Biology subjects

Hauser, A. R.

Publications and source records attributed to Hauser, A. R..

12 recordsLinked to original sources

bioRxiv2026

Transposon insertion sequencing of Pseudomonas aeruginosa identifies multiple intersecting pathways essential for extreme colistin resistance

Colistin is used to treat antibiotic resistant gram-negative infections, including those caused by Pseudomonas aeruginosa (Pa). Using a diverse collection of clinical isolates, we identified BWH047, a colistin-resistant isolate with an extremely high minimum inhibitory concentration (MIC, 1280 {micro}g/mL). To characterize the genes conditionally essential for colistin resistance in BWH047, we employed transposon insertion sequencing and identified 20 gene candidates. In-frame deletion validated 75% of the candidates and identified genes in several novel pathways that contribute to colistin resistance, including algU and wapH. We also identified several candidate genes from previously reported colistin resistance pathways (e.g. arn, pmrAB). We further investigated the impact of a colistin resistance-associated inner membrane DedA-family undecaprenyl phosphate flippase, which we named DpcA (DedA of Pseudomonas necessary for colistin resistance A). Deletion of dpcA in BWH047 restored sensitivity to colistin (MIC = 0.5 {micro}g/mL) and resulted in several unique changes to the structure of lipopolysaccharide (LPS), including production of decreased amounts of the colistin resistance-conferring 4-amino-4-deoxy-L-arabinose (L-Ara4N) modification on lipid A. To date, this work represents the most complete analysis of colistin resistance in Pa and identifies novel intersecting pathways that contribute to extreme phenotypic resistance. Author summaryPseudomonas aeruginosa is a bacterium that causes a wide variety of infections. It is especially problematic given its propensity to become resistant to antibiotics. One antibiotic used to treat multidrug-resistant P. aeruginosa infections is colistin. In this study, we investigated colistin resistance mechanisms in a patient-derived, extremely phenotypically resistant P. aeruginosa isolate, BWH047, using transposon insertion sequencing and mass spectrometry. We identified 13 genes conditionally essential for colistin resistance and investigated the role of one of these genes, dpcA, on the composition of the bacterial outer membrane, the target of colistin. Additionally, our study identified novel colistin resistance genes residing in several intersecting pathways that could be targeted to prevent the development of antimicrobial resistance.

microbiology↗

bioRxiv2026

Comparison of Galleria mellonella, Epithelial Cell Cytotoxicity, and Mouse Model of Bacteremia to Measure Pseudomonas aeruginosa Virulence

Considerable effort has focused on identifying alternatives to mouse models in research studies. In the field of bacterial pathogenesis, Galleria mellonella and epithelial cell lines have been widely used for this purpose, but the concordance of these models with mice remains unclear. To begin to address this knowledge gap, we used 105 clinical isolates of Pseudomonas aeruginosa for which the virulence had been previously determined in a mouse bacteremia model. A semistrong correlation was observed between G. mellonella median time to 50% mortality and mouse 50% pre-lethal dose (LD50) values (Spearmans rank correlation coefficient [{rho}] = 0.75), whereas percent A549 epithelial-like cell lysis during co-culture showed a weak correlation to mouse LD50 values ({rho} = -0.47). Given the stronger correlation between G. mellonella and mouse virulence, we next examined whether G. mellonella could substitute for mice when asking questions about the virulence of large numbers of P. aeruginosa isolates. Results from mice indicated that isolates with resistance to more antibiotics were significantly less virulent, and the use of G. mellonella identified the same inverse correlation. Furthermore, both models found no evidence for the existence of hypervirulent clonal lineages. In particular, isolates belonging to sequence types defined as high-risk clones were not consistently more virulent than other isolates, despite the known association of high-risk clones with poor clinical outcomes. These findings suggest that G. mellonella can serve as an adequate substitute for mice when addressing specific population-based virulence questions, although conclusions should be confirmed in mice. Author SummaryWe found that virulence measurements in a G. mellonella infection model showed a semistrong correlation with those from a mouse bacteremia model and that this insect larval model adequately detected population-level trends similarly to mice. In contrast, A549 epithelial-like cell lysis during bacterial co-culture correlated less well with mouse virulence. Together, these results support the use of G. mellonella as a scalable, low-cost, and humane first-line model for assessing P. aeruginosa virulence but also indicate that conclusions should be validated in mice.

