTS:A 66-year-old man who presented with progressive floaters and blurred vision was found to have isolated vitritis of the left eye. Diagnostic vitrectomy revealed acid-fast bacilli in the vitreous. Whole genome sequencing identified the organism as M. chelonae subspecies gwanakae , a recently identified novel subspecies. The patient was admitted for further evaluation and treatment. Punch biopsies of the numerous ulcerative skin lesions revealed acid-fast bacilli. Magnetic resonance imaging revealed osteomyelitis underlying the soft tissue infections, requiring incision and drainage. Biopsy of the bone also revealed acid-fast bacilli. He was treated with weekly intravitreal amikacin and empiric IV azithromycin, imipenem, and tobramycin. His ocular infection responded well to treatment with resolution of the vitritis and improvement in visual acuity. Unfortunately, his systemic condition deteriorated, and he declined further intervention, ultimately succumbing to his systemic infection 12 weeks after presentation. CONCLUSION:Isolated vitritis can be the presenting feature of a severe disseminated M. chelonae subspecies gwanakae infection.

Methicillin-resistant Staphylococcus aureus (MRSA) causes considerable morbidity and mortality in both community acquired and healthcare associated infections, but detecting colonization with MRSA has been shown to improve patient outcomes in certain clinical settings. MRSA colonization detection has been carried out in a variety of ways with molecular assays having superior sensitivity in most studies relative to culture, but culture is disadvantaged in some comparisons by utilization of low specimen volumes. We compared a commercial molecular assay to both low volume (10 µL) and high volume (650 µL) culture and found that increasing the volume utilized for culture led to detection of 25% more cases than low volume culture.

Vaccination can help prevent infection and can also be used to treat cancer, allergy, and potentially even drug overdose. Adjuvants enhance vaccine responses, but currently, the path to their advancement and development is incremental. We used a phenotypic small-molecule screen using THP-1 cells to identify nuclear factor-κB (NF-κB)–activating molecules followed by counterscreening lead target libraries with a quantitative tumor necrosis factor immunoassay using primary human peripheral blood mononuclear cells. Screening on primary cells identified an imidazopyrimidine, dubbed PVP-037. Moreover, while PVP-037 did not overtly activate THP-1 cells, it demonstrated broad innate immune activation, including NF-κB and cytokine induction from primary human leukocytes in vitro as well as enhancement of influenza and SARS-CoV-2 antigen-specific humoral responses in mice. Several de novo synthesis structural enhancements iteratively improved PVP-037’s in vitro efficacy, potency, species-specific activity, and in vivo adjuvanticity. Overall, we identified imidazopyrimidine Toll-like receptor-7/8 adjuvants that act in synergy with oil-in-water emulsion to enhance immune responses.

