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Antimicrobial Agents and Chemotherapy

American Society for Microbiology

Preprints posted in the last 30 days, ranked by how well they match Antimicrobial Agents and Chemotherapy's content profile, based on 167 papers previously published here. The average preprint has a 0.11% match score for this journal, so anything above that is already an above-average fit.

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Mechanisms involved in cefiderocol resistance in French Pseudomonas aeruginosa clinical strains

GAUTHIER, E.; PISANI, M.; BOUR, M.; GROSJEAN, M.; Plesiat, P.; SAFARI, S.; Hartkoorn, R. C.; SOURO, L.; Pretot, E.; Jeannot, K.

2026-04-16 microbiology 10.64898/2026.04.12.718081 medRxiv
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Cefiderocol exhibits excellent in vitro activity against Pseudomonas aeruginosa; however, resistance can emerge. We investigated the molecular mechanisms underlying cefiderocol resistance (MIC >2 mg/L) in 103 clinical strains collected from 61 hospitals (2021-2024). MICs ranged from 4 to >128 mg/L, with 39.8% of strains showing MICs >8 mg/L. Although 37.8% were classified as difficult-to-treat resistant (DTR), acquired {beta}-lactamases were detected in 72.8% of strains, including carbapenemases (39.8%), mainly NDM-1 (29.1%), and Extended Spectrum {beta}-Lactamases (ESBLs) (38.8%). Cloning of 11 {beta}-lactamases into pUCP24, including the acquired cephalosporinase PAC-1 and ESBLs (VEB-1, and VEB-9), resulted in marked increases in cefiderocol MICs (up to 128-fold). Introduction of 6 mutations in the PDC enzyme into a PAO1{Delta}blaPDC-1 background increased MICs up to 4 mg/L and conferred cross-resistance to ceftolozane/tazobactam, notably F121L, G157D, T70I, and E219K. Alterations in siderophore transporters or regulators were identified in 38.8% of strains, most frequently a PirR frameshift (R132fs), consistent with PirR inactivation, which was confirmed in the PAO1 strain to contribute to cefiderocol resistance. Overall, cefiderocol resistance in clinical strains is multifactorial, mainly involving acquired {beta}-lactamases (ESBLs, carbapenemases) and impaired siderophore uptake (PiuA/PiuD, PirA, PiuC), leading to high-level resistance (>8 mg/L). The polyclonal distribution and diversity of mechanisms highlight the need for routine susceptibility testing and surveillance. Detection of NDM producers is critical, as cefiderocol should be used with caution in this context.

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Rv0783c of Mycobacterium tuberculosis acts as a proton-motive force dependent multidrug efflux transporter involved in the efflux of structurally unrelated antibiotics and enhancing biofilm formation

Bhattacharyya, D.; Chatterjee, D.; Panda, A. P.; Ghosh, A. S.

2026-04-01 microbiology 10.64898/2026.04.01.715825 medRxiv
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Despite multiple treatment strategies and extensive research on resistance mechanisms, tuberculosis (TB) remains a major global health threat, largely because of the rise of multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. Among various mechanisms complicating the situation, active antibiotic export via efflux pumps is particularly significant, yet largely unexplored. Mycobacterium sp. encodes numerous transporters, many of which are overexpressed in clinical isolates or under drug stress. Here, we examined the possible role of Rv0783c, a putative transporter that is reportedly overexpressed in drug-stressed conditions. Rv0783c conferred resistance to multiple structurally diverse antibiotics, fluoroquinolones and anti-TB drugs in the heterologous hosts, namely, Escherichia coli and Mycobacterium smegmatis. Reduced drug accumulation and active efflux of ethidium bromide (EtBr) confirmed its transport activity, which in turn gets nullified upon using the proton-motive force blocker, CCCP. On the other hand, its expression enhanced biofilm formation, linking antibiotic resistance to persistence-associated phenotype. Furthermore, site-directed mutagenesis confirmed the presence of crucial interacting residues with antibiotics that were identified by in silico analysis. Overall, we demonstrate the role of Rv0783c in the extrusion of first and second-line anti-TB drugs and enhancing biofilm formation.

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Does Infection Progression of Mycobacterium abscessus Depend on Sex, Age, and Mouse strain?

Rima, M.; Chauffour, A.; Tournebize, R.; Poignon, C.; Coradin, T.; Aubry, A.; Veziris, N.

2026-03-30 microbiology 10.64898/2026.03.25.714167 medRxiv
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The lack of a reliable chronic murine model limits drugs evaluation against Mycobacterium abscessus. Models show discrepancies, especially regarding host factors (mouse strain, sex and age). Using beads-model, we compared BALB/cJRJ and C57BL/6NCrl across sexes and ages. BALB/cJRJ showed more sustained infection and lower variability, with no significant sex- or age-related differences. Considering these results and the higher prevalence of NTM pulmonary infections in female patients, 5-6 weeks-old female BALB/cJRJ are appropriate for M. abscessus beads-model.

