Structural insights into the mechanism of action of a biparatopic anti-HER2 antibody.

Pathways of human epidermal growth factor (EGF) receptors are activated upon ligand-dependent or -independent homo- or heterodimerization and their subsequent transphosphorylation. Overexpression of these receptors positively correlates with transphosphorylation rates and increased tumor growth rates. MEDI4276, an anti-human epidermal growth factor receptor 2 (HER2) biparatopic antibody-drug conjugate, has two paratopes within each antibody arm. One, 39S, is aiming at the HER2 site involved in receptor dimerization and the second, single chain fragment (scFv), mimicking trastuzumab. Here we present the cocrystal structure of the 39S Fab-HER2 complex and, along with biophysical and functional assays, determine the corresponding epitope of MEDI4276 and its underlying mechanism of action. Our results reveal that MEDI4276's uniqueness is based first on the ability of its 39S paratope to block HER2 homo- or heterodimerization and second on its ability to cluster the receptors on the surface of receptor-overexpressing cells.

Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following In Vitro Incubation in Broiler Ceca.

The chicken gastrointestinal tract harbors microorganisms that play a role in the health and disease status of the host. The cecum is the part of the gut that carries the highest microbial densities, has the longest residence time of digesta, and is a vital site for urea recycling and water regulation. Therefore, the cecum provides a rich environment for bacteria to horizontally transfer genes between one another via mobile genetic elements such as plasmids and bacteriophages. In this study, we used broiler chicken cecum as a model to investigate antibiotic resistance genes that can be transferred in vitro from cecal flora to Salmonella enterica serovar Heidelberg. We used whole-genome sequencing and resistome enrichment to decipher the interactions between S Heidelberg, the gut microbiome, and acquired antibiotic resistance. After 48 h of incubation of ceca under microaerophilic conditions, we recovered one S Heidelberg isolate with an acquired IncK2 plasmid (88 kb) carrying an extended-spectrum-ß-lactamase gene (blaCMY-2). In vitro, this plasmid was transferable between Escherichia coli and S Heidelberg strains but transfer was unsuccessful between S Heidelberg strains. An in-depth genetic characterization of transferred plasmids suggests that they share significant homology with P1-like phages. This study contributes to our understanding of horizontal gene transfer between an important foodborne pathogen and the chicken gut microbiome.IMPORTANCES. Heidelberg is a clinically important serovar, linked to foodborne illness and among the top 5 serovars isolated from poultry in the United States and Canada. Acquisition of new genetic material from the microbial flora in the gastrointestinal tract of food animals, including broilers, may contribute to increased fitness of pathogens like S. Heidelberg and may increase their level of antibiotic tolerance. Therefore, it is critical to gain a better understanding of the interactions that occur between important pathogens and the commensals present in the animal gut and other agroecosystems. In this report, we show that the native flora in broiler ceca were capable of transferring mobile genetic elements carrying the AmpC ß-lactamase (blaCMY-2) gene to an important foodborne pathogen, S Heidelberg. The potential role for bacteriophage transduction is also discussed.

Non-lethal isolation of the fungal pathogen Batrachochytrium dendrobatidis (Bd) from amphibians.

The ability to isolate and purify pathogens is important for the study of infectious disease. A protocol for isolating Batrachochytrium dendrobatidis (Bd), a lethal pathogen of amphibians, has been available for over a decade, but the method relies on sacrificing infected animals. We validated a non-lethal protocol for Bd isolation that uses biopsy punches from toe webbing to collect skin samples from live amphibians in remote field locations. We successfully isolated Bd from the Cascades frog Rana cascadae and found a positive association between Bd infection and probability of Bd growth in culture. Recapture rates of sampled animals suggest that our isolation protocol did not affect frog survival. The ability to collect isolates from live animals will facilitate investigations of the biology of Bd and enhance amphibian conservation efforts.

Use of Molecular Markers to Compare Escherichia coli Transport with Traditional Groundwater Tracers in Epikarst.

