Microorganisms

BackgroundReliable detection of Salmonella remains a major challenge for public health surveillance and food safety due to the growing diversity of circulating serovars and the limitations of existing molecular targets. This study aimed to identify an optimal molecular target and develop a TaqMan real-time PCR assay for the detection of Salmonella spp. MethodsBased on the results screening for Salmonella genes suitability as molecular markers, a TaqMan real-time PCR assay targeting the hilA gene was developed and validated. Analytical sensitivity, analytical specificity, and performance on bacterial isolates and artificially contaminated food samples were assessed. ResultsAmong all candidate targets, hilA demonstrated the broadest coverage and was detected in all tested Salmonella isolates, including representatives of rare serological groups, whereas invA conventionally used for this pathogen detection, was absent in a subset of strains. The assay exhibited a limit of detection of 100 bacterial cells/mL and 100 fg/L of genomic DNA. No cross-reactivity was observed with DNA from Shigella flexneri, Shigella sonnei, Yersinia pestis, Y. pseudotuberculosis, Y. enterocolitica, Y. kristensenii, Bacillus anthracis, Vibrio cholerae, or Francisella tularensis. The assay successfully detected Salmonella DNA in all artificially contaminated food samples tested. Evaluation using a collection of 25 bacterial isolates demonstrated positive amplification in all 24 confirmed Salmonella strains, while a strain initially identified by conventional bacteriology as Salmonella but subsequently confirmed by whole-genome sequencing as Proteus mirabilis yielded a negative result. ConclusionsThe hilA gene represents a highly conserved and reliable molecular target for the detection of Salmonella spp. The developed TaqMan real-time PCR assay demonstrated high analytical sensitivity, excellent specificity, and broad serovar coverage, supporting its application in laboratory detection of Salmonella, food safety monitoring, and epidemiological surveillance.

This study describes the characteristics of NATIVEDY162T (= JL13D10T = NRRL B-68525T) a novel bacterium isolated from the rumen of a healthy Holstein dairy cow. NATIVEDY162T was discovered to be an obligately anaerobic, slightly curved, rod that stains Gram-negative, and presents as singlets or short chains. Tests confirmed it is indole-, catalase-, oxidase-negative, and it is not motile. NATIVEDY162T indicated a growth preference within the pH range of 6.5-7.5 with optimal growth at pH 7.0. Carbon panel assays found NATIVEDY162T can utilize D-glucose, L-rhamnose, esculin/ferric citrate, D-lactose, and D-trehalose, whereas weak growth was observed on D-xylose and D-cellobiose. It was also capable of degrading starch and digesting both soluble and insoluble forms of cellulose, with genomic analysis providing further support by revealing a diverse array of carbohydrate-active enzymes (CAZymes) targeting starch and plant structural components like pectin and cellulose. Fermentation of glucose by NATIVEDY162T resulted in the major fermentation products lactate and butyrate. Phylogenetic analysis of the 16S rRNA gene positioned NATIVEDY162T in close relation to other Butyrivibrio species. Genome comparisons using BLAST ANI identified its closest relative as Butyrivibrio proteoclasticus (75.7% identity); however, the similarity did not meet the 95% threshold for species identification. Phylogenetic, genomic, and chemotaxonomic findings highlight differences between NATIVEDY162T and other Butyrivibrio species, indicating it is a novel species. NATIVEDY162T was isolated from a lactating Holstein dairy cow located in Californias San Joaquin Valley, a region rich in Portuguese influence from Azorean migrants who played a key role in the development of the California dairy industry, producing most of the states milk by the mid-20th century. Given this historical context, we propose the name Butyrivibrio azoria type strain NATIVEDY162T in honor of the significant contributions of Azorean and Portuguese dairy farmers in the region.

