Immunogenetics associated with severe coccidioidomycosis

Disseminated coccidioidomycosis (DCM) is caused by Coccidioides, pathogenic fungi endemic to the southwestern United States and Mexico. Illness occurs in approximately 30% of those infected, less than 1% of whom develop disseminated disease. To address why some individuals allow dissemination, we enrolled patients with DCM and performed whole-exome sequencing. In an exploratory set of 67 patients with DCM, 2 had haploinsufficient STAT3 mutations, and defects in β-glucan sensing and response were seen in 34 of 67 cases. Damaging CLEC7A and PLCG2 variants were associated with impaired production of β-glucan-stimulated TNF-α from PBMCs compared with healthy controls. Using ancestry-matched controls, damaging CLEC7A and PLCG2 variants were overrepresented in DCM, including CLEC7A Y238* and PLCG2 R268W. A validation cohort of 111 patients with DCM confirmed the PLCG2 R268W, CLEC7A I223S, and CLEC7A Y238* variants. Stimulation with a DECTIN-1 agonist induced DUOX1/DUOXA1-derived hydrogen peroxide [H2O2] in transfected cells. Heterozygous DUOX1 or DUOXA1 variants that impaired H2O2 production were overrepresented in discovery and validation cohorts. Patients with DCM have impaired β-glucan sensing or response affecting TNF-α and H2O2 production. Impaired Coccidioides recognition and decreased cellular response are associated with disseminated coccidioidomycosis.

Controversies in the Management of Central Nervous System Coccidioidomycosis

Central nervous system infection with Coccidioides spp is fatal if untreated, and complications occur even when therapy is directed by experienced clinicians. We convened a panel of clinicians experienced in the management of coccidioidal meningitis to summarize current controversies and provide consensus for the management of this difficult infection.

Antimicrobial-Resistant Shigella spp. in San Diego, California, USA, 2017-2020

Annually, Shigella spp. cause ≈188 million cases of diarrheal disease globally, including 500,000 cases in the United States; rates of antimicrobial resistance are increasing. To determine antimicrobial resistance and risk factors in San Diego, California, USA, we retrospectively reviewed cases of diarrheal disease caused by Shigella flexneri and S. sonnei diagnosed during 2017-2020. Of 128 evaluable cases, S. flexneri was slightly more common than S. sonnei; most cases were in persons who were gay or bisexual cisgender men, were living with HIV, were unhoused, or used methamphetamines. Overall, rates of resistance to azithromycin, fluoroquinolones, ampicillin, and trimethoprim/sulfamethoxazole (TMP/SMX) were comparable to the most recent national data reported from the Centers for Disease Control and Prevention; 55% of isolates were resistant to azithromycin, 23% to fluoroquinolones, 70% to ampicillin, and 83% to TMP/SMX. The rates that we found for TMP/SMX were slightly higher than those in national data.

Utility of Plasma Microbial Cell-Free DNA Decay Kinetics After Aortic Valve Replacement for Bartonella Endocarditis: Case Report

Background

Detection and sequencing of circulating microbial cell-free DNA (mcfDNA) in plasma is an increasingly popular tool for diagnosing many infectious diseases, but could also be used to monitor the progress of infection. However, the decay of this microbial cell-free DNA in blood following treatment has not been previously characterized.

Case Presentation

A 53 year-old male was diagnosed with Bartonella quintana bioprosthetic aortic valve endocarditis by sequencing of the mcfDNA in the blood (Karius, Redwood City, CA). We then monitored the kinetics of decay of mcfDNA after parenteral antibiotics and valve resection in this individual. We measured plasma mcfDNA (Karius) in serial samples obtained in the operating room to calculate mcfDNA half-life after valve resection. After four weeks of parenteral antibiotics, Bartonella mcfDNA signal decreased by 78%. The signal subsequently rose during operative manipulation of the infected valve but dropped 81-fold over four hours following valve resection. The half-life of mcfDNA between the time shortly following resection of the infected valve and 24 to 48 hours post-operatively was between 35 and 115 minutes. The trend in mcfDNA signal was characterized by rapid and then slower phases of decay within 24 hours, and little change between 24 and 48 hours.

Conclusions

This study is one of the first to characterize decay kinetics of mcfDNA and highlights the potential of monitoring mcfDNA in addressing major challenges in infective endocarditis management, including monitoring the response to therapy, and as an early screen for recurrence.

Decoding Transcription Regulatory Mechanisms Associated with Coccidioides immitis Phase Transition Using Total RNA

New or emerging infectious diseases are commonly caused by pathogens that cannot be readily manipulated or studied under common laboratory conditions. These limitations hinder standard experimental approaches and our abilities to define the fundamental molecular mechanisms underlying pathogenesis. The advance of capped small RNA sequencing (csRNA-seq) now enables genome-wide mapping of actively initiated transcripts from genes and other regulatory transcribed start regions (TSRs) such as enhancers at a precise moment from total RNA. As RNA is nonpathogenic and can be readily isolated from inactivated infectious samples, csRNA-seq can detect acute changes in gene regulation within or in response to a pathogen with remarkable sensitivity under common laboratory conditions. Studying valley fever (coccidioidomycosis), an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health, we show how csRNA-seq can unravel transcriptional programs driving pathogenesis. Performing csRNA-seq on RNA isolated from different stages of the valley fever pathogen Coccidioides immitis revealed alternative promoter usage, connected cis-regulatory domains, and a WOPR family transcription factor, which are known regulators of virulence in other fungi, as being critical for pathogenic growth. We further demonstrate that a C. immitis WOPR homologue, CIMG_02671, activates transcription in a WOPR motif-dependent manner. Collectively, these findings provide novel insights into valley fever pathogenesis and provide a proof of principle for csRNA-seq as a powerful means to determine the genes, regulatory mechanisms, and transcription factors that control the pathogenesis of highly infectious agents. IMPORTANCE Infectious pathogens like airborne viruses or fungal spores are difficult to study; they require high-containment facilities, special equipment, and expertise. As such, establishing approaches such as genome editing or other means to identify the factors and mechanisms underlying caused diseases, and, thus, promising drug targets, is costly and time-intensive. These obstacles particularly hinder the analysis of new, emerging, or rare infectious diseases. We recently developed a method termed capped small RNA sequencing (csRNA-seq) that enables capturing acute changes in active gene expression from total RNA. Prior to csRNA-seq, such an analysis was possible only by using living cells or nuclei, in which pathogens are highly infectious. The process of RNA purification, however, inactivates pathogens and thus enables the analysis of gene expression during disease progression under standard laboratory conditions. As a proof of principle, here, we use csRNA-seq to unravel the gene regulatory programs and factors likely critical for the pathogenesis of valley fever, an emerging endemic fungal infection that increasingly impacts livestock, pet, and human health.