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Potential Efficacy of Streptomycin in Amikacin-resistant Mycobacterium avium-intracellulare complex Pulmonary Disease

Kodama, T.; Morimoto, K.; Murase, Y.; Aono, A.; Furuuchi, K.; Fujiwara, K.; Ito, M.; Ohe, T.; Watanabe, F.; Chikamatsu, K.; Yoshida, S.; Minato, Y.; Tanaka, Y.; Hiramatsu, M.; Shiraishi, Y.; Yoshiyama, T.; Mitarai, S.

2026-04-05 respiratory medicine 10.64898/2026.04.03.26350100 medRxiv
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Aminoglycoside drugs, amikacin, streptomycin, and amikacin liposome inhalation suspension are crucial for treating refractory Mycobacterium avium-intracellulare complex pulmonary disease. In Mycobacterium tuberculosis, cross-resistance occurs between amikacin and kanamycin, but not between amikacin and streptomycin in genetic drug susceptibility testing. However, the occurrence of cross-resistance among aminoglycosides remains unclear in M. avium-intracellulare complex. We aimed to evaluate cross-resistance among aminoglycosides to determine whether streptomycin or kanamycin remains effective after the development of amikacin resistance. This single-center retrospective study included 20 patients with amikacin-resistant M. avium-intracellulare complex harboring rrs mutations. Paired analyses of streptomycin and kanamycin minimum inhibitory concentration values before and after amikacin resistance development were performed. In addition, streptomycin- and kanamycin-resistant strains were generated in vitro and resistance-associated mutations were identified using whole-genome sequencing. No significant increase was observed in streptomycin minimum inhibitory concentration values following amikacin resistance. In contrast, kanamycin values uniformly increased to >256 g/mL after the acquisition of amikacin resistance. Furthermore, amikacin- and kanamycin-resistant isolates shared mutations at position 1408 in the rrs gene, whereas streptomycin-resistant isolates exhibited mutations at position 20 in the rrs gene. These results suggest that amikacin and kanamycin exhibit cross-resistance in M. avium-intracellulare complex, whereas amikacin and streptomycin may not. Two cases in our cohort in which streptomycin treatment was effective after the acquisition of amikacin resistance further support these findings. In conclusion, streptomycin may be a potential therapeutic alternative for amikacin-resistant M. avium-intracellulare complex pulmonary disease. Future studies correlating streptomycin minimum inhibitory concentration values with clinical outcomes are required.

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HIV-1 Reverse Transcriptase interactions with Long-acting NNRTI, Depulfavirine (VM1500A)

Snyder, A. A.; Kaufman, I. L.; Risener, C. J.; Kirby, K. A.; Sarafianos, S. G.

2026-04-07 biochemistry 10.64898/2026.04.06.715899 medRxiv
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Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are key components of combination antiretroviral therapy (ART) for the treatment of human immunodeficiency virus type 1 (HIV-1) infection, binding an allosteric pocket of reverse transcriptase (RT) and inhibiting viral replication. Although second-generation NNRTIs have improved potency and resistance profiles compared to first-generation NNRTIs, the continued emergence of resistant viral strains and the need for long-acting therapeutic options underscore the importance of developing next-generation compounds. Depulfavirine (VM1500A) is a potent NNRTI being developed as a long-acting formulation. Its prodrug, elsulfavirine (ESV), is approved for HIV-1 treatment in Eurasian countries as a once-daily oral regimen and has demonstrated favorable antiviral efficacy, pharmacokinetics, and tolerability in clinical studies. Here, we report the 2.4 [A] crystal structure of HIV-1 RT in complex with depulfavirine, revealing an extended binding conformation within the NNRTI pocket that reaches from the back of the binding pocket to the entrance. These interactions may shed light on mechanisms of resistance to the F227C mutation, with and without V106 substitution, and Y188L. Notably, depulfavirine maintains potent inhibition of common NNRTI-resistant RT variants, including K103N and Y181C. Combination studies of ESV with antivirals from diverse inhibitor categories demonstrated additive or near-synergistic activity with islatravir (ISL), cabotegravir (CAB), lenacapavir (LEN), and tenofovir (TDF). These findings highlight the broad resistance profile and potential of the depulfavirine combination.

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In silico structural analysis of EthA substitutions for ranking priority mutations leading to ethionamide resistance in Mycobacterium tuberculosis

Machado, R. F.; Cardoso, S. L.; Pinheiro, I. C.; Ramos, J. P.; Antunes, C.; Capriles, P.; Galvao, T. C.

