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At least 19 recordsLinked to original sources
PubMed2019

Large-scale genome analysis of bovine commensal Escherichia coli reveals that bovine-adapted E. coli lineages are serving as evolutionary sources of the emergence of human intestinal pathogenic strains.

How pathogens evolve their virulence to humans in nature is a scientific issue of great medical and biological importance. Shiga toxin (Stx)-producing Escherichia coli (STEC) and enteropathogenic E. coli (EPEC) are the major foodborne pathogens that can cause hemolytic uremic syndrome and infantile diarrhea, respectively. The locus of enterocyte effacement (LEE)-encoded type 3 secretion system (T3SS) is the major virulence determinant of EPEC and is also possessed by major STEC lineages. Cattle are thought to be the primary reservoir of STEC and EPEC. However, genome sequences of bovine commensal E. coli are limited, and the emerging process of STEC and EPEC is largely unknown. Here, we performed a large-scale genomic comparison of bovine commensal E. coli with human commensal and clinical strains, including EPEC and STEC, at a global level. The analyses identified two distinct lineages, in which bovine and human commensal strains are enriched, respectively, and revealed that STEC and EPEC strains have emerged in multiple sublineages of the bovine-associated lineage. In addition to the bovine-associated lineage-specific genes, including fimbriae, capsule, and nutrition utilization genes, specific virulence gene communities have been accumulated in stx- and LEE-positive strains, respectively, with notable overlaps of community members. Functional associations of these genes probably confer benefits to these E. coli strains in inhabiting and/or adapting to the bovine intestinal environment and drive their evolution to highly virulent human pathogens under the bovine-adapted genetic background. Our data highlight the importance of large-scale genome sequencing of animal strains in the studies of zoonotic pathogens.

Animals↗
PubMed1978

A diagnostic key employing biological reactions for differentiating pathogenic Corynebacterium genitalium (NSU corynebacteria) from commensals of the urogenital tract.

More than 100 strains of Corynebacterium genitalium, probably responsible for coryneform urethritis and other infections, and 600 commensals of the male and female urogenital tracts have been studied and grouped into five pathogenic types numbered I to V and six saprophytic types designated C-1 to C-6 on the basis of eight biological reactions. This preliminary classification has been based on differences in requirements for oxygen, on the fermentation of fructose, dextrose, sucrose, and starch together with the production of the enzymes gelatinase, lipase, and urease. One criterion differentiated the pathogens from the commensals: All pathogens were nonfructose fermenters whereas every commensal fermented this sugar.

Bacteriological Techniques↗
PubMed2026

Commensal Dysbiosis Alters Primary Bile Acid Signaling to Drive Mammary Gland Inflammation and Breast Tumor Dissemination.

UNLABELLED: Breast cancer is the most commonly diagnosed malignancy and a leading cause of cancer-related mortality. Hormone receptor-positive (HR+) tumors represent the most prevalent metastatic subtype, and early dissemination remains a major clinical challenge. Commensal dysbiosis, defined as an inflammatory gut microbiome with low biodiversity, promotes metastasis by inducing mammary gland inflammation. In this study, we investigated systemic mechanisms governing dysbiosis-induced metastasis. Metabolomic profiling revealed elevated primary bile acids (BA) in the dysbiotic fecal microbiome. Sequestration and supplementation approaches demonstrated that beyond driving metabolic disease and mammary gland inflammation, primary BAs orchestrated enhanced HR+ tumor dissemination via a prostaglandin E2 (PGE2)-dependent pathway. Analysis of The Cancer Genome Atlas showed that BA, insulin resistance, and PGE2 gene signatures are associated with reduced survival in patients with HR+ tumors. In complementary analyses using the Epic Cosmos electronic health record database, BA sequestrant use was associated with longer restricted mean survival time among patients with metastatic disease. Together, these findings reveal that commensal dysbiosis-associated loss of microbial BA metabolism elevates primary BAs and promotes HR+ metastatic progression through PGE2 signaling. SIGNIFICANCE: Dysbiosis-induced bile acids drive systemic and mammary tissue-specific inflammation that promotes HR+ breast tumor metastasis, supporting the development of strategies targeting microbiome-derived metabolites to reduce metastatic risk in vulnerable populations.