Invasive Non-typhoidal Salmonella (iNTS) Infections

Salmonella enterica invade the host via the intestinal tract. There are ~ 2 thousand distinct serovars of non-typhoidal Salmonella (NTS) that can cause gastroenteritis in normal hosts, but bacteremia is an uncommon complication of gastroenteritis except at the extremes of age [1]. In contrast, enteric fever and invasive NTS infections (iNTS) are each caused by only a few serovars of S. enterica (Table 1), and bacteremia not gastroenteritis is their principal manifestation.

Transcriptional Analysis of Coccidioides immitis Mycelia and Spherules by RNA Sequencing

Coccidioides immitis and C. posadasii are dimorphic fungi that transform from mycelia with internal arthroconidia in the soil to a tissue form known as a spherule in mammals. This process can be recapitulated in vitro by increasing the temperature, CO₂ and changing other culture conditions. In this study, we have analyzed changes in gene expression in mycelia and young and mature spherules. Genes that were highly upregulated in young spherules include a spherule surface protein and iron and copper membrane transporters. Genes that are unique to Coccidioides spp. are also overrepresented in this group, suggesting that they may be important for spherule differentiation. Enriched GO terms in young spherule upregulated genes include oxidation-reduction, response to stress and membrane proteins. Downregulated genes are enriched for transcription factors, especially helix–loop–helix and C2H2 type zinc finger domain-containing proteins, which is consistent with the dramatic change in transcriptional profile. Almost all genes that are upregulated in young spherules remain upregulated in mature spherules, but a small number of genes are differentially expressed in those two stages of spherule development. Mature spherules express more Hsp31 and amylase and less tyrosinase than young spherules. Some expression of transposons was detected and most of the differentially expressed transposons were upregulated in spherules.

42. Common Population Variants Cause Susceptibility to Disseminated Coccidioidomycosis

Background

Coccidioides are endemic, dimorphic fungi found in soils of southwestern United States, Mexico and Central America. Infection occurs via inhalation of arthroconidia which swell, differentiate into spherules and rupture releasing endospores. While the majority of infected individuals will never report illness, roughly 1/3 seek medical attention for fungal pneumonia and ~1% of those present with disseminated coccidioidomycosis (DCM). IL12-IFNγ pathway mutations have been reported in DCM but are exceedingly rare and cannot account for the ~500–600 cases of DCM/year.

Methods

We performed whole exome sequencing on 66 individuals with DCM, retaining variants predicted damaging (CADD >15) with a population frequency < 10%.

Results

Homozygous CLEC7A c.714T >G; p.Y238* causing a truncated Dectin-1 receptor was overrepresented (OR=9.8449, 95% CI 3.0841 to 31.4260, P=0.0001). Dectin-1 signaling pathway variants included 3 homozygous and 11 heterozygous CLEC7A p.Y238* individuals, one each CLEC7A p.I223S and MALT1 p.R149Q and five PLCG2 p.R268W. Since Dectin-1 is the receptor for b-glucan, a major Coccidioides cell-wall component, we hypothesized that Dectin-1 pathway variants could affect fungal recognition and cellular response. Healthy control PBMCs stimulated with purified β-glucan or heat-killed Candida albicans induced 6-fold more TNFα than patients with homozygous or heterozygous CLEC7A, PLCG2 or MALT1 variants (P=0.0022, Ordinary one-way ANOVA). Additionally, one patient with a family history of DCM but lacking a defined mutation also failed to up-regulate TNFα after stimulation.

Normalized TNF production from healthy control and DCM patient’s peripheral blood mononuclear cells

Conclusion

Disclosures

Michail Lionakis, MD, ScD, Matinas BioPharma (Research Grant or Support)

711. Rapid, non-invasive detection and monitoring of Bartonella quintana endocarditis by plasma-based next-generation sequencing of microbial cell-free DNA

Background

There are up to 50,000 new cases of infective endocarditis each year in the United States, of which approximately 20% are culture negative endocarditis (CNE). In-hospital mortality remains high at 20 to 30%. Despite advances in diagnostic testing, determining the timing of surgery and duration of treatment in CNE are significant challenges for clinicians. Plasma next-generation sequencing (NGS) for circulating microbial cell-free DNA (mcfDNA) has shown utility in diagnosing and monitoring the response to treatment in endocarditis.

Methods

Serial blood samples were obtained prior to and after aortic valve replacement in a patient with culture negative endocarditis. Microbial cfDNA was extracted from plasma and NGS was performed by Karius, Inc. (Redwood City, California). Human sequences were removed and remaining sequences were aligned to a curated database of over 1,400 pathogens. Organisms present above a predefined statistical significance threshold were reported and quantified in DNA molecules per microliter (MPM). Chart review was performed for clinical correlation.

