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Microscopic and bacteriological comparison of paired sputa and transtracheal aspirates.

Ninety-six sputum specimens from patiens with pneumonia were microscopically screened for leukocytes and buccal squamous epithelial (BSE) cells. Cultures of these specimens were compared with cultures of paired transtracheal aspirates (TTA). Agreement between sputa with less than 25 BSE cells per 100X field and TTA was good (79%). Only 27% of the specimens with greater than 25 BSE cells per 100X field agreed with TTA. Sixty-six of the sputa were of group 5 quality, i.e., greater than 25 leukocytes and less than 10 BSE cells per 100X field. A potential pathogen growing in one of these specimens was 94% predictive of growth in the TTA. If a group 5 sputum was negative for a potential pathogen, there was a 45% chance that a fastidious organism had been overgrown or overlooked. The presence of definite lower tract secretions in group 5 sputa as determined by visualizing bronchial epithelial cells and alveolar macrophages did not significantly increase the diagnostic value of these specimens. Microscopic screening of sputum before culture with rejection of selected specimens can increase the value of sputum in determining the etiology of bacterial pneumonia.

Adult

The microbial flora in extended-wear soft contact-lens wearers.

Of 857 cultures of material collected from the eyelids, conjunctivae, and contact lenses of 51 extended-wear soft-contact-lens wearers, 44 (5%) grew potential pathogens. The aphakic patients wearing contact lenses had fewer recoverable pathogens (24 of 295 or 8%) than a group of preoperative cataract patients (63 of 295 or 21%). On five occasions, positive cultures accompanied clinical symptoms, and on three occasions, repeated cultures grew the same potential pathogen.

Aphakia, Postcataract

Bacteriological criteria for feeding raw breast-milk to babies on neonatal units.

Aerobic cultures of 207 samples of drip breast-milk from seventy mothers in hospital showed that 6 (3%) were sterile and 170 (82%) contained only the commensal organisms coagulase-negative staphylococci and Streptococcus viridans. 25 (15%) grew potential pathogens--Staphylococcus aureus in 13 (6%); enterobacteria in 15 (7%); and group-B streptococci in 3 (2%). It is proposed that milk with commensals in any numbers may be considered for use unheated but not milk containing any potential pathogens.

Aerobiosis

First characterization of Staphylococcus felis in diabetic foot osteomyelitis: from intracellular persistence to phage treatment.

Staphylococcus felis is a coagulase-negative Staphylococcus (CoNS) primarily associated with the feline microbiota and only rarely reported in human disease. Here, we report its implication in diabetic foot osteomyelitis, and provide the first comprehensive characterization of its pathogenic potential. Two isolates (NSF001 and NSF002), recovered 5 months apart from bone biopsies of the same patient, were analyzed for growth kinetics, biofilm formation, and intracellular persistence in macrophages and osteoblasts. Both isolates proliferated efficiently, produced robust biofilm, and persisted within host cells, most markedly in osteoblasts. In a zebrafish embryo infection model, both isolates caused significant mortality, confirming their pathogenic potential in vivo. Whole-genome sequencing revealed conserved virulence determinants, a narrow resistome, and strain-specific genomic variations affecting genes involved in virulence regulation, phage defense, and iron acquisition. The lytic phage SAVM02, previously characterized for activity against other Staphylococcus species, effectively inhibited S. felis growth in vitro and conferred protection in vivo against lethal infection. Notably, the two sequential isolates differed in their in vivo virulence and phage susceptibility, paralleling these within-host microevolutionary changes and illustrating bacterial adaptation during chronic infection. Altogether, this study establishes S. felis as a CoNS capable of intracellular persistence, biofilm formation, and in vivo virulence in chronic human infection. Our findings also highlight the therapeutic potential of lytic phages against virulent CoNS species and support further investigation of phage therapy for chronic staphylococcal infections.IMPORTANCECoagulase-negative staphylococci (CoNS) are increasingly recognized as genuine agents of chronic infection, yet the pathogenic capacity of most individual species remains undefined. Staphylococcus felis, a commensal of cats only exceptionally reported in humans, had never been implicated in a chronic human infection. Here, we describe two sequential S. felis isolates recovered from bone biopsies of a patient with diabetic foot osteomyelitis and show that this species combines biofilm formation, intracellular persistence in macrophages and osteoblasts, and lethality in a zebrafish embryo model. Whole-genome comparison of the two isolates uncovered microevolutionary changes, most notably in iron-acquisition and genome-defense loci, that paralleled differences in virulence and phage susceptibility. These findings extend the list of CoNS capable of causing invasive human disease and provide a rationale for lytic phage therapy against emerging, difficult-to-treat staphylococcal pathogens.