Female↗
PubMed2026

Antimicrobial susceptibility patterns of commensal fecal bacteria isolated from pigs with an intentional genomic alteration that included the selectable marker gene nptII.

INTRODUCTION: Animals with intentional genomic alterations (IGAs) hold promise for meeting increasing worldwide demand for animal-source proteins. As part of regulatory risk assessment for introducing animals with IGAs into the food chain, monitoring commensal bacterial microbiota is recommended due to concern that antimicrobial resistance genes used during IGA selection could be transferred, via horizontal gene transfer, to gastrointestinal or environmental bacterial populations, potentially contributing to antimicrobial resistance. The objective of this study was to assess the antimicrobial susceptibility patterns in commensal bacteria isolated from fecal samples of GalSafe™ pigs that have an IGA that includes the aminoglycoside resistance gene nptII. METHODS: Antimicrobial resistance rates observed in Escherichia coli, Salmonella, Campylobacter and Enterococcus isolated from GalSafe™ pigs were compared to resistance rates observed in conventional pigs at slaughter. Bacterial isolates were tested for antimicrobial resistance genes by PCR and one isolate underwent whole genome sequencing. RESULTS: In total, 137 bacterial isolates recovered from 55 fecal samples collected from 47 individual adult GalSafe™ pigs were evaluated. Prevalence of antimicrobial resistance in GalSafe™ pigs was generally similar to, or lower than, resistance prevalence reported from conventional pigs at slaughter, based on National Antimicrobial Resistance Monitoring System (NARMS) data. Higher resistance rates in GalSafe™ pigs were observed only for quinolones in Campylobacter coli (ciprofloxacin and nalidixic acid) and nitrofurantoin in Enterococcus spp. One isolate (E. coli) was positive for nptII neomycin resistance gene, the same gene used for IGA selection in GalSafe™ pigs, and the remaining 136 isolates were negative for nptII. However, the positive isolate did not appear to contain nptII derived from the GalSafe™ pig genome as the sequences flanking the gene did not match the IGA. DISCUSSION: We did not detect evidence of nptII gene transformation into bacterial species of potential human health importance in this population of GalSafe™ pigs.

NARMS↗
PubMed1975

Some factors influencing colicin activity between pathogenic and commensal Escherichia coli from the pig.

Commensal strains of Escherichia coli derived from pigs had a broad spectrum of in vitro colicin acitivity against pathogenic serotypes. Of eight pathogenic serotypes tested, only three were colicinogenic and were active against relatively few commensal strains. Colicin activity was influenced by temperature, pH and oxygen tension as well as by the availability of certain nutrients and the presence of trypsin. Lack of colicin activity in intestinal supernatant fluid was ascribed to the concentration of trypsin present. It was concluded that colicins are unlikely to influence the dominance of pathogenic Escherichia coli serotypes in the pig's intestine, except possibly in the colon and rectum where the concentration of trypsin is low.

Animals↗
PubMed2026

Herd-level heterogeneity of antimicrobial resistance in commensal Escherichia coli: A nationwide high-throughput survey of Australian pig herds.

Antimicrobial resistance in commensal Escherichia coli provides a useful indicator for overall antimicrobial resistance burden. We applied this approach to assess antimicrobial resistance within and between commercial pig herds across Australia. A high-throughput robotic workflow was used to isolate 2730 E. coli colonies from rectal contents collected in 2022 from healthy slaughter pigs (n = 300) representing 30 herds (∼70% of national production). Up to 94 isolates per herd underwent antimicrobial susceptibility testing using the Robotic Antimicrobial Susceptibility Platform. Isolate- and herd-level antimicrobial resistance indices were calculated, weighting antimicrobials by their human health importance. Resistance to first-line agents was widespread: ampicillin 77% and tetracycline 79%. By contrast, resistance to critically important antimicrobials was rare (ciprofloxacin 0.11%; extended-spectrum cephalosporins 0.04%), and no clinical resistance to carbapenems or colistin was detected. Overall, 56.9% of isolates were multi-class resistant. Herd-level antimicrobial resistance within indices ranged from 1.51 to 5.76, revealing substantial between-herd heterogeneity. Three herds carried critically important antimicrobials-resistant isolates that would likely have been missed using conventional, lower-density sampling approaches. Whole-genome sequencing identified fluoroquinolone-resistant isolates belonging to ST10 and ST69 (both qnrS1), and ST744 (Quinolone Resistance Determining Region mutations plus blaCTX-M-27). By testing approximately tenfold more isolates than conventional surveys, we uncovered considerable antimicrobial resistance with heterogeneity within and between animals and herds, including farm-specific variability. This expanded sampling also enabled detection of critically important antimicrobial resistance at very low prevalence. In conclusion, high-throughput, high-density testing offers a practical early-warning system and herd-level benchmark to inform surveillance and targeted interventions.

