Biology subjects

Hanson, B. M.

Publications and source records attributed to Hanson, B. M..

10 recordsLinked to original sources

bioRxiv2026

Carbapenem-resistant Klebsiella pneumoniae lineage CG307 displays urinary tract tropism

Carbapenem-resistant (CR) Klebsiella pneumoniae (Kp) are designated by the WHO as a top-priority pathogen due to their antibiotic resistance profiles, capacity to disseminate resistance, and associated mortality. The prototypical CRKp clade, CG258, is associated with acute respiratory infections; however, urinary tract infections (UTIs) caused by CRKp are increasing, and frequently linked to the emergent clade CG307. Notably, CG307 isolates have extensive accessory genomes that may drive adaptation to the urinary tract, including a novel capsule gene cluster and high-affinity urea transporter. In this study, we show that UTIs caused by Kp are increasing across the Southern US and that in addition to CG307s circulating within Houston, TX hospital systems, the lineage was also detected in healthcare systems in the broader Gulf Coast region. Characterization of CG307 isolates demonstrate that while these strains exhibit similar mucoviscosity compared to the reference UTI strain TOP52, the lineage displays significantly higher i) growth in artificial urine, ii) urease activity, and iii) UTI in a mouse model. These results suggest that CG307 is spreading across the Southern US and encodes distinct pathogenic features that promote urinary tract tropism, underscoring a need for targeted surveillance and future studies that mechanistically examine the factors that promote UTI.

microbiology↗

bioRxiv2025

Pangenome Analysis of Proteus mirabilis Reveals Lineage-Specific Antimicrobial Resistance Profiles and Discordant Genotype-Phenotype Correlations

Urinary tract infections (UTIs) impose a large healthcare burden, with escalating antimicrobial resistance (AMR) and treatment failure. Proteus mirabilis is an under-characterized and challenging UTI pathogen due to intrinsic resistances and biofilm formation. To understand P. mirabilis population genomics, we combined pangenome analysis, in silico AMR predication, and phenotypic antimicrobial susceptibility testing (AST) across 1,027 P. mirabilis genomes derived from human urine specimens. This revealed a mosaic pangenome driven by extensive accessory genome plasticity. Multilocus sequence typing (MLST) identified 213 MLSTs with only 7% having [≥]10 genomes, highlighting strain diversity. AMR gene profiles were largely lineage specific, with 25% of genomes harboring resistances for >6 antimicrobial subclasses. ST135 was identified as a highly MDR lineage, with 95% of genomes carrying [≥]16 resistance genes. Mobile genetic element (MGE) analysis of 22 clinical isolates with complete, reference level genomes revealed that Tn7 transposons, IS26-mediated genomic islands, and class 1 integrons act as vehicles for high AMR gene dissemination, including IS26-mediated gene stacking within a Proteus mirabilis Genomic Resistance Island 1 (PmGRI1) in ST135 isolates. While presence of genes like aph(3)-la reliably predicted kanamycin resistance, discordance for antibiotics such as trimethoprim-sulfamethoxazole and chloramphenicol revealed that AMR gene stacking, regulatory context, and intrinsic mechanisms, like efflux pumps, modulate phenotypic outcomes. In summary, our study provides a comprehensive and phenotypic resolution of P. mirabilis AMR, establishing that resistance architecture is lineage structured, MGE-driven, and phenotypically non-deterministic. We emphasize the need to shift towards standardized, genome-informed surveillance framework to translate into diagnostic and therapeutic strategies.

microbiology↗

bioRxiv2025

Clinical and Genomic Characterization of Recalcitrant Enterococcal Bacteremia: A Multicenter Prospective Cohort Study (VENOUS)