Bacterial contamination of karst aquifers is a global concern as water quality deteriorates in the face of decreasing water security. Traditional abiotic groundwater tracers, which do not exhibit surface properties similar to bacteria, may not be good proxies for risk assessment of bacterial transport in karst environments. This study examined the transport and attenuation of two isolates of in relation to traditional groundwater tracers (rhodamine WT dye and 1-µm-diam. latex microspheres) through ∼30 m of epikarst in western Kentucky. Differential movement of the four tracers was observed, with tracer behavior dependent on flow conditions. Dye arrived at the sampling site prior to particulates. Molecular biology techniques successfully detected bacteria in the cave and showed attenuation was greater for a bacterial isolate with high attachment efficiency compared with an isolate known to have low attachment efficiency. Microspheres were first detected simultaneously with the low-attachment isolate but attained maximum concentrations during increases in discharge >11 d post-injection. Bacteria were remobilized by storm events >60 d after injection, illustrating the storage capacity of epikarst with regard to potential contaminants. The two bacterial strains were not transported at the same rate within the epikarst, showing breakthroughs during differing storm events and illustrating the importance of cell surface chemistry in the prediction of microorganism movement. Moreover, this study has shown that molecular analysis can be successfully used to target, quantify, and track introduced microbial tracers in karst terrains.

Proposed Epidemiological Cutoff Values for Ceftriaxone, Cefepime, and Colistin in Salmonella.

We tested a diverse set of 500 isolates of nontyphoidal Salmonella enterica subsp. enterica from various animal, food, and human clinical sources for susceptibility to antimicrobials currently lacking epidemiological cutoff values (ECOFFs) set by the European Committee on Antimicrobial Susceptibility Testing. A consortium of five different laboratories each tested 100 isolates, using broth microdilution panels containing twofold dilutions of ceftriaxone, cefepime, and colistin to determine the minimum inhibitory concentrations of each drug when tested against the Salmonella isolates. Based on the resulting data, new ECOFFs of 0.25 µg/mL for ceftriaxone, 0.12 µg/mL for cefepime, and 2 µg/mL for colistin have been proposed. These thresholds will aid in the identification of Salmonella that have phenotypically detectable resistance mechanisms to these important antimicrobials.

Prevalence of mcr-1 in the Cecal Contents of Food Animals in the United States.

A survey of 2,003 cecal content samples from chickens, turkeys, cattle, and swine at slaughter facilities in the United States was conducted to estimate the prevalence of the mcr-1 gene conferring resistance to colistin in Enterobacteriaceae Two cecal samples from swine had Escherichia coli with IncI2 plasmids bearing the mcr-1 gene.

MULTIHORMONAL ISLET CELL CARCINOMAS IN THREE KOMODO DRAGONS (VARANUS KOMODOENSIS).

Multihormonal pancreatic islet cell carcinomas were found in one female and two male captive geriatric Komodo dragons (Varanus komodoensis). Gross changes in the pancreas were visible in two of the cases. Clinical signs noted in the Komodo dragons were lethargy, weakness, and anorexia. Histologically, the tumors were comprised of nests and cords of well-differentiated neoplastic islet cells with scant amounts of eosinophilic cytoplasm and round, euchromatic nuclei, with rare mitoses. Infiltration by the islet cell tumor into the surrounding acinar tissue was observed in all cases, but no metastatic foci were seen. Multihormone expression was observed in all tumors, which labeled strongly positive for glucagon and somatostatin and focally positive for polypeptide. Pancreatic islet cell neoplasms should be considered in the differential diagnosis for geriatric Komodo dragons presenting with weakness, lethargy, and poor appetite.

How Should We Be Determining Background and Baseline Antibiotic Resistance Levels in Agroecosystem Research?

Although historically, antibiotic resistance has occurred naturally in environmental bacteria, many questions remain regarding the specifics of how humans and animals contribute to the development and spread of antibiotic resistance in agroecosystems. Additional research is necessary to completely understand the potential risks to human, animal, and ecological health in systems altered by antibiotic-resistance-related contamination. At present, analyzing and interpreting the effects of human and animal inputs on antibiotic resistance in agroecosystems is difficult, since standard research terminology and protocols do not exist for studying background and baseline levels of resistance in the environment. To improve the state of science in antibiotic-resistance-related research in agroecosystems, researchers are encouraged to incorporate baseline data within the study system and background data from outside the study system to normalize the study data and determine the potential impact of antibiotic-resistance-related determinants on a specific agroecosystem. Therefore, the aims of this review were to (i) present standard definitions for commonly used terms in environmental antibiotic resistance research and (ii) illustrate the need for research standards (normalization) within and between studies of antibiotic resistance in agroecosystems. To foster synergy among antibiotic resistance researchers, a new surveillance and decision-making tool is proposed to assist researchers in determining the most relevant and important antibiotic-resistance-related targets to focus on in their given agroecosystems. Incorporation of these components within antibiotic-resistance-related studies should allow for a more comprehensive and accurate picture of the current and future states of antibiotic resistance in the environment.

