Biology subjects

Pierce, V. M.

Publications and source records attributed to Pierce, V. M..

7 recordsLinked to original sources

bioRxiv2026

LP.8.1-directed COVID-19 mRNA vaccines boost neutralizing antibodies and mitigate ancestral immune imprinting

As SARS-CoV-2 evolves, it evades existing immunity elicited by exposure to earlier strains of the virus. In response, vaccine manufacturers have updated COVID-19 vaccines annually since 2022, though immune imprinting to the ancestral strain has blunted antibody responses to modern viral variants. In early 2025, the JN.1 subvariant LP.8.1 was dominant and manufacturers updated mRNA vaccine formulations to target LP.8.1 (LP.8.1 MV). However, by late 2025, other subvariants were dominant (XFG and NB.1.8.1) or emerging (e.g., PE.1.4, BA.3.2, PY.1.1.1) around the world. It is critical to understand the extent to which updated vaccine boosters elicit titers against both their target strain and recent variants. Further, it is important to quantify the extent to which immune imprinting continues to shape antiviral immune responses. Using pseudoviruses, we measured neutralizing antibody titers against a panel of 11 SARS-CoV-2 variants in serum samples from 36 adult participants in the United States before and approximately 1 month after LP.8.1 MV booster. We found that neutralizing antibody titers were substantially increased by the boost, with the greatest increases elicited against LP.8.1 and XFG. For the first time since 2022, post-boost titers were higher against the homologous vaccine target (LP.8.1) than against D614G (representing the ancestral strain). Combined, these results indicate that ancestral immune imprinting is mitigated to the greatest extent observed to date by LP.8.1 MV. Lastly, for a subset of participants, we measured neutralizing titers at approximately 4 months post-booster and found that LP.8.1-directed antibody titers were durable, with an estimated average half-life of approximately 66 days.

microbiology↗

bioRxiv2025

Antibody evasion and receptor binding of SARS-CoV-2 LP.8.1.1, NB.1.8.1, XFG, and related subvariants

SARS-CoV-2 continues to evolve, causing repeated waves of infections around the world. It is critical to understand the features of the virus that explain its growth advantages. Recently, the SARS-CoV-2 Omicron JN.1 subvariants KP.3.1.1 and XEC were outcompeted by later JN.1 progenies, most prominently LP.8.1 and LP.8.1.1. Other recent JN.1 subvariants, such as LF.7.2.1, which became prevalent in Asia, and MC.10.1, have also been under monitoring. Subsequently, NB.1.8.1 and XFG subvariants began increasing in prevalence, as well. We found that serum neutralizing antibody titers against LP.8.1, LP.8.1.1, LF.7, LF.7.2.1, MC.10.1 were similar to XEC in a cohort of 20 KP.2-based monovalent mRNA vaccine (KP.2 MV) recipients and in a cohort 20 adults who did not receive KP.2 MV. NB.1.8.1 and XFG were more evasive of serum neutralization than LP.8.1.1. We then characterized subvariant susceptibility to monoclonal antibody (mAb) neutralization using a panel of 12 mAbs spanning several epitopes on the SARS-CoV-2 spike, and found that LP.8.1 and XFG, MC.10.1 and NB.1.8.1, and LF.7.2.1 evade different classes of mAbs relative to earlier JN.1 subvariants, even if the tested polyclonal serum neutralizing antibody titers were not different overall. Next, we found that the receptor-binding affinity of LP.8.1 to ACE2 was the highest among the tested viruses, while that of LF.7.2.1 was lowest. Therefore, unlike most prior SARS-CoV-2 sublineage evolutionary trajectories, receptor-binding affinity, possibly reflecting enhanced transmissibility-and not increased antibody evasion-better explained the rise of LP.8.1, while the expansion of NB.1.8.1 and XFG again appear correlated with their enhanced antibody evasion.

microbiology↗

bioRxiv2025

Do Existing COVID-19 Vaccines Need to Be Updated in 2025?