Animals↗
PubMed2026

Transferable IncX3-blaKPC-2 plasmid and chromosomal blaCTX-M-27 in a commensal Escherichia coli ST7854 isolated from a healthy companion dog.

OBJECTIVES: Carbapenemase-producing Enterobacterales have disseminated globally, largely via highly transmissible plasmids. Their emergence in companion animals is of particular concern, indicating that clinically important carbapenem-resistance determinants have spread beyond healthcare settings. This study characterized a multidrug-resistant Escherichia coli isolate from a healthy dog in South Korea. METHODS: Antimicrobial susceptibility was determined by standardized reference methods. Hybrid whole-genome assembly resolved chromosomal and plasmid architectures, and plasmid transferability was assessed by conjugation assays. Comparative genomic analysis based on nucleotide identity and alignment coverage evaluated relatedness to publicly available blaKPC-carrying IncX3 plasmids. RESULTS: The E. coli ST7854 isolate was resistant to carbapenems (imipenem MIC = 8 µg/mL), third-generation cephalosporins, fluoroquinolones, tetracycline, gentamicin, phenicols, and trimethoprim-sulfamethoxazole, but susceptible to amikacin and colistin. Assembly resolved a 4.77 Mb circular chromosome and seven plasmids. The ESBL gene blaCTX-M-27 was chromosomally integrated, whereas carbapenem resistance was conferred by blaKPC-2 on a 54,805 bp IncX3 plasmid. This IncX3-blaKPC-2 plasmid was transferred to E. coli J53 at a frequency of 5.91 × 10⁻⁴, whereas the large IncFIB multidrug resistance plasmid was not co-transferred. Comparative analysis revealed extensive structural similarity with Korean clinical IncX3 plasmids, whereas most representative international plasmids shared only the conserved IncX3 backbone. CONCLUSIONS: A commensal E. coli ST7854 isolate from a healthy companion dog carried a conjugative IncX3-blaKPC-2 plasmid and chromosomally integrated blaCTX-M-27. Similarity to Korean clinical plasmids suggests potential human-animal dissemination, and this asymptomatic carriage of mobile carbapenem-resistance determinants supports continued genomic surveillance of antimicrobial resistance in companion animals within a One Health framework.

Bla(CTX-M-27)↗
PubMed1979

Adhesion of commensal bacteria to the large intestine wall in humans.

Biopsies taken during colonoscopic examination of the human large bowel were used to examine the relationship of the commensal bacterial to the mucosal epithelial cell surface. Bacteria were seen adhering to the exposed epithelial cell surface and also to the mucus sheet. Isolation of aerobic organisms showed that Escherichia coli are closely associated with the gut wall throughout the large intestine. One strain of E. coli predominated in each biopsy, and this strain was present along the whole length of bowel. Adhesion of bacteria to the gut wall does occur in vivo and may be one of the factors involved in the ability of an organism to colonize and persist.

Escherichia coli↗
PubMedDate not supplied

[Presence of antibodies in human colostral secretory IgA against enteric commensal bacteria: biological implications (author's transl)].

Antisecretory component, anti-alpha, anti-mu and anti-Fc (gamma) fluorescent antibodies were used to detect the presence of immunoglobulins with antibody activity against enteric commensal bacteria in human colostrum and serum. Forty nine colostrum samples were studied; all of them displayed secretory IgA (sIgA) antibodies reacting with Bacteroides thetaiotaomicron, Clostridium perfringens and Escherichia coli serotype O141:H32 without any K antigen. The amount of sIgA antibodies was always related to the sIgA colostral concentration varying greatly from one patient to another. For the 3 lactating women studied, the colostrum sIgA antibodies were largely predominant as compared to the antibodies of other classes; in their sera, no antibody having the same anticommensal specificity was detected in the IgA fraction while these antibodies were found in IgM and IgG. Our results are incompatible with the existence of local antigenic stimulation, and the IgA transfer from serum into mammary secretion appears unlikely, but these results are perfectly compatible with the antigenic stimulation of gut associated lymphoid tissue and subsequent migration in mammary tissue.

