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Animals : An Open Access Journal From... Jan 2024Antimicrobials are extensively utilized in dairy farms to prevent and control diseases in cattle. However, their use contributes to the emergence of...
Antimicrobials are extensively utilized in dairy farms to prevent and control diseases in cattle. However, their use contributes to the emergence of antimicrobial-resistant bacteria (ARB) and antimicrobial-resistant genes (ARG), and these can be transmitted to the environment. Regular monitoring of antimicrobial resistance (AMR) is crucial for implementing effective mitigation strategies. This research aimed to assess the environmental microbial species present on dairy farms in Shandong Province and characterize the antimicrobial resistance profiles of the isolates. Five dairy farms located in Shandong Province were selected, representing the prevalent large-scale farming patterns in the area. Sampling took place from April to June 2022, with a total of 223 isolates collected from various environmental locations within each farm (bedding, sports field, and milking parlor). Matrix-assisted laser desorption/ionization-time-of-flight mass spectrometry (MALDI-TOF MS) was employed to identify the species of the clinical isolates. The main pathogens isolated were (5.38%, = 12), (4.93%, = 11), and (4.03%, = 9). Among the bacterial isolates, resistance to lincomycin was highest at 91%, and 88% were resistant to sulfadiazine. Antimicrobial resistance genes were detected in only a small proportion of the isolates, the most common of which was . These findings highlight the necessity for careful evaluation of antimicrobial usage in maintaining their effectiveness in human medicine. Understanding the microbial species present and their antimicrobial resistance profiles aids in focusing efforts toward sustainable antimicrobial use and safeguarding human health.
PubMed: 38200891
DOI: 10.3390/ani14010160 -
Infection and Drug Resistance 2023This study compared microbial compositions of midstream and catheter urine specimens from patients with suspected complicated urinary tract infections to determine if...
Emerging and Fastidious Uropathogens Were Detected by M-PCR with Similar Prevalence and Cell Density in Catheter and Midstream Voided Urine Indicating the Importance of These Microbes in Causing UTIs.
INTRODUCTION
This study compared microbial compositions of midstream and catheter urine specimens from patients with suspected complicated urinary tract infections to determine if emerging and fastidious uropathogens are infecting the bladder or are contaminants.
METHODS
Urine was collected by in-and-out catheter (n = 1000) or midstream voiding (n = 1000) from 2000 adult patients (≥60 years of age) at 17 DispatchHealth sites across 11 states. The two groups were matched by age (mean 81 years), sex (62.1% female, 37.9% male), and ICD-10-CM codes. Microbial detection was performed with multiplex polymerase chain reaction (M-PCR) with a threshold for "positive detection" ≥ 10,000 cells/mL for bacteria or any detection for yeast. Results were divided by sex.
RESULTS
In females, 28 of 30 microorganisms/groups were found by both collection methods, while in males 26 of 30 were found by both. There were significant overlaps in the detection and densities of classical uropathogens including , and , as well as emerging uropathogens including and . In females, detection rates were slightly higher in midstream voided compared to catheter-collected (p = 0.0005) urine samples, while males showed the opposite trend (p < 0.0001). More polymicrobial infections were detected in midstream voided compared to catheter-collected samples (64.4% vs 45.7%, p < 0.0001) in females but the opposite in males (35.6% vs 47.0%, p = 0.002).
DISCUSSION
In-and-out catheter-collected and midstream voided urine specimens shared significant similarities in microbial detections by M-PCR, with some differences found for a small subset of organisms and between sexes.
CONCLUSION
Non-invasive midstream voided collection of urine specimens for microbial detection and identification in cases of presumed UTI does not result in significantly more contamination compared to in-and-out catheter-collected specimens. Additionally, organisms long regarded as contaminants should be reconsidered as potential uropathogens.
PubMed: 38148772
DOI: 10.2147/IDR.S429990 -
Microorganisms Dec 2023is an aerobic Gram-positive coccus that grows as tiny alpha-hemolytic colonies. is a slow-growing facultative anaerobic Gram-positive rod. These bacteria are part of...
