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Animal Microbiome Nov 2023Infectious bovine keratoconjunctivitis (IBK) is a common cause of morbidity in cattle, resulting in significant economic losses. This study aimed to characterize the...
BACKGROUND
Infectious bovine keratoconjunctivitis (IBK) is a common cause of morbidity in cattle, resulting in significant economic losses. This study aimed to characterize the bovine bacterial ocular surface microbiome (OSM) through conjunctival swab samples from Normal eyes and eyes with naturally acquired, active IBK across populations of cattle using a three-part approach, including bacterial culture, relative abundance (RA, 16 S rRNA gene sequencing), and semi-quantitative random forest modeling (real-time polymerase chain reaction (RT-PCR)).
RESULTS
Conjunctival swab samples were obtained from eyes individually classified as Normal (n = 376) or IBK (n = 228) based on clinical signs. Cattle unaffected by IBK and the unaffected eye in cattle with contralateral IBK were used to obtain Normal eye samples. Moraxella bovis was cultured from similar proportions of IBK (7/228, 3.07%) and Normal eyes (1/159, 0.63%) (p = 0.1481). Moraxella bovoculi was cultured more frequently (p < 0.0001) in IBK (59/228, 25.88%) than Normal (7/159, 4.40%) eyes. RA (via 16 S rRNA gene sequencing) of Actinobacteriota was significantly higher in Normal eyes (p = 0.0045). Corynebacterium variabile and Corynebacterium stationis (Actinobacteriota) were detected at significantly higher RA (p = 0.0008, p = 0.0025 respectively) in Normal eyes. Rothia nasimurium (Actinobacteriota) was detected at significantly higher RA in IBK eyes (p < 0.0001). Alpha-diversity index was not significantly different between IBK and Normal eyes (p > 0.05). Alpha-diversity indices for geographic location (p < 0.001), age (p < 0.0001), sex (p < 0.05) and breed (p < 0.01) and beta-diversity indices for geographic location (p < 0.001), disease status (p < 0.01), age (p < 0.001), sex (p < 0.001) and breed (p < 0.001) were significantly different between groups. Modeling of RT-PCR values reliably categorized the microbiome of IBK and Normal eyes; primers for Moraxella bovoculi, Moraxella bovis, and Staphylococcus spp. were consistently the most significant canonical variables in these models.
CONCLUSIONS
The results provide further evidence that multiple elements of the bovine bacterial OSM are altered in the context of IBK, indicating the involvement of a variety of bacteria in addition to Moraxella bovis, including Moraxella bovoculi and R. nasimurium, among others. Actinobacteriota RA is altered in IBK, providing possible opportunities for novel therapeutic interventions. While RT-PCR modeling provided limited further support for the involvement of Moraxella bovis in IBK, this was not overtly reflected in culture or RA results. Results also highlight the influence of geographic location and breed type (dairy or beef) on the bovine bacterial OSM. RT-PCR modeling reliably categorized samples as IBK or Normal.
PubMed: 37996960
DOI: 10.1186/s42523-023-00282-4 -
Biotech (Basel (Switzerland)) Oct 2023(1) Background: The COVID-19 pandemic left many intriguing mysteries. Retrospective vulnerability trends tie as strongly to odd demographics as to exposure profiles,...
(1) Background: The COVID-19 pandemic left many intriguing mysteries. Retrospective vulnerability trends tie as strongly to odd demographics as to exposure profiles, genetics, health, or prior medical history. This article documents the importance of nasal microbiome profiles in distinguishing infection rate trends among differentially affected subgroups. (2) Hypothesis: From a detailed literature survey, microbiome profiling experiments, bioinformatics, and molecular simulations, we propose that specific commensal bacterial species in the genus confer protection against SARS-CoV-2 infections by expressing proteases that may interfere with the proteolytic priming of the Spike protein. (3) Evidence: Various reports have found elevated fractions in the nasal microbiomes of subpopulations with higher resistance to COVID-19 (e.g., adolescents, COVID-19-resistant children, people with strong dietary diversity, and omnivorous canines) and less abundant ones in vulnerable subsets (the elderly, people with narrower diets, carnivorous cats and foxes), along with bioinformatic evidence that bacteria express proteases with notable homology to human TMPRSS2. Simulations suggest that these proteases may proteolyze the SARS-CoV-2 spike protein in a manner that interferes with TMPRSS2 priming.
PubMed: 37987478
DOI: 10.3390/biotech12040061 -
World Journal of Gastrointestinal... Oct 2023Postpolypectomy syndrome (PPS) is a rare postoperative complication of colonic polypectomy. It presents with abdominal pain and fever accompanied by coagulopathy and...
