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Journal of Research in Medical Sciences... 2021Nosocomial surfaces are potential pathogen reservoirs. Our aim was to describe the microbial diversity and analyze microbial patterns of healthcare-associated pathogens...
Nosocomial surfaces are potential pathogen reservoirs. Our aim was to describe the microbial diversity and analyze microbial patterns of healthcare-associated pathogens in two step-down-care-units at a tertiary care hospital. We monitored infected patients over 45 days to describe microbial diversity and colonization patterns. A total of 2762 isolates were recovered from the sampled sites, coagulase-negative staphylococci represented 44.64% (1233/2762) of the isolates. The most frequently recovered ESKAPE species (, , , , , and ) were (7.53%; 208/2762 isolates) and / (5.18%; 143/2762). We recovered a high diversity of species, including potential pathogens. was detected more frequently on diverse surfaces and persisted in patients' nostrils during the hospital stay.
PubMed: 35126589
DOI: 10.4103/jrms.JRMS_1074_20 -
Microbiology Spectrum Feb 2022species are classified as high-priority pathogens due to high prevalence of multidrug resistance from persistent antibiotic use. For infections caused by...
species are classified as high-priority pathogens due to high prevalence of multidrug resistance from persistent antibiotic use. For infections caused by multidrug-resistant isolates, colistin (polymyxin E), a last-resort antibiotic, is a potential treatment option. Treatment with colistin has been shown to lead to emergence of polymyxin resistance. The primary mechanism for colistin resistance is modification of terminal phosphate moieties of lipid A, leading to decreased membrane electronegativity and reducing colistin binding affinity. Detection of these modifications, including the addition of phosphoethanolamine and 4-amino-4-deoxy-l-arabinose (Ara4N), can be used for prediction of colistin resistance using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The objective of this study was to identify lipid A markers for colistin resistance in species and Klebsiella aerogenes (formerly Enterobacter aerogenes). Using a collection of and Klebsiella aerogenes clinical isolates, broth MICs for colistin were determined initially. Subsequently, killing assays were carried out to determine how the concentration of colistin at which there is approximately 50% survival (kill) equates to their MICs. Finally, lipid A analysis was conducted via MALDI-TOF MS using the novel rapid extraction method, termed fast lipid analysis technique (FLAT), to correlate MIC and killing efficacy with predictive lipid A modifications. Sensitivity and specificity of the MS assay compared to MIC interpretation were 100% and 53.4%, respectively. A receiver operator characteristic (ROC) demonstrated that MS was highly correlated with killing, with area under the curve of 0.97. This analysis demonstrated the potential utility of MALDI-TOF MS as a rapid diagnostic platform of colistin resistance in species. In this study, we develop a novel method for identifying colistin resistance in species and Klebsiella aerogenes without performing antimicrobial susceptibility testing. Typically, susceptibility testing requires an additional 24 to 48 h, while the MS assay described in this study allows for resistant identifications in under 1 h after initial culture. Identification using MALDI-TOF MS would save time and prevent inappropriate use of colistin. MALDI-TOF MS is an easy-to-use, readily available, robust diagnostic tool in clinical laboratories. Furthermore, this study highlights limitations of polymyxin susceptibility testing. Use of a killing assay best captures how colistin treats infection and is shown to be highly correlated with our MS assay; thus, the MS assay in this study effectively predicts how colistin would treat a patient's infection. Use of MALDI-TOF MS for accurate and early identification of antimicrobial resistance can improve antimicrobial stewardship and patient outcomes.
Topics: Anti-Bacterial Agents; Colistin; Drug Resistance, Bacterial; Enterobacter; Enterobacteriaceae Infections; Humans; Lipid A; Microbial Sensitivity Tests; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Tandem Mass Spectrometry
PubMed: 35107363
DOI: 10.1128/spectrum.01445-21 -
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 -
Frontiers in Nutrition 2021A diverse group of rhizobacteria persists in the rhizospheric soil, on the surface of roots, or in association with rice plants. These bacteria colonize plant root...