is an aerobic Gram-positive coccus that grows as tiny alpha-hemolytic colonies. is a slow-growing facultative anaerobic Gram-positive rod. These bacteria are part of the urogenital microbiota of healthy patients, but can also be involved in urinary tract infections (UTIs), particularly in elderly men and young children. Because and are fastidious and are difficult to identify with phenotypic methods, they are underestimated causes of UTIs. Their growth is slow and requires a blood-enriched medium incubated under an anaerobic or 5% CO atmosphere for 48 h and from 24 to 48 h for and , respectively. Furthermore, accurate identification is only possible using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) or molecular-based methods. In rare cases, these bacteria can be responsible for invasive infections. We describe, here, an unusual case of bacteremic UTI caused by both and in an 89-year-old woman. She presented with dyspnea, and bacteriuria was noted. This challenging clinical and microbiological diagnosis was made in our laboratory by Gram staining urine with a leucocyte count >50/μL and/or a bacterial count >14/μL urinary culture on a blood agar plate. After 10 days of antimicrobial treatment consisting of 2 g amoxicillin PO t.i.d., the patient was discharged with a complete clinical and biological recovery. and are probably still underestimated causes of UTIs. Microbiologists could consider the presence of these two bacteria using appropriate culture and identification methods in cases where a positive direct examination of urine reveals small Gram-positive rods or cocci, where undocumented UTIs are present in elderly patients, but also where a urinary dipstick is negative for nitrites and is associated with leukocyturia.
PubMed: 38138052
DOI: 10.3390/microorganisms11122908 -
Journal of Dairy Science May 2024Udder cleft dermatitis (UCD) is a skin condition affecting the anterior parts of the udder in dairy cattle. In the present study, we aimed to shed light on the...
Udder cleft dermatitis (UCD) is a skin condition affecting the anterior parts of the udder in dairy cattle. In the present study, we aimed to shed light on the microbiota in severe UCD lesions versus healthy udder skin by putting forward a taxonomic and functional profile based on a virulence factor analysis. Through shotgun metagenomic sequencing, we found a high proportion of bacteria in addition to a low abundance of archaea. A distinct clustering of healthy udder skin versus UCD lesion samples was shown by applying principal component analysis and (sparse) partial least squares analysis on the metagenomic data. Proteobacteria, Bacillota, and Actinomycetota were among the most abundant phyla in healthy udder skin samples. In UCD samples, Bacteroidota was the most abundant phylum. At genus level, Bifidobacterium spp. had the highest relative abundance in healthy skin samples, whereas Porphyromonas spp. and Corynebacterium spp. had the highest relative abundance in UCD samples. In the differential abundance analysis, Porphyromonas spp. and Bacteroides spp. were significantly differentially abundant in UCD samples, whereas Bifidobacterium spp., Staphylococcus sp. AntiMn-1, and Staphylococcus equorum were more commonly found in healthy samples. Moreover, the abundance of several treponeme phylotypes was significantly higher in lesion samples. The streptococcal cysteine protease speB was among the most abundant virulence factors present in severe UCD lesions, while a plethora of virulence factors such as the antitoxin relB were downregulated, possibly contributing to creating the ideal wound climate for the dysbiotic community. Network analysis showed healthy lesion samples had a large network ofpositive, correlations between the abundances of beneficial species such as Aerococcus urinaeequi and Bifidobacterium angulatum, indicating that the healthy skin microbiome forms an active protective bacterial network, which is disrupted in case of UCD. In UCD samples, a smaller microbial network mainly consisting of positive correlations between the abundances of Bacteroides fragilis and anaerobic Bacteroidota was exposed. Moreover, a high correlation between the taxonomic data and virulence factors was revealed, concurrently with 2 separate networks of microbes and virulence factors. One network, matching with the taxonomic findings in the healthy udder skin samples, showcased a community of harmless or beneficial bacteria, such as Bifidobacterium spp. and Butyrivibrio proteoclasticus, associated with hcnB, hcnC, relB, glyoxalase, and cupin 2. The other network, corresponding to UCD samples, consisted of pathogenic or facultative pathogenic and mainly anaerobic bacteria such as Treponema spp., Mycoplasmopsis spp., and bovine gammaherpesvirus 4, that correlated with virulence factors SpvB, fhaB, and haemagglutination activity domain-associated factor. Our results point toward a dysbiotic community with a notable decrease in diversity and evenness, with a loss of normal skin inhabitants and innocuous or useful species making way for predominantly anaerobic, facultative pathogens. The shift in the abundance of virulence factors such as fhaB and SpvB could play a role in the manifestation of a local micro-environment favorable to the microbiome associated with udder skin lesions. Lastly, the presence of specific networks between microbial species, and between microbes and virulence factors was shown.