BACKGROUND
Postpolypectomy syndrome (PPS) is a rare postoperative complication of colonic polypectomy. It presents with abdominal pain and fever accompanied by coagulopathy and elevated inflammatory markers. Its prognosis is usually good, and it only requires outpatient treatment or observation in a general ward. However, it can be life-threatening.
CASE SUMMARY
The patient was a 58-year-old man who underwent two colonic polypectomies, each resulting in life-threatening sepsis, septic shock, and coagulopathy. Each of the notable manifestations was a rapid drop in blood pressure, an increase in heart rate, loss of consciousness, and heavy sweating, accompanied by shortness of breath and decreased oxygen in the finger pulse. Based on the criteria of organ dysfunction due to infection, we diagnosed him with sepsis. The patient also experienced severe gastrointestinal bleeding after the second operation. Curiously, he did not complain of any abdominal pain throughout the course of the illness. He had significantly elevated concentrations of inflammatory markers and coagulopathy. Except for the absence of abdominal pain, his fever, significant coagulopathy, and elevated inflammatory marker concentrations were all consistent with PPS. Abdominal computed tomography and superior mesenteric artery computed tomography angiography showed no free air or vascular damage. Thus, the diagnosis of colon perforation was not considered. The final blood culture results indicated . The patient was transferred to the intensive care unit and quickly improved after fluid resuscitation, antibiotic treatment, oxygen therapy, and blood transfusion.
CONCLUSION
PPS may induce dysregulation of the systemic inflammatory response, which can lead to sepsis or septic shock, even in the absence of abdominal pain.
PubMed: 37969719
DOI: 10.4240/wjgs.v15.i10.2343 -
Research Square Oct 2023Otitis media (OM) is primarily a bacterial middle-ear infection prevalent among children worldwide. In recurrent and/or chronic OM cases, antibiotic-resistant bacterial...
Otitis media (OM) is primarily a bacterial middle-ear infection prevalent among children worldwide. In recurrent and/or chronic OM cases, antibiotic-resistant bacterial biofilms can develop in the middle ear. A biofilm related to OM typically contains one or multiple bacterial strains, the most common include and . Optical coherence tomography (OCT) has been used clinically to visualize the presence of bacterial biofilms in the middle ear. This study used OCT to compare microstructural image texture features from primary bacterial biofilms and . The proposed method applied supervised machine-learning-based frameworks (SVM, random forest (RF), and XGBoost) to classify and speciate multiclass bacterial biofilms from the texture features extracted from OCT B-Scan images obtained from cultures and from clinically-obtained images from human subjects. Our findings show that optimized SVM-RBF and XGBoost classifiers can help distinguish bacterial biofilms by incorporating clinical knowledge into classification decisions. Furthermore, both classifiers achieved more than 95% of AUC (area under receiver operating curve), detecting each biofilm class. These results demonstrate the potential for differentiating OM-causing bacterial biofilms through texture analysis of OCT images and a machine-learning framework, which could provide additional clinically relevant data during real-time characterization of ear infections.
PubMed: 37961282
DOI: 10.21203/rs.3.rs-3466690/v1 -
The American Journal of Tropical... Dec 2023Infectious conjunctivitis outbreaks remain a public health burden. This study focuses on the pathogen and antimicrobial resistance (AMR) profiles identified in Niger....
Infectious conjunctivitis outbreaks remain a public health burden. This study focuses on the pathogen and antimicrobial resistance (AMR) profiles identified in Niger. Sixty-two patients with acute infectious conjunctivitis who presented to health posts were enrolled from December 2021 to May 2022. Nasal and conjunctival swabs were obtained from each patient. Unbiased RNA deep sequencing (RNA-seq) was used to identify associated pathogens. A pathogen was identified in 39 patients (63%; 95% CI, 50-74). Of those, an RNA virus was detected in 23 patients (59%; 95% CI, 43-73). RNA viruses were diverse and included human coronaviruses (HCoVs): SARS-CoV-2, HCoV-229E, HCoV-HKU1, and HCoV-OC43. A DNA virus was identified in 11 patients (28%; 95% CI, 17-44). Of those, four patients had a coinfection with an RNA virus and two patients had a coinfection with both an RNA virus and a bacterium. DNA viruses were predominantly human herpesvirus (cytomegalovirus, Epstein-Barr virus, human herpesvirus 8) and human adenovirus species B, C, and F. Eighteen patients (46%; 95% CI, 32-61) had a bacteria-associated infection that included Haemophilus influenza, Haemophilus aegyptius, Staphylococcus aureus, Streptococcus pneumoniae, and Moraxella spp. Antimicrobial resistance determinants were detected in either the conjunctiva or nasal samples of 20 patients (32%; 95% CI, 22-45) and were found to be more diverse in the nose (Shannon alpha diversity, 1.12 [95% CI, 1.05-1.26] versus 1.02 [95% CI, 1.00-1.05], P = 0.01). These results suggest the potential utility of leveraging RNA-seq to surveil pathogens and AMR for ocular infections.