Results

A 53-year old man with history of homelessness, well-controlled HIV infection and a bioprosthetic aortic valve presented with symptomatic severe aortic stenosis and elevated inflammatory markers 3 years following valve surgery. Transesophageal echocardiography showed a paravalvular leak. Bartonella quintana was detected by Karius NGS (in parallel Bartonella henselae serologies were positive). After 4 weeks of parenteral antibiotics, repeat Karius testing demonstrated a 94% (16-fold) decrease in the Bartonella quintana mcfDNA signal to 8813 MPM. He underwent surgical valve replacement; twenty-four hours after removal of the infected valve repeat Karius testing showed a rapid decay of the Bartonella quintana mcfDNA signal to 103 MPM. The patient completed 3 months of oral antibiotics post-operatively, ultimately returning to his former performance status.

Conclusion

Plasma-based next-generation sequencing assays for circulating microbial cell-free DNA offer a unique means of pathogen detection, assessment of infection burden and monitoring of response to both medical treatment and surgical debridement/definitive source control in a case of Bartonella quintana endocarditis.

Disclosures

Asim A. Ahmed, MD, Karius (Employee)

A 37-Year-Old Man With Pleuritic Chest Pain

CASE PRESENTATION

A 37-year-old man with poorly controlled type 2 diabetes presented with severe right-sided pleuritic chest pain, respiratory splinting, and cough. Two weeks earlier, he had been evaluated at an urgent care for cough and was prescribed a 5-day course of azithromycin for bronchitis. He then presented to our ED reporting mild, right-sided pleuritic chest pain. Vital signs were normal, and his chest radiograph showed a trace right pleural effusion (Fig 1A). He was discharged with naproxen for pleurisy. Three days later, he returned, reporting a dramatic increase in the severity of his pleuritic chest pain and a cough that had become productive of yellow-brown sputum. He denied fever, but endorsed chills and night sweats. His medications included atorvastatin, lisinopril, metformin, and saxagliptin. His parents were from Guam, although he was born and raised in San Diego, CA. He was employed as a social worker and denied any history of cigarette smoking, alcohol, or drug use.

2110. Treatment of Coccidioidomycosis with Isavuconazole

Background

There are limited prospective data available to guide the management of severe coccidioidomycosis. In particular, the treatment of disseminated coccidioidomycosis often requires extended courses of antifungal therapy, for which there are often intolerable side-effects, toxicities, and failures. In recent years, newer oral triazole antifungals with in vitro activity against Coccidioides have become available, but data are lacking on their efficacy in coccidioidomycosis. Isavuconazole lacks many of the toxicities of older triazole antifungals, such as QT prolongation and certain key drug interactions, making it an appealing option in selected patients.

Methods

Based on pharmacy prescription history at two federal facilities in southern California, we identified adult patients with coccidioidomycosis who received isavuconazole from 2017 to 2019. Patient records were reviewed to identify age, sex, ethnicity, sites of infection, prior antifungal therapy, indication for switch to isavuconazole, duration of follow-up, and outcomes.

Results

12 patients were identified between the ages of 36 and 86 years; 3 were women. 6 were of Pacific Islander descent, 4 were African American, 1 European-American, and 1 Latino. 6 (50%) had significant pre-infection comorbidities. 8 (67%) had evidence of extrapulmonary dissemination, including 1 patient with meningitis. All but one had received prior treatment with other azoles; two had previously been treated with amphotericin B. Six (50%) were switched to isavuconazole due failure or progression of disease on prior therapy; 3 (25%) due to drug toxicity; and 2 (17%) due to drug interactions. Seven (58%) patients improved on isavuconazole; 4/12 (33%) were stable; one developed hepatotoxicity but improved on posaconazole, and one patient deteriorated.

Conclusion

Isavuconazole appears to be a promising agent for the treatment of coccidioidomycosis. Long-term follow-up will be required to assess the risks of toxicity, disease progression, or relapse. For patients who are clinically stable but with an extensive disease burden or toxicity from older agents, isavuconazole may present an amphotericin-sparing option.

Disclosures

All authors: No reported disclosures.

A case of inguinal lymphogranuloma venereum imitating malignancy on CT imaging

Lymphogranuloma venereum is a sexually transmitted infection caused by serovars L1, L2, and L3 of Chlamydia trachomatis. We here report a case of Lymphogranuloma venereum, confirmed by PCR testing, which mimicked malignancy on CT imaging.

A review of innate and adaptive immunity to coccidioidomycosis

Coccidioidomycosis is a human fungal disease cause by inhalation of aerosol spores produced by Coccidioides posadasii or Coccidioides immitis. This disease is a common cause of community-acquired pneumonia in the endemic areas of the Southwestern United States. It also can present as a life-threatening disease as the fungal cells disseminate to skin, bone, and central nervous system. The outcome of coccidioidomycosis is largely determined by the nature of host immune response to the infection. Escalation of symptomatic infections and increased cost of long-term antifungal treatment warrant a concerted effort to better understand the innate and adaptive immune responses and the genetics associated with coccidioidomycosis susceptibility. This knowledge can be harnessed for development of a human vaccine against Coccidioides and advance clinic management of this disease. This review discusses recently reported studies on innate and adaptive immunity to Coccidioides infection, Mendelian susceptibility to disseminated disease and progress toward a human vaccine against this formidable disease.