CASE A38-year-old male with a past medical history of poorly controlled diabetes mellitus type 2 and hidradenitis suppurativa, a chronic inflammatory condition affecting apocrine glands of the axilla and groin, presented with 1 week of posterior neck swelling and pain. He noted having chronic, stable draining lesions in the axilla and groin but developed a new area of swelling and tenderness in the left posterior neck over the week prior to presentation. On presentation he was afebrile with a heart rate of 130 beats per min (bpm). Other vital signs were within normal limits. His exam was notable for a left-sided occiput large indurated area with mild erythema and tenderness to palpation without active drainage. Laboratory studies were notable for white blood cells, 22.2 103/mm3 (reference range, 4.0 103 to 11.0 103/mm3), and hemoglobin, 10.8 g/dL (reference range, 14.0 to 17.0 g/dL). Computed tomography of the soft tissues of the neck with contrast demonstrated a rim-enhancing hypodense collection in the subcutaneous tissues of the posterior neck measuring 3.1 by 6.1 by 3 cm with surrounding fat infiltration and phlegmonous change (Fig. 1). He was taken to the operating room by the Otolaryngology Department for incision and drainage. In the operating room he was found to have a left occipital abscess with copious purulence expressed with multiple pockets of pus and murky fluid. He was initially given one dose of vancomycin and piperacillin-tazobactam, which were stopped, and ampicillin-sulbactam was started postoperatively. Purulent fluid and a tissue specimen were collected during the incision and drainage procedure for the posterior neck abscess and were submitted for routine bacterial aerobic and anaerobic, fungal, and acid-fast bacillus (AFB) cultures. The direct Gram stain of the fluid showed Gram-variable rods with poor retention of crystal violet (Fig. 2A), but no organisms were observed on the Gram stain from tissue. Auramine-rhodamine (AR) stain of the fluid was read as positive (41,.30 organisms seen per 400 field) for acid-fast bacilli (AFB), and the tissue was also AR positive but with considerably fewer organisms (11, 2 to 20 organisms seen in a total of 50 400 fields). The aerobic (sheep’s blood, chocolate, and MacConkey agar, 3 days of incubation) and anaerobic (CDC anaerobic agar, 5 days of incubation in anaerobic environment) cultures showed no growth. Similarly, fungal cultures of the neck fluid aspirate showed no growth after 28 days, and AFB cultures on 7H11 and LJ-Gruff agar media and BD MGIT broth medium had no growth after 12 weeks (extended culture time because of positive smear). To confirm the AR result when the organism did not grow in culture, both Kinyoun (weakly positive) and modified Kinyoun (strongly positive) (Fig. 2B) stains were performed on the fluid aspirate. Because no organism grew in culture, the fluid specimen was sent to a reference lab (University of Washington) to be tested for tuberculous and nontuberculous mycobacteria by rpoB and hsp65 PCR and sequencing. Mycobacterium-specific targets were negative, but Lawsonella clevelandensis was identified via 16S rRNA primer sets included with the nontuberculousmycobacterium evaluation and subsequent 16S amplicon sequencing. He was treated with 7 days of intravenous ampicillin-sulbactam, 3 g every 6 h, while admitted as an inpatient. He was discharged with an additional 10 days of oral amoxicillin-clavulanate, 875 to 125 mg every 12 h. At outpatient follow-up his posterior Editor Carey-Ann D. Burnham, Pattern Bioscience Copyright © 2023 American Society for Microbiology. All Rights Reserved. Address correspondence to Elizabeth Gancher, elizabeth.gancher@jefferson.edu. The authors declare no conflict of interest. Published 23 May 2023

Blood culture is the standard diagnostic modality for detection of bloodstream infections, and the sensitivity of blood culture detection is directly predicated on the blood culture fill volume (1–3). Previously published studies of quality improvement projects have demonstrated that targeted education can improve blood culture fill volumes (4–6). As part of a quality improvement (QI) project, in addition to other educational interventions, individual collector data were obtained for analysis and distribution to collector managers. Our lab uses BD Bactec FX blood culture instruments and BD EpiCenter middleware. We were able to access individual collector data in EpiCenter using the Reports tab in Bactec FX Instrument reports and accessing the Blood Volume Monitoring Reports folder. Then, we selected Blood Volume Summary, set the study period for Collection Date Selection, and under Group Selection we checked Collected By, where we displayed a list of collectors' ID numbers, and we selected all ID numbers and then selected Print Preview and exported the data as a spreadsheet. In our case, the individual collector ID numbers were converted to employee names and direct reports by our EPIC lab information system group. Only collectors (or locations) with at least 25 collections per study period were included in the report. Individual collector data were used both for creating reports for nurse managers and phlebotomy supervisors and to study a 2-year period of individual collectors, correlating their average volume and the individual collector positive blood culture rate. The latter activity was approved by our institutional review board (IRB control number 20E.112). For the 2-year study period (calendar years 2018 to 2019), collectors who averaged 0 to 2.5, 2.6 to 5.0, 5.1 to 7.5, and .7.5 mL per blood culture had positive culture rates of 7.10%, 7.72%, 7.76%, and 8.00%, respectively (from 9,889 to 28,722 total cultures per category). In 2018, nurse managers were provided with location-specific blood culture fill volume (BCFV) data and education regarding proper BCFV levels. In fiscal year 2018 (FY18, July 2017 to June 2018), the average BCFV was 4.63 mL, with a true positive blood culture rate of 7.0%. In 2019, a health system-wide screen saver with information about appropriate BCFV was implemented for 1 month on all hospital computers. Beginning in the first quarter of 2020, nurse managers were provided with collector-specific BCFV data, which they used for team meeting presentations and individual discussions with low collectors, and this format of data was subsequently provided annually as shown in Fig. 1. In addition to the data used for corrective instruction, gold and silver blood culture bottle-shaped lapel pins were provided for collectors achieving.9.5 and 9.0 to 9.5 mL/bottle averages, respectively, which nurse managers indicated created some healthy competitive behavioral changes and provided a regular discussion opportunity to reinforce education on correct collection practices. Percent change in average blood culture volume was calculated for each quarter and compared to the previous quarter (for each pair for which sufficient data were available for a given ward in each quarter) and separated into the following groups: no intervention (no educational activities in the previous quarter), other intervention (presentation to nursing key personnel, initiation EditorWilliam Lainhart, University of Arizona/ Banner Health Copyright © 2023 Kirby et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Matthew A. Pettengill, Matthew.Pettengill@jefferson.edu. The authors declare no conflict of interest.