Topics: Humans; Anti-Bacterial Agents; Respiratory Tract Infections; Niger; Coinfection; Epstein-Barr Virus Infections; Drug Resistance, Bacterial; Herpesvirus 4, Human; Conjunctivitis
PubMed: 37931292
DOI: 10.4269/ajtmh.23-0498 -
Microorganisms Sep 2023Aerosols in caves are natural tracers and, together with climatic parameters, provide a detailed insight into atmospheric conditions, responses to climatic changes and...
Aerosols in caves are natural tracers and, together with climatic parameters, provide a detailed insight into atmospheric conditions, responses to climatic changes and anthropogenic influences in caves. Microbiological air monitoring in show caves is becoming increasingly useful to understand changes in cave ecosystems and to implement and review measures for sustainable cave use and tourism development. In 2017 and 2018, air along tourist trails in caves Postojnska jama and Škocjanske jame (Slovenia) was sampled before and after tourist visits. Samples were analysed using culture-dependent methods, flow cytometry, detection of β-D-glucan and lipopolysaccharide and compared with CO and temperature data to measure anthropogenic influences and seasonality on aerobiota. While the presence of tourists significantly increased concentrations of airborne microorganisms ( < 0.05), β-D-glucan and CO did not show such a trend and were more dependent on seasonal changes. Locally, concentrations of cultivable microorganisms above 1000 CFU/m were detected, which could have negative effects on the autochthonous microbiota and possibly on human health. A mixture of bacteria typically associated with humans was found in the air and identified with MALDI-TOF MS. Using MALDI-TOF MS, we achieved a 69.6% success rate in identification. , , and spp. were recognized as good indicators of cave anthropisation.
PubMed: 37894039
DOI: 10.3390/microorganisms11102381 -
Update on novel validly published taxa of bacteria isolated from domestic animals described in 2022.Journal of Clinical Microbiology Dec 2023Expansion of our knowledge of the microbial world continues to progress at a rapid rate and carries with it an associated need for recognizing and understanding the... (Review)
Review
Expansion of our knowledge of the microbial world continues to progress at a rapid rate and carries with it an associated need for recognizing and understanding the implications of those changes. Here, we describe additions of novel taxa from domestic animals published in 2022 that are validly published per the International Code of Nomenclature of Prokaryotes. These included new members of , sp. nov. in sheep with respiratory disease, three additions to (including one from chickens with spotty liver disease), and multiple additions of organisms from the microbiota of dogs, pigs, and especially honeybees and other important pollinators. Noteworthy additions were associated with diseases of cattle, including mastitis, endocarditis, orchitis, and endometritis. Also described in 2022 was sp. nov., a member of the family, isolated from the mammary lymph nodes of cows.
Topics: Male; Animals; Cattle; Dogs; Sheep; Swine; Animals, Domestic; Phylogeny; Chickens; Bacteria
PubMed: 37889054
DOI: 10.1128/jcm.00839-23 -
Metabolites Sep 2023Maintaining a diverse and well-balanced nasal and oral microbiota is vital for human health. However, the impact of indoor microbiome and metabolites on nasal and oral...
