Patel, Robin

Abstract Background Staphylococcus aureus is a challenging pathogen which causes a multiplicity of human diseases around the globe, acquired in the community and healthcare settings alike. Treatment of S. aureus infection can be challenging and is further compromised by antimicrobial resistance. Understanding of its pathogenesis, transmission pathways and the dynamics of its genome evolution and associated adaptations is incomplete. One strategy to assess genome evolution is to assess codon bias. Historically, studies have focused on the consequences of coding changes; assessing silent mutations in the form of synonymous codon usage bias represents a novel approach to studying genetic adaptation.Figure 1.Principal component analysis (PCA) (A) and sPLS-DA (B) separate S. aureus from complex mates.sPLS-DA component 1 relies on a hypothetical protein, identified here by its NCTC 8325 genomic coordinates, as important for separating S. aureus from complex mates (C). Methods Here, the codon bias of 2,872 genes was queried against all publicly available complete S. aureus plasmids and genomes. Using public BioSample data, genomes were sorted by disease state (e.g., bacteremia, pulmonary infection) and geographical collection site. Results Isolates from Nairobi, Kenya were most different from other isolates, suggesting that geographical isolation may shape codon bias signature. In addition, codon bias of two MSCRAMM proteins implicated in human disease - SdrC and FnBPB - varied between isolation sources, suggesting a role for codon bias in S. aureus genetic adaptation to selective pressures of infection. Additionally, codon bias out-performed coding and nucleic acid mutational metrics in separating members of the S. aureus complex, S. aureus, Staphylococcus argenteus, Staphylococcus schweitzeri, and Staphylococcus roterodami; Fig 1, sparse partial least squares analysis (sPLS-DA) mean AUC codon: 0.89762, nucleic acid: 0.82266, codon bias: 0.9996 (relying on hypothetical protein NC_007795.1:516850-517419). Conclusion This analysis suggests that codon bias in S. aureus is a source of genetic adaptation that can be used to separate strains by geographical isolation source, and separate S. aureus sensu stricto from other S. aureus complex members. Disclosures Nicholas Bedard, MD, Stryker: Advisor/Consultant Robin Patel, MD, a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection: a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection|MicuRx Pharmaceuticals and bioMérieux: Grant/Research Support|PhAST, Day Zero Diagnostics, DEEPULL DIAGNOSTICS, S.L., Nostics, HealthTrackRx, bioMérieux and CARB-X: Advisor/Consultant|Up-to-Date and the Infectious Diseases Board Review Course: Honoraria

Abstract Background Carbapenem-resistant Acinetobacter baumannii (CRAb) is a multi-drug resistant, opportunistic pathogen. Colistin is one of a few remaining treatment options, but resistance exists globally. Methods Between 2017 and 2019, 551 CRAb isolates were collected through the international Study Network of Acinetobacter as a Carbapenem-Resistant Pathogen (SNAP). Demographics, clinical characteristics, mortality, and a desirability of outcome ranking (DOOR) measure combining lack of clinical response, unsuccessful discharge, renal failure, and C. difficile infection, were recorded for each patient. A central laboratory measured colistin minimum inhibitory concentrations (MICs), and each isolate was classified as colistin-intermediate (MIC ≤2µg/mL) or resistant (MIC ≥4µg/mL). All isolates were sequenced on the Illumina platform, and the genomes were used to construct a phylogenetic tree and assess for variants within known colistin resistance-related genes. Results 18% of the 551 isolates were colistin-resistant. Compared to patients with colistin-intermediate isolates, patients with resistant strains were more likely to have been admitted from a healthcare facility, but otherwise had similar demographics and Charlson comorbidity indices. Focusing on patients with bloodstream or respiratory infections (n=217) uncovered increased 30-day mortality in patients with monomicrobial, colistin-resistant infections (11/19, p=0.008) when compared to monomicrobial-intermediate (41/102), polymicrobial-resistant (4/20) and polymicrobial-intermediate infections (18/76). Comparative genomics indicated that the majority of isolates belonged to clonal complex 2 (CC2), and that colistin resistance concentrated in certain genetic lineages. Variant analysis uncovered nonsynonymous mutations near and within the histidine kinase domain of pmrB, part of the PmrAB two-component system that regulates lipopolysaccharide modifications which can alter colistin susceptibility. Conclusion In this global cohort, patients with monomicrobial, colistin-resistant CRAb infections had increased mortality. New treatment options are needed for multidrug-resistant CRAb, and this study provides further evidence that pmrB may serve as a worthwhile drug development target. Disclosures Madison Stellfox, MD, PhD, Cumberland Pharmaceuticals: Grant/Research Support Robin Patel, MD, a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection: a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection|MicuRx Pharmaceuticals and bioMérieux: Grant/Research Support|PhAST, Day Zero Diagnostics, DEEPULL DIAGNOSTICS, S.L., Nostics, HealthTrackRx, bioMérieux and CARB-X: Advisor/Consultant|Up-to-Date and the Infectious Diseases Board Review Course: Honoraria David van Duin, MD, PhD, British Society for Antimicrobial Chemotherapy: Editor stipend|Merck: Advisor/Consultant|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Roche: Advisor/Consultant|Shionogi: Advisor/Consultant Yohei Doi, MD, PHD, GSK: Advisor/Consultant|Meiji Seika Pharma: Advisor/Consultant|Shionogi: Advisor/Consultant|Shionogi: Honoraria