microbiology↗

bioRxiv2026

A novel mechanism of ceftolozane-tazobactam resistance in Pseudomonas aeruginosa mediated by L2 β-lactamase

The prevalance of non-susceptibility to ceftolozane-tazobactam (C/T) among Pseudomonas aeruginosa remains low but novel mechanisms of C/T resistance are of concern. Herein, we describe a novel Pseudomonas aeruginosa genotype associated with high-level C/T resistance (>256/4 {micro}g/mL) in a single patient. Whole genome sequencing of the isolate was compared to that of a susceptible isolate cultured from the same patient two months earlier. Analysis of the sequences revealed two different P. aeruginosa high-risk clones: ST111 followed by ST235. The C/T-resistant ST235 isolate contained five copies of a genetic element comprised of an L2 {beta}-lactamase gene (blaL2) and a truncated ampRL2 transcriptional regulator gene, which are commonly found together in Stenotrophomonas maltophilia strains and have not been reported to mediate resistance to C/T. Comparative genomic analysis with other P. aeruginosa isolates failed to identify alternative explanations for the observed C/T resistance. We found that exogenous expression of blaL2 modestly increased C/T MICs in genetically distinct P. aeruginosa strains. A screen of our archived isolates identified two P. aeruginosa clinical isolates, PS2045 and PS2046, with one and two copies, respectively, of the genetic element containing blaL2 and truncated ampRL2. Interestingly, disruption of the gene blaL2 but not the truncated ampRL2 in PS2045 led to a significant decrease in C/T MIC. Thus, we report a novel mechanism of C/T resistance in P. aeruginosa mediated by an L2 {beta}-lactamase independently of its canonical regulator AmpRL2.

microbiology↗

bioRxiv2024

Pseudomonas aeruginosa population dynamics in a vancomycin-induced murine model of gastrointestinal carriage

Pseudomonas aeruginosa is a common nosocomial pathogen and a major cause of morbidity and mortality in hospitalized patients. Multiple reports highlight that P. aeruginosa gastrointestinal colonization may precede systemic infections by this pathogen. Gaining a deeper insight into the dynamics of P. aeruginosa gastrointestinal carriage is an essential step in managing gastrointestinal colonization and could contribute to preventing bacterial transmission and progression to systemic infection. Here, we present a clinically relevant mouse model relying on parenteral vancomycin pretreatment and a single orogastric gavage of a controlled dose of P. aeruginosa. Robust carriage was observed with multiple clinical isolates, and carriage persisted for up to 60 days. Histological and microbiological examination of mice indicated that this model indeed represented carriage and not infection. We then used a barcoded P. aeruginosa library along with the sequence tag-based analysis of microbial populations (STAMPR) analytic pipeline to quantify bacterial population dynamics and bottlenecks during the establishment of the gastrointestinal carriage. Analysis indicated that most of the P. aeruginosa population was rapidly eliminated in the stomach, but the few bacteria that moved to the small intestine and the caecum expanded significantly. Hence, the stomach constitutes a significant barrier against gastrointestinal carriage of P. aeruginosa, which may have clinical implications for hospitalized patients. IMPORTANCEWhile P. aeruginosa is rarely part of the normal human microbiome, carriage of the bacterium is quite frequent in hospitalized patients and residents of long-term care facilities. P. aeruginosa carriage is a precursor to infection. Options for treating infections caused by difficult-to-treat P. aeruginosa strains are dwindling, underscoring the urgency to better understand and impede pre-infection stages, such as colonization. Here, we use vancomycin-treated mice to model antibiotic-treated patients who become colonized with P. aeruginosa in their gastrointestinal tracts. We identify the stomach as a major barrier to the establishment of gastrointestinal carriage. These findings suggest that efforts to prevent gastrointestinal colonization should focus not only on judicious use of antibiotics but also on investigation into how the stomach eliminates orally ingested P. aeruginosa.