Antibiograms are cumulative reports of antimicrobial susceptibility results that are used to guide the selection of empirical antibiotic therapy. Although Clinical and Laboratory Standards Institute (CLSI) guidelines recommend including only organisms that have at least 30 isolates in an antibiogram, previous studies demonstrated that adherence to this recommendation is highly variable. This paper aims to model the impact of small sample sizes on expected levels of error in cumulative antibiograms by comparing percent susceptibility results for random samples to those of the larger, entire data set. The results demonstrate relatively high error rates when utilizing low numbers of isolates in cumulative antibiograms, and provide a discussion point for considering the appropriate number of isolates that could be utilized, and the impact of increasing isolate numbers by including multiple years of data. IMPORTANCE Antibiograms are reports of local antimicrobial susceptibility patterns for common bacteria and yeast that are used to make empirical decisions for patient therapy and also to inform institution therapy guidelines. This study evaluates the impact of low isolate counts on the reliability of antibiograms, and suggests that more institutions should utilize multiple years of data to overcome this issue.

Background: Current pharmacy practice guidelines recommend 24-h area-under-curve (AUC24) targets for use of vancomycin against methicillin-resistant Staphylococcus aureus (MRSA). AUC protocol-specific vancomycin orders were begun recently (2022) at our institution. We reviewed initial AUC protocol-associated data and calculations.Methods: AUC24 calculations are derived from timed, paired measurements of vancomycin (V1, V2). We retrieved paired (V1,V2) measurements for a 90-day interval. Calculations to obtain AUC24 were performed according to two accepted methods (A, B) that assume first-order kinetics for vancomycin elimination between V1 and V2.esults: 44 (V1,V2) measurement pairs were from among 27 patients. Dosing intervals were 8, 12, or 24 h. The first-order rate constant k was normally distributed (k = 0.096 +/- 0.046 1/h); t1/2 ranged from 3 to 30 h. For target AUC24 = 400-600 h x mu g/mL, 55% of calculated AUC24 results were within target. Imprecision for calculated k was predicted to be least when V2 is a trough level. Method B results were greater than Method A results by a factor of 1.07.onclusions: 45% of AUC24 results indicated need for change in dosage. Recommendations are that average results from A and B methods of calculation should be used, and that V1 and V2 should be as widely separated as possible.

Campylobacter ureolyticus is an emerging pathogen increasingly appreciated as a common cause of gastroenteritis and extra-intestinal infections in humans. Outside the setting of gastroenteritis, little work has been done to describe the genomic content and relatedness of the species, especially regarding clinical isolates. We reviewed the epidemiology of clinical C. ureolyticus cultured by our institution over the past 10 years. Fifty-one unique C. ureolyticus isolates were identified between January 2010 and August 2022, mostly originating from abscesses and blood cultures. To clarify the taxonomic relationships between isolates and to attribute specific genes with different clinical manifestations, we sequenced 19 available isolates from a variety of clinical specimen types and conducted a pangenomic analysis with publicly available C. ureolyticus genomes. Digital DNA:DNA hybridization suggested that these C. ureolyticus comprised a species complex of 10 species clusters (SCs) and several subspecies clusters. Although some orthologous genes or gene functions were enriched in isolates found in different SCs and clinical specimens, no association was significant. Nearly a third of the isolates possessed antimicrobial resistance genes, including the ermA resistance gene, potentially conferring resistance to macrolides, the treatment of choice for severe human campylobacteriosis. This work effectively doubles the number of publicly available C. ureolyticus genomes, provides further clarification of taxonomic relationships within this bacterial complex, and identifies target SCs for future analysis.

Campylobacter ureolyticusis an emerging pathogen increasingly appreciated as a common cause of gastroenteritis and extra-intestinal infections in humans. Outside the setting of gastroenteritis, little work has been done to describe the genomic content and relatedness of the species, especially regarding clinical isolates.