Topics: Animals; Cattle; Mammary Glands, Animal; Virulence Factors; Skin Diseases; Microbiota; Treponema; Bacteria; Bacteroidetes; Dermatitis
PubMed: 38135052
DOI: 10.3168/jds.2023-24180 -
Veterinary Sciences Dec 2023Subclinical mastitis is a common disease that threatens the welfare and health of dairy cows and causes huge economic losses. Somatic cell count (SCC) is the most...
Subclinical mastitis is a common disease that threatens the welfare and health of dairy cows and causes huge economic losses. Somatic cell count (SCC) is the most suitable indirect index used to evaluate the degree of mastitis. To explore the relationship between SCC, diversity in the microbiome, and subclinical mastitis, we performed next-generation sequencing of the 16S rRNA gene of cow's milk with different SCC ranges. The data obtained showed that the microbiota was rich and coordinated with SCC below 2 × 10. SCC above 2 × 10 showed a decrease in the diversity of microbial genera. When SCC was below 2 × 10, the phylum Actinobacteriota accounted for the most. When SCC was between 2 × 10 and 5 × 10, Firmicutes accounted for the most, and when SCC exceeded 5 × 10, Firmicutes and Proteobacteria accounted for the most. Pathogenic genera such as Streptococcus spp. were absent, while SCC above 2 × 10 showed a decrease in the diversity of microbial genera. SCC was positively correlated with the percentage of , , and and negatively correlated with the percentage of , , , and . decreased 6.19 times after the SCC exceeded 2 × 10; the SCC increased exponentially from 2 × 10 to 5 × 10 and above 1 × 10 in . Analysis of the microbiota of the different SCC ranges suggests that the development of mastitis may not only be a primary infection but may also be the result of dysbiosis in the mammary gland.
PubMed: 38133250
DOI: 10.3390/vetsci10120699 -
Topics in Spinal Cord Injury... 2023Neurogenic bladder is associated with bacterial colonization and frequent urinary tract infections.
BACKGROUND
Neurogenic bladder is associated with bacterial colonization and frequent urinary tract infections.
OBJECTIVES
To explore the effects of one to two doses of intravesical (LGG) on the urobiomes of adults with spinal cord injury/disease (SCI/D) who manage their bladders with intermittent catheterization (IC).
METHODS
This was a pilot substudy within an 18-month phase 1 clinical trial of self-instilled intravesical LGG for urinary symptoms as directed by the Self-Management Protocol using Probiotics (SMP-Pro). Urine samples were collected monthly when participants were asymptomatic. When SMP-Pro "trigger" symptoms (cloudier and/or more foul-smelling urine) occurred, urine samples were collected immediately pre-LGG instillation and 24 to 48 hours after LGG instillation. Urine was collected via a new catheter, immediately placed on ice/freezer, and processed within 12 hours. Genomic DNA was isolated, and the V4 region of the 16S rRNA bacterial gene was amplified and high throughput sequenced. Amplicon sequence variants were inferred and bacterial composition, community structure, and variation across clinical phenotypes were determined.
RESULTS
126 urine samples were collected from 26 participants (SCI/D = 23; multiple sclerosis = 2; spina bifida = 1) between 20 and 57 years of age. The urobiomes were characterized by four dominant phyla (>1%): Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria, which were comprised of six dominant genera (>3%): (29.1%), (22.4%), (15.2%), (6.3%), (6.0%), and (3.0%). Post-LGG samples were associated with a decline in predominance ( < .001) and altered bacterial diversity ( < .05).
CONCLUSION
Among people with SCI/D who use IC, intravesical LGG alters the bacterial composition and diversity of the urine ecosystem, potentially disrupting the uropathogenic urobiome.
Topics: Adult; Humans; Lacticaseibacillus rhamnosus; Microbiota; RNA, Ribosomal, 16S; Spinal Cord Injuries; Urinary Bladder, Neurogenic; Urinary Tract; Pilot Projects
PubMed: 38076286
DOI: 10.46292/sci23-00004 -
International Journal of Molecular... Nov 2023() is a swine pathogen that can cause sepsis, meningitis, endocarditis, and other infectious diseases; it is also a zoonotic pathogen that has caused a global surge in...