microbiology↗

bioRxiv2023

Genome-wide screens reveal shared and strain-specific genes that facilitate enteric colonization by Klebsiella pneumoniae

Gastrointestinal (GI) colonization by Klebsiella pneumoniae is a risk factor for subsequent infection as well as transmission to other patients. Additionally, colonization is achieved by many strain types that exhibit high diversity in genetic content. Thus, we aimed to study strain-specific requirements for K. pneumoniae GI colonization by applying transposon insertion sequencing to three classical clinical strains: a carbapenem-resistant strain, an extended-spectrum beta-lactamase producing strain, and a non-epidemic antibiotic-susceptible strain. The transposon insertion libraries were screened in a murine model of GI colonization. At three days post-inoculation, 27 genes were required by all three strains for colonization. Isogenic deletion mutants for three genes/operons (acrA, carAB, tatABCD) confirmed colonization defects in each of the three strains. Additionally, deletion of acrA reduced bile tolerance in vitro, while complementation restored both bile tolerance in vitro and colonization ability in vivo. Transposon insertion sequencing suggested that some genes were more important for colonization of one strain than the others. For example, deletion of the sucrose porin-encoding gene scrY resulted in a colonization defect in the carbapenemase-producing strain but not in the extended-spectrum beta-lactamase producer or the antibiotic-susceptible strain. These findings demonstrate that classical K. pneumoniae strains use both shared and strain-specific strategies to colonize the mouse GI tract. IMPORTANCEKlebsiella pneumoniae is a common cause of difficult-to-treat infections due to its propensity to express resistance to many antibiotics. For example, carbapenem-resistant K. pneumoniae (CR-Kp) has been named an urgent threat by the United States Centers for Disease Control and Prevention. Gastrointestinal colonization of patients with K. pneumoniae has been linked to subsequent infection, making it a key process to control in prevention of multidrug-resistant infections. However, the bacterial factors which contribute to K. pneumoniae colonization are not well understood. Additionally, individual strains exhibit large amounts of genetic diversity, begging the question of whether some colonization factors are strain-dependent. This study identifies the enteric colonization factors of 3 classical strains using transposon mutant screens to define a core colonization program for K. pneumoniae as well as detecting strain-to-strain differences in colonization strategies.

microbiology↗

bioRxiv2022

Genomic evaluation of a case of Lacticaseibacillus rhamnosus endocarditis: comparison with commercial yogurt isolates and examination of global population structure

