Tailored Treatment Based on Helicobacter pylori Genetic Markers of Resistance Is Associated With Higher Eradication Success.

INTRODUCTION: Increasing antimicrobial resistance with Helicobacter pylori infection has focused efforts to tailor eradication therapy based on identifying genetic markers of resistance to predict antimicrobial susceptibility. METHODS: In this retrospective study, we report the effect of routine inclusion of antimicrobial susceptibility testing and recommendations for eradication therapy with gastric specimens with H. pylori . RESULTS: The use of a recommended treatment regimen based on genetic markers of resistance was associated with an 84% rate of eradication success and 4.4 greater odds of eradication relative to unrecommended treatment. DISCUSSION: This is the first study describing the use of H. pylori genetic resistance testing as standard of care.

Seroprevalence of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) among healthcare providers prior to the vaccine era in an integrated midwestern healthcare system.

We performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) antinucleocapsid IgG testing on 5,557 healthcare providers and found a seroprevalence of 3.9%. African Americans were more likely to test positive than Whites, and HCWs with household exposure and those working on COVID-19 cohorting units were more likely to test positive than their peers.

SARS-CoV-2 antibody profile of naturally infected and vaccinated individuals detected using qualitative, semi-quantitative and multiplex immunoassays.

This study measured antibodies against different antigen targets in healthcare workers (HCW) who have been fully vaccinated with mRNA vaccines, recovered from natural infection, or patients during active infection. All vaccinated individuals were positive for anti-RBD, anti-S1, and anti-S2 antibodies. The nonvaccinated recovered cohort showed 90% seropositivity by Atellica total antibody, 73% by Atellica IgG, 84% by Bioplex anti-RBD, 77% by Bioplex anti-S1, 37% by Bioplex anti-S2, and 79% by Bioplex antinucleocapsid respectively. The active infection cohort exhibited a similar pattern as the recovered cohort. About 88% and 78% of the recovered and active infection cohort produced both anti-spike and anti-N antibodies with Anti-S1/anti-N ratios ranging from 0.07 to 16.26. In summary, fully vaccinated individuals demonstrated an average of 50-fold higher antibody levels than naturally infected unvaccinated individuals with immune reactivity strongly towards RBD/S1 and a weak response to S2. The results support vaccination regardless of previous COVID-infection status.

Determining the Clinical Utility of 16S rRNA Sequencing in the Management of Culture-Negative Pediatric Infections.

The use of 16S rRNA sequencing in culture-negative infections has improved identification of bacterial pathogens in select scenarios, but its clinical impact requires further elucidation, especially in the pediatric population. This retrospective study aims to determine the clinical utility of 16S rRNA sequencing on the clinical management of pediatric culture-negative infections in our institution. Significant clinical utility was identified in 30 (40.5%) of 74 clinical samples (p < 0.0001). Of all specimens, pulmonary samples yielded the most clinical utility (n = 9, 30%), followed equally by joint fluid (n = 6, 20%) and bone (n = 6, 20%), with no difference between fluid and fresh tissue specimens (p = 0.346). Although the difference was not statistically significant (p = 0.4111), the overall use of broad-spectrum coverage was decreased. The median number of antibiotics was decreased from two to one (p < 0.0001) based on 16S rRNA sequencing results. The results suggest that 16S rRNA sequencing has a significant impact on decreasing the number of antibiotics used in the treatment of pediatric culture-negative infections. 16S rRNA sequencing performed on pulmonary specimens has the highest likelihood of identifying a pathogen compared to other specimen types. Additional cost-benefit analysis needs to be completed to further determine clinical benefit.

High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants.