ObjectiveThis study aimed to establish an efficient isolation, culture, and preservation system for lactic acid bacteria from Mongolian horse feces by systematically evaluating the effects of sampling methods, culture conditions, media types, and cryopreservation protocols. MethodsFecal samples were collected using rectal and natural defecation methods, and bacteria were isolated by the spread plate technique, with isolates subcultured and identified via 16S rRNA gene sequencing. The performance of five commercial media (A-E), aerobic versus anaerobic conditions, and different glycerol concentrations (10% and 30%), temperatures (-20 {degrees}C and -80 {degrees}C), and storage durations (7, 15, and 30 days) were compared. ResultsRectal sampling showed significantly higher lactic acid bacterial survival and greater species diversity (12 vs. 8). Anaerobic culture yielded substantially higher counts and diversity (707 strains, 12 species) compared to aerobic conditions (36 strains, 5 species). Medium C (M.R.S. AGAR) exhibited the best isolation performance, producing the highest number of strains (311) and species (11), with selective enrichment for both bacilli and cocci. Glycerol effectively improved strain survival during sample cryopreservation, with the optimal short-term storage ([≤]15 days) achieved at -20 {degrees}C with 30% glycerol. Functional screening of randomly selected strains from optimized conditions demonstrated promising growth, acid and bile salt tolerance, and antimicrobial activity. ConclusionRectal sampling combined with anaerobic incubation using Medium C is recommended for optimal isolation. For samples that cannot be processed immediately, short-term preservation at -20 {degrees}C with 30% glycerol prior to isolation is effective. This study provides practical technical references for the acquisition and preservation of equine intestinal lactic acid bacteria resources.

From Brazilian limestone caves, we isolated 29 bacteria utilizing phenol (23 bacteria), toluene (all bacteria), and/or benzene (all bacteria) as sole carbon sources. One isolate showed phosphate solubilization, while lipase/esterase activity occurred in two isolates; no amylase activity was detected, but 16 isolates ([~]55%) exhibited protease activity. Among them, Nocardioides sp. SF1 was selected for whole-genome sequencing due to its aromatic compound tolerance and protease activity. Additionally, catechol cleavage assays yielded unexpected purple pigmentation, suggesting non-canonical aromatic metabolism. Its high-quality draft genome (4.25 Mbp, 16 contigs, N50 of 887 kb) lacks canonical phenol hydroxylase but encodes alternative oxidation systems, phenylacetyl-CoA pathway, besides, desferrioxamine siderophore, biosurfactants, and phosphate solubilization, key adaptations for oligotrophic caves and biotechnologically interesting activities. Whole-genome comparisons (TYGS/GGDC, OrthoANI and k-mer) suggest potential new species. Lacks acquired antimicrobial resistance genes (ResFinder) and pathogenicity potential (PathogenFinder). Nocardioides sp. SF1 emerges as a non-pathogenic candidate for aromatic bioremediation and plant growth promotion in contaminated, nutrient-poor environments, highlighting cave actinobacterias unexplored biotechnological potential.

Purpose: Human Parvovirus B19 (B19V) infection is associated with a broad spectrum of clinical manifestations, including erythema infectiosum, arthropathy, transient red cell aplasia, hepatitis, and adverse fetal outcomes. Due to nonspecific presentations and limited routine testing, B19V infection often remains undiagnosed. Despite recent reports of increased B19V activity worldwide, contemporary data on its presence in Brazil remain scarce. We investigated the circulation of underdiagnosed pathogens in patients with suspected infectious diseases, prioritizing severe and fatal cases. Methods: In this descriptive study, hybrid capture-based whole-genome sequencing was used for a broad-range viral detection and characterization. We analyzed 472 clinical specimens selected for diagnostic investigation between 2024 and 2025, according to surveillance criteria for respiratory and arboviral infections, referred to the Public Health Laboratory of the state of Rio de Janeiro, Brazil. Results: B19V was the second most frequently detected viral pathogens, being identified in 190/472 specimens. Of these, just one sample had been previously tested for this pathogen. Thirty-one cases had higher B19V genomic coverage and were therefore selected for further analysis. Notably, B19V was the only virus detected with substantial genomic coverage in nine individuals, including elderly patients, and meningitis cases with B19V-positive cerebrospinal fluid. Phylogenetic analysis showed that recovered genomes clustered within genotype 1A2. Conclusions: B19V was frequently detected in patients undergoing investigation for infectious diseases and its circulation may represent an important and underrecognized pathogen. These findings support the incorporation of B19V testing into diagnostic algorithms for unexplained infectious diseases, especially in patients presenting atypical symptoms.