2026-04-17 molecular biology 10.64898/2026.04.16.718980 medRxiv
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BackgroundTuberculosis (TB) is the second-leading cause of deaths from infectious agents and remains a global health threat. Ethionamide (ETH) is a prodrug used in regimens for multidrug-resistant TB, and, partly due to side effects that can lead to low treatment adhesion, resistance arises. Changes in EthA, the monooxygenase that activates ETH, are the main mechanism of resistance. Yet, of hundreds of EthA substitutions found in resistant isolates, only a handful have been annotated as resistance determinants. ResultsAn in silico analysis was carried out on a previously described panel of Mycobacterium tuberculosis clinical isolates for which genomes and ETH susceptibility testing results were available. EthA substitutions were mapped, revealing the existence of hotspots in its sequence. Visualization of the hotspots in the EthA structural model shows that they cluster in three regions, including ligand binding pockets. Models were built of twenty-three variants found in resistant isolates and changes in local configuration was mapped to identify investigate impact on ETH activation. Information from these models contributed to establishing five criteria for scoring whether substitutions are most likely to lead to resistance. Using these criteria, EthA D58G was selected and its expression is shown to increase growth in high ETH concentrations. ConclusionFunctionally relevant regions of EthA are revealed and point out priority substitutions for functional studies, enhancing identification and detection of substitutions not been previously associated with resistance.

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Commonly prescribed medicines antagonise anti-MRSA antibiotics and select for resistance

Douglas, E.; Edwards, A. M.; claireaux, H.; Sohail, Z.

2026-04-01 microbiology 10.64898/2026.03.31.715408 medRxiv
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Many commonly prescribed non-antibiotic medicines have off-target antimicrobial activity, yet their impact on antibiotic efficacy remains poorly understood. In this study, we investigated eight widely used UK prescription medicines and identified simvastatin, amlodipine, and fluoxetine as growth inhibitory towards methicillin-resistant Staphylococcus aureus (MRSA). These drugs disrupt bacterial membranes, with amlodipine and fluoxetine also triggering stress responses linked to cell wall and membrane damage. Further mechanistic analysis using transposon mutant screening revealed that simvastatin impairs cell wall synthesis by inhibiting the mevalonate pathway. Notably, checkerboard assays demonstrated antagonistic interactions: simvastatin reduced the efficacy of {beta}-lactams and vancomycin, amlodipine with vancomycin and daptomycin, and fluoxetine with vancomycin activity. Prolonged exposure to these drugs also accelerated resistance development to vancomycin and daptomycin. Together, these findings underscore the potential for commonly prescribed non-antibiotic medicines to undermine antibiotic therapy, warranting further study given the rising S. aureus treatment failures.

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Novel regimens for treatment of Mycobacterium avium lung disease based on advanced in vitro systems and the mathematics of basis functions

Srivastava, S.; Singh, S.; Boorgula, G. D.; McShane, P. J.; Gumbo, T.

2026-03-31 microbiology 10.64898/2026.03.30.715241 medRxiv
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Azithromycin plus ethambutol plus rifabutin (azithromycin-ethambutol-rifabutin) is the standard-of-care (SOC) for Mycobacterium avium-complex lung disease. The SOC achieves sustained sputum culture conversion in only 43-53% of patients, after an average of 18 months of therapy. Recent quantitative analyses ranked omadacycline, ceftriaxone, and minocycline highest for microbial kill. Azithromycin-minocycline-ethambutol, azithromycin-omadacycline-ethambutol, epetraborole-omadacycline-ethambutol, ceftriaxone-omadacycline-rifabutin, and the SOC were compared in the intracellular hollow fiber system model of M. avium lung disease (HFS-MAC). HFS-MAC units were treated once daily for 28 days to mimic the intrapulmonary pharmacokinetics of each drug. The ceftriaxone concentrations measured in the HFS-MAC were only 1% of those achieved in the lung by standard clinical doses. Changes in the bacterial burden were described using basis functions (BF). For liquid cultures, BF 1 (BF1) was described by a linear regression-based slope, with steepest kill slope (95% Confidence interval) of 7.87 (1.52 to14.23) by ceftriaxone-omadacycline-rifabutin versus 1.04 (-0.84 to 2.92) for SOC. For the CFU/mL readout, the BF1 steepest non-linear kill slope was for ceftriaxone-omadacycline-rifabutin of 0.55 (0.35 to 0.98) log10 CFU/mL/day versus 0.16 (0.07 to 0.25) log10 CFU/mL/day for the SOC. Thus, ceftriaxone-omadacycline-rifabutin is potentially better than the SOC, even though further ceftriaxone dose optimization is required. BF2 described rebound growth and drug-resistant subpopulation growth, and demonstrated that contrary to popular belief, SOC rebound was best explained by ethambutol-resistance (r2>0.99, p=0.01) and not by azithromycin-resistance (r2=0.27, p=0.32), questioning ethambutols role in the SOC. The BF framework is potentially easy to adapt for modeling other anti-infective agents across many infectious diseases.