OBJECTIVES: Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is rapid, accurate, adaptable, and able to detect new low-level variants built with existing hospital infrastructure. METHODS: We used a tiered high-throughput SARS-CoV-2 screening program to characterize variants in a supraregional health system over 76 days. Combining targeted reverse transcription-polymerase chain reaction (RT-PCR) and selective sequencing, we screened SARS-CoV-2 reactive samples from all hospitals within our health care system for genotyping dominant and emerging variants. RESULTS: The median turnaround for genotyping was 2 days using the high-throughput RT-PCR-based screen, allowing us to rapidly characterize the emerging Delta variant. In our population, the Delta variant is associated with a lower cycle threshold value, lower age at infection, and increased vaccine-breakthrough cases. Detection of low-level and potentially emerging variants highlights the utility of a tiered approach. CONCLUSIONS: These findings underscore the need for fast, low-cost, high-throughput monitoring of regional viral sequences as the pandemic unfolds and the emergence of SARS-CoV-2 variants increases. Combining RT-PCR-based screening with selective sequencing allows for rapid genotyping of variants and dynamic system improvement.

Parasitic Disease Surveillance, Mississippi, USA.

Surveillance for soil-transmitted helminths, strongyloidiasis, cryptosporidiosis, and giardiasis was conducted in Mississippi, USA. PCR performed on 224 fecal samples for all soil-transmitted helminths and on 370 samples for only Necator americanus and Strongyloides stercoralis identified 1 S. stercoralis infection. Seroprevalences were 8.8% for Toxocara, 27.4% for Cryptosporidium, 5.7% for Giardia, and 0.2% for Strongyloides parasites.

How the Pathologist Can Help the Surgeon Collect Better Specimens for Microbiology Culture.

CONTEXT.­: Specimen quality is paramount for microbiology culture in order to ensure the testing is performed appropriately and the results, generated accurately, reflect the patient's clinical situation and guide proper treatment. Several factors play a critical role in guaranteeing the accuracy of the culture results, including adequate specimen collection by the surgeon, proper labeling, and timely transport to the laboratory. OBJECTIVE.­: To educate pathologists, surgeons, and other medical personnel involved in the collection and processing of surgical specimens submitted for microbiologic culture. To assure the pathogen is correctly identified, proper protocols must be followed. The accurate identification of the infectious microorganisms from surgical specimens is vital for the treating clinician to ensure the correct antimicrobial therapy is administered. DATA SOURCES.­: An analysis of relevant literature was performed by using PubMed. Articles were selected on the basis of their relevance to the topic as well as their date of publication. Articles published between 2000 and 2018 were deemed sufficient for inclusion, while older references, regardless of relevance, were excluded. CONCLUSIONS.­: The process of properly obtaining specimens for microbiology culture from the operating room is a complex process that requires collaboration between the collecting surgeon and the pathologist and microbiology laboratory in order to provide the highest quality of results from which important treatment decisions are then implemented. Engaging leadership to develop mutually agreed-upon institutional best practices will help not only to standardize practices but also to improve the quality of microbiology results reported.

Routine Broad-Range Fungal Polymerase Chain Reaction With DNA Sequencing in Patients With Suspected Mycoses Does Not Add Value and Is Not Cost-Effective.

CONTEXT.­: New molecular diagnostic tests regularly become available, and they may be assumed to be superior to traditional diagnostic studies. The added cost of these studies should be considered in conjunction with the value provided for patient care. OBJECTIVE.­: To assess the cost and diagnostic value of broad-range polymerase chain reaction (PCR) and DNA sequencing for the diagnosis of fungal infections compared with traditional studies. DESIGN.­: We reviewed the cost and clinical impact of broad-range fungal PCR/DNA sequencing for 65 specimens for which this test, a direct fungal examination, fungal culture, and a histopathologic assessment were performed. RESULTS.­: The sensitivity, specificity, and positive and negative predictive values for each of the assays studied were, respectively: histopathology (83.3%, 100%, 100%, and 98.3%); direct examination (66.7%, 100%, 100%, and 96.7%); fungal culture (83.3%, 100%, 100%, and 98.3%); and broad-range fungal PCR/DNA sequencing (83.3%, 95.0%, 62.5%, and 98.3%). The cost for broad-range fungal PCR/DNA sequencing was $32,500, compared with $8,591.70 for all traditional tests combined, for the 65 specimens included in this review. CONCLUSIONS.­: Broad-range fungal PCR/DNA sequencing did not detect any infecting fungal pathogen that was not detected by at least 1 of the traditional methods, but 3 false-positives occurred. Broad-range fungal PCR/DNA sequencing is not a substitute for traditional laboratory studies and should be used judiciously to promote care affordability.