Stony coral tissue loss disease (SCTLD), a coral pathology with rapid tissue loss and high mortality rate has affected nearly 30 species with a variable degree of susceptibility across species. It has been suggested that SCTLD has a systemic effect within coral colonies, but little is known about within-colony changes of the microbial communities associated with this disease. Here we evaluate the microbial shifts within coral colonies: apparently healthy tissue and SCTLD tissue. The study was done in three species following a gradient of susceptibility to the disease: Dendrogyra cylindrus (Dcyl, n = 11) and Pseudodiploria strigosa (Pstr, n = 6) two highly susceptible species; and Orbicella faveolata (Ofav, n = 8), a moderately affected species. 16S rRNA Illumina sequences analysis showed differential microbial community structure within two species (Dcyl, p = 0.01, Pstr, p = 0.01) but not for Ofav (p = 0.28). Taxonomic profiles of bacterial groups were species-specific in SCTLD tissue, but healthy tissue shared similarities between species including Pirelullales, NB1-J and SAR324. Our results reveal that the microbial communities effects associated to the disease follow a similar pattern to the species susceptibility to SCTLD, providing new insights into the disease dynamics in the Mexican Caribbean.

This study investigated the genomic and biochemical characteristics of two amylolytic microbial strains, NATIVEDY160T (= JE7B6T = NRRL B-68523T) and NATIVEDY161T (= JL13D9T, = NRRL B-68524T) isolated from the rumen of healthy Holstein dairy cattle. Both strains are obligately anaerobic, non-motile, Gram positive, catalase-negative, and oxidase-negative. Morphologically, NATIVEDY160T grows in long coccoid chains while NATIVEDY161T grows in short chains or pairs. NATIVEDY160T can catabolize amygdalin, esculin/ferric citrate, and starch, compared to NATIVEDY161T which utilizes amygdalin, arbutin, esculin/ferric citrate, glycogen, and D-maltose as determined by API 50 CH carbon panels. Starch degradation ability was verified for both strains, but neither showed cellulolytic activity as confirmed by starch agar and Congo red agar assays, respectively. HPLC analysis revealed that lactate was the primary end product of both strains carbohydrate fermentation, while strain NATIVEDY161T also produced small amounts of acetate. 16S rRNA sequences from both strains cluster with the Oscillospiraceae (formerly Ruminococcaceae) lineage Ruminococcus species, but average nucleotide identity of either strain compared to closely related Ruminococcus members was under the species threshold (95%). Genomic, phylogenetic, and phenotypic interrogation support NATIVEDY160T and NATIVEDY161T as novel species. Each strain was isolated from the rumen of dairy cows located within the central valley of southern California, which has a rich history of Dutch and Basque dairy farm ownership and is still the case today in the region. In recognition of the contributions and heritage of the central and southern California dairy industry, the names Ruminococcus hollandia and Ruminococcus vasco are proposed with NATIVEDY160T and NATIVEDY161T as their respective type strains.

Syngas fermentation by carbon monoxide (CO)-utilising acetogens offers a sustainable route for converting gasified waste materials into value-added chemicals. In this study, we isolated a novel thermophilic CO-utilising bacterium, strain AZ2, from marine hydrothermal sediment collected on the island of Sao Miguel, Azores, Portugal. Strain AZ2 is an obligately anaerobic, spore-forming bacterium. Average nucleotide identity (ANI; 78.4-86.7%) and digital DNA-DNA hybridization (dDDH; 23.4-32.5 %) analyses indicate that strain AZ2 represents a novel species within a previously uncharacterised lineage represented by the GTDB placeholder genus UBA2545 in the Neomoorellaceae family. Strain AZ2 was able to grow fermentatively on CO, producing acetate. We further demonstrated that its closest isolated relatives - Thermanaeromonas toyohensis, T. burensis, and Thermanaeromonas sp. strain 9S - are capable of growing on CO, producing either acetate or hydrogen gas (H2). Additionally, we unveiled the genomic potential for CO utilisation within other members of the GTDB placeholder class DSM-521 (previously Moorellia) to which our isolate belongs, expanding the list of possible thermophilic CO-utilising acetogens. We propose that strain AZ2T represents the type strain of a novel genus and species, named Thermobium azorense gen. nov., sp. nov. (= DSM 121889T = JCM 39698T).