COVID-19 vaccines have been updated each year since 2022 to improve protection against evolving SARS-CoV-2 variants. However, it is unclear whether a reformulation will be necessary for 2025. KP.2-based monovalent COVID-19 mRNA vaccines (KP.2 MV) were authorized for use in 2024, and they conferred substantial protection against hospitalizations caused by viral variants that emerged and dominated later, such as KP.3.1.1 and XEC. Today, LP.8.1 and its subvariant LP.8.1.1 have become dominant worldwide, particularly so in North America. Other variants, such as the LF.7 subvariant LF.7.2.1, have emerged with a growth advantage in Asia. To characterize the antigenicity of LP.8.1, LP.8.1.1, LF.7, LF.7.2.1, and another variant under monitoring, MC.10.1, we tested serum samples from 20 individuals who recently received KP.2 MV in neutralization assays against JN.1, KP.2, KP.3, KP.3.1.1, XEC, LP.8.1, LP.8.1.1, LF.7, LF.7.2.1, or MC.10.1 pseudoviruses. Serum neutralizing antibody titers against LP.8.1, LP.8.1.1, LF.7, LF.7.2.1, and MC.10.1 were comparable to those against KP.3.1.1 and XEC, indicating that LP.8.1.1 and other recently dominant subvariants are antigenically similar to their predecessors. Therefore, the currently authorized KP.2 MV may not need to be updated for 2025, if the vaccine manufacturers could demonstrate comparable immunogenicity for KP.2 MV and LP.8.1-based mRNA vaccines and, of course, in the absence of an antigenically divergent SARS-CoV-2 variant emerging.

microbiology↗

bioRxiv2023

The carbapenem inoculum effect provides insight into the molecular mechanisms underlying carbapenem resistance in Enterobacterales

Carbapenem-resistant Enterobacterales (CRE) are important pathogens that can develop resistance via multiple molecular mechanisms, including hydrolysis or reduced antibiotic influx. Identifying these mechanisms can improve pathogen surveillance, infection control, and patient care. We investigated, both phenomenologically and mechanistically, how resistance mechanisms influence the carbapenem inoculum effect (IE), a phenomenon where inoculum size affects antimicrobial susceptibility testing (AST). We demonstrated that any of seven different carbapenemases were sufficient to impart a meropenem IE when transformed into a laboratory strain of Escherichia coli. Across 106 clinical CRE isolates spanning 6 genera and 12 species, the carbapenem IE strictly depended on resistance mechanism: all 36 carbapenemase-producing CRE (CP-CRE) exhibited a clear IE, whereas 43 porin-deficient CRE displayed none. 27 isolates with both carbapenemase production and porin deficiency exhibited high-level resistance at all inocula, and still displayed an IE, albeit smaller in magnitude than CP-CRE with intact porins. Mechanistically, we found that clinical CP-CRE release carbapenemase activity into culture supernatant to protect other cells. Further, this released activity markedly increased upon exposure to lethal antibiotic doses, functionally consistent with altruism. Concerningly, 50% and 24% of CP-CRE isolates changed susceptibility classification to meropenem and ertapenem, respectively, across the allowable inoculum range in clinical testing guidelines. The meropenem IE, and the ratio of ertapenem to meropenem minimal inhibitory concentration (MIC) at standard inoculum, reliably identified CP-CRE. Understanding how resistance mechanisms affect AST could improve diagnosis and guide therapies for CRE infections. ImportanceInfections caused by carbapenem-resistant Enterobacterales (CRE) pose significant threats to patients and public health worldwide. Carbapenem resistance can occur through several molecular mechanisms, including enzymatic hydrolysis by carbapenemases and reduced influx via porin mutations. Identifying carbapenemase-producing isolates could enable tailored antibiotic selection to improve patient outcomes, and infection control measures to prevent further carbapenemase transmission. In a large collection of CRE isolates, we found that only carbapenemase-producing CRE exhibit an inoculum effect, in which their measured resistance varies markedly with cell density, which risks misdiagnosis. Further, this inoculum effect occurs under conditions where bacteria release carbapenemases to the community upon exposure to antibiotic that results in cell death, functionally consistent with altruism. Measuring this inoculum effect, or integrating other data from routine antimicrobial susceptibility testing, enhances carbapenem resistance detection, paving the way for more effective strategies to combat this growing public health crisis.

