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Frontiers in Microbiology 202216S rRNA amplicon sequencing was used to investigate changes in the broiler gastrointestinal tract (GIT) microbiota throughout the rearing period and in combination with...
16S rRNA amplicon sequencing was used to investigate changes in the broiler gastrointestinal tract (GIT) microbiota throughout the rearing period and in combination with antibiotic treatment. Thirty birds (from a commercial flock) were removed at multiple points throughout the rearing period on days 13, 27, and 33, euthanised, and their GIT aseptically removed and divided into upper (the crop, proventriculus, and the gizzard), middle (the duodenum, jejunum, and ileum) and lower (the large intestine, the caeca, and the cloaca) sections. In a separate commercial flock, on the same farm with similar husbandry practices and feed, doxycycline (100 mg/ml per kg body weight) was administered in drinking water between day 8 and 12 (inclusive) of the production cycle. Birds were removed on days, 13, 27, and 33 and GIT samples prepared as above. The contents of three merged samples from each GIT section were pooled ( = 60), the DNA extracted and analysed by 16S rRNA amplicon metagenomic sequencing and analysed. Major changes in the broiler microbiota were observed as the birds aged particularly with the Firmicutes/Bacteroidetes ratio (F:B) of the lower GIT. Moreover, Chao1, ACE, and Shannon indices showed the antibiotic treatment significantly altered the microbiota, and this change persisted throughout the rearing period. Further research is required to investigate the effect of these changes on bird performance, susceptibility to infections and carriage.
PubMed: 35875529
DOI: 10.3389/fmicb.2022.885862 -
Developmental Biology Sep 2020Congenital anomalies of external genitalia affect approximately 1 in 125 live male births. Development of the genital tubercle, the precursor of the penis and clitoris,...
Congenital anomalies of external genitalia affect approximately 1 in 125 live male births. Development of the genital tubercle, the precursor of the penis and clitoris, is regulated by the urethral plate epithelium, an endodermal signaling center. Signaling activity of the urethral plate is mediated by Sonic hedgehog (SHH), which coordinates outgrowth and patterning of the genital tubercle by controlling cell cycle kinetics and expression of downstream genes. The mechanisms that govern Shh transcription in urethral plate cells are largely unknown. Here we show that deletion of Foxa1 and Foxa2 results in persistent cloaca, an incomplete separation of urinary, genital, and anorectal tracts, and severe hypospadias, a failure of urethral tubulogenesis. Loss of Foxa2 and only one copy of Foxa1 results in urethral fistula, an additional opening of the penile urethra. Foxa1/a2 participate in an autoregulatory feedback loop with Shh, in which FOXA1 and FOXA2 positively regulate transcription of Shh in the urethra, and SHH feeds back to negatively regulate Foxa1 and Foxa2 expression. These findings reveal novel roles for Foxa genes in development of the urethral tube and in division of the embryonic cloaca.
Topics: Animals; Cloaca; Embryo, Mammalian; Hedgehog Proteins; Hepatocyte Nuclear Factor 3-alpha; Hepatocyte Nuclear Factor 3-beta; Mice; Mice, Transgenic; Ureter
PubMed: 32645357
DOI: 10.1016/j.ydbio.2020.06.009 -
Journal of Pediatric Urology Feb 2007'Persistent cloaca' is a severe malformation affecting females in which the urinary, genital and alimentary tracts share a single conduit. Previously, a Uroplakin IIIA...
OBJECTIVES
'Persistent cloaca' is a severe malformation affecting females in which the urinary, genital and alimentary tracts share a single conduit. Previously, a Uroplakin IIIA (UPIIIA) mutation was reported in one individual with persistent cloaca, and UPIIIA, Sonic Hedgehog (SHH), Ephrin B2 (EFNB2) and Hepatocyte Nuclear Factor 1beta (HNF1beta) are expressed during the normal development of organs that are affected in this condition. HNF1beta mutations have been associated with uterine malformations in humans, and mutations of genes homologous to human SHH or EFNB2 cause persistent cloaca in mice.
PATIENTS AND METHODS
We sought mutations of coding regions of UPIIIA, SHH, EFNB2 and HNF1beta genes by direct sequencing in a group of 20 patients with persistent cloaca. Most had associated malformations of the upper renal tract and over half had impaired renal excretory function. The majority of patients had congenital anomalies outside the renal/genital tracts and two had the VACTERL association.
RESULTS
Apart from a previously described index case, we failed to find UPIIIA mutations, and no patient had a SHH, EFNB2 or HNF1beta mutation.