() is a swine pathogen that can cause sepsis, meningitis, endocarditis, and other infectious diseases; it is also a zoonotic pathogen that has caused a global surge in fatal human infections. The widespread prevalence of multidrug-resistant strains and the decline in novel antibiotic candidates have necessitated the development of alternative antimicrobial agents. In this study, AVPL, the () phage lysin, was found to exhibit efficient bactericidal activity and broad lytic activity against multiple serotypes of . A final concentration of 300 μg/mL AVPL reduced counts by 4-4.5 log10 within 1 h in vitro. Importantly, AVPL effectively inhibited 48 h biofilm formation and disrupted preformed biofilms. In a mouse model, 300 μg/mouse AVPL protected 100% of mice from infection following the administration of lethal doses of multidrug-resistant type 2 (SS2) strain SC19, reduced the bacterial load in different organs, and effectively alleviated inflammation and histopathological damage in infected mice. These data suggest that AVPL is a valuable candidate antimicrobial agent for treating infections.
Topics: Animals; Swine; Humans; Mice; Bacteriophages; Aerococcus; Streptococcus suis; Streptococcal Infections; Bacteremia; Disease Models, Animal
PubMed: 38068990
DOI: 10.3390/ijms242316670 -
Animals : An Open Access Journal From... Nov 2023Food grinding is supposed to be influenced by multiple factors. However, how those factors affecting this behavior remain unclear. In this study, we investigated the...
Food grinding is supposed to be influenced by multiple factors. However, how those factors affecting this behavior remain unclear. In this study, we investigated the effect of food restriction on food grinding in Brandt's voles (), as well as the potential role of the gut microbiota in this process, through a comparison of the variations between voles with different food supplies. Food restriction reduced the relative amount of ground food to a greater extent than it lowered the relative food consumption, and altered the abundance of , , , and . Fecal acetate content for the 7.5 g-food supply group was lower than that for the 15 g-food supply group. Our study indicated that food restriction could effectively inhibit food grinding. Further, abundance, abundance, and acetate content were strongly related to food grinding. Variations in gut microbial abundance and short-chain fatty acid content induced by food restriction likely promote the inhibition of food grinding. These results could potentially provide guidance for reducing food waste during laboratory rodent maintenance.
PubMed: 37958179
DOI: 10.3390/ani13213424 -
IDCases 2023is a Gram-positive, catalase-negative coccus, rarely responsible for urinary tract infections and seldom described for musculoskeletal infections like spondylodiscitis....
is a Gram-positive, catalase-negative coccus, rarely responsible for urinary tract infections and seldom described for musculoskeletal infections like spondylodiscitis. An 86-year-old man presented to our hospital for groin pain without fever. Pelvic CT-guided biopsy revealed an pubic symphysis osteomyelitis. He received a treatment by amoxicillin for six weeks, and did not need any surgery. An eight -month- follow-up showed a favorable evolution. Pubic symphysis infection can be induced by a wide variety of pathogens, and may have very different clinical presentations. Some authors recommend systematic surgery, but in case of susceptible pathogen associated with a low level of joint destruction, medical treatment alone should be sufficient to cure and make surgery unnecessary.
PubMed: 37928817
DOI: 10.1016/j.idcr.2023.e01911 -
Cancers Oct 2023Colorectal cancer (CRC) is a significant global health concern. Microbial dysbiosis and associated metabolites have been associated with CRC occurrence and progression....
Colorectal cancer (CRC) is a significant global health concern. Microbial dysbiosis and associated metabolites have been associated with CRC occurrence and progression. This study aims to analyze the gut microbiota composition and the enriched metabolic pathways in patients with late-stage CRC. In this study, a cohort of 25 CRC patients diagnosed at late stage III and IV and 25 healthy participants were enrolled. The fecal bacterial composition was investigated using V3-V4 ribosomal RNA gene sequencing, followed by clustering and linear discriminant analysis (LDA) effect size (LEfSe) analyses. A cluster of ortholog genes' (COG) functional annotations and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were employed to identify enrichment pathways between the two groups. The findings showed that the fecal microbiota between the two groups varied significantly in alpha and beta diversities. CRC patients' fecal samples had significantly enriched populations of , , , , , , , , Family XIII_AD3001 Group, , , , , , , and (Q < 0.05). The enriched pathways identified in the CRC group were amino acid transport, signaling and metabolism, membrane biogenesis, DNA replication and mismatch repair system, and protease activity (Q < 0.05). These results suggested that the imbalance between intestinal bacteria and the elevated level of the predicated functions and pathways may contribute to the development of advanced CRC tumors. Further research is warranted to elucidate the exact role of the gut microbiome in CRC and its potential implications for use in diagnostic, prevention, and treatment strategies.
PubMed: 37894386
DOI: 10.3390/cancers15205019