Staphylococcus felis

Evaluation of some methods for the laboratory examination of sputum.

Methods for the quantitation of leucocytes, squamous epithelial cells, and potential pathogens in sputa are described. Microscopic examination showed that 58% of sputa tested (554/957) were purulent or moderately purulent and 48% were moderately or heavily contaminated by squamous epithelial cells. The presence of squamous epithelial cells indicated oropharyngeal contamination. A simple dilution technique was chosen to compare the isolation of potential pathogens from direct cultures and from dilutions of sputa (10(-7) per ml original sputum). The dilution technique permitted easier reading of sputum cultures and avoided the possible over-reporting of enterobacteria and Pseudomonas aeruginosa, which were frequently found on direct examination. Enterobacteria and Pseudomonas aeruginosa were more likely to be isolated from sputa moderately or heavily contaminated with squamous epithelial cells. The use of counter-current immunoelectrophoresis (CIE) and co-agglutination tests to detect pneumococcal antigen in sputa is described. The presence of antigen in sputum was a more reliable index of lower respiratory tract infection than a positive culture. Co-agglutination tests were simpler to perform and used smaller amounts of expensive antiserum than CIE.

Antigens, Bacterial

Ecophylaxis: preventive treatment with gentamicin of rabbit lincomycin-associated diarrhea.

In rabbits the oral or parenteral administration of lincomycin result in a severe and usually fatal form of diarrhea. The rabbits treated simultaneously with lincomycin and gentamicin do not present any sign of disease and behave exactly, therefore, as the control subjects. The same occurs in subjects treated with gentamicin alone. In all the subjects which died with diarrhea there was a marked alteration of the intestinal bacterial flora. Among the aerobic bacteria there was an overgrowth of coliforms and less frequently of enterococci, while bacilli were reduced and lactobacilli completely disappeared. Among the anaerobic bacteria, bacteroides and bifidobacteria disappeared and there was an overgrowth of clostridia instead. In rabbits treated contemporaneously with lincomycin and gentamicin, coliforms were absent and the mean number of clostridia was at least one hundred times lower; as in rabbits treated only with lincomycin, enterococci were present in greater number, while lactobacilli, bifidobacteria and bacteroides completely disappeared. Some of the bacteria which are able to overgrow in lincomycin treated subjects, in particular coliforms and clostridia, can be considered potentially pathogenic and their overgrowth could therefore explain the onset of diarrhea. Actually in faecal specimens of rabbits with lincomycin-associated diarrhea, together with the overgrowth of E. coli and clostridia, there is an absence of lactobacilli, bifidobacteria and bacteroides. It is known that these last bacteria contribute, in normal conditions, to maintaining the ecological equilibrium of the intestinal microbial flora. The diarrhea itself can be attributed most likely to the ecological alteration of intestinal microbial flora, with an overgrowth of some potentially pathogenic bacteria and the suppression of others which normally exert an inhibiting effect on the former. It has been suggested to call this form of gentamicin prophylaxis of lincomycin-associated diarrhea 'ecophylaxis', in the sense that it prevents or corrects certain types of ecological alteration of the intestinal microbial flora which lead to diarrhea.