IntroductionAcute myeloid leukemia (AML) is a hematological malignancy associated with muscle wasting. As the relative abundance of Lachnospira eligens was reduced in patients with AML compared to healthy individuals and correlated positively with muscle strength, we hypothesized that L. eligens positively impacts the muscle through the production of small metabolites reaching the systemic circulation. MethodsL. eligens levels were analyzed in two additional independent cohorts. Six L. eligens isolates were characterized through whole-genome sequencing to select clinically relevant strains. The composition of their culture supernatant was analyzed by metabolomics. The impact of L. eligens supernatant on dexamethasone- and interleukin-6-atrophied murine myotubes was assessed. Bioactive metabolites and their production mechanism were identified using among others bioactivity-guided fractionation. The underlying mechanism was also explored on the host side through myotubes transcriptome analysis and metabolic flux analysis. The relevance of bioactive metabolites and their production mechanism was evaluated through clinical data and samples analyses and in a mouse model of leukemia. ResultsThe levels of L. eligens are reduced in independent cohorts of patients with AML and its supernatant counteracts myotube atrophy. This anti-atrophic effect, conserved between strains of the same species, depends on the occurrence of mixed acid fermentation (MAF) in anoxic culture conditions and the presence of its acid end-products acetate, formate and D-lactate. Consistent with those results, blood levels of acetate are decreased and the relative abundance of fecal bacteria capable of performing aerobic respiration is increased in patients with AML. However, bacterial supernatant failed to prevent muscle atrophy and weakness in leukemic mice, likely due to insufficient sustained elevation of acid end-products in the blood. ConclusionThis work reveals the anti-atrophic effect of MAF end-products on myotubes and suggests the importance of considering gut electron acceptor levels (e.g. O2) in disorders affecting muscle health. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/729780v1_ufig1.gif" ALT="Figure 1"> View larger version (40K): org.highwire.dtl.DTLVardef@112529eorg.highwire.dtl.DTLVardef@1ee1929org.highwire.dtl.DTLVardef@b5f389org.highwire.dtl.DTLVardef@187bc40_HPS_FORMAT_FIGEXP M_FIG Mixed acid fermentation products from Lachnospira eligens counteract myotube atrophy. Our study suggests that gut anaerobiosis is disrupted in treatment-naive patients with acute myeloid leukemia (AML), leading to decreased circulating acetate levels and a reduced relative abundance of L. eligens, which significantly correlated with muscle strength. In line with this framework, in vitro experiments demonstrate that the culture supernatant of L. eligens, which contains mixed acid fermentation (MAF) end-products such as acetate, effectively counteracts C2C12 myotube atrophy in the presence of pro-atrophying stimuli. Further mechanistic experiments indicate a causal role for MAF end-products in this anti-atrophying effect. Created with BioRender.com. Legend: solid frames: experimental results; dashed frames: hypothetical conclusions derived from results; black solid arrow: established correlation; black dashed arrows: hypothetical causation. C_FIG

The obscure life histories of many kickxellalean genera remain a bottleneck for comprehensive taxon sampling and phylogenetic reconstruction of the order. While Kickxellales has long been regarded as saprobes inhabiting soil or dung, the discovery of "amphibious fungi" such as Unguispora, which exhibits dimorphic growth between the animal gut and feces, suggests a cryptic gut-dwelling stage within these genera. Given its phylogenetic proximity to Unguispora, ecophysiological traits of Linderina were investigated to evaluate its potential association with the animal gut. Two isolates of L. macrospora were obtained from Japanese soil, representing the first record of this species in Japan. Physiological assays revealed that the optimal temperature for both vegetative growth and sporulation was 25-30 {degrees}C. Furthermore, comparative growth assays on different media demonstrated that sporocladium abundance per sporangiophore is sensitive to nutrient availability, and nutrient-poor media were determined to be the most suitable for evaluating morphological characterization. Under anaerobic, nutrient-rich conditions which are known to induce yeast-like growth in Unguispora, sporangiospores of L. macrospora produce arthrospores. Although marked morphological plasticity was observed during the arthrospore formation, the occurrence of yeast-like unicellular proliferation suggests a potential relationship with the animal gut. Additionally, vegetative growth and sporulation were markedly inhibited by white light exposure; notably, a lethal effect on growth was observed during incubation at 20 {degrees}C, indicating that the natural niche of the species is restricted to light-shielded environments. Our findings will help to elucidate the cryptic life cycles and evolutionary trajectories within Kickxellales.