Vaccines have generally been developed with limited insight into their molecular impact. While systems vaccinology enables characterization of mechanisms of action, these tools have yet to be applied to infants, who are at high risk of infection and receive the most vaccines. Bacille Calmette-Guérin (BCG) protects infants against disseminated tuberculosis (TB) and TB-unrelated infections via incompletely understood mechanisms. We employ mass-spectrometry-based metabolomics of blood plasma to profile BCG-induced infant responses in Guinea-Bissau in vivo and the US in vitro. BCG-induced lysophosphatidylcholines (LPCs) correlate with both TLR-agonist- and purified protein derivative (PPD, mycobacterial antigen)-induced blood cytokine production in vitro, raising the possibility that LPCs contribute to BCG immunogenicity. Analysis of an independent newborn cohort from The Gambia demonstrates shared vaccine-induced metabolites, such as phospholipids and sphingolipids. BCG-induced changes to the plasma lipidome and LPCs may contribute to its immunogenicity and inform the development of early life vaccines.

In July 2021, the Virginia Department of Health notified CDC of a cluster of eight invasive infections with Burkholderia stabilis, a bacterium in the Burkholderia cepacia complex (BCC), among hospitalized patients at hospital A. Most patients had undergone ultrasound-guided procedures during their admission. Culture of MediChoice M500812 nonsterile ultrasound gel used in hospital A revealed contamination of unopened product with B. stabilis that matched the whole genome sequencing (WGS) of B. stabilis strains found among patients. CDC and hospital A, in collaboration with partner health care facilities, state and local health departments, and the Food and Drug Administration (FDA), identified 119 B. stabilis infections in 10 U.S. states, leading to the national recall of all ultrasound gel products produced by Eco-Med Pharmaceutical (Eco-Med), the manufacturer of MediChoice M500812. Additional investigation of health care facility practices revealed frequent use of nonsterile ultrasound gel to assist with visualization in preparation for or during invasive, percutaneous procedures (e.g., intravenous catheter insertion). This practice could have allowed introduction of contaminated ultrasound gel into sterile body sites when gel and associated viable bacteria were not completely removed from skin, leading to invasive infections. This outbreak highlights the importance of appropriate use of ultrasound gel within health care settings to help prevent patient infections, including the use of only sterile, single-use ultrasound gel for ultrasonography when subsequent percutaneous procedures might be performed.

Maybe 2021 wasn't so bad after all! It was like 2020, but with COVID vaccines and better access to plastic pipette tips, and clearly, 2022 is getting off to a bad start. Even better, 2021 had some exciting papers in clinical microbiology, which is what is highlighted in this 2021 year in review. None of them are about COVID-19. Of course, there were some interesting discoveries about SARS-CoV-2 and COVID-19, but this review is completely COVID-19 free (almost).

Background Elevated cytokine release and T cell exhaustion have been associated with COVID-19 disease severity. T cell activity may be indirectly measured through interferon gamma release assays (IGRAs), which use mitogen stimulation of T lymphocytes as a positive control. In our institution, an unexpectedly high rate of indeterminate IGRAs was noted in COVID-19–positive patients. We aimed to evaluate the clinical characteristics associated with indeterminate IGRA results and the difference in mitogen responses between COVID-19–positive and COVID-19–negative patients. Methods We reviewed all patients, regardless of COVID status, who were admitted between March 1, 2020, and May 31, 2020, and for whom an IGRA was collected. For COVID-19–positive individuals, we evaluated the statistical association of their IGRA results and clinical characteristics, including demographics, laboratory values, comorbidities, and hospitalization-related outcomes. For both COVID-19–positive and COVID-19–negative individuals, we evaluated IGRA mitogen control values relative to COVID-19 status as stratified by absolute lymphocyte count. Results In COVID-19–positive patients, indeterminate IGRA results were statistically associated with white blood cell count and other markers of inflammation. When comparing COVID-19–positive and COVID-19–negative patients, we noted a statistically significant difference in IGRA mitogen control values when stratified by absolute lymphocyte count. Conclusions Indeterminate IGRA results were associated with higher levels of inflammatory markers. Furthermore, when comparing mitogen responses between COVID-19–positive and COVID-19–negative patients, there was an observed difference in T cell reactivity between the groups. The mitogen response in IGRAs may serve as a surrogate for T cell function and a marker of disease severity in COVID-19.

From the onset of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/COVID-19 pandemic, there has been a major emphasis on molecular laboratory tests for the virus. Shortages in various testing supplies, the desire to increase testing capacity, and a push to make point-of-care or home-based testing available have fostered considerable innovation for SARS-CoV-2 molecular diagnostics, advancements likely to be applicable to other diagnostic uses. The authors attempt to cover some of the most compelling novel types of molecular assays or novel approaches in adapting established molecular methodologies for SARS-CoV-2 detection or characterization.