Animals

Enhanced HIF-1α cooperation by a human RORγt mutant potentiates Th17 pathogenicity.

T helper 17 (Th17) cells are pivotal in mucosal defense and autoimmune pathology, with their function governed by the transcription factor retinoic acid receptor-related orphan receptor gamma t (RORγt). Although genome-wide association studies link RORC variants to inflammatory diseases, their functional consequences remain poorly understood. We identify a pathogenic RORγt mutation N277D (mouse homolog N275D) that amplifies Th17 pathogenicity through cooperation with hypoxia-inducible factor HIF-1α. This mutation enhances IFN-γ and other Th1-type cytokine production by Th17 cells, exacerbating colitis without disrupting T cell development or homeostasis. Integrated transcriptomic and metabolomic profiling reveals activation of glycolytic and hypoxia-associated pathways, consistent with increased RORγtN275D recruitment by HIF-1α to the Pdk1 locus. Notably, silencing Pdk1 normalizes the excessive IFN-γ production in RORγtN275D Th17 cells. Together, these findings define a regulatory axis linking RORγt and HIF-1α that coordinates transcriptional and metabolic programs in pathogenic Th17 cells, providing a framework for dissecting the functional impact of autoimmune risk variants.

CP: immunology

Campylobacteriosis in man: pathogenic mechanisms and review of 91 bloodstream infections.

Five patients with Campylobacter fetus(previously called "Vibrio fetus") bacteremia are presented with enteric symptoms in four patients, a self-limited course in three, and with possible nosocomial infection in one patient who had disseminated malignancy. The clinical syndromes of 91 bacteremic patients with campylobacteriosis and C. fetus taxonomy and pathogenicity are reviewed. Studies of potential pathogenic mechanisms in enteric infections failed to reveal the production of either heat-stable or heat-labile, cholera-like enterotoxin, cytotoxicity or invasiveness. In comparison with different species of vibrio infections, C. fetus appears to produce disease by a different mechanism, one which involves a bloodstream infection, perhaps following penetration through the intestinal mucosa as has been demonstrated experimentally with salmonellae and yersinia. Such a pattern is consistent with the clinical pattern of C. fetus infections and the experimental studies reported herein.

Adult

Metagenomic profiling of gut microbiome in post-cholecystectomy patients with diarrhea: a nested case-control study.

BACKGROUND: Cholecystectomy can cause diarrhea, with an incidence as high as 57.2%, seriously impacting patient prognosis. To investigate the gut dysbiosis following cholecystectomy and identify microbial biomarkers and functional genomics associated with post-cholecystectomy diarrhea (PCD), we conducted a nested case-control study within a prospective cohort. METHODS: We enrolled a cohort of 160 patients. At follow-up completion, 30 patients who developed PCD were matched with 30 non-PCD (NPCD) controls. 16 S rRNA sequencing was used to analyze gut microbiota structure and diversity (mainly at genus level). Representative fecal samples underwent metagenomic sequencing for species level and genetic differential analysis. RESULTS: The potentially pathogenic bacterial species Coprococcus comes and Blautia sp. were significantly enriched in the gut microbiota of PCD patients, with their abundance positively correlated with the degree of intestinal inflammation. In contrast, the potentially beneficial bacterial species Bacteroides intestinalis and Prevotella copri, known to contribute to lipid metabolism and play a role in modulating gut immunity and suppressing inflammatory responses, were found to be significantly depleted in PCD patients. Further metagenomic functional analysis revealed significant enrichment of pathways related to cell motility, membrane transport, and sulfur metabolism in PCD patients. CONCLUSIONS: This work identified potential beneficial and pathogenic bacterial species associated with the onset of PCD, as well as significantly enriched functional pathways within the intestinal microbiota. These findings provide a scientific basis for elucidating the relationship between PCD and gut microbiota, and provide candidate microbial signatures and functional pathways that may inform future microbiota-targeted strategies, pending external and mechanistic validation.