Abstract Background Phage therapy has gained increasing interest as an approach to treat antimicrobial- resistant bacterial infections. Standardized, reproducible PST methods are needed to rapidly identify active phages for potential clinical use. Here, PST of 24 clinical isolates of carbapenem-resistant K. pneumoniae (CR-Kp) to 6 K. pneumoniae phages (3 from KlebPhaCol and 3 from phage hunting) was assessed using a plaque assay (PA) and a liquid assay (LA), and results compared. Phage Susceptibility Testing: Agreement Between Plaque Assay and Liquid Assay Methods For the PA, 2µL of 10−1-10−8 phage dilutions were spotted on bacterial laws of CR-Kp (double agar overlay), and plaques scored upon overnight incubation at 37°C [0 (no activity), 1+ (lysis from without), 2+ (concentration-dependent lysis), 3+ (clear plaques, small or medium size), 4+ (clear plaques of large size); scores ≥ 2+ were considered susceptible]. Testing was performed on 3 different days. If ≥ 2 replicates scored ≥ 2+, the result was classified as susceptible. For the LA, phages and bacteria were combined (MOI=10) in 96-well plates [phage-bacteria combinations (3 replicates), phage controls (106 PFU/mL), bacterial controls (BC, 105 CFU/mL), media sterility controls] and plates incubated at 37°C for 24h, with OD600 measured every 15 min. Hold time (HT) — delay in achieving inflection at the beginning of exponential growth phase — was calculated for phage-treated compared to BC wells. Testing was performed on 2 different days. Mean HT was computed for each phage-bacteria combination and results assessed as susceptible or not using cutoff HTs of 4h and 8h. Results Using a LA HT cutoff of 4h, there was complete agreement with results of the PA for 3 phages, and 96, 79 and 67% overall agreement for 3 other phages (Table). Using a LA HT cutoff of 8h, there was complete negative agreement for 4 phages, but lower overall agreement between the LA and PA (58-96%). Increased classification as susceptible by PA compared to LA was the main source of disagreement when using a LA HT cutoff of 8h. Conclusion Here, two PST assays were compared, and greater agreement was found when using a 4h compared to an 8h HT LA cutoff. These results represent a step forward in the standardization of PST methods, bearing in mind that correlation of results with pre-clinical and clinical outcomes is needed. Disclosures Robin Patel, MD, a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection: a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection|MicuRx Pharmaceuticals and bioMérieux: Grant/Research Support|PhAST, Day Zero Diagnostics, DEEPULL DIAGNOSTICS, S.L., Nostics, HealthTrackRx, bioMérieux and CARB-X: Advisor/Consultant|Up-to-Date and the Infectious Diseases Board Review Course: Honoraria