A diverse group of rhizobacteria persists in the rhizospheric soil, on the surface of roots, or in association with rice plants. These bacteria colonize plant root systems, enhance plant growth and crop yield. Indigenous rhizobacteria are known to promote soil health, grain production quality and serve as sustainable bioinoculant. The present study was aimed to isolate, identify and characterize indigenous plant growth promoting (PGP) diazotrophic bacteria associated with the rhizosphere of rice fields from different areas of Jammu and Kashmir, India. A total of 15 bacteria were isolated and evaluated for various PGP traits, antagonistic activity against phytopathogens, production of hydrolytic enzymes and biofilm formation under conditions. The majority of the isolated bacteria were Gram-negative. Out of 15 bacterial isolates, nine isolates produced IAA (12.24 ± 2.86 to 250.3 ± 1.15 μg/ml), 6 isolates exhibited phosphate solubilization activity (36.69 ± 1.63 to 312.4 ± 1.15 μg/ml), 7 isolates exhibited rock phosphate solubilization while 5 isolates solubilized zinc (10-18 mm), 7 isolates showed siderophore production, 8 isolates exhibited HCN production, 6 isolates exhibited aminocyclopropane-1-carboxylate (ACC) deaminase activity, 13 isolates exhibited cellulase activity, nine isolates exhibited amylase and lipase activity and six isolates exhibited chitinase activity. In addition, 5 isolates showed amplification with gene and showed a significant amount of nitrogenase activity in a range of 0.127-4.39 μmol CH/mg protein/h. Five isolates viz., IHK-1, IHK-3, IHK-13, IHK-15 and IHK-25 exhibited most PGP attributes and successfully limited the mycelial growth of and oxysporum . All the five bacterial isolates were identified based on morphological, biochemical and 16S rDNA gene sequencing study, as sp., sp., and . Rice plants developed from seeds inoculated with these PGP strains individually had considerably higher germination percentage, seed vigor index and total dry biomass when compared to control. These findings strongly imply that the PGP diazotrophic bacteria identified in this work could be employed as plant growth stimulators in rice.
PubMed: 35096930
DOI: 10.3389/fnut.2021.781764 -
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 -
Journal of Extracellular Vesicles Jan 2022Intestinal commensal bacteria contribute to maintaining gut homeostasis. Disruptions to the commensal flora are linked to the development and persistence of disease. The...
Intestinal commensal bacteria contribute to maintaining gut homeostasis. Disruptions to the commensal flora are linked to the development and persistence of disease. The importance of these organisms is further demonstrated by the widespread ability of enteric viruses to exploit commensal bacteria to enhance viral infection. These viruses interact directly with commensal bacteria, and while the impact of this interaction on viral infection is well described for several viruses, the impact on the commensal bacteria has yet to be explored. In this article, we demonstrate, for the first time, that enteric viruses alter the gene expression and phenotype of individual commensal bacteria. Human and murine norovirus interaction with bacteria resulted in genome-wide differential gene expression and marked changes in the surface architecture of the bacterial cells. Furthermore, the interaction of the virus with bacteria led to increased production of smaller outer membrane vesicles (OMVs). Enhanced production of smaller vesicles was also observed when noroviruses were incubated with other commensal bacteria, indicating a potentially broad impact of norovirus interaction. The vesicle production observed in the in vivo model followed a similar trend where an increased quantity of smaller bacterial vesicles was observed in stool collected from virus-infected mice compared to mock-infected mice. Furthermore, changes in vesicle size were linked to changes in protein content and abundance, indicating that viral binding induced a shift in the mechanism of the OMV biogenesis. Collectively, these data demonstrate that enteric viruses induce specific changes in bacterial gene expression, leading to changes in bacterial extracellular vesicle production that can potentially impact host responses to infection.
Topics: Animals; Bacterial Outer Membrane; Enterobacter cloacae; Extracellular Vesicles; Gastroenteritis; Gastrointestinal Microbiome; Humans; Mice; Microbial Interactions; Norovirus
PubMed: 34981901
DOI: 10.1002/jev2.12172 -
Veterinary World Sep 2021There is a worldwide controversy about the choice of microbial flora for use as process hygiene indicators. This study aimed to evaluate the pertinence of using either...