Structural insights into neonatal Fc receptor-based recycling mechanisms.

We report the three-dimensional structure of human neonatal Fc receptor (FcRn) bound concurrently to its two known ligands. More particularly, we solved the crystal structure of the complex between human FcRn, wild-type human serum albumin (HSA), and a human Fc engineered for improved pharmacokinetics properties (Fc-YTE). The crystal structure of human FcRn bound to wild-type HSA alone is also presented. HSA domain III exhibits an extensive interface of contact with FcRn, whereas domain I plays a lesser role. A molecular explanation for the HSA recycling mechanism is provided with the identification of FcRn His(161) as the only potential direct contributor to the corresponding pH-dependent process. At last, this study also allows an accurate structural definition of residues considered for decades as important to the human IgG/FcRn interaction and reveals Fc His(310) as a significant contributor to pH-dependent binding. Finally, we explain various structural mechanisms by which several Fc mutations (including YTE) result in increased human IgG binding to FcRn. Our study provides an unprecedented relevant understanding of the molecular basis of human Fc interaction with human FcRn.

Structural insights into the interaction of human IgG1 with FcγRI: no direct role of glycans in binding.

The three-dimensional structure of a human IgG1 Fc fragment bound to wild-type human FcγRI is reported. The structure of the corresponding complex was solved at a resolution of 2.4 Šusing molecular replacement; this is the highest resolution achieved for an unmutated FcγRI molecule. This study highlights the critical structural and functional role played by the second extracellular subdomain of FcγRI. It also explains the long-known major energetic contribution of the Fc `LLGG' motif at positions 234-237, and particularly of Leu235, via a `lock-and-key' mechanism. Finally, a previously held belief is corrected and a differing view is offered on the recently proposed direct role of Fc carbohydrates in the corresponding interaction. Structural evidence is provided that such glycan-related effects are strictly indirect.

A novel anti-PcrV antibody providing enhanced protection against Pseudomonas aeruginosa in multiple animal infection models.

Pseudomonas aeruginosa is a major cause of hospital-acquired infections, particularly in mechanically ventilated patients, and it is the leading cause of death in cystic fibrosis patients. A key virulence factor associated with disease severity is the P. aeruginosa type III secretion system (T3SS), which injects bacterial toxins directly into the cytoplasm of host cells. The PcrV protein, located at the tip of the T3SS injectisome complex, is required for T3SS function and is a well-validated target in animal models of immunoprophylactic strategies targeting P. aeruginosa. In an effort to identify a highly potent and protective monoclonal antibody (MAb) that inhibits the T3SS, we generated and characterized a panel of novel anti-PcrV MAbs. Interestingly, some MAbs exhibiting potent inhibition of T3SS in vitro failed to provide protection in a mouse model of P. aeruginosa infection, suggesting that effective in vivo inhibition of T3SS with anti-PcrV MAbs is epitope dependent. V2L2MD, while not the most potent MAb as assessed by in vitro cytotoxicity inhibition assays, provided strong prophylactic protection in several murine infection models and a postinfection therapeutic model. V2L2MD mediated significantly (P < 0.0001) better in vivo protection than that provided by a comparator antibody, MAb166, a well-characterized anti-PcrV MAb and the progenitor of a clinical candidate, KB001-A. The results described here support further development of a V2L2MD-containing immunotherapeutic and may suggest even greater potential than was previously recognized for the prevention and treatment of P. aeruginosa infections in high-risk populations.

An analysis of culture-based methods used for the detection and isolation of Salmonella spp., Escherichia coli, and Enterococcus spp. from surface water: A systematic review.