CONCLUSION
Persistent cloaca is only rarely associated with UPIIIA mutation. Despite the fact that SHH and EFNB2 are appealing candidate genes, based on their expression patterns and mutant mice phenotypes, they were not mutated in these humans with persistent cloaca. Although HNF1beta mutations can perturb paramesonephric duct fusion in humans, HNF1beta was not mutated in persistent cloaca.
PubMed: 17476318
DOI: 10.1016/j.jpurol.2006.03.002 -
CEN Case Reports Aug 2022Persistent cloaca involves fusion of the bladder, vagina, and rectum into a single duct called the common duct. Although its pathogenesis remains unclear, it has been...
Persistent cloaca involves fusion of the bladder, vagina, and rectum into a single duct called the common duct. Although its pathogenesis remains unclear, it has been associated with hyperchloremic metabolic acidosis. Herein, we present the case of a neonatal girl with high-confluence type variant of persistent cloaca treated with vesicostomy (Blocksom) for refractory metabolic acidosis. She was diagnosed with persistent cloaca before birth; colostomy was performed and a urinary catheter was placed in the bladder. Voiding cystourethrography on day 19 after birth showed that most of the contrast material leaked into the rectum; hence, the urinary catheter was removed. On day 27, hyperchloremic metabolic acidosis was detected and treatment with oral sodium bicarbonate was initiated; however, the infant showed no response. Because hyperchloremia occurred after removal of the urinary catheter, continuous urine retention in the colon through the common duct was believed to have caused the progression of hyperchloremic metabolic acidosis through transporters in the intestinal mucosa. As reinstallation of a urinary catheter was technically difficult, vesicostomy was performed on day 29, after which the metabolic acidosis improved. This report suggests vesicostomy as an effective treatment for refractory hyperchloremic metabolic acidosis associated with high-confluence type persistent cloaca.
Topics: Acidosis; Animals; Cloaca; Colon; Cystostomy; Female; Humans; Infant; Infant, Newborn; Urinary Tract
PubMed: 35099756
DOI: 10.1007/s13730-022-00686-2 -
Journal of Neonatal Surgery 2013Hydrometrocolpos (HMC) develops as a result of vaginal outflow obstruction and the accumulation of secretions. It might be secondary to persistent cloaca, urogenital...
BACKGROUND
Hydrometrocolpos (HMC) develops as a result of vaginal outflow obstruction and the accumulation of secretions. It might be secondary to persistent cloaca, urogenital sinus, some syndromes, presence of the vaginal septum, vaginal atresia, and imperforate hymen. Each of them has different treatment options and follow-up protocols. This study was performed to identify the etiology and the related management of patients with HMC.
MATERIALS AND METHODS
A descriptive series of patients with HMC managed in our hospital between 2004 and 2011 is being presented. The medical record of these patients was analyzed for etiology, management, and outcome.
RESULTS
Eight patients with HMC were managed during 7 years at our department. Underlying etiologies included urogenital sinus (n=3), and 1 each of imperforate hymen, transverse vaginal septum, Herlyn-Werner-Wunderlich syndrome, persistent cloaca, and a variant of the cloaca. Four patients were prenatally diagnosed. The patient with imperforate hymen was managed successfully with incision and drainage. Abdominal vaginostomy was done in three patients with urogenital sinus as initial procedure. In patient with persistent cloaca, a colostomy and abdominal vaginostomy were performed. Patient with cloaca variant died due to persistent acidosis and salt wasting.
CONCLUSION
HMC may have different etiological factors which may dictate different surgical management. Etiology of HMC can be as simple as imperforate hymen to the most severe cloacal malformations.
PubMed: 26023425
DOI: No ID Found -
The Canadian Journal of Infectious... 2022Cystic fibrosis (CF) is an inherited recessive disorder characterized by recurrent and persistent pulmonary infections, resulting in lung function deterioration and...
BACKGROUND
Cystic fibrosis (CF) is an inherited recessive disorder characterized by recurrent and persistent pulmonary infections, resulting in lung function deterioration and early mortality.
METHODS
A cross-sectional study was conducted on the bacterial profile and antibiotic resistance pattern of 103 respiratory specimens from CF patients with signs of pulmonary exacerbation. Antibiotic susceptibility testing and biofilm formation of and isolates were performed by the Kirby-Bauer disc diffusion method and microtiter plate assay, respectively. Molecular typing of and isolates was carried out by spa typing and repetitive extragenic palindromic element PCR.