Antibiotic susceptibility, cytotoxicity, and protease activity of viridans group streptococci causing endophthalmitis.

The viridans group streptococci comprise multiple species and have gained more recognition in recent years as common etiologic agents of bacterial endophthalmitis. The purpose of this study was to identify the species of human endophthalmitis isolates of viridans streptococci and to characterize their potential virulence attributes. The species of 22 endophthalmitis strains of viridans streptococci were identified by Matrix Assisted Laser Desorption Ionization Time-of-Flight. Susceptibilities to 3 antibiotics commonly used for bacterial endophthalmitis were determined. The extracellular milieu of each strain was tested for cytotoxicity of retinal pigmented epithelial cells, hemolysis of sheep erythrocytes, and protease activity using gelatin zymography. Identified species were Streptococcus mitis/oralis, S. salivarius, S. vestibularis, S. parasanguinis, S. mutans, S. constellatus, and S. gordonii. One strain of S. pseudoporcinus was also identified. All strains were sensitive to vancomycin, 77% were resistant to amikacin, and 27% had intermediate resistance to ceftazidime. Extracellular milieu from all strains except one (S. pseudoporcinus) were largely devoid of toxicity to retinal pigmented epithelial cells and sheep erythrocytes. Twelve strains, 10 of which were S. mitis/oralis, produced protease activity. Interestingly, not all of the S. mitis/oralis strains were proteolytic. These findings highlight the diversity of virulence factor production in ocular strains of the viridans streptococci not only at the group level but also at the species level.

A Quality Improvement Initiative: Reducing Blood Culture Contamination in a Children's Hospital.

BACKGROUND AND OBJECTIVE: Blood culture contamination is a safety and quality concern in children's hospitals; it leads to increased unnecessary testing, admissions, antibiotic exposure, and cost. The standard benchmark for blood culture contamination is 3%. Our aim with the quality improvement project was to reduce the contamination rate at our children's hospital from a mean of 2.85% to <1.5% in 2 years. METHODS: After initial unit-specific efforts, we formed a multidisciplinary team, created a process map and a cause-and-effect analysis, sent out surveys to nurses, and created observation sheets used to identify problem areas and record the most common deviations during the collection process. We also standardized the blood culture collection protocol and reemphasized nurse education in person and with online modules. During our project, we noted that nurses were collecting 1 to 3 mL of blood on all children regardless of weight. We developed optimal weight-based blood volumes and, after educating ordering providers, we updated our electronic medical record to reflect appropriate volumes in the order. RESULTS: Despite a steady increase in the number of blood cultures collected at our children's hospital, we were able to decrease the average contamination rate from 2.85% to 1.54%, saving the hospital an estimated average of $49 998 per month. CONCLUSIONS: By standardizing blood culture collection methods, optimizing blood volume, creating checklists, and reinforcing nurse education, we were able to develop a best practice for pediatric blood culture collection and reduce blood culture contamination to a sustainable low rate at our children's hospital.

Mycobacterium genavense-induced spindle cell pseudotumor in a pediatric hematopoietic stem cell transplant recipient: Case report and review of the literature.

We describe the first reported pediatric patient to our knowledge with a spindle cell pseudotumor caused by Mycobacterium genavense in a hematopoietic stem cell transplant recipient, and review the literature of such an entity in the transplant population.

Recessive nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum is caused by homozygous protein-truncating mutations of WDR73.