The aim of this study was to evaluate the impact of two sustainable dietary protein sources on the structure and composition of the gut microbiota in European sea bass (Dicentrarchus labrax) juveniles. These protein sources were incorporated to the aquafeeds containing (a) Lupinus albus meal, treated with either exogenous enzymes (Solid state hydrolysis-SSH) or fermented with Saccharomyces cerevisiae (Solid state fermentation, SSF) and (b) Lagocephalus sceleratus meal. In the first case (a), the control aquafeed simulated a standard commercial diet, containing soybean meal whereas in the rest of the diets soybean meal was partially or totally replaced by hydrolysed or fermented Lupin meal. In the second case (b) the fish were fed Lagocephalus sceleratus unprocessed fishmeal as well as treated at different temperatures to deactivate tetrodotoxin (TTX). A control diet with 30% commercial fish meal was also fed as a reference diet. Both diets in all inclusion levels did not cause any significant gut microbiota change, suggesting their neutral role in this aspect. However, the gut bacterial communities of the fish fed with 12.5% lupin meal inclusion, had increased amino acid biosynthetic pathways suggesting a beneficial effect.

Predatory protists are important in shaping terrestrial microbial ecosystems, but their roles in the phyllosphere, or the communities on aerial plant surfaces, are poorly understood. Previous work found that the order Colpodida dominated heterotrophic protist communities in the phyllosphere. While most protists were sporadically present, a few Colpodida variants were prevalent and abundant, indicating that these variants may represent species adapted to the phyllosphere. To identify these organisms, we cultured colpodids from field-collected tomato leaves and performed phylogenetic analysis of the 18S rRNA gene. Five of nine independent isolates matched the most prevalent Colpodida variant previously identified as leaf-enriched through amplicon sequencing, and these isolates comprised a novel clade of Paracolpoda steinii. When compared to a maize root isolate of Colpoda inflata, an abundant rhizosphere ciliate, a P. steinii isolate was similar in size and growth yield on E. coli, but grew to higher yields and formed large cyst clusters when incubated with model phyllosphere bacteria prey Erwinia and Pseudomonas. We developed and validated quantitative PCR (qPCR) methods for detection and cell abundance estimation of the P. steinii phyllosphere clade, C. inflata, and the order Colpodida in environmental samples. In inoculated greenhouse plants, qPCR-estimated protist populations matched measured inoculum levels, and protist inoculum was still detectable after five days. In an uninoculated tomato field, P. steinii was detected on all plants, with greatest abundances observed in lower leaves and after a rain event. P. steinii comprised up to 18.7% of total leaf Colpodida populations, which were estimated at up to [~]1400 organisms per gram of fresh weight. The findings demonstrate that Colpodida communities are consistently present on tomato leaves, dynamically affected by the abiotic environment, and include significant populations of P. steinii. We propose that the P. steinii isolates and qPCR tools presented can be used as a model system to investigate colonization and distribution patterns, biotic interactions, genetic adaptations, and agricultural applications of leaf predation.

BackgroundHuman head lice (Pediculus humanus capitis de Geer) are known to harbor diverse maternally inherited bacterial symbionts. These endosymbiotic bacteria may contribute to insecticide degradation, potentially helping lice withstand particular environmental pressures. Using next-generation sequencing (NGS), this study investigated the bacterial symbionts present in wild head-louse populations and characterized their phylogenetic relationships in mutant and permethrin-susceptible strains. MethodsHead lice specimens were collected from 10 locations across Fars Province, Iran. Following DNA extraction, the samples were analyzed using polymerase chain reaction (PCR), and the resulting amplicons were sequenced to detect mutations in specimens from each location. Lice were then classified according to the presence or absence of mutations and subjected to NGS to characterize the symbiotic bacterial communities in mutant and putatively permethrin-susceptible strains. ResultsMutant strains were detected at only three sampling stations. Bioinformatic analysis of the nucleic acid sequences revealed three exons and two introns, with an expected amplicon length of 582 bp. NGS analysis showed that Candidatus Riesia pediculicola (Arsenophonus), belonging to the phylum Proteobacteria, was the predominant bacterial genus. Actinobacteria and Firmicutes were the second- and third-most abundant phyla, respectively. Most of the remaining 25 bacterial taxa were associated with the mutant strain. Additionally, two previously unreported bacterial genera were deposited in GenBank. ConclusionsThe distinct distribution of Arsenophonus species between susceptible and mutant head-lice strains--along with the greater abundance of Escherichia, Shigella, Lawsonella, and Megamonas in mutant strains--highlights the need for advanced metagenomic analyses to determine how these endosymbionts may help their hosts withstand specific environmental disturbances.