microbiology↗

bioRxiv2022

A novel rRNA hybridization-based approach to rapid, accurate Candida identification directly from blood culture

Invasive fungal infections are increasingly common and carry high morbidity and mortality, yet fungal diagnostics lag behind bacterial diagnostics in rapidly identifying the causal pathogen. We previously devised a fluorescent hybridization-based assay to identify bacteria within hours directly from blood culture bottles without subculture, called phylogeny-informed rRNA-based strain identification (Phirst-ID). Here, we adapt this approach to unambiguously identify 11 common pathogenic Candida species, including C. auris, with 100% accuracy from laboratory culture (33 of 33 strains in a reference panel, plus 33 of 33 additional isolates tested in a validation panel). In a pilot study on 62 consecutive positive clinical blood cultures from two hospitals that showed yeast on Gram stain, Candida Phirst-ID matched the clinical laboratory result for 58 of 59 specimens represented in the 11-species reference panel, without misclassifying the 3 off-panel species. It also detected mixed Candida species in 2 of these 62 specimens, including the one discordant classification, that were not identified by standard clinical microbiology workflows; in each case the presence of both species was validated by both clinical and experimental data. Finally, in three specimens that grew both bacteria and yeast, we paired our prior bacterial probeset with this new Candida probeset to detect both pathogen types using Phirst-ID. This simple, robust assay can provide accurate Candida identification within hours directly from blood culture bottles, and the conceptual approach holds promise for pan-microbial identification in a single workflow.

microbiology↗

bioRxiv2021

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

BackgroundCarbapenem-resistant Enterobacterales (CRE) are an urgent global health threat. Inferring the dynamics of local CRE dissemination is currently limited by our inability to confidently trace the spread of resistance determinants to unrelated bacterial hosts. Whole genome sequence comparison is useful for identifying CRE clonal transmission and outbreaks, but high-frequency horizontal gene transfer (HGT) of carbapenem resistance genes and subsequent genome rearrangement complicate tracing the local persistence and mobilization of these genes across organisms. MethodsTo overcome this limitation, we developed a new approach to identify recent HGT of large, near-identical plasmid segments across species boundaries, which also allowed us to overcome technical challenges with genome assembly. We applied this to complete and near-complete genome assemblies to examine the local spread of CRE in a systematic, prospective collection of all CRE, as well as time- and species-matched carbapenem susceptible Enterobacterales, isolated from patients from four U.S. hospitals over nearly five years. ResultsOur CRE collection comprised a diverse range of species, lineages and carbapenem resistance mechanisms, many of which were encoded on a variety of promiscuous plasmid types. We found and quantified rearrangement, persistence, and repeated transfer of plasmid segments, including those harboring carbapenemases, between organisms over multiple years. Some plasmid segments were found to be strongly associated with specific locales, thus representing geographic signatures that make it possible to trace recent and localized HGT events. Functional analysis of these signatures revealed genes commonly found in plasmids of nosocomial pathogens, such as functions required for plasmid retention and spread, as well survival against a variety of antibiotic and antiseptics common to the hospital environment. ConclusionsCollectively, the framework we developed provides a clearer, high resolution picture of the epidemiology of antibiotic resistance importation, spread, and persistence in patients and healthcare networks.

genomics↗

bioRxiv2021

DNA spike-ins enable confident interpretation of SARS-CoV-2 genomic data from amplicon-based sequencing

The rapid global spread and continued evolution of SARS-CoV-2 has highlighted an unprecedented need for viral genomic surveillance and clinical viral sequencing. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but suffer a high potential for contamination, which can undermine lab processes and results. This challenge will only increase with expanding global production of sequences by diverse research groups for epidemiological and clinical interpretation. We present an approach which uses synthetic DNA spike-ins (SDSIs) to track samples and detect inter-sample contamination through a sequencing workflow. Applying this approach to the ARTIC Consortiums amplicon design, we define a series of best practices for Illumina-based sequencing and provide a detailed characterization of approaches to increase sensitivity for low-viral load samples incorporating the SDSIs. We demonstrate the utility and efficiency of the SDSI method amidst a real-time investigation of a suspected hospital cluster of SARS-CoV-2 cases.

molecular biology↗