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The structure-interaction model of polymyxin lipopeptides with human oligopeptide transporter 2

Jiang, X.; Luo, Y.; Azad, M. A. K.; Xu, L.; Xiao, M.; Velkov, T.; Roberts, K. D.; Thamlikitkul, V.; Zhou, Q. T.; Zhou, F.; Li, J.

2026-04-02 biochemistry 10.64898/2026.04.01.715775 medRxiv
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BackgroundMultidrug-resistant (MDR) Gram-negative bacteria have triggered a critical global health crisis. Polymyxin lipopeptide antibiotics are used as a last-line therapy against these problematic pathogens, but their clinical use is largely limited by severe nephrotoxicity. Human oligopeptide transporter 2 (hPepT2) is a membrane transporter mediating the reabsorption of polymyxins in renal proximal tubular cells, substantially contributing to their nephrotoxicity. However, it remains unclear how polymyxins interact with hPepT2. MethodsIn this study, we investigated the structure-interaction relationship (SIR) of polymyxins with hPepT2 by integrating computational, chemical and cell biology approaches. Bioinformatic modelling predicted the residues essential for the binding of polymyxins with hPepT2. Transporter mutagenesis and molecular analysis were employed to explore the role of each residue in the interaction of hPepT2 and polymyxins. Moreover, we synthesised a series of polymyxin-like analogues with altering the moieties that are critical for binding with hPepT2. The antibacterial activity and nephrotoxicity of these analogues were subsequently assessed. ResultsOur bioinformatic modelling proposed an outward-facing structure of hPepT2 with a possible transport pathway that polymyxins bind to the lateral opening site of hPepT2 (e.g. E214, D215, D317, D342, E622). Molecular assays for transporter function and expression confirmed that D215 residue of hPepT2 is critical for polymyxin binding, while several other residues significantly impact on transporter turnover rate and/or protein expression. Our experimental validations showed that the lipopeptide analogues with altering the Dab1, Dab3, Dab5 and Dab9 moieties of polymyxins demonstrated decreased interactions with hPepT2. Among these synthetic analogues, alanine substitution at Dab3 showed reduced nephrotoxicity in mice while reserved antibacterial activity against a range of bacterial strains. ConclusionsOverall, this proof-of-concept study demonstrated that the computationally predicted and experimentally validated polymyxin-hPepT2 SIR model provides a viable approach for the discovery of novel, safer lipopeptide antibiotics.

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Application of Engineered NK-92 Cell Extracellular Vesicles in the Treatment of Systemic Lupus Erythematosus

Sun, Y.; Tang, Z.; Guo, M.; Zhai, Z.; Wu, Z.; Wang, X.; Li, F.; An, W.; Dou, X.

2026-04-15 synthetic biology 10.64898/2026.04.14.718139 medRxiv
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IntroductionSystemic Lupus Erythematosus (SLE) is a chronic autoimmune disease characterized by loss of immune tolerance, autoantibody production, and multi-organ damage. Current therapies, including glucocorticoids and CAR-T/CAR-NK cell therapies, are limited by adverse effects, high cost, and safety concerns. ObjectivesTo develop engineered NK-92 cell-derived extracellular vesicles displaying CD19 single-chain variable fragment (V-CD19-Exo) and evaluate their therapeutic efficacy in an MRL/lpr mouse model of SLE. MethodsThe CD19scFv-LAMP-2B fusion construct was stably expressed in NK-92 cells via lentiviral transduction. Extracellular vesicles were isolated by differential centrifugation and characterized by NTA, TEM, and Western Blot. In vivo efficacy was assessed in MRL/lpr mice through B cell depletion analysis, renal function monitoring, cytokine profiling, autoantibody detection, and survival observation. ResultsV-CD19-Exo significantly reduced splenic CD19{square}CD20{square} B cells from 10.53% to 1.51% (p < 0.0001). Treatment attenuated proteinuria, ameliorated lupus nephritis pathology, reversed splenomegaly, and downregulated serum IgE, IL-17A, IFN-{gamma}, anti-dsDNA, and ANA levels. Notably, V-CD19-Exo improved survival to approximately 80% compared to 25% in untreated controls. ConclusionEngineered NK-92 cell-derived extracellular vesicles represent a novel, safe, and effective cell-free therapeutic strategy for SLE, offering advantages over conventional cell therapies including lower immunogenicity, scalable production, and no requirement for lymphodepletion.

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Levosimendan inhibits HIV-1 infection in myeloid cells in the RIOK1-dependent manner

He, J.; Ma, J.; Park, Y.; Zhou, D.; Wang, X.; Fiches, G. N.; Shanaka, K. A.; Lepcha, T. T.; Liu, Y.; Eleya, S.; Santoso, N. G.; Ho, W.-Z.; Zhu, J.