APX001 and Other Gwt1 Inhibitor Prodrugs Are Effective in Experimental Coccidioides immitis Pneumonia

Coccidioidomycosis is a systemic fungal infection caused by the inhalation of the arthroconidia of either of two closely related dimorphic fungi, Coccidioides immitis and C. posadasii, that are endemic in the southwestern United States and other areas in the Western Hemisphere. Chronic cavitary pulmonary infections and extrapulmonary sites of infection are very difficult to treat and often require lifelong azole therapy. APX001A is the first in a new class of broad-spectrum antifungal agents that inhibit Gwt1, an enzyme which is required for cell wall localization of glycosylphosphatidylinositol (GPI)-anchored mannoproteins in fungi. APX001A and several analogs were highly active against clinical isolates of Coccidioides, inhibiting hyphal growth at low nanogram/ml concentrations. APX001 is the N-phosphonooxymethyl prodrug of APX001A, currently in clinical trials for the treatment of invasive fungal infections. Mice were treated orally once daily with 26 mg/kg/day of APX001 and the prodrug analog APX2097, 2 h after administration of the pan-cytochrome P450 inhibitor 1-aminobenzotriazole, which was used to enhance drug half-life and exposures to more closely mimic human pharmacokinetics of APX001A. Five days of treatment reduced lung colony counts by nearly 3 logs and prevented dissemination, similar to the efficacy of fluconazole dosed orally at 25 mg/kg twice daily. In a survival experiment, both APX001- and APX2097-treated mice survived significantly longer than control and fluconazole-treated mice. APX001 and other members of this new class of antifungal agents may offer great promise as effective therapies for coccidioidomycosis.

Listeria monocytogenes endocarditis: case report, review of the literature, and laboratory evaluation of potential novel antibiotic synergies

Endocarditis is a rare but serious manifestation of Listeria monocytogenes (LM). However, the optimal treatment strategy for LM endocarditis has yet to be established. Current antibiotic strategies for listeriosis include penicillin G or ampicillin (AMP) monotherapy, or AMP + gentamicin combination therapy which is often favored for endocarditis. The primary objective of our investigation was to assess the utility of AMP + ceftriaxone (CRO) and AMP + daptomycin (DAP) against LM, modeling less nephrotoxic antibiotic combinations traditionally used to manage resistant enterococcal endocarditis. Here we report a case of LM endocarditis, review the world literature, and evaluate alternative treatment strategies for listeriosis utilizing in vitro and ex vivo studies. The combination of AMP + CRO and AMP + DAP were each noted to have synergistic activity against a LM endocarditis isolate. Additionally, co-incubation of the isolate with sub-lethal concentrations of antibiotics (AMP, CRO, DAP, AMP + CRO or AMP + DAP) sensitized the bacterium to whole blood killing while pretreatment with CRO and DAP (at 1/4 MIC) sensitized the bacterium to neutrophil killing. However, these effects did not reflect potentiation of antibiotic activity to human cathelicidin peptide LL-37, which is abundant in neutrophils and highly active against LM. Interestingly, AMP pretreatment of the LM endocarditis isolate resulted in increased DAP binding to the bacterium when assessed by fluorescence microscopy. These in vitro and ex vivo studies suggest further investigation of combination therapy using AMP + CRO or AMP + DAP as an alternative treatment for LM infection is warranted.

Actinotignum schaalii Infection: A Clandestine Cause of Sterile Pyuria?

Actinotignum schaalii is an underappreciated cause of urinary tract infections (UTIs) in older adults. The diagnosis may be missed due to difficulty isolating and identifying the organism. Complications can result because the organism is intrinsically resistant to 2 commonly used drugs to treat UTI, as illustrated by this case.

Coccidioides immitis and posadasii; A review of their biology, genomics, pathogenesis, and host immunity

Coccidioides immitis and C. posadasii are two highly pathogenic dimorphic fungal species that are endemic in the arid areas of the new world, including the region from west Texas to southern and central California in the USA that cause coccidioidomycosis (also known as Valley Fever). In highly endemic regions such as southern Arizona, up to 50% of long term residents have been infected. New information about fungal population genetics, ecology, epidemiology, and host-pathogen interactions is becoming available. However, our understanding of some aspects of coccidioidomycosis is still incomplete, including the extent of genetic variability of the fungus, the genes involved in virulence, and how the changes in gene expression during the organism's dimorphic life cycle are related to the transformation from a free-living mold to a parasitic spherule. Unfortunately, efforts to develop an effective subunit vaccine have not yet been productive, although two potential live fungus vaccines have been developed.

Successful treatment of Aureobasidium pullulans central catheter-related fungemia and septic pulmonary emboli

INTRODUCTION

Aureobasidium pullulans is a saprophytic fungus that is widely distributed in the environment, and in the right host can be an opportunistic human pathogen.

PRESENTATION OF CASE

A 66-year-old man with Crohn's disease with a single kidney, and requiring total parenteral nutrition via a Hickman catheter, was admitted with a 10-week history of progressive shortness of breath, fevers and weight loss. Chest imaging demonstrated new multifocal lung parenchymal opacities compatible with septic pulmonary emboli. Blood culture grew a yeast-like organism that transformed into a black mold on subculture, eventually identified as A. pullulans. Due to triazole resistance, the patient was treated with liposomal amphotericin and micafungin. Serum (1,3)-β-d-glucan level was used to monitor therapy, initially measured at >500 pg/mL and decreasing to 66 pg/mL after one year of therapy.

DISCUSSION

We describe the successful treatment of a case of catheter related fungemia and septic pulmonary emboli due A. pullulans. While initially appearing as an oval yeast on blood culture, subsequent growth as a black mold led to identification of the fungus as A. pullulans. The infection was cured with a combination of antifungal agents, even though the foreign body could not be safely removed. Nephrotoxicity required dosing adjustment of the amphotericin to biweekly during the maintenance phase of treatment. The serum (1,3)-β-d-glucan level proved to be useful in monitoring response to therapy.

CONCLUSION

We report here successful treatment of a disseminated A. pullulans infection with an induction and maintenance approach to liposomal amphotericin dosing, and monitoring response to therapy with serum (1,3)-β-d-glucan levels.