Abstract Background Staphylococci are the most frequent microorganisms in periprosthetic joint infection (PJI) and treatment remains challenging. Phage is being considered as a potential treatment. Here, the in vitro activity of phages SaMD07FSphi1or SaNSI1469phi1, alone and in combination with vancomycin against staphylococcal biofilms was evaluated. Figure 1 In vitro activity of phage SaMD07FSphi1 against S. aureus and S. epidermidis biofilms Figure 2 In vitro activity of phage SaNSI1469phi1 against S. aureus and S. epidermidis biofilms Methods Biofilms were grown at 37°C on 4 cm stainless steel K-wires in tryptic soy broth (TSB) with 106 cfu/ml of S. epidermidis or S. aureus (8 PJI isolates with phage activity against planktonically-grown bacteria). After 24 h, 3 K-wires were quantitatively cultured to define pre-treatment bacterial loads, with the remaining assigned to one of four treatment groups: TSB, phage (4 x 106 plaque forming units/ml), vancomycin (16 µg/ml) or phage/vancomycin. K-wires were incubated for 6 or 24 h at 37°C, rinsed, sonicated, and quantitatively cultured. Testing was performed in triplicate and on 3 separate days and mean log10 cfu/K-wire reduction factors (LRFs) versus TSB calculated. Results Phage SaMD07FSphi1 (Figure 1) plus vancomycin showed LRFs of 2.8 (p, 0.0003) and 2.3 (p, 0.0177) log10 cfu/K-wire at 24 h for S. aureus IDRL-6121 and S. aureus IDRL-8454, respectively, whereas phage alone showed was 3.1 (p, 0.0003) and 3.0 (p, 0.0003), respectively. All treatments were ≤1.0 log10 cfu/K-wire 24 h LRFs for S. aureus IDRL-6175, S. epidermidis IDRL-5966 and S. epidermidis IDRL-6108.This phage plus vancomycin showed LRFs of 0.6 log10 cfu/K-wire at 6 h for S. epidermidis IDRL-5966 and S. aureus IDRL-6175, with bacterial regrowth at 24 h. Phage SaNSI1469phi1 (Figure 2) plus vancomycin showed 24 h LRFs of 2.0 (p, 0.02) and 3.2 (p, 0.003) log10 cfu/K-wire for S. epidermidis IDRL-6955 and S. aureus IDRL-7299, respectively, whereas phage alone was 0.2 (p, 0.17) and 0.5 (p, 0.03) log10 cfu/K-wire, respectively. All treatments showed ≤1.0 log10 cfu/K-wire 24-hour LRFs log10 cfu/K-wire for S. epidermidis IDRL-10273. This phage alone showed 6 h LRFs of 1.0 and 1.3 for S. epidermidis IDRL-6955 and S. aureus IDRL-7299, with bacterial regrowth at 24 h. Conclusion Phages SaMD07FSphi1 and SaNSI1469phi1 alone and with vancomycin showed activity against staphylococcal biofilms formed by 4 isolates. Increased activity was observed at 6 h in some cases, with bacterial regrowth at 24 h. Disclosures Robin Patel, MD, a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection: a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication, a patent on PET imaging of bacterial infection|MicuRx Pharmaceuticals and bioMérieux: Grant/Research Support|PhAST, Day Zero Diagnostics, DEEPULL DIAGNOSTICS, S.L., Nostics, HealthTrackRx, bioMérieux and CARB-X: Advisor/Consultant|Up-to-Date and the Infectious Diseases Board Review Course: Honoraria

Abstract Background Streptococcus agalactiae (group B Streptococcus [GBS]) may cause pneumonia or may colonize the respiratory tract, making its clinical significance uncertain when detected in respiratory specimens. This study aimed to assess whether clinicians interpreted GBS detected by the BIOFIRE Pneumonia Panel (BF-PP) as a pathogen implicated in pneumonia. Methods This retrospective cohort study included adult patients hospitalized with suspected pneumonia at Mayo Clinic, Rochester, between September 2020 and February 2025. Cases were independently classified into pathogen and nonpathogen groups by 2 infectious diseases (ID) specialists, with a third reviewer resolving disagreements. Clinical characteristics and outcomes of both groups were recorded. A subgroup analysis of patients who had an ID consultation was performed. Results A total of 109 cases were included. GBS was considered a pneumonia pathogen in 47.7% of cases and a nonpathogen in 52.3%. ID consultation was performed in 33.0% of cases, with GBS considered a pathogen in 30.6% of those. Common comorbid conditions included pulmonary, gastrointestinal, neurologic, and cardiovascular disease and obesity. Rates of endotracheal intubation were similar in the pathogen and nonpathogen groups (51.9% vs 50.9%, respectively), with the in-hospital mortality rate being numerically but not significantly higher in the former versus the latter (21.2% vs 14.0%; P = .33); findings were similar in the ID-assessed subgroup. In 76.1% of GBS detections, other microorganisms—most commonly Staphylococcus aureus—were codetected. Only 10.2% of BF-PP GBS-positive specimens were culture positive for GBS. Conclusions While GBS is not an uncommon pneumonia pathogen, the clinical significance of its detection by BF-PP is uncertain in many cases.

37 cases of Mycoplasma pneumoniae pneumonia were diagnosed in children in North Dakota, over 3.5 months (35 by PCR); 44% harbored macrolide-resistance. Children with macrolide-resistant M. pneumoniae had a longer period of coughing prior to diagnosis (+ 3.9 days, p=0.048), a longer duration of illness (+ 5.4 days, p=0.011) and earlier resolution of fever after initiation of doxycycline (- 0.92 days, p=0.025) compared to those without macrolide resistant M. pneumoniae.