BackgroundPatients with recalcitrant enterococcal bloodstream infections are at greater risk of adverse outcomes. We identified patients in the 2016-2022 Vancomycin-Resistant Enterococcal Bacteremia Outcomes Study (VENOUS) cohort experiencing recalcitrant bloodstream infections for further clinical and genomic characterization. MethodsBacteremia episodes were considered "persistent" if there was a lack of clearance on day four while receiving [≥] 48 hours of active therapy and recurrent if there was clearance during hospitalization with a subsequent positive culture (collectively, "recalcitrant" bacteremia). A matched comparison group of non-recalcitrant bacteremia patients was chosen in a 2:1 control:case ratio. Isolates were subjected to short- and long-read whole-genome sequencing. Hybrid assemblies were created using a custom pipeline. Findings. A total of 46 recalcitrant infections from 41 patients were identified. Patients with persistent bacteremia were more often admitted to the ICU upon admission relative to controls. E. faecalis strains causing persistent infections had a significantly higher proportion of genes associated with carbohydrate utilization relative to controls. Representation of functional groups associated with mutated genes was disparate between E. faecium and E. faecalis index and persistent isolates, suggesting species-specific adaptation. DiscussionEnterococcal isolates causing recalcitrant bacteremia were genomically diverse, indicating that strain-specific signatures are not drivers of persistence. However, comparisons of index vs. persistent isolates revealed that E. faecium may be genetically pre-adapted to cause persistent infection, and site-specific structural variation during infection suggests the role of differential gene expression in adaptation and persistence. This data lays groundwork for future studies to define signatures of enterococcal adaptation during bacteremia.

genomics↗

bioRxiv2024

Cefiderocol heteroresistance associated with mutations in TonB-dependent receptor genes in Pseudomonas aeruginosa of clinical origin

The siderophore-cephalosporin cefiderocol(FDC) presents a promising treatment option for carbapenem-resistant (CR) P. aeruginosa (PA). FDC circumvents traditional porin and efflux mediated resistance by utilizing TonB-dependent receptors (TBDRs) to access the periplasmic space. Emerging FDC resistance has been associated with loss of function mutations within TBDR genes or the regulatory genes controlling TBDR expression. Further, difficulties with antimicrobial susceptibility testing (AST) and unexpected negative clinical treatment outcomes have prompted concerns for heteroresistance, where a single lineage isolate contains resistant subpopulations not detectable by standard AST. This study aimed to evaluate the prevalence of TBDR mutations among clinical isolates of P. aeruginosa and the phenotypic effect on FDC susceptibility and heteroresistance. We evaluated the sequence of pirR, pirS, pirA, piuA or piuD from 498 unique isolates collected before the introduction of FDC from 4 clinical sites in Portland, OR (1), Houston, TX (2), and Santiago, Chile (1). At some clinical sites, TBDR mutations were seen in up to 25% of isolates, and insertion, deletion, or frameshift mutations were predicted to impair protein function were seen in 3% of all isolates (n=15). Using population analysis profile testing, we found that P. aeruginosa with major TBDR mutations were enriched for a heteroresistant phenotype and undergo a shift in the susceptibility distribution of the population as compared to susceptible strains with wild type TBDR genes. Our results indicate that mutations in TBDR genes predate the clinical introduction of FDC, and these mutations may predispose to the emergence of FDC resistance.

microbiology↗

bioRxiv2023

LiaX is a surrogate marker for cell-envelope stress and daptomycin non-susceptibility in Enterococcus faecium

Daptomycin (DAP) is often used as a first line therapy to treat vancomycin-resistant Enterococcus faecium (VREfm) infections but emergence of DAP non-susceptibility threatens the effectiveness of this antibiotic. Moreover, current methods to determine DAP MICs have poor reproducibility and accuracy. In enterococci, DAP resistance is mediated by the LiaFSR cell membrane stress response system and deletion of liaR encoding the response regulator results in hypersusceptibility to DAP and antimicrobial peptides. The main genes regulated by LiaR are a cluster of three genes, designated liaXYZ. In Enterococcus faecalis, LiaX is surface exposed with a C-terminus that functions as a negative regulator of cell membrane remodeling and an N-terminal domain that is released to the extracellular medium where it binds DAP. Thus, in E. faecalis, LiaX functions as a sentinel molecule recognizing DAP and controlling the cell membrane response, but less is known about LiaX in E. faecium. Here, we found that liaX is essential in E. faecium (Efm) with an activated LiaFSR system. Unlike E. faecalis, Efm LiaX is not detected in the extracellular milieu and does not appear to alter phospholipid architecture. We further postulated that LiaX could be used as a surrogate marker for cell envelope activation and non-susceptibility to DAP. For this purpose, we developed and optimized a LiaX ELISA. We then assessed 86 clinical E. faecium BSI isolates for DAP MICs and used whole genome sequencing to assess for substitutions in LiaX. All DAP-R clinical strains of E. faecium exhibited elevated LiaX levels. Strikingly, 73% of DAP-S isolates by standard MIC determination had elevated LiaX ELISAs above the established cut-off. Phylogenetic analyses of predicted amino acid substitutions showed 12 different variants of LiaX without a specific association with DAP MIC or LiaX ELISA values. Our findings also suggest that many Efm isolates that test DAP susceptible by standard MIC determination are likely to have an activated cell stress response that may predispose to DAP failure. As LiaX appears to be essential for the cell envelope response to DAP, its detection could prove useful to improve the accuracy of susceptibility testing by anticipating therapeutic failure.