Antibodies, Bacterial↗
PubMed1979

Corynebacterium pseudogenitalium sp. nov. Commensals of the human male and female urogenital tracts.

Antisera to Corynebacterium genitalium Types C-1 to C-6 were prepared in rabbits and the titers of complement fixing antibodies to the homologous strains, to the heterologous strains, to C. genitalium Types I to V, and to the reference species Corynebacterium xerosis and Corynebacterium minutissimum ascertained. Five Types stimulated low levels of cross-reacting antibodies to all corynebacteria tested including Type C-3. In contrast the antiserum to Type C-3 had antibodies to only two heterologous strains suggesting that these corynebacteria usually shared more than one minor cell wall antigen. The biologic reactions and serotypes of C. genitalium Types C-1 to C-6 have been compared with those of Types I to V. It is considered that C. genitalium should be retained for corynebacteria having the properties of Types I to V whereas corynebacteria having the characteristics of Types C-1 to C-6 that are commensals of the male and female urogenital tracts should be incorporated in a new species Corynebacteria pseudogenitalium sp. nov. The differences in the biologic characteristics of the two species have been discussed and summarized.

Antibodies, Bacterial↗
PubMed2026

From commensal to pathobiont: The emergence of virulence-enhanced Escherichia coli in China's food-animal systems - insights with future implications.

A fundamental shift in Escherichia coli epidemiology is being driven by convergence of virulence determinants and antimicrobial resistance within linked human-animal-environment systems. In China, the rapid growth of food-animal production, extensive antimicrobial use, and complex food networks are accelerating the emergence and dissemination of virulence-enhanced E. coli pathobionts. This review synthesizes recent epidemiological, genomics, and outbreak data to characterize China's evolving landscape of food-animal-associated E. coli. We highlight a significant shift from classical pathotypes to hybrid lineages that simultaneously carry virulence factors and last-resort antibiotic resistance determinants, including mcr-1, tet(X4), and blaNDM. These traits disseminate rapidly via plasmid-mediated horizontal gene transfer, facilitating rapid adaptation and enabling cross-sectoral One Health transmission. National surveillance, foodborne outbreak investigations, and whole-genome sequencing data show that food-animal reservoirs are active evolutionary niches that drive pathogen diversity and fitness, rather than serving merely as contamination sources. Whole-genome sequencing also pinpoints high-risk clones (e.g., ST394) and plasmid-mediated co-selection of virulence and AMR. The emergence of hybrid pathotypes (e.g., STEC/ETEC) and AMR-virulence co-selection challenges traditional classification and limits the effectiveness of conventional surveillance approaches. The 2017 colistin ban reduced mcr-1, yet ongoing resistance and emerging tet(X4) demand integrated surveillance. Collectively, these findings call for reconceptualizing E. coli as a dynamic genomic entity embedded within a unified ecological network. Addressing this threat requires an integrated One Health strategy including genomic surveillance, agricultural antimicrobial stewardship, and coordinated food-environment-clinical monitoring to prevent high-risk clone emergence and global spread.

Animals↗
PubMed1977

Continuous-culture studies of interactions among human skin-commensal bacteria.

Chemostat studies were made of an antibiotic-producing Staphylococcus epidermidis strain (S6+), a similar, but antibiotic non-producing S. epidermidis strain (S6-), and a sensitive indicator strain of Micrococcus sp. (M7). Pure and mixed continous cultures were investigated at low population levels (in 0-1% peptone water) and at higher levels (in 0-5% peptone water). Strain S6+ antagonised the growth of strain M7 when its colony count was maintained above 10(7-0) per ml, while strain S6- remained unaffected.

Anti-Bacterial Agents↗
PubMed2026

Functional analysis of Candida albicans protein kinases identifies Crk1 as a modulator of epithelial cell damage.