Probiotics, including yogurt commonly containing bacteria of the Lactobacillus group, are widely used to promote microbiome health and to prevent gastrointestinal or other infections, especially in the setting of antibiotic use. Rarely, however, Lactobacillus bacteria have caused invasive or severe infections in patients. In this report, we present a patient with fatal Lacticaseibacillus bacteremia and endocarditis who frequently consumed yogurt. Whole genome sequencing identified the patients bloodstream isolate as Lacticaseibacillus (formerly Lactobacillus) rhamnosus, and sequencing of Lactobacillus isolates from selected commercial yogurt preparations revealed one isolate nearly identical to the patients isolate, differing by only one nucleotide (adenine to guanine substitution leading to a M1A amino acid change in the start codon of the nrdR gene). To place these sequences into broader context of L. rhamnosus strains, we compared them to 602 L. rhamnosus genome sequences publicly available through the National Center for Biotechnology Information repository. Both isolates belonged to a clade, identified in this report as clade YC, composed of mostly gastrointestinal isolates from healthy individuals, some of which also differed by only a single nucleotide from the patients isolate. Members of clade YC had only rarely been previously identified in invasive infections. In summary, the Lacticaseibacillus strain causing this patients infection may have originated from a commercial dairy product or from the commensal flora of his gastrointestinal tract. This study demonstrates that whole genome sequencing may be insufficient to reliably determine the source of invasive infections caused by L. rhamnosus. IMPORTANCEActive culture and probiotic foods and supplements are often used to promote gut health. Though largely considered safe for human consumption, there are rare reports of severe infections linked to bacterial species used in these products. Using whole genome sequencing, we examined a case of fatal infection with Lacticaseibacillus rhamnosus in the patients blood. By comparing the bacterial genome sequence from the patient to strains cultured from 4 commercial yogurt samples and 602 publicly available sequences of L. rhamnosus from around the world, we found that it was nearly identical to one of the yogurt strains and equally similar to other strains from both probiotics and healthy individuals gastrointestinal tracts. These findings show that even with whole genome sequencing it can be difficult to determine the source of an invasive L. rhamnosus infection, whether from recent consumption of a probiotic or dairy product versus from the gastrointestinal microbiome.

microbiology↗

bioRxiv2021

Genomic and phenotypic characterization of Pseudomonas hygromyciniae, a novel bacterial species discovered from a commercially purchased antibiotic

A purchased lot of the antibiotic hygromycin B was found to be contaminated with a novel bacterial species, which we designate Pseudomonas hygromyciniae. Characteristics of P. hygromyciniae include its ability to use a variety of compounds as carbon sources, its pathogenicity towards lettuce and Galleria mellonella, and its ability to inhibit the growth of an E. coli strain. P. hygromyciniae is unlikely to be a human pathogen, as it did not survive at 37 {degrees}C and was not cytotoxic towards a mammalian cell line. The P. hygromyciniae strain harbors a novel 250 kb megaplasmid which confers resistance to hygromycin B and contains numerous other genes predicted to encode replication and conjugation machinery. These findings indicate that commercially manufactured antibiotics represent another extreme environment that may support the growth of novel bacterial species. IMPORTANCEMicrobial ecologists have surveyed numerous natural and manmade environments in search of new microbial species. In some instances, these microbes are discovered in harsh conditions, such as deep-sea vents, and their discovery leads to better understanding of how microbes adapt to their environment. Here, we have discovered a new species of bacteria from an extreme manmade environment: a lyophilized, commercially available bottle of the antibiotic hygromycin B.

microbiology↗

bioRxiv2021

Functional and Structural Characterization of OXA-935, a Novel OXA-10-family β-lactamase from Pseudomonas aeruginosa

Resistance to antipseudomonal penicillins and cephalosporins is often driven by the overproduction of the intrinsic {beta}-lactamase AmpC. However, OXA-10-family {beta}-lactamases are a rich source of resistance in Pseudomonas aeruginosa. OXA {beta}-lactamases have a propensity for mutation leading to extended spectrum cephalosporinase and carbapenemase activity. In this study, we identified isolates from a subclade of the multidrug-resistant (MDR) high risk clonal complex CC446 with resistance to ceftazidime. Genomic analysis revealed that these isolates harbored a plasmid containing a novel allele of blaOXA-10, named blaOXA-935, which was predicted to produce an OXA-10 variant with two amino acid substitutions: an aspartic acid instead of glycine at position 157 and a serine instead of phenylalanine at position 153. The G157D mutation, present in OXA-14, is associated with resistance to ceftazidime. Deletion of blaOXA-935 restored sensitivity to ceftazidime and susceptibility profiling of P. aeruginosa laboratory strains expressing blaOXA-935 revealed that OXA-935 conferred ceftazidime resistance. To better understand the impact of the variant amino acids, we determined the crystal structures of OXA-14 and OXA-935. In OXA-14, one of two monomers contained the canonical carbamylated lysine-70 (K70). In contrast, both monomers of OXA-935 were decarbamylated at K70, and the F153S mutation conferred increased flexibility to the omega ({Omega}) loop. Compared to OXA-14, the catalytic efficiency of OXA-935 for nitrocefin was significantly reduced. Amino acid changes that confer extended spectrum cephalosporinase activity to OXA-10-family {beta}-lactamases are concerning given rising reliance on novel {beta}-lactam/{beta}-lactamase inhibitor combinations such as ceftolozane-tazobactam and ceftazidime-avibactam to treat MDR P. aeruginosa infections.