Gordonia sternal wound infection treated with ceftaroline: case report and literature review

Introduction. Case reports have emerged with identification of Gordonia bronchialis infections including sternal wound infections and foreign bodies such as central lines and shunts. Case presentation. We present a case that demonstrates the need to consider Gordonia infection as a cause of sternal wound infection and highlights the utility of novel diagnostics to aid in the identification of unusual pathogens that can cause post-operative infections. We report here the first successful use of ceftaroline for treatment of a G. bronchialis sternal wound infection. Conclusion. There are only case reports and in vitro assays to date to guide treatment of this infection, and we now add ceftaroline as a new drug to consider, though adequate surgical debridement is paramount.

Bacteremia and Skin Infections in Four Patients Caused by Helicobacter-Like Organisms

Background

Enterohepatic Helicobacter-like organisms (HLO) have been recognized as causes of human infection since 1984, primarily as a cause of bacteremia and cellulitis in immunocompromised individuals, but the spectrum of illness due to HLO has expanded based on numerous reports from Japan.

Methods

We report 4 epidemiologically unrelated immunocompetent patients with HLO bacteremia diagnosed within a 2-year period. Three patients had cellulitis and 1 patient had unexplained fever. 16S ribosomal deoxyribonucleic acid (rDNA) sequence analysis of 2 isolates suggested that they were Helicobacter cinaedi, and whole-genome sequencing showed that they differed only slightly from reference strains.

Conclusions

We believe that this syndrome is more common than reported, but it is easily overlooked because the skin lesions resemble streptococcal cellulitis and respond very rapidly to β-lactam antibiotics, and the organism is difficult to isolate from the blood. All HLO in our series were isolated from blood using the ESP system and were not detected in 2 other widely used commercial blood culture systems.

Fluoroquinolone resistance colonization from initial to repeat prostate biopsy

Purpose:

Fluoroquinolone (FQ) resistant (FQR) bacteria are a major cause of infection after transrectal prostate biopsy (TRPB). We determined the prevalence of FQR in initial and subsequent rectal cultures from men undergoing repeat prostate biopsies.

Materials and methods:

After IRB approval, men presenting for TRPB at the San Diego Veterans Affairs Medical Center between January 1, 2010, and February 6, 2014, underwent pre-TRPB rectal culture. The rectal swab was collected from the patient immediately prior to TRPB. Rectal swabs were streaked onto locally prepared ciprofloxacin-supplemented (4 mg/L) MacConkey agar plates. A representative colony was selected for identification and susceptibility testing.

Results:

Of 617 patients who had rectal cultures done, 7% (43/617) had a repeat rectal culture performed in relation to a second prostate biopsy. All cipro-resistant bacteria isolated were Escherichia coli. The median time and interquartile range between first and second biopsy was 2.3 years (range 1.2–3.6 years). On first biopsy, 16.3% (7/43) had FQR, which was not statistically different from the 18.6% of patients who had FQR on their second biopsy ( p=0.78). Overall, 74% (32/43) of patients tested absent for FQR at both prostate biopsies, and 9.3% (4/43) tested present at both ( p=0.015). However, 9.3% (4/43) converted from absent to present FQR, and 7.0% (3/43) converted from present FQR to absent ( p=0.69). Seventy percent of the FQR E. coli were also resistant to gentamicin, and 22% were resistant to cefepime.

Conclusions:

Patients undergoing prostate biopsy should be examined for FQR prior to each individual biopsy because prior culture results do not always predict whether a patient will be colonized with FQR E. coli.

A Novel Shiga Toxin 1a-Converting Bacteriophage of Shigella sonnei With Close Relationship to Shiga Toxin 2-Converting Pages of Escherichia coli

In recent studies, strains of non-dysenteriae 1 Shigella (NDS) expressing Shiga toxin have been reported. In this study, we report a novel stx1a-converting bacteriophage of Shigella sonnei associated with travel to Mexico. Phylogenetic comparison between this and other stx-converting phages suggests that toxigenic NDS strains have arisen through separate horizontal transfer events from toxigenic Escherichia coli.

Rapid Identification of Rectal Multidrug-resistant Escherichia coli Before Transrectal Prostate Biopsy

OBJECTIVE

To develop and evaluate a rapid multiplex-quantitative polymerase chain reaction (qPCR) to identify fecal carriers of multidrug-resistant extraintestinal pathogenic Escherichia coli (MDR-ExPEC) clonal groups.

METHODS

Men presenting for transrectal prostate biopsy (TPB) at the San Diego Veterans Affairs Medical Center underwent rectal culture immediately before TPB. Rectal swabs were streaked onto ciprofloxacin-supplemented (4 mg/L) MacConkey agar plates, identified, and susceptibility tested. The same swab was sent to the University of Washington for qPCR test (EST200) targeting 2 major MDR-ExPEC clonal groups--ST131 and ST69--that combined were expected to represent majority of fluoroquinolone (FQ)- and trimethoprim-sulfamethoxazole-resistant E coli. We calculate test characteristics including the area under the receiver operative curve (AUC).

RESULTS

We enrolled 104 men from 11/5/2013 to 6/10/2014. FQ-resistant E coli were cultured from 19.2% (20/104) of rectal swabs, and 26% (27/104) of all swabs were positive for EST200 by PCR. The test characteristics comparing the EST200 to the culture-based detection of FQ resistance were 75%, 86%, 94%, and 56%, respectively. The AUC was 0.84 for the EST200 to detect FQ resistance before TPB.

CONCLUSION

Compared to the reference standard rectal culture, EST200 was able to detect majority of FQ-resistant E coli on rectal swabs before prostate biopsy.