Humans

Evaluation of industrial yeasts for pathogenicity.

Eleven yeasts representative of species of industrial interest were compared with Candida albicans for their potential pathogenicity for untreated and cortisone-treated mice. Only C. tropicalis produced a progressive infection similar to that produced by C. albicans. Candida lipolytica, Torulopsis spp., and Hansenula polymorpha were not recovered from mice 6 days after inoculation. Kluyveromyces fragilis, C. pseudotropicalis, C. utilis, C. guilliermondii and C. maltosa were recovered from mice but did not produce evidence of infection.

Animals

[Pathogenicity of aerobically sporulating microorganisms: Bacillus subtilis].

Bioassays were made on white mice and rats to find the potential pathogenicity of B. subtilis and its metabolites. The peroral and intraperitoneal application of several strains of B. subtilis to white mice did not cause any changes either in the behaviour or health condition of the animals until the first to seventh day after test. B. subtilis cultures or cellular suspensions on the one hand and non-cellular filtrates of cultures represented by the B. subtilis metabolism products on the other hand were given to the animals. No changes in the health condition of the mice and rats were observed when feed artificially infected with B. subtilis was fed. Dissection did not reveal any macroscopic changes on the organs of the abdominal and thoracic cavity. Cultures from the individual body organs (liver, spleen, kidneys, parts of the small and large intestines, stomach) perorally infected with B. subtilis showed the presence of the microbe only in parts of the digestive tracts.

Aerobiosis

[Acholeplasma laidlawii--a pathogenic or apathogenic species?].

The question is discussed, whether Acholeplasma laidlawii is a pathogenic or apathogenic species. Studies have shown that it is a species of potential pathogenicity, however, with virulence properties differing greatly by strains. Nothing so far has become known of contributive factors which might be needed for an infectious disease to develop.

Acholeplasma laidlawii

Deciphering the genomic landscape of novel Acinetobacter non-baumannii lineages causing neonatal septicemia: carbapenem resistance and virulence.

BACKGROUND: Acinetobacter non-baumannii (Anb) species are reported worldwide to cause infections in both adults and neonates, although less frequently than Acinetobacter baumannii. However, limited information is available on their genomic diversity, resistance mechanisms, and virulence potential. This study investigates novel Anb isolates causing neonatal septicemia in India to characterize their resistance and pathogenic traits. METHODS: Anb isolates from neonatal blood cultures (2007-2025) were identified by VITEK2 Compact system, MALDI-TOF MS, and Whole-genome sequencing (WGS). Antimicrobial susceptibility was tested by VITEK2. Genomic analysis included MLST, resistome, virulome, plasmid typing, integrons, and core-genome phylogeny analysis. In vitro and in vivo studies assessed pathogenic potential of Anb species. RESULTS: Anb infections were low (11%) among the neonates during the study period. WGS revealed 11 novel Sequence Types (STs) which include A. indicus, A. variabilis, A. schindleri, and A. bereziniae. Six out of these eleven Anbs harbored carbapenemases such as bla NDM-1 and/or bla OXA-58-like genes (bla OXA-58, bla OXA-420). bla NDM-1 was acquired via Tn125 transposon. ISAba125 was located upstream of bla NDM-1, and a conserved structure extending to IS91 family transposase was detected in bla NDM-1-harboring genomes. bla OXA-58-like genes were found to be associated with ISAba3. Most carbapenemases were likely located on chromosome. Class 1 integrons carrying multiple antimicrobial resistance genes (ARGs) and diverse plasmid replicase families were detected in Anbs. Core genome phylogeny showed that the study Anbs were not closely related to the global Anbs. In vitro virulence-associated assays (biofilm formation, surface motility, adherence/invasion, apoptosis) and in vivo lethality in murine infection model showed reduced pathogenicity, reinforcing earlier observations that Anb species are generally less virulent than A. baumannii. Several virulence factors (VFs) were detected; however, no clear correlation was observed between virulence genes, in vitro pathogenicity, and in vivo lethality. CONCLUSION: These results indicate the multifactorial nature of Anb pathogenicity and the current limitations of knowledge of its VFs. However, the presence of numerous VFs suggests a capacity to cause disease, particularly in vulnerable host populations such as neonates. Furthermore, the presence of multiple ARGs indicates a strong potential for persistence and dissemination in hospital environments with high antibiotic pressure. Overall, these findings underscore the importance of continued AMR surveillance, genome characterization and further investigations into Anb pathogenicity.