microbiology↗

bioRxiv2020

Prevalence of Hypervirulence-Associated Pathogenicity Loci Among Klebsiella pneumoniae Bloodstream Isolates at a United States Hospital

BackgroundKlebsiella pneumoniae (K. pneumoniae) strains have been divided into two major categories: classical K. pneumonia, which are frequently multidrug-resistant and cause hospital-acquired infections in patients with impaired defenses, and hypervirulent K. pneumoniae, which cause severe disseminated community-acquired infections in immunologically normal hosts. Both types of infections may lead to bacteremia and are associated with significant morbidity and mortality. The relative burden of these two types of K. pneumoniae among bloodstream isolates within the United States is not well understood. MethodsWe examined consecutive K. pneumoniae isolates cultured from the blood of hospitalized patients at Northwestern Memorial Hospital (NMH) in Chicago, Illinois April 2015 - April 2017. Bloodstream isolates underwent whole genome sequencing, and clinically relevant data (sequence type [ST], capsule loci, virulence factors, and antimicrobial resistance genes) were inferred from the genome using the bioinformatic tools Kleborate and Kaptive. Patient demographic, comorbidity, and infection information, as well as phenotypic antimicrobial resistance of the isolate were extracted from the electronic medical record. Candidate hypervirulent isolates were tested in a murine model of pneumonia. Complete genome sequences of these candidate hypervirulent isolates were obtained and plasmid content was evaluated. ResultsK. pneumoniae bloodstream isolates (n=104) from NMH were highly diverse consisting of 75 distinct STs and 51 unique capsule loci. The majority of these isolates (n=58, 55.8%) were susceptible to all tested antibiotics except ampicillin, but 17 (16.3%) were multidrug-resistant. A total of 32 (30.8%) of these isolates were STs of known high-risk clones, including ST258 and ST45. In particular, 18 (17.3%) were resistant to ceftriaxone, 17 harbored extended-spectrum beta-lactamases, and 9 (8.7%) were resistant to meropenem. Four (3.8%) of the 104 isolates were hypervirulent K. pneumoniae, as evidenced by hypermucoviscous phenotypes, high levels of virulence in a murine model of pneumonia, and the presence of large plasmids similar to characterized hypervirulence plasmids. Of particular concern, several of these plasmids contained tra conjugation loci suggesting the potential for transmission. Two of these hypervirulent strains belonged to the well characterized ST23 lineage and one to the emerging ST66 lineage. ConclusionsWhile NMH K. pneumoniae bloodstream infections are caused by highly diverse strains, the most prevalent STs were those of multidrug-resistant high-risk clones. A small number of hypervirulent K. pneumoniae were observed in patients with no recent travel history, suggesting that these isolates are undergoing community spread in the United States.