2026-04-09 microbiology 10.64898/2026.04.08.717218 medRxiv
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Despite of the highly potent antiretroviral therapies, HIV-1 establishes persistent infection and causes chronic inflammation in AIDS patients. Beyond CD4+ T cells, HIV-1 infects myeloid cells, including circulating monocytes and tissue-resident macrophages, and integrates with host genomes to form stable viral reservoirs. To achieve a functional HIV cure, latency-promoting agents (LPAs) have been developed for the "block-and-lock" strategy to reinforce deep HIV-1 latency and permanently silence proviruses. However, most LPAs have been tested mainly in CD4+ T cells, and their efficacy in myeloid cells remains unclear. In this study, we reported that levosimendan (LSM), a drug approved for clinic use to treat heart failures, is able to inhibit HIV lytic infection and reactivation in myeloid cells. LSM blocked viral lytic reactivation in HIV-1 latently infected monocytic cells (TH89GFP, U1) and microglial cells (HC69). LSM also inhibited HIV infection in human induced pluripotent stem cell (iPSC) derived microglia (iMG), primary human resident liver macrophages (Kupffer cells) as well as human monocyte-derived macrophages (MDMs). Furthermore, we demonstrated that overexpression of a predicted drug target of LSM, the conserved serine/threonine kinase RIOK1 (RIO kinase 1), overcomes LSMs anti-HIV effect. Overall, our studies concluded that LSM is a promising LPA to inhibit HIV-1 infection in myeloid cells in the RIOK1-dependent manner.

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Secretome-Mediated Antimicrobial and Immunomodulatory Activity of Lactobacillus johnsonii Against Multidrug-Resistant Enteroaggregative Escherichia coli

VASAMSETTI, S. M.; G L, M.; Khaderbad, Y.; Gupta, A.; Morampudi, V.

2026-04-03 microbiology 10.64898/2026.04.02.716048 medRxiv
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Enteroaggregative Escherichia coli (EAEC) is a leading cause of persistent diarrhea in children in low- and middle-income countries, and the emergence of multidrug-resistant (MDR) strains necessitates non-antibiotic therapeutic strategies. This study evaluates Lactobacillus johnsonii, previously characterized by our group, as a probiotic candidate against a clinically confirmed MDR EAEC isolate resistant to ampicillin, ciprofloxacin, azithromycin, amoxicillin, and gentamicin. L. johnsonii demonstrated robust gastrointestinal resilience, high cell surface hydrophobicity, phenol tolerance, and rapid autoaggregation reaching 80.4 {+/-} 2.3% by 4 hours, collectively supporting mucosal colonization potential. In antimicrobial assays, L. johnsonii produced zones of inhibition against MDR EAEC substantially exceeding those of gentamicin, reduced viable biofilm-associated EAEC by over 80%, and displaced pre-adhered EAEC from HCT-116 intestinal epithelial cells in a time-dependent manner. L. johnsonii also attenuated MDR EAEC-induced gas production and reduced nitric oxide levels by 67.7% in infected RAW 264.7 macrophages, suggesting immunomodulatory activity. Nutrient competition did not appear to contribute to EAEC suppression under tested conditions, indicating inhibition is predominantly secretome-dependent. Fractionation of the L. johnsonii cell-free supernatant by fast protein liquid chromatography yielded five fractions below 75 kDa; fractions S5 and S6 exhibited sustained bactericidal activity at 6 hours. Gram staining confirmed that both fractions reduced viable EAEC cell numbers, with S6 producing a greater reduction than S5, indicating quantitatively distinct bactericidal potencies. These in vitro findings support the potential of L. johnsonii as a biotherapeutic candidate for antibiotic-resistant enteric infections. In vivo validation and chemical characterization of active fractions remain important next steps.

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Proviral dynamics and HIV-1C viral diversity in the context of HIV-TB co-infection

Bhowmick, S.; Bhagat, S.; Yadav, S.; Kadam, K.; Kamble, P.; Shrivas, S.; Devadiga, P.; Kaginkar, S.; Padwal, V.; Neman, N.; Musale, S.; Mohite, N.; Nagar, V.; Patil, P.; Agrawal, S.; Gaikwad, S.; Shastri, J.; Mukherjee, N.; Munne, K.; Bhor, V. M.; Madan, T.; Sutar, J.; Bhattacharya, J.; Patel, V.