Identification of methods for the standardized assessment of bacterial pathogens and antimicrobial resistance (AMR) in environmental water can improve the quality of monitoring and data collected, support global surveillance efforts, and enhance the understanding of environmental water sources. We conducted a systematic review to assemble and synthesize available literature that identified methods for assessment of prevalence and abundance of bacterial fecal indicators and pathogens in water for the purposes of monitoring bacterial pathogens and AMR. After screening for quality, 175 unique publications were identified from 15 databases, and data were extracted for analysis. This review identifies the most common and robust methods, and media used to isolate target organisms from surface water sources, summarizes methodological trends, and recognizes knowledge gaps. The information presented in this review will be useful when establishing standardized methods for monitoring bacterial pathogens and AMR in water in the United States and globally.

Hemorrhagic diathesis in avian species following intramuscular administration of polysulfated glycosaminoglycan.

Polysulfated glycosaminoglycans (PSGAGs) have been used for decades in a variety of species for the management of osteoarthritic pain. However, reports on the use of PSGAGs in avian species are scarce. In domestic cats and dogs, PSGAG injections have caused prolongation of clotting times but are considered to be an efficacious drug with a wide margin of safety. This publication documents four cases of fatal coagulopathies in different avian species (one coraciiforme, two raptors, and one psittacine) following the intramuscular administration of PSGAG. All affected birds received varying dosages and dosing intervals of PSGAG. Three of the four birds experienced fatal hemorrhage into the pectoral muscle, while the fourth bled continuously from the injection site. Only one bird had chronic, severe pre-existing disease; the remainder were being managed for osteoarthritis. This report highlights the importance of species-specific dosing of PSGAG and warrants further investigation into the etiopathogenesis of this process.

Management and environmental factors influence the prevalence and abundance of food-borne pathogens and commensal bacteria in peanut hull-based broiler litter.

In this study, we conducted a longitudinal sampling of peanut hull-based litter from a farm under a "no antibiotics ever" program. Our objective was to determine broiler management practices and environmental factors that are associated with the occurrence of food-borne pathogens (Salmonella and Campylobacter) and the abundance of commensal bacteria (Escherichia coli, Enterococcus spp., and Staphylococcus spp.). Litter (n = 288) was collected from 4 broiler houses over three consecutive flocks, starting with a complete house cleanout and fresh peanut hull. Litter was sampled at the beginning of each grow-out cycle and at the end of the cycle. Logistic and linear regression models were used to model the relationships between pathogen prevalence, commensal abundance and management practices, and environmental factors. The number of flocks raised on litter, grow-out period, broiler house, litter pH, litter moisture, and house temperature were associated with the prevalence of pathogens and the abundance of commensal bacteria in litter. The final logistic model for pathogens showed that a higher probability of detecting Salmonella in litter was associated with the number of flocks raised on litter and the grow-out period. A higher probability of detecting Campylobacter in litter was associated with the number of flocks raised on litter, broiler house and the sections of the house, and the pH of litter. Our results suggest that management practices and environmental factors affect Salmonella and Campylobacter differently and suggest that each pathogen will require its own tailored intervention to stop their persistence in broiler litter.

A comparison of methods to detect low levels of Salmonella enterica in surface waters to support antimicrobial resistance surveillance efforts performed in multiple laboratories.