Acinetobacter non-baumannii

Whole-genome prediction of bacterial pathogenic capacity on novel bacteria using protein language models with PathogenFinder2.

MOTIVATION: Infectious diseases continue to be a leading cause of mortality and pose a significant global health threat. Thus, the development of tools for surveillance and early detection of emerging pathogens is needed. RESULTS: We introduce PathogenFinder2, a novel, alignment-free, taxonomy-agnostic model for predicting bacterial pathogenic capacity in humans using protein language models. It outperforms previous methods, particularly for novel taxa, and provides interpretable outputs by highlighting proteins most relevant to pathogenic potential. These insights aid the identification of virulence factors, vaccine targets, and infection-related metabolic pathways. Furthermore, we introduce the Bacterial Pathogenic Capacity Landscape, which reveals patterns linked to host condition, infection site, microbial antagonism, and environmental origin. AVAILABILITY: The model is freely available online at https://genepi.dk/pathogenfinder2, or as a standalone program (https://github.com/genomicepidemiology/PathogenFinder2).

Genome, Bacterial

Calcium release channel deficiency syndrome in patients diagnosed with idiopathic ventricular fibrillation and decedents classified as sudden unexplained death in the young.

AIMS: Calcium release channel deficiency syndrome (CRCDS) results from loss-of-function (LOF) variants in the RYR2-encoded type 2 ryanodine receptor (RyR2), predisposing patients to sudden cardiac arrest/death (SCA/SCD) without abnormalities on a stress electrocardiogram (ECG). Undetected CRCDS may underlie idiopathic ventricular fibrillation (IVF) and sudden unexplained death in the young (SUDY). We aimed to determine the prevalence of potential CRCDS-causative RYR2 variants in IVF and SUDY. METHODS AND RESULTS: We reviewed clinical evaluation and RYR2 genetic analysis of 169 IVF patients and 279 SUDY victims. Only ultra-rare (<0.005% in gnomAD) nonsynonymous RYR2 variants were considered potentially pathogenic. Among IVF patients, 6/169 (3%) overall-and 6/67 (9%) with exertion-related SCA-harboured an RYR2 variant and represent potential CRCDS cases. All exhibited normal resting and stress ECGs. Genetic analysis revealed six distinct RYR2 variants, two previously characterized as LOF. In SUDY, 31/279 victims (11%) had a RYR2 variant (30 unique variants), predominantly observed in exertion-related SCD 20/83 (24%) vs. rest-related 11/196 (6%). Of the 14 SUDY victims with functionally characterized RYR2 variants, five (2% of total cohort) had a LOF variant; among the 56 exertion-related SUDY cases, four (7%) had a LOF variant. CONCLUSION: CRCDS may account for 3% of IVF overall and 9% of exertion-related SCA in IVF. Ultra-rare RYR2 variants may underlie up to 11% of SUDY, with 65% of RYR2-positive cases occurring during exertion. LOF-RYR2 variants may contribute to &#x2265;7% of exercise-associated SUDY. Accurate identification of the underlying ryanodinopathy is essential for clinical management of affected patients.

Humans

Multimodal genomic surveillance for respiratory pathogens at four U.S. international airports: A comparison of air, wastewater, clinical, and national surveillance data.