UNLABELLED: The commensal and pathogenic lifestyles of the opportunistic fungal pathogen Candida albicans require complex signaling networks regulated by protein kinases. To investigate the role of C. albicans protein kinases at the intestinal epithelial interface, we screened a comprehensive protein kinase deletion library for the capacity of the mutants to damage intestinal epithelial cells (IEC). Mutants showing altered IEC cytotoxicity relative to the wild type were further analyzed for their growth and morphology, focusing on hyper-damaging strains to identify kinases that rather prevent host cell damage. Deletion of CRK1 caused increased IEC-specific damage, despite slower growth, reduced hyphal length, and reduced adhesion as compared to wild-type cells. While tissue invasion levels and the formation of transcellular tunnels of the crk1Δ/Δ mutant were increased, the translocation capacity through the IEC barrier was reduced. Transcriptional and metabolic profiling suggested a role for Crk1 in metabolic adaptation to carbon and nitrogen sources, which was validated by showing that high glucose and amino acids are required for crk1Δ/Δ to cause increased IEC damage. Deletion of CRK1 rendered C. albicans more susceptible to cell wall and membrane stressors, but caused higher resistance to a catalase-specific and histidine biosynthesis inhibitor. This phenotypic pattern of medium- and epithelial cell type-specific cytotoxicity displayed by a C. albicans protein kinase mutant suggests that Crk1 regulates processes linked to carbon and amino acid metabolism that are relevant to interactions with intestinal epithelial cells. IMPORTANCE: Microbial signal transduction pathways regulate adaptation to changing environmental conditions and facilitate the success of many microbes during interactions with their hosts. The fungal pathobiont Candida albicans exists as a harmless commensal on mucosal surfaces of most humans but can also cause superficial and invasive infections under certain circumstances. Both lifestyles require complex signaling networks, predominantly regulated by protein kinases. The C. albicans genome was predicted to encode 108 protein kinases, yet nearly 50% remain uncharacterized. We aimed to dissect the role of C. albicans protein kinases during the transition from commensal to pathogen. We showed that multiple protein kinase genes are involved in epithelial cell damage. Particularly, the protein kinase gene Crk1 was of interest because deletion of CRK1 caused increased damage to intestinal epithelial cells under distinct conditions. Our study links Crk1 with regulation of metabolic processes relevant for commensalism and pathogenicity of C. albicans.

Candida albicans↗
PubMed2026

Human Milk Oligosaccharides Modulate Nitrogen Utilization in Lactobacillus crispatus in a Glucose-Dependent Manner.

The vaginal microbiome's transition to a dysbiotic state increases susceptibility to pathogens like group B Streptococcus. While human milk oligosaccharides are established prebiotics in the neonatal gut, their impact on the vaginal niche remains largely unexplored. This study investigated the effects of pooled human milk oligosaccharides on the growth and physiology of vaginal (Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners) and gut-derived (Lactobacillus reuteri, Lactobacillus rhamnosus) commensals. Growth analyses revealed that human milk oligosaccharides significantly and selectively stimulated growth across all vaginal strains tested, whereas gut commensals exhibited variable or inhibited growth. Carbohydrate utilization assays and comparative genomics against Bifidobacterium infantis showed that Lactobacillus crispatus and Lactobacillus reuteri lack the canonical metabolic machinery to catabolize human milk oligosaccharides. Instead, nitrogen utilization assays identified a glucose-dependent pathway where human milk oligosaccharides are associated with the depletion of primary amines and amino acids in Lactobacillus crispatus supernatants. These results suggest that human milk oligosaccharides act as noncatabolic modulators of vaginal lactobacilli. Collectively, these in vitro findings may warrant investigation of human milk oligosaccharides as modulators of vaginal commensal physiology in more complex experimental systems.

Humans↗
PubMed1979

The reproductive ecology of the house mouse.