Developing effective and sensitive detection methods for antimicrobial resistant Salmonella enterica from surface water is a goal of the National Antimicrobial Resistance Monitoring System (NARMS). There are no specified methods for recovery of S. enterica in surface waters in the U.S. A multi-laboratory evaluation of four methods - bulk water enrichment (BW), vertical Modified Moore Swab (VMMS), modified Standard Method 9260.B2 (SM), and dead-end ultrafiltration (DEUF) - was undertaken to recover S. enterica from surface water. In Phase 1, one-liter volumes of water were collected from the same site on five different dates. Water was shipped and analyzed at four different laboratory locations (A, B, C, and D) for recovery of 1) inoculated fluorescent S. Typhimurium strain (ca. 30 CFU/L) and 2) Salmonella present in the water sampled. At each location, BW, VMMS, or SM recovery was performed on five separate 1 L water samples. Twenty 1 L water samples were subjected to each recovery method, and overall, sixty 1 L samples were assayed for Salmonella. Inoculated, fluorescent Salmonella Typhimurium and environmental Salmonella spp. were recovered from 65 % (39/60) and 45 % (27/60) of water samples, respectively. BW, VMMS, and SM recovered fluorescent S. Typhimurium from 60 %, 60 %, and 75 % of inoculated samples, respectively. Analysis by Chi-squared test determined laboratory location had a significant (p < 0.05) effect on fluorescent S. Typhimurium recovery compared to method or date of water collection. In Phase 2, recovery of inoculated fluorescent S. Typhimurium from 1 L samples by SM and DEUF was compared at laboratory locations B and D. SM and DEUF recovered fluorescent S. Typhimurium from 100 % (20/20) and 95 % (19/20) of inoculated water samples, respectively; laboratory location (p > 0.05) did not affect Salmonella recovery. Uniform laboratory methodology and training should be prioritized in conducting Salmonella recovery from surface water in laboratories.

Impact of growth conditions on transport behavior of E. coli.

The aim of this investigation is to determine the effect that growth solution has on the cell surface properties and transport behavior of eleven Escherichia coli isolates through saturated porous media. The two growth solutions used were a standard laboratory growth medium (LB) and a dairy manure extract solution. In general, cells grown in manure extract were more hydrophobic, had a more negative zeta potential, had lower amounts of surface macromolecules, and had lower attachment efficiencies than isolates grown in LB. An inverse relationship between the natural log of zeta potential and the attachment efficiency of the isolates for the cells grown in LB media was the only statistically significant correlation observed between transport behavior and cell characteristics of the isolates. This study shows the need to consider growth conditions when studying bacteria to better mimic the environmental stresses that bacteria undergo in the natural environment. This approach could lead to a better understanding of the behavior of manure-derived bacteria in aquatic and terrestrial environments.

Improved process intermediate stability through the identification and elimination of reactive glycation residues - a monoclonal antibody case study.

The manufacturing of therapeutic biologics can result in a heterogeneous population of charge variants, encompassing many quality attributes which could impact activity and pharmacokinetics. Monitoring the relative abundance of these charge variants to demonstrate process consistency is an expectation of regulatory agencies. Control of the relative abundance of charge variants is also necessary to ensure product comparability across the product lifecycle. We have observed a significant shift in the relative abundance of charged species, as measured by capillary isoelectric focusing, during clarified cell culture fluid holds for several monoclonal antibodies. This lack of stability requires that the hold time for this process intermediate be significantly curtailed, eliminating manufacturing flexibility. We have identified the cause of this shift in relative abundance of charged species as changes in glycation levels, focused predominantly on three conserved, solvent accessible, lysine residues. Mutants of a model protein were generated that show increased charge state stability can be gained by eliminating these reactive lysines. Further, characterization studies were conducted on these mutants to determine the impact to biological activity and stability of the molecule, with no detrimental effects observed. Incorporating this knowledge into the assessments of candidate drugs could allow for the selection of molecules less susceptible to this product degradation pathway, allowing for greater manufacturing flexibility. This process of identifying and removing reactive lysine residues could be useful in the design of drug candidates with improved charge state stability, across a range of modalities.

Transferability of ESBL-encoding IncN and IncI1 plasmids among field strains of different Salmonella serovars and Escherichia coli.