RESULTS
In a total of 129 isolates, the most prevalent organisms were (55.3%) and (41.7%). Other less prevalent bacterial isolates include coagulase-negative staphylococci, , , , and . The highest rate of resistance for was observed to azithromycin and erythromycin (80%), ciprofloxacin (52.3%), clindamycin (44.6%) and tetracycline (43%). Twenty percent of isolates were methicillin-resistant (MRSA) and 47.6% were MDR . For isolates the highest resistance was to cefepime (38.3%) and levofloxacin (33.3%) and 20% showed MDR phenotype.
CONCLUSION
Our study demonstrated a significant decline in the prevalence of infections in comparison to previous studies. We found to be more prevalent in younger patients, whereas mucoid showed a shift in prevalence toward older ages. Molecular typing methods showed great diversity between isolates.
PubMed: 36593975
DOI: 10.1155/2022/5831139 -
Microbiology Spectrum Feb 2022Prior study has demonstrated that gut microbiota at the genus level is significantly altered in patients with growth hormone (GH)-secreting pituitary adenoma (GHPA)....
Prior study has demonstrated that gut microbiota at the genus level is significantly altered in patients with growth hormone (GH)-secreting pituitary adenoma (GHPA). Yet, no studies exist describing the state of gut microbiota at species level in GHPA. We performed a study using 16S rRNA amplicon sequencing in a cohort of patients with GH-secreting pituitary adenoma (GHPA, = 28) and healthy controls ( = 67). Among them, 9 patients and 10 healthy controls were randomly chosen and enrolled in metagenomics shotgun sequencing, generating 280,426,512 reads after aligning to NCBI GenBank DataBase to acquire taxa information at the species level. Weighted UniFrac analysis revealed that microbial diversity was notably decreased in patients with GHPA, consistent with a previous study. With 16S rRNA sequencing, after correction for false-discovery rate (FDR), rank-sum test at the genus level revealed that the relative abundance of and was remarkably increased in patients and and genera predominated in the controls, augmented by additional LEfSe (linear discriminant analysis effect size) analysis. As for further comparison at the species level with metagenomics sequencing, rank-sum test together with LEfSe analysis confirmed the enrichment of Alistipes shahii and Odoribacter splanchnicus in the patient group. Notably, LEfSe analysis with metagenomics also demonstrated that sp. and sp. , derived from , were both significantly enriched in patients. Functional analysis showed that amino acid metabolism pathway was remarkably enriched in GHPA, while carbohydrate metabolism pathway was notably enriched in controls. Further, significant positive correlations were observed between and baseline insulin-like growth factor 1 (IGF-1), indicating that may be strongly associated with GH/IGF-1 axis in GHPA. Our data extend our insight into the GHPA microbiome, which may shed further light on GHPA pathogenesis and facilitate the exploration of novel therapeutic targets based on microbiota manipulation. Dysbiosis of gut microbiota is associated not only with intestinal disorders but also with numerous extraintestinal diseases. Growth hormone-secreting pituitary adenoma (GHPA) is an insidious disease with persistent hypersecretion of GH and IGF-1, causing increased morbidity and mortality. Researches have reported that the GH/IGF-1 axis exerts its own influence on the intestinal microflora. Here, the results showed that compared with healthy controls, GHPA patients not only decreased the alpha diversity of the intestinal flora but also significantly changed their beta diversity. Further, metagenomics shotgun sequencing in the present study exhibited that sp. and sp. were enriched in patients. Also, we were pleasantly surprised to find that the genus was strongly positively correlated with baseline IGF-1 levels. Collectively, our work provides the first glimpse of the dysbiosis of the gut microbiota at species level, providing a better understanding of the pathophysiological process of GHPA.
Topics: Adult; Bacteria; Case-Control Studies; DNA, Bacterial; Dysbiosis; Feces; Female; Gastrointestinal Microbiome; Growth Hormone; Growth Hormone-Secreting Pituitary Adenoma; Humans; Insulin-Like Growth Factor I; Male; Metagenomics; Middle Aged; Phylogeny; RNA, Ribosomal, 16S
PubMed: 35019688
DOI: 10.1128/spectrum.00425-21 -
BMC Medicine Aug 2018Antibiotic resistance is an urgent global problem, but reversibility is poorly understood. We examined the development and decay of bacterial resistance in community... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Antibiotic resistance is an urgent global problem, but reversibility is poorly understood. We examined the development and decay of bacterial resistance in community patients after antibiotic use.