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acquired respiratory syndrome coronavirus 2 (SARS-CoV-2), began in China in the fall of 2019 and started making international news by early January 2020.At that time it was unclear if it would develop into a localized epidemic level infectious disease, similar to severe acquired respiratory syndrome virus (SARS-CoV, or SARS-CoV-1) or Middle East respiratory syndrome virus (MERS), or something more widespread.The pandemic scope of COVID-19 was clear by the end of February, 2020, but diagnostic testing lagged behind.Regulatory issues revolving around both the granting of Emergency Use Authorizations (EUAs) for test development and supply chain constrictions were major impediments to building testing infrastructure.The first assay in the US was developed by the CDC and distributed to public health laboratories, though its rollout was badly hampered by manufacturing issues and supply availability (particularly for RNA extraction).Commercial assays became selectively available by mid-March but not widely accessible with reasonable turnaround times (<24 h) until May.However, the scale of the ramp-up in lab-developed and commercial tests from March 2020 to July 2020 is staggering-from unavailable to around 1 million SARS-CoV-2 tests performed each day in the US and eventually testing would peak in January 2021 at around 2 million SARS-CoV-2 tests performed each day in the US.We herein present our opinion on what has been, and what may be, the role and contribution of SARS-CoV-2 viral testing during the COVID-19 pandemic.Diagnostic testing is necessary to guide clinical and public health decision making, but to do so effectively it needs to be both accessible and of high quality.In March of 2020 the lack of access to SARS-CoV-2 testing with <24 h turnaround times impaired efforts to curb the pandemic.Many testing decisions were made

We present a case of a young healthy female who developed recurrent cranial wound infections after a traumatic injury, the etiologic organism finally identified as Mycoplasma hominis, an uncommon and difficult to isolate bacterium.

A 3-dimensional printed swab was invented to address supply chain disruptions caused by coronavirus disease 2019 that result in shortages of standard nasopharyngeal swab used for severe acute respiratory syndrome coronavirus 2 testing. A clinical trial compared the 2 swabs. Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes coronavirus disease 2019 (COVID-19), can be detected in respiratory samples by real-time reverse transcriptase polymerase chain reaction (RT-PCR) or other molecular methods. Accessibility of diagnostic testing for COVID-19 has been limited by intermittent shortages of supplies required for testing, including flocked nasopharyngeal (FLNP) swabs. Methods We developed a 3-dimensional printed nasopharyngeal (3DP) swab as a replacement of the FLNP swab. The performance of 3DP and FLNP swabs were compared in a clinical trial of symptomatic patients at 3 clinical sites (n = 291) using 3 SARS-CoV-2 emergency use authorization tests: a modified version of the Centers for Disease Control and Prevention (CDC) RT-PCR Diagnostic Panel and 2 commercial automated formats, Roche Cobas and NeuMoDx. Results The cycle threshold-C(t)-values from the gene targets and the RNase P gene control in the CDC assay showed no significant differences between swabs for both gene targets (P = .152 and P = .092), with the RNase P target performing significantly better in the 3DP swabs (P < .001). The C(t) values showed no significant differences between swabs for both viral gene targets in the Roche cobas assay (P = .05 and P = .05) as well as the NeuMoDx assay (P = .401 and P = .484). The overall clinical correlation of COVID-19 diagnosis between all methods was 95.88% (Kappa 0.901). Conclusions The 3DP swabs were equivalent to standard FLNP in 3 testing platforms for SARS-CoV-2. Given the need for widespread testing, 3DP swabs printed onsite are an alternate to FLNP that can rapidly scale in response to acute needs when supply chain disruptions affect availability of collection kits.

A male patient in his thirties presented to the hospital with meningismus and altered mental status. Cerebrospinal fluid (CSF) analysis confirmed meningitis, but no microorganisms were identified. Head imaging (MRI) revealed multiple brain abscesses. Surgically-collected brain specimens revealed Gram-positive cocci and subsequently grew Streptococcus intermedius. MRI of the thoracic spine subsequently also identified an intramedullary spinal abscess. While brain abscesses and spinal abscesses caused by S. intermedius have been previously reported, the extent of disseminated disease in the patient was noteworthy.

RT-PCR is the gold-standard for the diagnosis of SARS-CoV-2 infection, however, testing has been complicated by supply shortages and long turn-around times.….