Background: Phages are being assessed for treatment of periprosthetic joint infection (PJI). Staphylococci are the most common cause of PJI. Phages are traditionally considered to be strain-specific and restricted to specific species. We aimed to assess the in vitro activity of a collection of staphylococcal phages against a selection of clinical Staphylococcus isolates recovered from PJI over a 20-year period. Methods: The activity of 37 staphylococcal phages was evaluated against 204 staphylococcal isolates, including 102 Staphylococcus aureus, 81 Staphylococcus epidermidis , and 21 Staphylococcus lugdunensis , using a tetrazolium dye–based metabolic assay. Standardized inocula of bacteria and phage were incubated over 48 hours. Growth inhibition ≥8 hours was considered indicative of phage activity. Results: A total of 7,548 phage-isolate pairs were assessed. Overall, 31 of 37 phages had activity against at least 1 isolate. The most broadly active phage showed activity against 50 of 195 isolates (26%) tested. Twenty-three phages showed cross-species activity, with 11 phages active against all 3 Staphylococcus species, and 12 phages active against 2 species. Of all S. aureus isolates tested, 61% were susceptible to at least 1 phage, while 31% and 76% of S. epidermidis and S. lugdunensis isolates were susceptible to at least 1 phage, respectively. Conclusions: This is the largest library of phages evaluated against staphylococci from PJI. Results show that staphylococcal phages can have cross-species activity, suggesting that phage libraries may offer cross-species coverage of clinically encountered staphylococcal isolates from PJI. Level of Evidence: Level V . Mechanism-based reasoning. See Instructions for Authors for a complete description of levels of evidence.

Three previously uncharacterized bacterial species, designated strains BD586 T , BD613 T and BD626 T , isolated from human clinical specimens, were identified at Mayo Clinic, Rochester, Minnesota, USA. Initial identification efforts using matrix-assisted laser desorption ionization-time-of-flight MS and partial 16S rRNA gene sequencing proved inconclusive. Comprehensive analysis involving phenotypic characterization, biochemical assays and whole-genome sequencing was undertaken. The isolates were Gram-negative, motile, facultatively anaerobic rods, occurring singly, in pairs and in short chains; BD613 T additionally formed small aggregates. The isolates tested positive for catalase and negative for oxidase. Their colonies appeared smooth, white, opaque and non-haemolytic. Growth was observed at 35 °C under aerobic, anaerobic and CO₂-enriched conditions, as well as in media with NaCl concentrations up to 10% and at pH 7-9. Phylogenetic relationships were inferred from core gene alignments, average nucleotide identity and digital DNA–DNA hybridization comparisons. Results confirmed the placement of BD586 T , BD613 T and BD626 T within the recently established Dryocola genus, while also indicating their novelty as distinct species. The major cellular fatty acids were C 16:0 and C 17:0 cyclo. Based on these findings, a formal description of three new species, Dryocola mayonis sp. nov. (type strain BD586 T =TSD 474 T , =NCTC 15089 T , =DSM 119465 T ), Dryocola sharpae sp. nov. (type strain BD613 T =TSD 475 T , =NCTC 15090 T , =DSM 119466 T ) and Dryocola baronae sp. nov. (type strain BD626 T =TSD 476 T , =NCTC 15091 T , =DSM 119479 T ), is proposed, and the genus description of Dryocola is emended to refine its genomic, morphological and chemotaxonomic boundaries.

ABSTRACT The genomic sequences of seven phages isolated from municipal sewage in Rochester, Minnesota, USA, using Klebsiella pneumoniae strains ( bla KPC carriers) as hosts are reported. These phages are lytic and belong to the Ackermannviridae, Drexlerviridae , and Zobellviridae families. No known antimicrobial resistance or virulence genes were found within their genomes.

ABSTRACT Biofilms hinder wound infection healing, making wound infections a healthcare challenge for which innovative treatments are needed. A 1.77 cm 2 electrochemical bandage (e-bandage), which generates the biocide hypochlorous acid (HOCl), has shown promising anti-biofilm activity in vitro , ex vivo , and in vivo . The e-bandage is a three-electrode system operationalized by a hydrogel. In addition to providing a conductive electrolyte for the electrodes, the hydrogel provides a protective barrier for the wound. How different hydrogels impact e-bandage functionality is not completely defined. Here, the in vitro activity of seven clinically available hydrogels (xanthan gum, 3M, Duoderm, Prontosan, Purilon, Skintegrity, and Solosite) was evaluated with 1.77 cm 2 HOCl-generating e-bandages using a potentiostat with a multiplexer in a membrane biofilm model against methicillin-resistant Staphylococcus aureus IDRL-6169 and Acinetobacter baumannii ATCC-17978. When applied with polarized HOCl-producing e-bandages, all evaluated hydrogels except Solosite yielded ≥5.5 log 10 CFU/cm 2 reductions in bacterial quantities after 6 h of treatment, with most being below the detection limit at that time point. Prontosan exhibited antibacterial activity independent of e-bandage. Results of this study inform the selection of clinically available hydrogels that may be suitable for use with a 1.77 cm 2 HOCl-producing e-bandage. IMPORTANCE In this study, it was shown that some clinically available hydrogels, combined with a 1.77 cm 2 HOCl-generating electrochemical bandage, deliver time-dependent antimicrobial activity against methicillin-resistant Staphylococcus aureus and Acinetobacter baumannii biofilms, offering a potential approach to treat wound infections, including those caused by antimicrobial-resistant bacteria.