Massively parallel combination screen reveals small molecule sensitization of antibiotic-resistant Gram-negative ESKAPE pathogens

Antibiotic resistance, especially in multidrug-resistant ESKAPE pathogens, remains a worldwide problem. Combination antimicrobial therapies may be an important strategy to overcome resistance and broaden the spectrum of existing antibiotics. However, this strategy is limited by the ability to efficiently screen large combinatorial chemical spaces. Here, we deployed a high-throughput combinatorial screening platform, DropArray, to evaluate the interactions of over 30,000 compounds with up to 22 antibiotics and 6 strains of Gram-negative ESKAPE pathogens, totaling to over 1.3 million unique strain-antibiotic-compound combinations. In this dataset, compounds more frequently exhibited synergy with known antibiotics than single-agent activity. We identified a compound, P2-56, and developed a more potent analog, P2-56-3, which potentiated rifampin (RIF) activity against Acinetobacter baumannii and Klebsiella pneumoniae. Using phenotypic assays, we showed P2-56-3 disrupts the outer membrane of A. baumannii. To identify pathways involved in the mechanism of synergy between P2-56-3 and RIF, we performed genetic screens in A. baumannii. CRISPRi-induced partial depletion of lipooligosaccharide transport genes (lptA-D, lptFG) resulted in hypersensitivity to P2-56-3/RIF treatment, demonstrating the genetic dependency of P2-56-3 activity and RIF sensitization on lpt genes in A. baumannii. Consistent with outer membrane homeostasis being an important determinant of P2-56-3/RIF tolerance, knockout of maintenance of lipid asymmetry complex genes and overexpression of certain resistance-nodulation-division efflux pumps - a phenotype associated with multidrug-resistance - resulted in hypersensitivity to P2-56-3. These findings demonstrate the immense scale of phenotypic antibiotic combination screens using DropArray and the potential for such approaches to discover new small molecule synergies against multidrug-resistant ESKAPE strains.

Critical role of growth medium for detecting drug interactions in Gram-negative bacteria that model in vivo responses

The rise in infections caused by multidrug-resistant (MDR) bacteria has necessitated a variety of clinical approaches, including the use of antibiotic combinations. Here, we tested the hypothesis that drug-drug interactions vary in different media, and determined which in vitro models best predict drug interactions in the lungs. We systematically studied pair-wise antibiotic interactions in three different media, CAMHB, (a rich lab medium standard for antibiotic susceptibility testing), a urine mimetic medium (UMM), and a minimal medium of M9 salts supplemented with glucose and iron (M9Glu) with three Gram-negative ESKAPE pathogens, Acinetobacter baumannii (Ab), Klebsiella pneumoniae (Kp), and Pseudomonas aeruginosa (Pa). There were pronounced differences in responses to antibiotic combinations between the three bacterial species grown in the same medium. However, within species, PaO1 responded to drug combinations similarly when grown in all three different media, whereas Ab17978 and other Ab clinical isolates responded similarly when grown in CAMHB and M9Glu medium. By contrast, drug interactions in Kp43816, and other Kp clinical isolates poorly correlated across different media. To assess whether any of these media were predictive of antibiotic interactions against Kp in the lungs of mice, we tested three antibiotic combination pairs. In vitro measurements in M9Glu, but not rich medium or UMM, predicted in vivo outcomes. This work demonstrates that antibiotic interactions are highly variable across three Gram-negative pathogens and highlights the importance of growth medium by showing a superior correlation between in vitro interactions in a minimal growth medium and in vivo outcomes.

IMPORTANCE

Drug-resistant bacterial infections are a growing concern and have only continued to increase during the SARS-CoV-2 pandemic. Though not routinely used for Gram-negative bacteria, drug combinations are sometimes used for serious infections and may become more widely used as the prevalence of extremely drug-resistant organisms increases. To date, reliable methods are not available for identifying beneficial drug combinations for a particular infection. Our study shows variability across strains in how drug interactions are impacted by growth conditions. It also demonstrates that testing drug combinations in tissue-relevant growth conditions for some strains better models what happens during infection and may better inform combination therapy selection.

Allosteric site variants affect GTP hydrolysis on Ras

RAS GTPases are proto-oncoproteins that regulate cell growth, proliferation, and differentiation in response to extracellular signals. The signaling functions of RAS, and other small GTPases, are dependent on their ability to cycle between GDP-bound and GTP-bound states. Structural analyses suggest that GTP hydrolysis catalyzed by HRAS can be regulated by an allosteric site located between helices 3, 4, and loop 7. Here we explore the relationship between intrinsic GTP hydrolysis on HRAS and the position of helix 3 and loop 7 through manipulation of the allosteric site, showing that the two sites are functionally connected. We generated several hydrophobic mutations in the allosteric site of HRAS to promote shifts in helix 3 relative to helix 4. By combining crystallography and enzymology to study these mutants, we show that closure of the allosteric site correlates with increased hydrolysis of GTP on HRAS in solution. Interestingly, binding to the RAS binding domain of RAF kinase (RAF-RBD) inhibits GTP hydrolysis in the mutants. This behavior may be representative of a cluster of mutations found in human tumors, which potentially cooperate with RAF complex formation to stabilize the GTP-bound state of RAS.