Maintaining a diverse and well-balanced nasal and oral microbiota is vital for human health. However, the impact of indoor microbiome and metabolites on nasal and oral microbiota remains largely unknown. Fifty-six children in Shanghai were surveyed to complete a questionnaire about their personal and environmental characteristics. The indoor microbiome and metabolites from vacuumed indoor dust were profiled via shotgun metagenomics and untargeted liquid chromatography-mass spectrometry (LC-MS). The nasal and oral microbiota in children was characterized using full-length 16S rRNA sequencing from PacBio. Associations between personal/environmental characteristics and the nasal/oral microbiota were calculated using PERMANOVA and regression analyses. We identified 6247, 431, and 342 microbial species in the indoor dust, nasal, and oral cavities, respectively. The overall nasal and oral microbial composition showed significant associations with environmental tobacco smoke (ETS) exposure during pregnancy and early childhood ( = 0.005 and 0.03, respectively), and the abundance of total indoor flavonoids and two mycotoxins (deoxynivalenol and nivalenol) ( = 0.01, 0.02, and 0.03, respectively). Notably, the abundance of several flavonoids, such as baicalein, eupatilin, isoliquiritigenin, tangeritin, and hesperidin, showed positive correlations with alpha diversity and the abundance of protective microbial taxa in nasal and oral cavities ( < 0.02), suggesting their potential beneficial roles in promoting nasal/oral health. Conversely, high carbohydrate/fat food intake and ETS exposure diminished protective microorganisms while augmenting risky microorganisms in the nasal/oral cavities. Further, potential microbial transfer was observed from the indoor environment to the childhood oral cavity (, , and ), which could potentially increase virulence factors related to adherence and immune modulation and vancomycin resistance genes in children. This is the first study to reveal the association between the indoor microbiome/metabolites and nasal/oral microbiota using multi-omic approaches. These findings reveal potential protective and risk factors related to the indoor microbial environment.
PubMed: 37887365
DOI: 10.3390/metabo13101040 -
Nature Communications Oct 2023Culture techniques have associated colonization with pathogenic bacteria in the airways of neonates with later risk of childhood asthma, whereas more recent studies...
Culture techniques have associated colonization with pathogenic bacteria in the airways of neonates with later risk of childhood asthma, whereas more recent studies utilizing sequencing techniques have shown the same phenomenon with specific anaerobic taxa. Here, we analyze nasopharyngeal swabs from 1 month neonates in the COPSAC prospective birth cohort by 16S rRNA gene sequencing of the V3-V4 region in relation to asthma risk throughout childhood. Results are compared with previous culture results from hypopharyngeal aspirates from the same cohort and with hypopharyngeal sequencing data from the later COPSAC cohort. Nasopharyngeal relative abundance values of Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis are associated with the same species in the hypopharyngeal cultures. A combined pathogen score of these bacteria's abundance values is associated with persistent wheeze/asthma by age 7. No other taxa are associated. Compared to the hypopharyngeal aspirates from the COPSAC cohort, the anaerobes Veillonella and Prevotella, which have previously been implicated in asthma development, are less commonly detected in the COPSAC nasopharyngeal samples, but correlate with the pathogen score, hinting at latent community structures that bridge current and previous results. These findings have implications for future asthma prevention efforts.
Topics: Humans; Infant, Newborn; Infant; Child; Prospective Studies; RNA, Ribosomal, 16S; Asthma; Bacteria; Nasopharynx; Microbiota
PubMed: 37863895
DOI: 10.1038/s41467-023-42309-z -
Veterinary World Sep 2023Infectious bovine keratoconjunctivitis (IBK) causes a significant economic loss to cattle industries in many countries, including Kazakhstan. Although is recognized as...
BACKGROUND AND AIM
Infectious bovine keratoconjunctivitis (IBK) causes a significant economic loss to cattle industries in many countries, including Kazakhstan. Although is recognized as an etiologic agent of IBK, other bacterial and viral agents have been suspected to play a role in the pathogenesis of this disease. This study aimed to evaluate samples collected from the eyes of IBK-affected cattle in Eastern Kazakhstan at different stages of IBK for the presence of , , , , and Bovine Herpes Virus Type 1 (BHV-1) and to characterize gene sequence diversity from positive samples.
MATERIALS AND METHODS
Individual ocular swabs (n = 168) were collected from cattle that had clinical signs of IBK during the summer of 2022 on farms in the Abay region of Kazakhstan. Eye lesion scores (1, 2, and 3) were assigned depending on the degree of ocular damage. Infectious bovine keratoconjunctivitis-associated organisms were detected using a multiplex real-time polymerase chain reaction assay. The gene was sequenced from positive samples.
RESULTS
and BHV-1 were not detected in any of the collected samples. was identified in the majority of samples overall, usually in mixed infection with spp. was detected in 76.2% of animals and predominated in animals with eye lesion scores 2 and 3. was detected only in association with and/or in animals with eye lesion scores 2 and 3. was found in 57.7% of animals and was always identified in association with another organism. Sequencing of the gene in 96 samples from positive samples identified five PilA groups. The majority belonged to PilA group A. However, three new PilA groups were identified and designated PilA groups N, O, and P.
CONCLUSION
The results indicate a high prevalence of and in eyes of cattle with IBK on livestock farms in Eastern Kazakhstan. Additional novel PilA groups were identified.
PubMed: 37859972
DOI: 10.14202/vetworld.2023.1833-1839