Salmonella-induced Diarrhea Occurs in the Absence of IL-8 Receptor (CXCR2)-Dependent Neutrophilic Inflammation

BACKGROUND

Gastroenteritis is the most common manifestation of nontyphoidal Salmonella enterica infections, but little is known about the pathogenesis of diarrhea in this infection

METHODS

To determine whether polymorphonuclear neutrophils (PMNs) are required for diarrhea for Salmonella colitis, we infected kanamycin-pretreated interleukin 8R (IL-8R) mutant mice and controls, both with nonmutant Slc11a1 (Nramp1, ItyR). We compared the 2 mouse strains for increases in fecal water content (diarrhea) 3 days after infection, changes in expression of ion transporters in colonic epithelial cells, proliferation of epithelial cells, and severity of infection as measured by colony-forming units (CFUs).

RESULTS

The IL-8R knockout mice had fewer PMNs in the colon but the other variables we measured were unaffected except for an increase in CFUs in the colon. The pathologic changes in the cecum were similar in both groups except for the lack of PMNs in the IL-8R knockout mice. There was minimal damage to the colon more distally.

CONCLUSIONS

In the early stage of Salmonella colitis, PMNs are not required for diarrhea or for the decrease in expression of colonic epithelial cell apical ion transporters. They contribute to defense against infection in the cecum but not extracolonically at this stage of Salmonella colitis.

tPA Alu (I/D) polymorphism associates with bacterial osteomyelitis

BACKGROUND

Coagulation and fibrinolysis are important in infections and systemic inflammatory response syndrome. Polymorphisms in plasminogen activator inhibitor-1 (PAI-1, SERPINE1) and tissue plasminogen activator (tPA, PLAT), such as PAI-1 (-675 4G/5G deletion/insertion) and tPA (Alu insertion/deletion [I/D]), are associated with strokes, myocardial infarctions, bacterial infections and septic shock severity, and trauma. Osteomyelitis is a mostly posttraumatic, Staphylococcal bone infection.

PATIENTS AND METHODS

tPA Alu (I/D) (rs4646972) and PAI-1 (4G/5G) (rs1799889) polymorphisms were studied by DNA amplification with polymerase chain reaction in 261 patients with osteomyelitis and in 299 matched blood donors. Plasma PAI-1/tPA complex was assessed by enzyme-linked immuosorbent assay.

RESULTS

II homozygotes (37.9% vs 19.1%) and I allele carriers (56.3% vs 46.3%) for the tPA Alu (I/D) polymorphism were significantly more frequent in osteomyelitis patients compared to controls (P < .001). II genotype carrier osteomyelitis patients had lower PAI-1/tPA complex levels compared to those with the D allele (P ≤ .04). There was no association between these genotypes and chronicity of osteomyelitis, post-traumatic etiology, or with a specific bacterial etiology. PAI-1 (4G/4G) homozygotes were not significantly different between osteomyelitis patients and controls (P = .1).

CONCLUSIONS

We report for the first time to our knowledge an association between the tPA Alu (I/D) polymorphism and susceptibility to bacterial osteomyelitis, perhaps by fibrinolysis dysfunction.

The use of ceftaroline fosamil in methicillin-resistant Staphylococcus aureus endocarditis and deep-seated MRSA infections: a retrospective case series of 10 patients

There are many limitations to the current antibiotics used for the treatment of severe methicillin-resistant Staphylococcus aureus (MRSA) infections. Ceftaroline is a new fifth-generation cephalosporin approved for the treatment of skin and soft tissue infections caused by MRSA and community-acquired pneumonia. We propose that ceftaroline can also be used successfully in more severe MRSA infections, including endocarditis. We conducted a retrospective chart review in a university-affiliated Department of Veterans Affairs hospital in San Diego, California (USA) of ten inpatients treated with ceftaroline for severe MRSA infection, including five cases of probable endocarditis (including two endocardial pacemaker infections), one case of pyomyositis with possible endocarditis, two cases of pneumonia (including one case of empyema), two cases of septic arthritis (including one case of prosthetic joint infection), and two cases of osteomyelitis. Seven of the 10 patients achieved microbiological cure. Six of the 10 patients achieved clinical cure. Seven patients were discharged from the hospital. Three patients were placed on comfort care and expired in the hospital; one achieved microbiological cure before death, and two remained bacteremic at time of death. In most patients, ceftaroline was effective for treatment of MRSA bacteremia and other severe MRSA infections. Adverse effects seen included rash, eosinophilia, pruritus, and Clostridium difficile infection. Ceftaroline can be a safe and effective drug for treatment of severe MRSA infections, and further comparative studies are warranted.

Group B Streptococcus CovR regulation modulates host immune signalling pathways to promote vaginal colonization

Streptococcus agalactiae (Group B Streptococcus, GBS) is a frequent commensal organism of the vaginal tract of healthy women. However, GBS can transition to a pathogen in susceptible hosts, but host and microbial factors that contribute to this conversion are not well understood. GBS CovR/S (CsrR/S) is a two component regulatory system that regulates key virulence elements including adherence and toxin production. We performed global transcription profiling of human vaginal epithelial cells exposed to WT, CovR deficient, and toxin deficient strains, and observed that insufficient regulation by CovR and subsequent increased toxin production results in a drastic increase in host inflammatory responses, particularly in cytokine signalling pathways promoted by IL-8 and CXCL2. Additionally, we observed that CovR regulation impacts epithelial cell attachment and intracellular invasion. In our mouse model of GBS vaginal colonization, we further demonstrated that CovR regulation promotes vaginal persistence, as infection with a CovR deficient strainresulted in a heightened host immune response as measured by cytokine production and neutrophil activation. Using CXCr2 KO mice, we determined that this immune alteration occurs, at least in part, via signalling through the CXCL2 receptor. Taken together, we conclude that CovR is an important regulator of GBS vaginal colonization and loss of this regulatory function may contribute to the inflammatory havoc seen during the course of infection.