Identification, characterization and benefits of an exclusion system in an integrative and conjugative element of Bacillus subtilis

Integrative and conjugative elements (ICEs) are mobile genetic elements that transfer from cell to cell by conjugation (like plasmids) and integrate into the chromosomes of bacterial hosts (like lysogenic phages or transposons). ICEs are prevalent in bacterial chromosomes and play a major role in bacterial evolution by promoting horizontal gene transfer. Exclusion prevents the redundant transfer of conjugative elements into host cells that already contain a copy of the element. Exclusion has been characterized mostly for conjugative elements of Gram-negative bacteria. Here, we report the identification and characterization of an exclusion mechanism in ICEBs1 from the Gram-positive bacterium Bacillus subtilis. We found that cells containing ICEBs1 inhibit the activity of the ICEBs1-encoded conjugation machinery in other cells. This inhibition (exclusion) was specific to the cognate conjugation machinery and the ICEBs1 gene yddJ was both necessary and sufficient to mediate exclusion by recipient cells. Through a mutagenesis and enrichment screen, we identified exclusion-resistant mutations in the ICEBs1 gene conG. Using genes from a heterologous but related ICE, we found that the exclusion specificity was determined by ConG and YddJ. Finally, we found that under conditions that support conjugation, exclusion provides a selective advantage to the element and its host cells.

Primary ovarian carcinoid tumors

Primary ovarian carcinoid tumors were reviewed from Mayo Clinic and Colorado Tumor Registry data. A total of 17 patients with this diagnosis were identified. Histologic analysis of these carcinoid tumors revealed 9 (53%) were insular, 5 (29%) were trabecular, and 4 (26%) were strumal carcinoid with or without a mature dermoid component. There were 11 patients with stage I and 6 patients with stage III or IV disease at diagnosis. Carcinoid syndrome was found in 29% of patients. Pressure or pain with defecation was noted in 41% of cases. Recurrence of tumor occurred in 1 of 11 patients with suspected stage I disease 13 years after initial diagnosis. Overall survival was excellent in the 11 patients whose disease was confined to one ovary (100% 5-year survival), but only 1 of 6 patients survived (33% 5-year survival) if advanced stage at diagnosis. Systemic chemotherapy for advanced disease achieved a complete response in 1 patient and stable disease in another. Although rare, primary ovarian carcinoid tumors treated with surgery alone and found to be confined to the ovary can be expected to have an excellent overall outcome.

Invasive vaginal carcinoma: analysis of early-stage disease

From 1960 through 1987, 89 patients with stage I (44 patients) or II (45 patients) vaginal carcinoma (excluding melanomas) were treated primarily at the Mayo Clinic. Treatment consisted of surgery alone in 52 patients, surgery plus radiation in 14, and radiation alone in 23. The median duration of follow-up was 4.4 years. The 5-year survival (Kaplan-Meier method) was 82% for patients with stage I disease and 53% for those with stage II disease (p = 0.009). Analysis of survival according to treatment did not show statistically significant differences. This report is consistent with previous studies showing that stage is an important prognostic factor and that treatment can be individualized, including surgical treatment for primary early-stage vaginal cancer.

Cervical mucus immunoglobulins as an indicator of ovulation

A practical and accurate method of determining ovulation using cervical mucus is described. Ovulatory cycles from 32 healthy women were assessed using hormonal and nonhormonal methods. Cervical mucus extractable immunoglobulins were assayed for the complete cycles of nine women and randomly collected from 23 additional women with normal cycles. All normal ovulatory women showed a minimum concentration present at midcycle when optimum conditions for fertilization existed. Using newer laser nephelometry techniques, the content of extractable immunoglobulin G and immunoglobulin A per sample weight confirmed the cyclic nature of the concentration of immunoglobulin in cervical mucus, and correlated well with previously defined biophysical properties of cervical mucus. Nephelometry proved to be rapid, accurate, and an inexpensive technique for determining ovulation and has potential for clinical use.

A comparison of homogeneous and heterogeneous platinum as catalysts for the deuteration of polyphenyl aromatic hydrocarbons

Polyphenyl aromatic compounds exchange with heavy water in the presence of both homogeneous and heterogeneous platinum with high M values. Diphenyl, m- and p-terphenyls exhibit similar isotope orientations during initial rates in both catalytic systems whereas o-terphenyl does not. The first three compounds show ortho steric effects and appear to exchange by n-dissociative processes. In m- and p-terphenyls, the deactivated ortho protons exchange heterogeneously at rates which may be directly related to their degrees of steric hindrance. With o- terphenyl, all ortho hydrogens are deactivated in homogeneous exchange whereas heterogeneously, all centre ring ortho hydrogens exchange readily. A novel catalytic intermediate has been proposed to explain this orientation. These results show that o-terphenyl is a unique compound for differentiating between homogeneous and heterogeneous metal catalysed exchange processes. The data from the polyphenyls and the condensed polycyclics support the π-complex theory of catalysis.

A comparison of homogeneous and heterogeneous platinum as catalysts for the deuteration of condensed polycyclic aromatic hydrocarbons

A comparison has been made of homogeneous sodium chloroplatinate(II) with heterogeneous platinum metal as catalysts for the exchange in D2O of naphthalene, anthracene and pyrene, three representative condensed polycyclic aromatic hydrocarbons. For this purpose, very careful detailed experiments have been designed so that the progressive deuteration of the aromatics could be followed with time especially in both catalytic systems. Initial isotope orientation is similar for both catalysts although specificity is better with homogeneous platinum. Naphthalene during the initial stages of exchange yields ,&orientation with an M value of 1, ultimately giving naphthalene[β-D4]. Only with heterogeneous platinum does prolonged exchange yield naphthalene[D8]. A unique scrambling reaction of naphthalene[β-D4] has been observed only with heterogeneous platinum. The reactivities of anthracene and pyrene are similar to naphthalene. Present data have been interpreted in terms of bond localization concepts, in particular the role of π-olefin type complexes in both catalytic systems. The results also indicate that π- dissociative, as compared with π-associative, mechanisms predominate both homogeneously and heterogeneously.