OBJECTIVES: This study aimed to sequence, assemble, and annotate three plasmids (two IncN and one IncI1) carrying the blaCTX-M-1 gene and assess their transferability rates between homologous and heterologous serovars and/or species of bacteria. METHODS: First, the plasmids were sequenced, assembled, and annotated. They were then transferred from three donor strains (Escherichia coli/IncN, S. Heidelberg/IncN, and S. Heidelberg/IncI1) into nine recipient strains (S. Enteritidis, S. Heidelberg, S. Saintpaul, S. Cero, S. Infantis, S. Braenderup, E. coli 50, and E. coli 2010). The blaCTX-M-1 gene polymerase chain reaction (PCR), plasmid isolation, and antimicrobial susceptibility testing were used on the transconjugants to confirm the successful transfer of extended-spectrum beta lactamase (EBSL) plasmids into the recipient strains. RESULTS: Both IncN plasmids were 42,407 bp in size and showed >99.4% similarity to the S. Bredeney pET1.2-IncN (GenBank accession CP043224.1), whereas the IncI1 plasmid was 107,635 bp in size and demonstrated >99.9% similarity to the E. coli pCOV33 plasmid (GenBank accession MG649046.1). Successful plasmid transfer was observed between donor ​E. coli (IncN) and all recipient strains except for E. coli 50 and between donor S. Heidelberg (IncN) and all recipient strains. Successful plasmid transfer was also observed between S. Heidelberg (IncI1) and E. coli 50. CONCLUSION: Transfer of the blaCTX-M-1 encoding IncN and IncI1 plasmids via conjugation is possible and yet occurs at different frequencies depending on the donor strain of bacteria, with S. Heidelberg (IncN) having the highest donor-dependent transfer frequency, followed by E. coli 9079 (IncN) and S. Heidelberg (IncI1).

Antimicrobial prophylaxis does not improve post-surgical outcomes in SIV/SHIV-uninfected or SIV/SHIV-infected macaques (Macaca mulatta and Macaca fascicularis) based on a retrospective analysis.

Surgical antimicrobial prophylaxis is indicated when performing contaminated surgeries, when specific surgical implants are placed, and for prolonged surgical procedures. Unnecessary prophylactic antibiotics are often utilized for macaque surgeries, despite medical and veterinary guidelines. In this study we compared complication rates in macaques receiving peripheral lymph node (PLN) and laparoscopic biopsies, with and without antimicrobial prophylaxis. A majority of animals were SIV or SHIV infected at the time of surgery, so we also compared post-operative complication rates based on infection status. We found no significant difference in PLN biopsy complication rates for animals that received antimicrobial prophylaxis versus those that did not. Animals who underwent laparoscopic procedures and received prophylactic antibiotics had a higher complication rate than those who did not receive them. Complication rates did not differ significantly for SIV/SHIV infected versus uninfected animals for both laparoscopic biopsy procedures and PLN biopsy procedures. SIV/SHIV infected animals that underwent PLN biopsies had no significant difference in complication rates with and without antimicrobial prophylaxis, and SIV/SHIV infected animals receiving prophylactic antibiotics for laparoscopic biopsies had a higher complication rate than those that did not. This study suggests that perioperative prophylactic antibiotics have no role in the management of SIV/SHIV-infected and uninfected macaques undergoing clean, minimally invasive surgeries. Additionally, we recommend eliminating unnecessary antibiotic use in study animals due to their potential confounding impacts on research models and their potential to promote antimicrobial resistance.

Use of Whole Genome Sequencing by the Federal Interagency Collaboration for Genomics for Food and Feed Safety in the United States.

ABSTRACT: This multiagency report developed by the Interagency Collaboration for Genomics for Food and Feed Safety provides an overview of the use of and transition to whole genome sequencing (WGS) technology for detection and characterization of pathogens transmitted commonly by food and for identification of their sources. We describe foodborne pathogen analysis, investigation, and harmonization efforts among the following federal agencies: National Institutes of Health; Department of Health and Human Services, Centers for Disease Control and Prevention (CDC) and U.S. Food and Drug Administration (FDA); and the U.S. Department of Agriculture, Food Safety and Inspection Service, Agricultural Research Service, and Animal and Plant Health Inspection Service. We describe single nucleotide polymorphism, core-genome, and whole genome multilocus sequence typing data analysis methods as used in the PulseNet (CDC) and GenomeTrakr (FDA) networks, underscoring the complementary nature of the results for linking genetically related foodborne pathogens during outbreak investigations while allowing flexibility to meet the specific needs of Interagency Collaboration partners. We highlight how we apply WGS to pathogen characterization (virulence and antimicrobial resistance profiles) and source attribution efforts and increase transparency by making the sequences and other data publicly available through the National Center for Biotechnology Information. We also highlight the impact of current trends in the use of culture-independent diagnostic tests for human diagnostic testing on analytical approaches related to food safety and what is next for the use of WGS in the area of food safety.