We describe a novel nephrocerebellar syndrome on the Galloway-Mowat syndrome spectrum among 30 children (ages 1.0 to 28 years) from diverse Amish demes. Children with nephrocerebellar syndrome had progressive microcephaly, visual impairment, stagnant psychomotor development, abnormal extrapyramidal movements and nephrosis. Fourteen died between ages 2.7 and 28 years, typically from renal failure. Post-mortem studies revealed (i) micrencephaly without polymicrogyria or heterotopia; (ii) atrophic cerebellar hemispheres with stunted folia, profound granule cell depletion, Bergmann gliosis, and signs of Purkinje cell deafferentation; (iii) selective striatal cholinergic interneuron loss; and (iv) optic atrophy with delamination of the lateral geniculate nuclei. Renal tissue showed focal and segmental glomerulosclerosis and extensive effacement and microvillus transformation of podocyte foot processes. Nephrocerebellar syndrome mapped to 700 kb on chromosome 15, which contained a single novel homozygous frameshift variant (WDR73 c.888delT; p.Phe296Leufs*26). WDR73 protein is expressed in human cerebral cortex, hippocampus, and cultured embryonic kidney cells. It is concentrated at mitotic microtubules and interacts with α-, ß-, and γ-tubulin, heat shock proteins 70 and 90 (HSP-70; HSP-90), and the carbamoyl phosphate synthetase 2/aspartate transcarbamylase/dihydroorotase multi-enzyme complex. Recombinant WDR73 p.Phe296Leufs*26 and p.Arg256Profs*18 proteins are truncated, unstable, and show increased interaction with α- and ß-tubulin and HSP-70/HSP-90. Fibroblasts from patients homozygous for WDR73 p.Phe296Leufs*26 proliferate poorly in primary culture and senesce early. Our data suggest that in humans, WDR73 interacts with mitotic microtubules to regulate cell cycle progression, proliferation and survival in brain and kidney. We extend the Galloway-Mowat syndrome spectrum with the first description of diencephalic and striatal neuropathology.

Absolute immature platelet count dynamics in diagnosing and monitoring the clinical course of thrombotic thrombocytopenic purpura.

BACKGROUND: Thrombotic thrombocytopenic purpura (TTP) is a life-threatening diagnosis requiring prompt initiation of therapeutic plasma exchange (TPE). Measurement of immature platelet (PLT) fraction (%-IPF) differentiates PLT consumption or destruction from hypoproduction. STUDY DESIGN AND METHOD: Our study evaluated %-IPF changes over the course of TTP treated with TPE and as a measure of treatment efficacy. Eleven idiopathic TTP patients, two human immunodeficiency virus (HIV)-associated TTP patients, and five non-TTP patients with thrombocytopenia were enrolled into our study. All patients were treated with TPE and had ADAMTS13 activity measured. RESULTS: All idiopathic TTP patients had a significantly increased %-IPF and decreased absolute immature PLT count (A-IPC) and PLT count at presentation. An A-IPC value of less than 5 × 10(9) /L at presentation has 84.6% sensitivity, 80% specificity, and 91.7% positive predictive value for diagnosing TTP. A concurrent steady decline in %-IPF and increased PLT counts toward normal was observed in TTP patients undergoing TPE. The A-IPC, however, showed an increase and decrease curve that was not seen in the two HIV-associated TTP patients with no response to TPE and the five non-TTP patients. More importantly, reaching an A-IPC ratio of 3 compared to baseline value during TPE can readily differentiate idiopathic TTP from the other two groups and is correlated with good clinical responses to TPE. An abrupt increase of A-IPC during TPE was also noted in a TTP patient who relapsed 3 days before PLT count decrease. A-IPC is positively correlated with ADAMTS13 activity at presentation but negatively correlated with ADAMTS13 activity during recovery. CONCLUSION: A-IPC should be routinely analyzed for diagnosing and monitoring TTP patients.

Immature platelet fraction can help adjust therapy in refractory thrombotic microangiopathic hemolytic anemia cases.

Hemolytic uremic syndrome and thrombotic thrombocytopenic purpura share presentations, therapies and diagnostic evaluation of activity of the metalloprotease ADAMTS13. Here, we report a patient with the clinical presentation of thrombotic microangiopathic thrombocytopenia, normal ADAMTS13, prolonged regimen of therapeutic plasma exchanges (TPEs), bone marrow biopsy showing adequate tri-lineage hematopoiesis, and low immature platelet fraction (%-IPF) (<1.0%). Low %-IPF suggested platelet hypoproduction; high steroid therapy, in conjunction with TPEs, resulted in the recovery of platelet count. Further investigation is needed to determine if %-IPF can guide therapy in cases of microangiopathic hemolytic anemias refractory to therapy.