In spite of well-established global immune landscape, SARS-CoV-2 is still able to further spread and continue causing infection waves. The current understanding about the reason behind is limited, and it is still difficult to predict the evolution or spreading tread of SARS-CoV-2. Therefore, it is necessary to investigate whether the establishment of population immunity has changed the virus evolution or spreading pattern. In this investigation, one overall analysis of the SARS-CoV-2 spreading in the past several years have been carried out through one thorough genomic epidemiology study, with Germany being chosen as one representative location in view of the systemic efforts for genomic surveillance. The growth advantage of a few predominant variants in its early spreading period has been evaluated through a logistic regression model. The results have revealed that the major circulating SARS-CoV-2 variants since 2023 are mainly derived from the Omicron BA.2 family. Since middle of 2024, most predominant variants were produced primarily through recombination, indicating that the evolution derived from recombination might be the major driving force for the continuous spread of SARS-CoV-2 despite the existence of population immunity. Furthermore, the lower growth advantage of recently emerged variants might possibly lead to a tread of reduction in the frequency of infection wave. The information revealed from this investigation suggests that although short-term spreading tread can be affected by specific virus feature as well as local immunity landscape, the long-term spreading tread is mainly decided by the genomic diversity of the viruses, and can be predicted through phylogenetic and genomic epidemiology investigation. The results have emphasized the importance of maintaining the efforts for genomic surveillance of SARS-CoV-2, which is essential from both medical and research perspectives.

Background Otitis media is a leading cause of childhood morbidity and presents a significant healthcare burden worldwide. Streptococcus pneumoniae is a major aetiological agent of OM, and the introduction of pneumococcal conjugate vaccines into the Malaysian National Immunisation Programme in 2020 would have altered pneumococcal carriage and serotype distribution. This study aimed to determine pneumococcal carriage, serotype distribution, and associated risk factors among children with OM in the early post-PCV era in Peninsular Malaysia. Methods and Findings A total of 360 children with OM were recruited from hospitals on the east and west coasts of Peninsular Malaysia between 2023 and 2025. Nasopharyngeal and middle ear fluid samples were collected for Spn isolation by culture, followed by serotyping using multiplex PCR. Sociodemographic, environmental, and medical history data were analysed for associations with pneumococcal carriage using chi-square, Fishers exact tests, and logistic regression. Pneumococcal carriage was detected in 26.7% of children in either NP or MEF samples, with carriage rates of 25.6% and 1.9% in NP and MEF samples, respectively. The most prevalent serotypes were 23A, 15B/15C, non-typable strains, 19F, and 11A/11D. Daycare attendance (p = 0.012, aOR [95% CI]: 2.177 [1.186 - 3.995] and residence in rural areas (p = 0.019, aOR [95% CI]: 2.476 [1.159 - 5.292] were significantly associated with pneumococcal carriage. The main limitation of the study was the reliance on self-reported questionnaire data, which may have introduced recall bias and reporting errors. Conclusions The predominance of non-vaccine serotypes and non-typable Spn indicates ongoing serotype replacement and the emergence of phase-variant strains in the early post-PCV era. Continued surveillance is essential to monitor these changes and inform the development of next-generation pneumococcal vaccines. This study was registered under clinical trial registration number NCT05429541.