2026-04-08 microbiology 10.64898/2026.04.08.712756 medRxiv
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BackgroundART effectively suppresses HIV replication and restores CD4+ T cells; however, long-lived HIV latent reservoirs enable viral persistence. Tuberculosis (TB) co-infection further impacts HIV latency and enhances viral replication. Given the high prevalence of latent TB infection (LTBI) in TB-endemic settings, understanding its impact on HIV biology is critical. Our study aims to investigate the influence of TB co-infection on HIV reservoir dynamics, viral diversity, and drug resistance mutations in ART-naive individuals. MethodologySamples from 90 ART-naive HIV-1C individuals, stratified based on IGRA and TB diagnosis, were used in this study. Plasma and PBMCs were isolated for viral RNA and DNA extraction respectively. Total proviral DNA was quantified using gag PCR. Full-length env and pol genes were amplified, purified and sequenced using ONT and Illumina platforms. Pol sequences were subjected to Drug Resistance Mutation (DRM) analysis via Stanford HIVdb with a minimum threshold mutation frequency of [&ge;]10%. Full length env sequences were used for phylogenetic analysis by aligning with Indian Subtype C reference sequence and phylogenetic tree was generated using ggplot2. ResultProviral load analysis showed no significant differences across HIV+LTBI-, HIV+LTBI+, and HIV+TB+ groups, although a trend toward higher levels was observed in HIV+TB+ individuals. Correlation analysis revealed distinct immune associations, with HIV+LTBI+ individuals showing positive correlations with activation and PD-1 expression. Longitudinal analysis of proviral loads demonstrated a modest decline in proviral load post-ART but remained persistent for up to 18-20 months following initiation of ART accompanied by low level ongoing viral replication. DRM analysis revealed a 33% prevalence in ART-naive individuals, with higher occurrence in HIV+LTBI+ group. Of the identified DRMs, 38% (5/13) and 71% (5/7) in sequences obtained from PBMC and plasma respectively were attributed to polymorphic mutations associated with Integrase strand transfer inhibitors (INSTIs). DRMs within plasma and PBMC derived viruses showed high concordance. Phylogenetic analysis of env sequences indicated overlapping viral populations between the 3 groups, with greater diversity in PBMCs compared to plasma. ConclusionThe study highlights that HIV reservoir dynamics, drug resistance, and viral diversity are significantly influenced by TB co-infection. While proviral loads were comparable, LTBI-associated immune activation and granuloma niches may have driven viral diversification and DRM emergence. High concordance between compartments and presence of transmitted resistance underscore the need for baseline screening, multi-compartment analysis, and sustained surveillance.

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Retinal Pigment Epithelium Injury in Pentosan Polysulfate Exposure: Morphologic Changes, Phagocytic Deficits, and Mitochondrial Dysfunction

Rajagopalan, A.; Satyanarayana, G.; Kumpakha, R.; Shiromani, S.; Boatright, J.; Jain, N.; Datta, S.

2026-03-31 molecular biology 10.64898/2026.03.28.715018 medRxiv
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Pentosan polysulfate (PPS) is a semisynthetic sulfated polysaccharide that was approved by the United States Food and Drug Administration (FDA) for treatment of interstitial cystitis (IC). A 2018 study by our group described a vision-threatening macular toxicity associated with long-term use of PPS. However, given the relatively recent characterization of PPS maculopathy, we have limited knowledge of its pathophysiology. The present study therefore investigated the pathophysiology of PPS maculopathy in a cell culture model, assessing impacts of PPS exposure on morphology and mitochondrial function. We treated ARPE-19 cells with increasing doses of PPS and investigated both mitoprotective and cytoprotective mechanisms, mitochondrial reactive oxygen species production (ROS) and respiration, cellular structure, and retinal pigment epithelium (RPE) dysfunction through phagocytosis assays. We found that PPS increased mitochondrial superoxide accumulation and that increased doses of PPS impaired basal and maximal respiration in a Seahorse assay without the expected response of increases in the cellular energy sensor pAMPK. PPS exposure disrupted mitochondrial and cell protective mechanisms against ROS accumulation as assessed through examination of mitochondrial biogenesis markers PGC-1 and SIRT1 and autophagy markers LC3 and p62. PINK1 expression increased with increasing duration of exposure to PPS. Further, we found that PPS led to functional and structural changes to RPE cells, which exhibited an increase in cell aspect ratio and impaired phagocytosis with higher doses of PPS. Lastly, we found an increase in cell death in response to higher doses of PPS, evident through ethidium homodimer cell viability assays. Taken together, our study shows PPS exposure has profound effects on RPE viability and function through impairment of mitochondrial respiration and mito- and cyto-protective mechanisms and highlights mitochondrial insult as a potential focus of future PPS research.

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Economic value of resistance-guided gonorrhea treatment: cost-neutrality thresholds for resistance test pricing in the United States

Nichols, B. E.; Wonderly Trainor, B.; Hampson, G.; Grad, Y. H.; Klausner, J. D.