This paper attempts to integrate the physiological and ecological perspectives of the reproductive biology of the house mouse (Mus musculus). The endeavor is made within a larger context to provide a prototype for mammalian reproductive ecology in general. Specifically, the environmental regulation of the reproduction of Mus musculus is examined in relation to its ecological opportunism and, in particular, in relation to its history of global colonization. House mice can live as commensals of man or under totally feral conditions. Stable, high density, commensal populations are characterized by an insular division of the living space into demeterritories, each dominated by a single male. Feral populations typically are characterized by temporal, spatial, and social instability. Territoriality is improbable under such conditions, particularly given the necessity for large home ranges in most feral habitats. In both feral and commensal populations, however, male aggressiveness promotes the large-scale dispersal of young, all of which are potential colonizers. Of the ten or so environmental factors known to influence reproduction in house mice, seven probably are of routine importance in natural populations: diurnal modulation by daily light:dark cycles; caloric intake; nutrition; extreme temperature; agaonistic stimuli; socio-tactile cues; and priming pheronomes. The last two factors named operate directly on the secretion of luteinizing hormone or prolactin; the others act at many points in the reproductive system. Reproduction in the house mouse seems divorced from photoperiodically induced seasonality; indeed, this species breeds well even in constant darkness. Seasonal breeding may or may not then occur, depending upon dietary considerations, with or without a secondary interaction with variation in ambient temperature. There is no evidence for a dependence upon secondary plant compounds. Some of the effects of priming pheromones that have been observed previously in laboratory mice probably play no meaningful role in wild populations. The remaining pheromonal phenomena can be conceptualized as a single cueing system that has three components: (a) urinary cues of socially dominant males can accelerate ovulation in females, adult or prepubertal; (b) female urinary cues may elevate pheromonal potency in adult males, thereby forming a feedback loop by which the females elicit their own ovulation; and (c) the male's action on prepubertal females can be blocked by urinary cues emanating from other females. When all of the above is viewed in toto, the reproductive biology of the house mouse seems uniquely suited to support ecological opportunism. The relatively few environmental inhibitors of reproduction in this species should enhance the ability of dispersing young to colonize an exceptionally wide variety of habitats and climates...

Animals↗
PubMed2025

Bacterial skin colonization with a specific Cutibacterium avidum clade as a risk factor for periprosthetic joint infections-a multicenter study.

Cutibacterium avidum is increasingly recognized as a causative agent of periprosthetic joint infections (PJIs), yet data on its pathogenic potential and distinguishing features from commensal strains remain limited. In this multicenter study, we compared 11 C. avidum isolates from PJIs with 32 isolates from healthy skin collected across four European hospitals. We investigated phylogenetic relationships, antibiotic susceptibility, biofilm formation, and bacterial fitness. Phylogenomic analysis revealed two main clades within the C. avidum population. All PJI isolates belonged exclusively to Clade 1, which also included skin isolates. Within Clade 1, gene content analysis showed no consistent genetic differences between PJI and skin isolates. All isolates exhibited moderate to strong biofilm formation, with no significant differences in either data set. Minimal inhibitory concentration (MIC) and minimal biofilm inhibitory concentration (MBIC) values were low and largely concordant, while minimal biofilm eradication concentration (MBEC) values were elevated for all antibiotics except rifampin. One isolate was resistant to clindamycin due to the erm(X) gene. Rifampin consistently showed the lowest MIC, minimal bactericidal concentration, MBIC, and MBEC values. Bacterial fitness, assessed via bacterial quantitative fitness analysis, was significantly lower in PJI isolates compared to skin isolates when all strains were analyzed (P = 0.039), but this difference was not statistically significant when restricted to Clade 1. In conclusion, C. avidum isolates are strong biofilm producers irrespective of clinical origin. PJI isolates are restricted to a single phylogenetic clade, yet lack distinct biofilm or fitness traits within that clade, suggesting that multiple Clade 1 strains may have the potential to cause PJIs. IMPORTANCE Cutibacterium avidum has long been considered a skin commensal, but it is increasingly associated with prosthetic joint infections (PJIs). Despite its clinical emergence, little is known about its virulence potential or how invasive strains differ from commensal ones. This multicenter study provides the most comprehensive comparative analysis to date, integrating phenotypic and genomic data from both PJI-associated and skin-derived isolates. We show that all isolates are strong biofilm formers and that invasive isolates exhibit reduced growth fitness-a phenotype linked to persistence and treatment failure in other pathogens. Notably, all PJI isolates belonged to a single phylogenetic clade, suggesting that specific lineages of C. avidum may be more likely to cause infection. These findings help clarify the biology of this emerging pathogen and provide a foundation for improved diagnostics, susceptibility testing, and future infection prevention and treatment strategies.

Biofilms↗