METHODS
This was a systematic review and meta-analysis. PubMed, EMBASE and CENTRAL (from inception to May 2017) were searched, with forward and backward citation searches of the identified studies. We contacted authors whose data were unclear, and of abstract-only reports, for further information. We considered controlled or times-series studies of patients in the community who were given antibiotics and where the subsequent prevalence of resistant bacteria was measured. Two authors extracted risk of bias and data. The meta-analysis used a fixed-effects model.
RESULTS
Of 24,492 articles screened, five controlled and 20 time-series studies (total 16,353 children and 1461 adults) were eligible. Resistance in Streptococcus pneumoniae initially increased fourfold after penicillin-class antibiotic exposure [odds ratio (OR) 4.2, 95% confidence interval (CI) 3.5-5.4], but this fell after 1 month (OR 1.7, 95% CI 1.3-2.1). After cephalosporin-class antibiotics, resistance increased (OR 2.2, 95%CI 1.7-2.9); and fell to (OR 1.6, 95% CI 1.2-2.3) at 1 month. After macrolide-class antibiotics, resistance increased (OR 3.8, 95% CI 1.9-7.6) and persisted for 1 month (OR 5.2, 95% CI 2.6-10.3) and 3 months (OR 8.1, 95% CI 4.6-14.2, from controlled studies and OR 2.3, 95% CI 0.6-9.4, from time-series studies). Resistance in Haemophilus influenzae after penicillins was not significantly increased (OR 1.3, 95% CI 0.9-1.9) initially but was at 1 month (OR 3.4, 95% CI 1.5-7.6), falling after 3 months (OR 1.0, 95% CI 0.5-2.2). Data were sparse for cephalosporins and macrolides. Resistance in Enterobacter increased post-exposure (OR 3.2, 95% CI 0.9-10.8, from controlled studies and OR 7.1, 95% CI 4.2-12, from time-series studies], but was lower after 1 month (OR 1.8, 95% CI 0.9-3.6).
CONCLUSIONS
Resistance generally increased soon after antibiotic use. For some antibiotic classes and bacteria, it partially diminished after 1 and 3 months, but longer-term data are lacking and urgently needed.
TRIAL REGISTRATION
PROSPERO CRD42015025499 .
Topics: Adolescent; Adult; Anti-Bacterial Agents; Bacterial Infections; Child; Child, Preschool; Drug Resistance, Microbial; Humans; Infant; Infant, Newborn; Young Adult
PubMed: 30081902
DOI: 10.1186/s12916-018-1109-4 -
Applied Microbiology Sep 1975The districution of Staphylococcus and Micrococcus species and associated coryneform bacteria, Acinetobacter, Klebsiella, Enterobacter, Bacillus, and Streptomyces on...
The districution of Staphylococcus and Micrococcus species and associated coryneform bacteria, Acinetobacter, Klebsiella, Enterobacter, Bacillus, and Streptomyces on skin was determined during October 1971 from samples collected on persons living in North Carolina and New Jersey. Persistence of these organisms on skin was estimated in temporal studies conducted during the period from June 1971 to June 1972 on persons living in North Carolina. Staphylococci and coryneforms were the most predominant and persistent bacteria isolated from the nares and axillae. Staphylococci, coryneforms, micrococci, and Bacillus were the most predominant and persistent bacteria isolated from the head, legs, and arms. Acinetobacters were most frequently isolated during the warmer months of the years. Staphylococcus aureus and S. epidermidis were the most predominant and persistent staphylococci isolated from the nares, whereas S. epidermidis and S. hominis were the most predominant and persistent staphylocicci isolated from the axillae, head, legs, and arms. S. capitis was often isolated from the head and arms and S. haemolyticus was often isolated from the head, legs, and arms. S. simulans, S. xylosus, S. cohnii, S. saprophyticus, S. warneri, and an unclassified coagulase-positive species were only occasionally isolated from skin. Micrococcus luteus was the most predominant and persistent Micrococcus isolated from skin and preferred regions of the head, legs, and arms. M. varians was the second most frequent Micrococcus isolated. M. lylae, M. sedentarius, M. roseus, M. kristinae, and M. nishinomiyaensis were only occasionally isolated from skin. M. lylae was most frequently isolated during the colder months of the years.
Topics: Acinetobacter; Actinomycetales; Aerobiosis; Arm; Axilla; Bacillus; Bacteria; Enterobacter; Head; Humans; Klebsiella; Leg; Micrococcus; New Jersey; North Carolina; Nose; Seasons; Skin; Species Specificity; Staphylococcus; Streptomyces
PubMed: 810086
DOI: 10.1128/am.30.3.381-395.1975