2026-04-07 health economics 10.64898/2026.04.07.26350302 medRxiv
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Background: Rising antimicrobial resistance in Neisseria gonorrhoeae threatens the effectiveness of existing therapies. Resistance-guided treatment (RGT) may reduce treatment failures, complications, and inappropriate use of last-line agents while slowing resistance emergence. Methods and Findings: We developed an individual-level stochastic simulation model of gonorrhea diagnosis and treatment in the United States, incorporating infection prevalence, symptom status, diagnostic accuracy, resistance profiles, treatment pathways, and partner management (costs in 2025 USD). We evaluated three resistance testing strategies, ciprofloxacin-only, ciprofloxacin+ceftriaxone, and triple-target (including a novel drug A), across a wide range of resistance scenarios. We quantified economic value across three dimensions: (1) per-episode direct medical cost savings, (2) system-level costs attributable to ceftriaxone resistance emergence among MSM, and (3) avoided costs of new antibiotic development, estimating the maximum per-test price at which RGT remains cost-neutral. Per-episode cost-neutrality thresholds ranged from near $0 when ceftriaxone resistance was absent to up to $45/test at 15% ceftriaxone resistance. At 50% ciprofloxacin and 5% ceftriaxone resistance, the population-weighted threshold was $4 (95% UI:$3-$8) for a CIP-only test and $11 (95% UI:$5-$14) for a triple-target test. Among MSM, incorporating system-level resistance emergence costs and avoided antibiotic development costs increased the total per-test value to $35-$145 for a single-target test and $84-$128 for a triple-target test, depending on whether prescribing practices shift when ceftriaxone resistance reaches 5%. Conclusions: Resistance-guided therapy offers economic benefits across multiple dimensions even at relatively high diagnostic prices, supporting investment in gonorrhea resistance testing to improve partner outcomes, delay resistance emergence, and enhance the long-term cost-efficiency of gonorrhea management.

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A Triple-Modality Peptide-Antibiotic-Phage Therapy Eradicates Multidrug-Resistant Serratia marcescens Biofilms

Duggal, A. P.; Alreja, A. B.; Vashee, I.; Nordstrom, H.; Harrelson, E.; Fallen, N.; Takano, K.-A.; Blaustein, R. A.; Fouts, D. E.; Gonzalez-Juarbe, N.

2026-04-09 microbiology 10.64898/2026.04.08.717253 medRxiv
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Serratia marcescens is an opportunistic pathogen that causes severe hospital-acquired infections, notable for its biofilm formation abilities and development of extensive antibiotic resistance. Here we evaluated the efficacy of bacteriophages, antibiotics, and antimicrobial peptides (BAP), alone and in combination, against fourteen multi-drug-resistant (MDR) S. marcescens isolates sourced from hospitals and other environmental settings in an in vitro biofilm model. Phage combination with a cocktail of sub-minimal inhibitory concentration (MIC) of penicillin-streptomycin, kanamycin, and ciprofloxacin, reduced biofilm biomass, however, complete decolonization was not achieved. Incorporating an antimicrobial peptide cocktail into this regimen eradicated 99.99% of multi-drug-resistant isolates grown planktonically or in surface-associated biofilms. Microscopy and viability assays confirmed extensive biofilm disruption and bacterial clearance without regrowth. These findings reveal that simultaneous interference of cell wall synthesis, protein translation, DNA replication, and membrane integrity can overcome S. marcescens antimicrobial defenses, establishing a multifaceted therapeutic framework for managing device-associated infections caused by MDR pathogens.

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Promising antimicrobial activity of Moringa oleifera seed extract fractions

Futagbi, G.; Donkor, M. T.; Obeng, B. C.; Achou, S.; Adjah-Tetteh, E.; Honyo, M. E.; Osei, M.-M.; Adukpo, S.; Chama, M. A.; Amoah, L. E.; Donkor, E. S.

2026-03-27 microbiology 10.64898/2026.03.23.713792 medRxiv
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This study investigated the antiplasmodial and antibacterial activities of fractionated extracts of Moringa oleifera seeds, focusing on the influence of solvent polarity on bioactivity. The results revealed a polarity-dependent distribution of activity. Polar aqueous extracts (crude and residual fractions) exhibited the most pronounced antiplasmodial effects against Plasmodium falciparum (3D7 strain), with IC values of 107-135 {micro}g/mL. Time-dependent analyses of the crude and residual fractions showed that parasitaemia declined steadily over time, and consequently, percentage inhibition increased with time, with both extracts reaching 70-80% inhibition by 48 hours at higher concentrations. In contrast, moderately polar organic fractions, notably ethyl acetate and dichloromethane, demonstrated strong antibacterial activity against both Gram-positive and Gram-negative clinical isolates, including resistant strains such as MRSA and ESBL-producing Escherichia coli. Minimum inhibitory concentrations (MICs) ranged from 6.3 to 25 mg/mL for the ethyl acetate fraction, and all active fractions exhibited bactericidal properties (MBC/MIC [&le;] 4). Comparative analysis showed that while antiplasmodial activity was moderate relative to the standard drug (chloroquine), antibacterial activity was robust and clinically promising. Fractionation revealed that distinct phytochemical classes underlie the two activities: polar compounds appear responsible for antiplasmodial effects, whereas moderately polar compounds drive antibacterial potency. The moderate antiplasmodial activity is significant in the context of adjunctive therapy and resistance management, while the strong antibacterial activity is highly relevant to the global challenge of antimicrobial resistance. Together, the results position Moringa oleifera as a promising source of phytochemicals for integrated infectious disease management, particularly in regions where malaria and bacterial co-infections are prevalent.