BACKGROUND AND AIM
There is a worldwide controversy about the choice of microbial flora for use as process hygiene indicators. This study aimed to evaluate the pertinence of using either coliforms or Enterobacteriaceae (EB) as process hygiene indicators in the pasteurized milk production line. Two flora families and total flora were used as bacterial indicators in some stages of pasteurized milk production line to identify the origin of post-pasteurization contamination and compare the results obtained for each flora. In addition, the bacteriological profile of isolated coliforms and EB was developed.
MATERIALS AND METHODS
One thousand and two hundred samples of pasteurized cow milk and surfaces (pipes and tank) at various processing stages were taken from two dairies in the northern region of Algeria. The total microbial flora (TF), total coliforms (TC), thermotolerant coliforms, and EB were enumerated, following the recommendations of ISO 4833:2006, ISO 4832:2006, and ISO 21528-2:2017 methods, respectively. The bacteriological profile was determined using the API 20E and 10S tests (bioMérieux, France). Furthermore, the cleaning efficiency and disinfection protocol of surfaces were evaluated using contact agar slides 1 (Liofilchem™, Italy).
RESULTS
Enumeration of the different indicators shows that the highest contamination rate is recorded by the total flora in the two units, 3.28 and 3.78 log CFU/mL, respectively. EB (-0.60 log CFU/mL) at post-pasteurization stage in Unit 1 and coliforms (0.44 log CFU/mL) at the pasteurized packaged milk stage in Unit 2 are the least significant germ families. The lowest compliance rates of bacterial contamination were reported for total flora (82-85%) at the three sampled sites in Unit 2. In comparison, the highest was reported in Unit 1 (99.8%) and 2 (98%) by the EB indicator. Assessing the surface cleaning and disinfection protocol compliance shows that the tank records the highest non-compliance rates for EB and TF (4% and 3%) in Unit 2. EB are represented in both units by various species. in Unit 1 and in Unit 2 are the common species of the three indicator families. and in Unit 1, , , , , and in Unit 2 are the most time persistent bacterial genera along the production line. , , and are common genera in both units.
CONCLUSION
The results obtained show no difference in the use of EB or TC as hygiene indicators. However, if the objective is to identify the species of bacterial populations, using EBs are the most appropriate.
PubMed: 34840449
DOI: 10.14202/vetworld.2021.2317-2324 -
Microbiology Spectrum Dec 2021The hospital environment has been reported as a source of transmission events and outbreaks of carbapenemase-producing Enterobacterales. Interconnected plumbing systems...
The hospital environment has been reported as a source of transmission events and outbreaks of carbapenemase-producing Enterobacterales. Interconnected plumbing systems and the microbial diversity in these reservoirs pose a challenge for outbreak investigation and control. A total of 133 clinical and environmental OXA-48-producing Enterobacter cloacae isolates collected between 2015 and 2021 were characterized by whole-genome sequencing (WGS) to investigate a prolonged intermittent outbreak involving 41 patients in the hematological unit. A mock-shower experiment was performed to investigate the possible acquisition route. WGS indicated the hospital water environmental reservoir as the most likely source of the outbreak. The lack of diversity of the harbouring plasmids was a challenge for data interpretation. The detection of -harboring E. cloacae strains in the shower area after the mock-shower experiment provided strong evidence that showering is the most likely route of acquisition. Initially, in 20 out of 38 patient rooms, wastewater traps and drains were contaminated with OXA-48-positive E. cloacae. Continuous decontamination using 25% acetic acid three times weekly was effective in reducing the trap/drain positivity in monthly environmental screening but not in reducing new acquisitions. However, the installation of removable custom-made shower tubs did prevent new acquisitions over a subsequent 12-month observation period. In the present study, continuous decontamination was effective in reducing the bacterial burden in the nosocomial reservoirs but was not sufficient to prevent environment-to-patient transmission in the long term. Construction interventions may be necessary for successful infection prevention and control. The hospital water environment can be a reservoir for a multiward outbreak, leading to acquisitions or transmissions of multidrug-resistant organisms in a hospital setting. The majority of Gram-negative bacteria are able to build biofilms and persist in the hospital plumbing system over a long period of time. The elimination of the reservoir is essential to prevent further transmission and spread, but proposed decontamination regimens, e.g., using acetic acid, can only suppress but not fully eliminate the environmental reservoir. In this study, we demonstrated that colonization with multidrug-resistant organisms can be acquired by showering in showers with contaminated water traps and drains. A construction intervention by installing removable and autoclavable shower inserts to avoid sink contact during showering was effective in containing this outbreak and may be a viable alternative infection prevention and control measure in outbreak situations involving contaminated shower drains and water traps.