Rapid progression to decompensated cirrhosis, liver transplant, and death in HIV-infected men after primary hepatitis C virus infection

BACKGROUND

We and others have shown that primary hepatitis C (HCV) infection in men infected with human immunodeficiency virus (HIV) causes early-onset liver fibrosis; however, little is known about the long-term natural history of the liver disease in these HIV-infected men.

METHODS

We followed a cohort of HIV-infected men with primary HCV infection in New York City.

RESULTS

Four men who were not cured after their primary HCV infection developed decompensated cirrhosis within 17 months to 6 years after primary HCV infection. Three died within 8 years of primary HCV infection, and 1 survived after liver transplant done 2 years after primary HCV infection. Three of the 4 men had AIDS at the time of primary HCV infection, and the most rapid progression occurred in the 2 men with the lowest CD4 counts at the time of HCV infection. Liver histopathology was most consistent with HCV-induced damage even though some had exposures to other potential hepatotoxins.

CONCLUSIONS

Primary HCV infection resulted in decompensated cirrhosis and death within 2-8 years in 4 HIV-infected men. The rapid onset of fibrosis due to primary HCV infection in HIV-infected men cannot therefore be considered benign. The rate of continued progression to liver failure may be proportional to the degree of underlying immunocompromise caused by HIV infection. More research is needed to better define the mechanisms behind accelerated liver damage.

Factors regulated by interferon gamma and hypoxia-inducible factor 1A contribute to responses that protect mice from Coccidioides immitis infection

Background

Coccidioidomycosis results from airborne infections caused by either Coccidioides immitis or C. posadasii. Both are pathogenic fungi that live in desert soil in the New World and can infect normal hosts, but most infections are self-limited. Disseminated infections occur in approximately 5% of cases and may prove fatal. Mouse models of the disease have identified strains that are resistant (e.g. DBA/2) or susceptible (e.g. C57BL/6) to these pathogens. However, the genetic and immunological basis for this difference has not been fully characterized.

Results

Microarray technology was used to identify genes that were differentially expressed in lung tissue between resistant DBA/2 and sensitive C57BL/6 mice after infection with C. immitis. Differentially expressed genes were mapped onto biological pathways, gene ontologies, and protein interaction networks, which revealed that innate immune responses mediated by Type II interferon (i.e., IFNG) and the signal transducer and activator of transcription 1 (STAT1) contribute to the resistant phenotype. In addition, upregulation of hypoxia inducible factor 1A (HIF1A), possibly as part of a larger inflammatory response mediated by tumor necrosis factor alpha (TNFA), may also contribute to resistance. Microarray gene expression was confirmed by real-time quantitative PCR for a subset of 12 genes, which revealed that IFNG HIF1A and TNFA, among others, were significantly differentially expressed between the two strains at day 14 post-infection.

Conclusion

These results confirm the finding that DBA/2 mice express more Type II interferon and interferon stimulated genes than genetically susceptible strains and suggest that differential expression of HIF1A may also play a role in protection.

Hypercalcemia in disseminated coccidioidomycosis: expression of parathyroid hormone-related peptide is characteristic of granulomatous inflammation

BACKGROUND

Hypercalcemia is an uncommon complication of disseminated granulomatous infections. The pathogenesis of hypercalcemia associated with infection is not clear.

METHODS

We investigated a case of disseminated coccidioidomycosis with hypercalcemia. We used a sensitive radioimmunoassay to measure serum parathyroid hormone-related peptide (PTHrP) and a mouse monoclonal antibody to PTHrP to immunostain biopsies.

RESULTS

We found elevated serum levels of PTHrP while the patient was hypercalcemic that became undetectable when serum calcium normalized. We also found that the inflammatory cells and some surrounding tissues in skin biopsies expressed PTHrP. PTHrP was expressed by all biopsied lesions of patients with coccidioidomycosis that we examined, whether localized to the lung or disseminated, but no other cases were hypercalcemic. PTHrP was also expressed by the 3 mycobacterial granulomas we examined, and in a lymph node from a patient with sarcoidosis.

CONCLUSIONS

The expression of PTHrP is a property of infectious granulomas regardless of etiology or the tissue involved, suggesting that PTHrP expression is part of the normal granulomatous immune response. Hypercalcemia may result if there is disseminated infection and multiple granulomas. We propose that excess production of PTHrP is the cause of hypercalcemia in granulomatous infections.

Biofilm formation and Klebsiella pneumoniae liver abscess: true, true and unrelated?

Klebsiella pneumoniae liver abscess is an emerging infectious disease. This syndrome was unknown before the late 1980s when it was first recognized in Taiwan. Over the next two decades it increased in prevalence in Taiwan and was reported from other nations of East Asia. It was then that the rest of the world became aware of this interesting new syndrome. The disease is no longer confined to East Asia, and is now an emerging infection in North America and Europe. How did this come about? We now understand some of the genetic changes that turn commensal E. coli into extra-intestinal pathogens. K pneumoniae is another member of the Enterobacteriaceae that is usually normal flora in the gut, but we know relatively little about how it evolved into an invasive pathogen capable of causing abscesses in normal livers. The phenotype of the liver-invasive strains is hyperviscosity of the polysaccharide capsules, but while the gene that determines that property is required it is not sufficient to create the pathogen, and more research is needed to discover the other virulence genes, and thus to potentially target them therapeutically.