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Using photoaffinity labelling to study pantothenamide uptake in malaria parasites

Akkerman, L. J.; Cassidy-Eulitz, S.; Velema, W. A.; Kooij, T. W. A.

2026-04-13 microbiology 10.64898/2026.04.13.718166 medRxiv
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6.5%
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Pantothenamides (PanAms) comprise a promising class of antimalarial compounds that kill asexual blood-stage Plasmodium falciparum parasites and block transmission. Intriguingly, the most advanced PanAm in drug development, MMV693183, is approximately 100 times more potent against female gametocytes than males. We hypothesized that this specificity is explained by a difference in PanAm uptake, which we studied using a PanAm-based photoaffinity labelling (PAL) probe. We successfully synthesized a probe that competed with MMV693183 in drug sensitivity assays, while the probe did not display high potency by itself. We observed no significant difference in median fluorophore-labelled probe signal intensity between male and female gametocytes, although there might be a difference in subcellular localization of the probe between the sexes. By combining PAL with affinity purification and mass spectrometry, we were not able to identify novel candidate PanAm transporters. We conclude that PAL provides evidence that differences in PanAm uptake do not underly differences in PanAm sensitivity between the gametocyte sexes.

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Local prevalence of ceftriaxone resistance informs optimal deploy-ment of new gonorrhea treatments

Oliveira Roster, K. I.; Rönn, M. M.; Gorenburg, E. R.; Partl, D. K.; Anderegg, N.; Abel zur Wiesch, P.; Au, C.; Kouyos, R. D.; Martinez, F. P.; Low, N.; Grad, Y. H.

2026-04-24 infectious diseases 10.64898/2026.04.23.26351610 medRxiv
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6.3%
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Numerous factors may influence the optimal rollout of new gonococcal antibiotics. We compared eight rollout strategies using a gonorrhea transmission model and ranked strategies by the number of gonococcal infections and clinically useful antibiotic lifespan. Rankings were most sensitive to the starting ceftriaxone resistance prevalence and screening frequency.

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Epidemiology and Predictors of Fluoroquinolone Resistance in ESBL-Producing Escherichia coli: Implications for Empirical Therapy in Mexico

Gallardo Mejia, A.; Almeida, J.

2026-04-22 infectious diseases 10.64898/2026.04.21.26351439 medRxiv
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Urinary tract infections (UTIs) are among the most common infectious diseases worldwide, with Escherichia coli being the predominant uropathogen. The increasing prevalence of extended-spectrum beta-lactamase (ESBL)-producing strains and their association with fluoroquinolone resistance pose a significant challenge to empirical therapy, particularly in community settings. The aim of this study was to determine the epidemiology and predictive factors associated with ESBL-producing E. coli and its concomitant fluoroquinolone resistance in community-acquired clinical isolates. A retrospective cross-sectional study was conducted analyzing 244 clinical E. coli isolates. Demographic and microbiological data were collected, including age, sex, sample type, and antibiotic susceptibility. Associations between variables and ESBL production were assessed using Pearsons chi-squared test, and odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. Of the isolates, 165 (68%) were ESBL-producing. A significant association was observed between age group and ESBL production (p < 0.001), with the highest frequency in the 20-39 age group. Most ESBL-positive isolates were obtained from women (73%), although odds ratio (OR) analysis suggested a non-significant trend toward a higher probability in men (OR = 1.29; 95% CI: 0.72-2.31). High rates of fluoroquinolone resistance were identified among the ESBL-producing isolates, with 30% resistance to levofloxacin and 35% to ciprofloxacin (p < 0.001). Urine samples showed the highest concentration of ESBL-positive isolates, with a significant association between sample type and resistance (p < 0.001). The high prevalence of ESBL-producing E. coli and its concomitant resistance to fluoroquinolones highlight a critical challenge for the empirical treatment of urinary tract infections in Mexico, underscoring the need to strengthen antimicrobial use management and local surveillance strategies.