microbiology↗

bioRxiv2022

Staphylococcus aureus Breast Implant Infection Isolates Display Recalcitrance to Antibiotic Pocket Irrigants

Breast implant-associated infections (BIAIs) are a common complication following breast prostheses placement and account for [~]100,000 infections annually. The frequency, high cost of treatment, and morbidity make BIAIs a significant health burden for women. Thus, effective BIAI prevention strategies are urgently needed. This study tests the efficacy of one infection prevention strategy: the use of a triple antibiotic pocket irrigant (TAPI) against Staphylococcus aureus, the most common cause of BIAIs. TAPI, which consists of 50,000 U bacitracin, 1 g cefazolin, and 80 mg gentamicin diluted in 500 mL of saline, is used to irrigate the breast implant pocket during surgery. We used in vitro and in vivo assays to test the efficacy of each antibiotic in TAPI, as well as TAPI at the concentration used during surgery. We found that planktonically grown S. aureus BIAI isolates displayed susceptibility to gentamicin, cefazolin, and TAPI. However, TAPI treatment enhanced biofilm formation of BIAI strains. Furthermore, we compared TAPI treatment of a S. aureus reference strain (JE2) to a BIAI isolate (117) in a mouse BIAI model. TAPI significantly reduced infection of JE2 at 1- and 7-days post infection (dpi). In contrast, BIAI strain 117 displayed high bacterial burdens in tissues and implants, which persisted out to 14-dpi despite TAPI treatment. Lastly, we demonstrated that TAPI was effective against P. aeruginosa reference (PAO1) and BIAI strains in vitro and in vivo. Together, these data suggest S. aureus BIAI strains employ unique mechanisms to resist antibiotic prophylaxis treatment and promote chronic infection.

microbiology↗

bioRxiv2019

SVants: A long-read based method for structural variation detection in bacterial genomes

MotivationMobile genetic elements (MGEs) are genetic material that can transfer between bacterial cells and move to new locations within a single bacterial genome. These elements range from several hundred to tens of thousands of bases, and are often bordered by repeat regions, which makes resolving these elements difficult with short-read sequencing data. The development and availability of long-read sequencing technologies has opened up new opportunities in the study of structural variation but there is a lack of bioinformatics tools designed to take advantage of these longer reads.\n\nResultsWe present an assembly-free method for identifying the location of these MGEs when compared to any reference genome (including draft genomes). Using an artificially constructed Escherichia coli genome containing single and tandem-repeats of a Tn9 transposon, we demonstrate the ability of SVants to accurately identify multiple insertion sites as well as count the number of repeats of this MGE. Additionally, we show that SVants accurately identifies the transposon of interest, Tn9, but does not erroneously identify existing IS1 regions present within the chromosome of the E. coli artificial reference.\n\nAvailability and ImplementationSVants is available as open-source software at https://github.com/EpiBlake/SVants

bioinformatics↗

bioRxiv2019

β-lactamase Amplification and Porin Loss Drive Progressive β-lactam Resistance in Recurrent ESBL Enterobacteriaceae Bacteremia