Early detection of outbreaks and emerging pathogens is critical for public health and global biosecurity. Airports, as major international travel hubs with dense, enclosed populations, are high-risk settings for disease transmission and potential pathogen introduction. The U.S. Centers for Disease Control and Prevention, in collaboration with Ginkgo Biosecurity and the University of Wisconsin-Madison, implemented air monitoring for pathogen surveillance in congregate areas at four U.S. international airports. From October 2023 to August 2024, SARS-CoV-2 was detected by PCR in 98.3% of air samples and influenza A in 17.2%. Influenza A positivity in air samples correlated with aviation wastewater (r&#x2009;=&#x2009;0.48), traveler nasal swab positivity (r&#x2009;=&#x2009;0.73), and national clinical surveillance (r&#x2009;=&#x2009;0.86), whereas SARS-CoV-2 measurements did not correlate significantly across these modalities. Targeted amplicon sequencing of SARS-CoV-2 from air samples identified contemporaneous lineages also detected in wastewater collected from the same airports. Targeted enrichment sequencing detected 30 viral species and recovered high-quality genomes for SARS-CoV-2, influenza, bocavirus, and seasonal coronaviruses. Together, these findings demonstrate that air sampling can complement aviation wastewater surveillance at ports of entry, although performance and concordance vary by pathogen and sample type.

Journal Article

Genomic and phenotypic characterization of mcr-9 carrying Enterobacter oligotrophicus recovered from bovine mastitis.

Bovine mastitis (BM) is a leading cause of economic loss in the dairy industry, driven by decreased milk yields, involuntary culling, and substantial veterinary costs. A single Gram-negative isolate recovered from BM was characterized in this study. For this, antimicrobial susceptibility testing (AST) was performed using the Neg-Urine-Combo 98 panel. Whole-genome sequencing (WGS) was employed to identify antimicrobial resistance genes (ARG), virulence factors (VF) genes, plasmid replicons and prophage sequences. Comparative genomic analysis was performed through phylogenetic analysis. The BM isolate was phenotypically identified as Citrobacter rodentium, however, WGS analysis reclassified the isolate as Enterobacter oligotrophicus. Phenotypic AST revealed a resistance profile of 12%, with the isolate exhibiting resistance to &#x3b2;-lactams antimicrobials, specifically amoxicillin-clavulanate, ampicillin and the cephalosporin-cefoxitin. Conversely, susceptibility was demonstrated for the remaining tested antimicrobials. Genomic profiling identified 31 ARG, 10 VF genes and 6 prophage sequences within the E. oligotrophicus genome. This study provides the first evidence of E. oligotrophicus as a causative agent of BM, expanding the known spectrum of pathogens affecting the dairy industry by delivering the second complete genome of E. oligotrophicus available globally. The identification of 31 ARG, 10 VF, and 6 prophage sequences underscore the potential pathogenic risk and environmental resilience of this isolate. These findings highlight the critical role of WGS-based surveillance in identifying non-conventional mastitis pathogens and underscore the need for targeted mitigation strategies in veterinary medicine.

Animals

Coxsackievirus B cardiopathy and angiopathy in the hypercholesterolemic host.

Studies on the pathogenic potential of the human cardiotropic enterovirus, coxsackievirus B5, show that this agent localizes and replicates in the aorta of mice. Nutritionally-induced hypercholesterolemia leads to an increased replication and persistence of virus in tissues, specifically the aorta. Coxsackievirus B cardiopathy is markedly augmented in the hypercholesterolemic host, resulting in a persistent cardiomyolysis which is not evident in virus-infected animals with normal cholesterol levels. Pathological changes in the aorta become evident only months after the acute infection, and only in hypercholesterolemic animals previously infected with coxsackievirus B5. Our findings of coxsackievirus B-induced angiopathy and cardiopathy in the hypercholesterolemic host extend the known pathogenic range of these human viruses, and further emphasizes their potential as etiological agents of cardiovascular disease.

Animals