microbiology↗

bioRxiv2020

A Genome-based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates

Variation in the genome of Pseudomonas aeruginosa, an important pathogen, can have dramatic impacts on the bacteriums ability to cause disease. We therefore asked whether it was possible to predict the virulence of P. aeruginosa isolates based upon their genomic content. We applied a machine learning approach to a genetically and phenotypically diverse collection of 115 clinical P. aeruginosa isolates using genomic information and corresponding virulence phenotypes in a mouse model of bacteremia. We defined the accessory genome of these isolates through the presence or absence of accessory genomic elements (AGEs), sequences present in some strains but not others. Machine learning models trained using AGEs were predictive of virulence, with a mean nested cross-validation accuracy of 75% using the random forest algorithm. However, individual AGEs did not have a large influence on the algorithms performance, suggesting instead that the virulence prediction derives from a diffuse genomic signature. These results were validated with an independent test set of 25 P. aeruginosa isolates whose virulence was predicted with 72% accuracy. Machine learning models trained using core genome single nucleotide variants and whole genome k-mers also predicted virulence. Our findings are a proof of concept for the use of bacterial genomes to predict pathogenicity in P. aeruginosa and highlight the potential of this approach for predicting patient outcomes. IMPORTANCEPseudomonas aeruginosa is a clinically important gram-negative opportunistic pathogen. As a species, P. aeruginosa has a large degree of heterogeneity both through variation in sequences found throughout the species (core genome) and the presence or absence of sequences in different isolates (accessory genome). P. aeruginosa isolates also differ markedly in their ability to cause disease. In this study, we used machine learning to predict the virulence level of P. aeruginosa isolates in a mouse bacteremia model based on genomic content. We show that both the accessory and core genome are predictive of virulence. This study provides a machine learning framework to investigate relationships between bacterial genomes and complex phenotypes such as virulence.

genomics↗

bioRxiv2019

Evaluation of Dose Fractionated Polymyxin B on Acute Kidney Injury: A Translational In Vitro Model

The polymyxins are last-line defense for highly resistant infections. Nephrotoxicity, however, is a dose-limiting factor. Yet, approaches to mitigate nephrotoxicity are poorly defined. This study aimed to investigate the impact of dose fractionated (once, twice and thrice daily) polymyxin B (PB) on acute kidney injury (AKI) in a pre-clinical model. Secondarily, we aimed to describe the pharmacokinetic (PK) profile of PB. Sprague-Dawley rats were assigned to experimental groups with different dosing intervals but constant total daily exposure (12 mg/kg/day into single, twice daily, and thrice daily doses) and controls received normal saline subcutaneously over 3 days. Blood and urine samples were collected, and kidneys were harvested at necropsy. A three-compartment model best described the data and Bayesian observed vs. predicted concentration demonstrated bias, imprecision, and R2 of 0.129 mg/L, 0.729 mg2/L2 and 0.652, respectively. PB exposure (i.e. AUC24h) were similar across treatment groups over time (p=0.87). As a representative, urinary KIM-1 were elevated on days 1 and 2 for experimental groups compared to controls, and thrice daily group experienced the most KIM-1 increase [mean increase (95% CI) day 1 from day -1, 4.44 (0.89, 8.00) ng/mL; p=0.018] as compared to control [mean increase (95% CI) day 1 from day -1, 0.03 (-0.42, 0.49) ng/mL; p=0.99]. Correspondingly, significant histopathological damage was observed with the same group (p=0.013) (controls as a referent). Our findings suggested that fractionating the PB dose thrice daily resulted in the most injury in a rat model.

pharmacology and toxicology↗

bioRxiv2019

Systemic Infection Facilitates Transmission of Pseudomonas aeruginosa

Health care-associated infections such as Pseudomonas aeruginosa (PA) bacteremia pose a major clinical risk for hospitalized patients, and efforts to limit them are a priority. The fitness pressures accounting for PA virulence factors that facilitate bloodstream infections are unclear, as these infections are presumed to be a \"dead-end\" and have no impact on transmission. Here, we used a mouse model to show that PA spreads from the bloodstream to the gallbladder, where it replicates to extremely high numbers. Bacteria in the gallbladder then seed the intestines and feces, leading to transmission to uninfected cage-mate mice. The findings demonstrate that the gallbladder is critical for spread of PA from the bloodstream to the feces during bacteremia, a process that promotes transmission.

microbiology↗