BackgroundCarbapenem resistant Enterobacterales (CRE) remain urgent antimicrobial resistance threats. Approximately half of CRE clinical isolates lack carbapenem hydrolyzing enzymes and develop carbapenem resistance through alternative mechanisms. The purpose of this study was to elucidate the development of carbapenem resistance mechanisms from clonal, recurrent extended-spectrum {beta}-lactamase positive Enterobacterales (ESBL-E) bacteremia isolates in a vulnerable patient population. MethodsThis study investigated a historical, retrospective cohort of ESBL-E bacteremia cases in the University of Texas MD Anderson Cancer Center (MDACC) from January 2015 to July 2016. Phylogenetic and comparative genomic analyses were performed to identify clonal, recurrent ESBL-E isolates developing carbapenem resistance. Oxford Nanopore Technology (ONT) long-read and Illumina short-read sequencing data were used to generate consensus assemblies and to identify signatures of mobile genetic element mediated amplification and transposition of antimicrobial resistance genes. Serial passaging experiments were performed on a set of clinical ST131 ESBL-E isolates to recapitulate in vivo observations. qPCR and qRT-PCR were used to determine respective copy number and transcript levels of {beta}-lactamase genes. Results116 ESBL-E bacteremia cases were identified, 16 of which had documented recurrent infections. Four serial, recurrent isolates displayed a carbapenem resistant phenotype, three without the acquisition of a known carbapenemase. These three isolates had non-carbapenemase-producing CRE (non-CP-CRE) mechanisms driven by IS26- and ISEcp1-mediated amplification of respective translocatable units (TU) and transposition units (TPU) harboring both blaOXA-1 and blaCTX-M variants with concomitant outer membrane porin disruption. The TU and TPU structures inserted into the open reading frames of outer membrane porin genes in a subset of non-CP-CRE isolates. Serial passage of an index ST131 ESBL-E isolate under selective carbapenem exposure resulted in chromosomal amplification of modular, TUs harboring {beta}-lactamase genes with concomitant porin inactivation, recapitulating the in vivo carbapenem resistance progression. Long-read sequencing of two additional MDACC bacteremia strains identified similar non-CP-CRE mechanisms observed in the serial isolates. ConclusionsNon-CP-CRE de novo mechanisms were the primary driver of CRE development in recurrent bacteremia cases within this vulnerable patient population. The incorporation of long-read ONT data into AMR surveillance platforms is critical to identify high-risk CRE isolates that are difficult to identify with low-resolution phenotypic and molecular characterization methods.

genomics↗

bioRxiv2017

Staphylococcus aureus Colonization And Familial Transmission Over A One Year Period

Methods177 adults and 86 minors comprising 95 family units were enrolled from two counties in Iowa and followed up for 52 weeks. Random effects logistic regression was used to test the effect of different risk factors on the probability of an individual falling into a different S. aureus colonization categories. Additionally, the frequency of S. aureus colonization events and familial transmission events were calculated.\n\nResultsThe number of positive environmental sites within a participants house was associated with being a persistent carrier compared to being a non-carrier or intermittent carrier. Age, sharing bath towels, and the number of positive environmental sites within a participants house were associated with being a persistent or intermittent carrier. Colonization events per year were 3.95 for adults and 3.04 for minors. Duration of colonization was longest for persistent carriers (92.3 days for adults and 97.8 days for minors), and intermittent carriers had the most colonization events.\n\nConclusionsThe average duration of colonization was significantly different when comparing intermittent carriers and non-carriers. We have also established estimates of the duration of colonization and the frequency of transmission events among family units in a non-healthcare population.

epidemiology↗

bioRxiv2017

The Oropharynx As A Distinct Colonization Site For Staphylococcus aureus In The Community

BackgroundS. aureus is a frequent cause of hospital and community associated infections and colonization is known to increase the risk of infection, with the nares considered the most important colonization site.\n\nMethodsWe compared the prevalence of nasal and oropharyngeal carriage in a yearlong, prospective cohort study of people from the community as well as assessed risk factors for nares-only and oropharynx-only colonization.\n\nResultsColonization at both anatomical sites was correlated; however, oropharynx only carriage occurred and oropharyngeal swabs were more sensitive than nasal swabs at detecting carriage (77.27% and 72.725 respectively). Non-Caucasian race, having a greater number of people living in your home and more children in your home all significantly increased the odds of oropharynx-only carriage. Having S. aureus present on home environmental sites, exercising in a fitness center, and sharing bath towels all increased the odds of nares-only carriage.\n\nConclusionsOropharyngeal swabs increase the detection of S. aureus colonization in community embers.

epidemiology↗