Improving reverse vaccinology with a machine learning approach

Reverse vaccinology aims to accelerate subunit vaccine design by rapidly predicting which proteins in a pathogenic bacterial proteome are putative protective antigens. Support vector machine classification is a machine learning approach that has been applied to solve numerous classification problems in biological sciences but has not previously been incorporated into a reverse vaccinology approach. A training data set of 136 bacterial protective antigens paired with 136 non-antigens was constructed and bioinformatic tools were used to annotate this data for predicted protein features, many of which are associated with antigenicity (i.e. extracellular localization, signal peptides and B-cell epitopes). Annotation was used to train support vector machine classifiers that exhibited a maximum accuracy of 92% for discriminating protective antigens from non-antigens as assessed by a leave-tenth-out cross-validation approach. These accuracies were superior to those achieved when annotating training data with auto and cross covariance transformations of z-descriptors for hydrophobicity, molecular size and polarity, or when classification was performed using regression methods. To further validate support vector machine classifiers, they were used to rank all the proteins in six bacterial proteomes for their antigenicity. Protective antigens from the training data were significantly recalled (enriched) in the top 75 ranked proteins for all six proteomes as assessed by a Fisher's exact test (p<0.05). This paper describes a superior workflow for performing reverse vaccinology studies and provides a benchmark training data set that can be used to evaluate future methodological improvements.

The Role of the spv Genes in Salmonella Pathogenesis

Salmonella strains cause three main types of diseases in people: gastroenteritis, enteric (typhoid) fever, and non-typhoid extra-intestinal disease with bacteremia. Genetic analysis indicates that each clinical syndrome requires distinct sets of virulence genes, and Salmonella isolates differ in their constellation of virulence traits. The spv locus is strongly associated with strains that cause non-typhoid bacteremia, but are not present in typhoid strains. The spv region contains three genes required for the virulence phenotype in mice: the positive transcriptional regulator spvR and two structural genes spvB and spvC. SpvB and SpvC are translocated into the host cell by the Salmonella pathogenicity island-2 type-three secretion system. SpvB prevents actin polymerization by ADP-ribosylation of actin monomers, while SpvC has phosphothreonine lyase activity and has been shown to inhibit MAP kinase signaling. The exact mechanisms by which SpvB and SpvC act in concert to enhance virulence are still unclear. SpvB exhibits a cytotoxic effect on host cells and is required for delayed cell death by apoptosis following intracellular infection. Strains isolated from systemic infections of immune compromised patients, particularly HIV patients, usually carry the spv locus, strongly suggesting that CD4 T cells are required to control disease due to Salmonella that are spv positive. This association is not seen with typhoid fever, indicating that the pathogenesis and immunology of typhoid have fundamental differences from the syndrome of non-typhoid bacteremia.

The role of reactive oxygen intermediates in experimental coccidioidomycois in mice

Background

Coccidioidomycosis is usually a self-limited infection in immunocompentent people. In immunocompentent human beings second infections due to Coccidioides are very rare, indicating that recovery from infection results in protective immunity. In experimental animals, immunization with several different proteins or attenuated mutants protects against a virulent challenge. To explore what mechanisms are responsible for protective immunity, we investigated the course of Coccidioides infection in the gp91^phox knock out mouse that has a defect in the oxidative burst that results in chronic granulomatous disease.

Results

We found that the gp91^phox knock out mice were somewhat more resistant to intraperitoneal infection and equally as resistant to low dose intranasal infection, but slightly more susceptible to high dose intranasal infection compared to control mice. The gp91^phox knock out mice made a more robust inflammatory response to infection than controls, as measured by histology and production of inflammatory cytokines. The gp91^phox knock out mice were as protected by immunization with the recombinant Coccidioides protein Ag2/PRA as the controls were against either intraperitoneal or intranasal infection. Coccidioides immitis arthroconidia and spherules were significantly more resistant to H₂O₂ treatment in vitro than Aspergillus fumigatus spores.

Conclusion

These data suggest that oxidative burst may not be required for protective immunity to coccidioidomycois.

Secondary syphilis with ocular manifestations in older adults

We describe 4 patients (age, >50 years) with secondary syphilis. All patients presented with ocular syphilis, and 2 presented with syphilis-negative rapid plasma reagin titers due to a prozone phenomenon. Three male patients reported sildenafil use. The presentation of these patients with ocular syphilis suggests the need for additional clinical studies involving older patients.

Susceptibility to Coccidioides species in C57BL/6 mice is associated with expression of a truncated splice variant of Dectin-1 (Clec7a)

Coccidioides posadasii spherules stimulate macrophages to make cytokines via TLR-2 and Dectin-1. We used formalin-killed spherules and 1,3-beta-glucan purified from spherules to stimulate elicited peritoneal macrophages and myeloid dendritic cells (mDCs) from susceptible (C57BL/6) and resistant (DBA/2) mouse strains. DBA/2 macrophages produced more TNF-alpha and IL-6 than macrophages from C57BL/6 mice, and the amount of TNF-alpha made was dependent on both TLR2 and Dectin-1. DCs from C57BL/6 mice made more IL-10 and less IL-23p19 and IL-12p70 than did DBA/2 DC. These responses were inhibited by a monoclonal antibody to Dectin-1. DBA/2 mice expressed full-length Dectin-1, whereas C57BL/6 mice spliced out exon 3, which encodes most of the stalk. RAW cells transduced to express the full-length Dectin-1 responded better to FKS than cells expressing truncated Dectin-1. We compared the isoform of Dectin-1 expressed by 34 C57BL/6 X DBA/2 recombinant inbred (BXD RI) lines with their susceptibility to Coccidioides immitis. In 25 of 34 RI lines susceptibility or resistance corresponded to short or full-length isoforms, respectively. These results suggest that alternative splicing of the Dectin-1 gene contributes to susceptibility of C57BL/6 mice to coccidioidomycosis, and affects the cytokine responses of macrophages and mDCs to spherules.