Salmonellosis continues to be one of the most important causes of food-borne illness in the U.S. An additional concern with this bacterial pathogen is that infections with multiple-antibiotic-resistant Salmonella strains are becoming untreatable infectious diseases. Poultry meat and eggs are major sources of Salmonella food-borne illness, due to carriage of these bacterial pathogens in the intestinal microbiome of chickens. A food safety priority, as stated by the USDA, is a significant reduction in carriage of pathogenic Salmonella species in poultry which would significantly improve food safety and reduce cases of human salmonellosis contracted from consumption of contaminated poultry. While this goal has been a priority for many years, basic research and animal management efforts have not achieved significant control of Salmonella carriage. This study represents an alternative approach to reduce or eliminate carriage of Salmonella in poultry flocks. We characterized a type 1 fimbrial allele of Salmonella that confers high levels of adherence to various host cells. We then engineered an E. coli Nissle 1917 probiotic strain that expresses this Salmonella adherence factor at high levels. The E. coli Nissle 1917 is used as the scaffold strain for this work since this E. coli strain has received the FDA designation of Generally Regarded As Safe (GRAS) and has been used for many years as a probiotic to treat human intestinal disorders. Our E. coli Nissle strain was engineered to use an in vivo selection system for a plasmid carrying the cloned Salmonella type 1 fimbrial genes, so that the strain can be used as a probiotic without any antibiotic resistance-encoding genes requiring antibiotic selection for maintenance of the desired phenotype. Our probiotic strain displays high levels of adherence to host cells, in fact higher levels of adherence than a Salmonella strain carrying the same type 1 fimbrial genes. We demonstrate that the probiotic strain significantly outcompetes pathogenic Salmonella strains for adherence to tissue culture cells and in vivo experimental challenges revealed that the probiotic strain mediates a significant exclusion of Salmonella from the intestines of broilers, layers, and turkeys.

Gonorrhea, caused by the Gram-negative bacterium Neisseria gonorrhoeae, poses a growing global public health threat due to the rapid emergence of multidrug-resistant strains and the limited availability of effective treatments. Since there are no known lytic gonophages, we explored prophages present in the genome of N. gonorrhoeae FA1090, with a particular focus on prophage-encoded endolysins. In this study, we evaluate antigonococcal properties of prophage-encoded endopeptidases with the NlpC/P60 enzymatic domain. Recombinant endolysin Phi1gp518 exhibits intrinsic bactericidal activity against non-permeabilized N. gonorrhoeae FA1090 cells. Furthermore, it shows an expanded host range against clinical gonococcal isolates. The gonolysin remains stable across all human body temperatures, a pH range of 5-10, and shows no cytotoxic effects toward human cervical epithelial cells, supporting its potential safety for therapeutic applications. Additionally, Phi1gp518 impairs the formation of gonococcal microcolonies and prevents proper biofilm establishment. The antigonococcal properties of Phi1gp518 endopeptidase make it a good candidate for further protein engineering and development as an alternative treatment strategy for drug-resistant N. gonorrhoeae infections.

IntroductionEnteric fever, being endemic with seasonal peaks in low- and middle-income countries, is a major health concern. Moreover, the rise in antibiotic resistance has exacerbated the situation. This study was undertaken to investigate the lytic bacteriophages against Salmonella Typhi with a potential for phage therapy. Materials and MethodsA hospital-based cross-sectional study was conducted from October 2023 to March 2024. Blood cultures were processed by the BACTEC automated culture system following standard microbiological techniques to isolate typhoidal Salmonella. Antibiotic susceptibility was tested by the modified Kirby-Bauer disc diffusion method. Lytic bacteriophages isolated by the double-layer agar method were assessed for their host range and lytic ability with spot and turbidimetric assays. ResultsOf the total 1054 blood specimens, 35 (3.2%) were positive for S. Typhi. All the isolates were susceptible to first-line antibiotics--ampicillin, chloramphenicol, and cotrimoxazole. The isolates were also sensitive to nalidixic acid (80%) as well as fluoroquinolones; ciprofloxacin (62.86%), levofloxacin (77.14%), and ofloxacin (80%). Fifteen lytic phages were isolated against S. Typhi Ty2 and CT18 strains. Four phages--vB_SaTy_ST2, vB_SaTy_ST7, vB_SaTy_ST17, and vB_SaTy_ST18--lysed all 35 clinical S. Typhi isolates. While vB_SaTy_ST17 and vB_SaTy_ST18 also lysed 7 out of 20 S. Paratyphi A isolates. Three phages (vB_SaTy_ST2, vB_SaTy_ST7, vB_SaTy_ST17) were tested against S. Typhi isolate S30. Individually, vB_SaTy_ST17 suppressed the growth for 13 hours, vB_SaTy_ST2 and vB_SaTy_ST7 for 10 hours. The phage cocktail vB_SaTy_ST2 + vB_SaTy_ST17 was the most effective, which extended the inhibition time to 15 hours. ConclusionThis study highlights the ongoing burden of enteric fever in Nepal and the increase in susceptibility of S. Typhi to nalidixic acid and fluoroquinolones. It also demonstrates the promising lytic potential of bacteriophages, particularly vB_SaTy_ST17 and the phage cocktail vB_SaTy_ST2 + vB_SaTy_ST17, against clinical S. Typhi, highlighting their potential as alternatives to antibiotics.

Endophytic yeasts of the Metschnikowia pulcherrima clade are recognized as natural producers of pulcherrimin, an iron-chelating red pigment associated with antimicrobial activity. However, endophytic isolates from arid Central Asian fruit trees remain unexplored, and their pulcherrimin biosynthetic capacity is poorly characterized. In this study, five endophytic M. pulcherrima strains were isolated from apricot, persimmon, peach and pomegranate fruits in Uzbekistan and identified using MALDI-TOF MS and ITS sequencing. The strains were cultivated in FeCl-supplemented Sabouraud medium, and pulcherrimin was extracted and quantified using a gravimetric workflow with biological triplicates. Pigment yields ranged from 420.6 to 776.4 mg/L, representing some of the highest values reported for non-engineered isolates under flask conditions. Antimicrobial activity was evaluated by agar well diffusion assays against Staphylococcus aureus, Bacillus subtilis, Escherichia coli, Pseudomonas aeruginosa and Candida albicans, with inhibition zones reaching 18-23 mm depending on the strain. Nano-LC-MS/MS analysis confirmed the presence of key intermediates of the pulcherrimin biosynthetic pathway, including cyclo(Leu-Leu) and pulcherriminic acid, supporting the metabolic origin of the pigment. These findings reveal that endophytic M. pulcherrima from Uzbekistan fruit trees and shrubs constitute highly productive natural sources of pulcherrimin and represent promising candidates for future fermentation optimization and development of natural antimicrobial pigments. Paragraph on importanceThis study provides the first systematic evidence that endophytic Metschnikowia pulcherrima yeasts isolated from fruit trees in Central Asia possess an exceptional capacity to produce pulcherrimin, a natural antimicrobial pigment. Strains obtained under the environmental conditions of Uzbekistan produced remarkably high levels of pulcherrimin (up to 776 mg/L) under simple, non-genetically modified fermentation conditions, exceeding yields previously reported for yeast and bacterial sources. The iron-chelating mechanism characteristic of pulcherrimin confers broad-spectrum antimicrobial activity against bacteria and yeasts. These findings highlight endophytic yeasts as environmentally safe and sustainable sources of natural antimicrobial pigments and identify Central Asia as a previously unexplored reservoir of high-value microbial resources with significant biotechnological potential.

Macrolides are key agents for treating infections caused by non-tuberculous mycobacteria (NTM). Nevertheless, chromosomal erm genes conferring inducible macrolide resistance are described in some NTM species, such as Mycobacterium abscessus and M. fortuitum, whereas M. chelonae had long been considered as lacking a functional erm. Recent descriptions from the USA and Japan of a new plasmid-borne erm(55) (erm(55)P) in M. chelonae and other rapidly growing mycobacteria (RGM) have challenged this assumption. We investigated erm(55)P occurrence in clinical RGM referred to the French National Reference Centre for Mycobacteria between 2012 and 2026 by genome screening and erm(55)P specific real-time PCR. Positive isolates underwent long-read whole genome sequencing (GridIon, Oxford Nanopore Technologies). Clarithromycin (CLR) minimum inhibitory concentration (MIC) was determined by broth microdilution (RAPMYCO and FRATMYC, Thermo Fisher) and read up to 14 days. Five clinical isolates showing inducible CLR resistance (MIC range <0.25-64 mg/L on day 3-4 and 128 - >128 mg/L on day 14) were positive for erm(55)P: one M. chelonae, three M. neoaurum, and one M. parafortuitum. erm(55)P-positive M. chelonae genomes from this and previous descriptions did not cluster together in the phylogenetic analysis of 263 genomes. The assembled plasmids showed high similarity to previously reported erm(55)-carrying plasmids, especially within the erm(55)P region. The upstream sequence of erm(55)P showed a secondary structure compatible with a possible translation attenuation mechanism. These findings document the first report of a plasmid-borne erm(55) in Europe in M. chelonae and other RGM and raise concern about the emergence of plasmid macrolide resistance in NTM.