Topics: Bacterial Proteins; Biofilms; Cross Infection; Disease Outbreaks; Enterobacter cloacae; Enterobacteriaceae Infections; Genome, Bacterial; Humans; Infection Control; Intensive Care Units; Sanitary Engineering; Water Microbiology; Whole Genome Sequencing; beta-Lactamases
PubMed: 34817232
DOI: 10.1128/Spectrum.01380-21 -
Journal of Medical Virology Apr 2022Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), may manifest as a life-threatening...
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), may manifest as a life-threatening respiratory infection with systemic complications. Clinical manifestations among children are generally less severe than those seen in adults, but critical cases have increasingly been reported in infants less than 1 year of age. We report a severe case of neonatal COVID-19 requiring intensive care and mechanical ventilation, further complicated by a multidrug-resistant Enterobacter asburiae super-infection. Chest X-rays, lung ultrasound, and chest computed tomography revealed extensive interstitial pneumonia with multiple consolidations, associated with persistent increased work of breathing and feeding difficulties. SARS-CoV-2 RNA was detected in respiratory specimens and stools, but not in other biological samples, with a rapid clearance in stools. Serological tests demonstrated a specific SARS-CoV-2 antibody response mounted by the neonate and sustained over time. The therapeutic approach included the use of enoxaparin and steroids which may have contributed to the bacterial complication, underlying the challenges in managing neonatal COVID-19, where the balance between viral replication and immunomodulation maybe even more challenging than in older ages.
Topics: COVID-19; Critical Care; Enterobacter; Enterobacteriaceae Infections; Female; Humans; Infant, Newborn; Lung; Neonatal Sepsis; SARS-CoV-2; Superinfection; Treatment Outcome
PubMed: 34812530
DOI: 10.1002/jmv.27472 -
Clinical Genetics Feb 2022The caudal type homeobox 2 (CDX2) gene encodes a developmental regulator involved in caudal body patterning. Only three pathogenic variants in human CDX2 have been...
The caudal type homeobox 2 (CDX2) gene encodes a developmental regulator involved in caudal body patterning. Only three pathogenic variants in human CDX2 have been described, in patients with persistent cloaca, sirenomelia and/or renal and anogenital malformations. We identified five patients with de novo or inherited pathogenic variants in CDX2 with clinical phenotypes that partially overlap with previous cases, that is, imperforate anus and renal, urogenital and limb abnormalities. However, additional clinical features were seen including vertebral agenesis and we describe considerable phenotypic variability, even in unrelated patients with the same recurrent p.(Arg237His) variant. We propose CDX2 variants as rare genetic cause for a multiple congenital anomaly syndrome that can include features of caudal regression syndrome and VACTERL. A causative role is further substantiated by the relationship between CDX2 and other proteins encoded by genes that were previously linked to caudal abnormalities in humans, for example, TBXT (sacral agenesis and other vertebral segmentation defects) and CDX1 (anorectal malformations). Our findings confirm the essential role of CDX2 in caudal morphogenesis and formation of cloacal derivatives in humans, which to date has only been well characterized in animals.
Topics: Abnormalities, Multiple; Alleles; CDX2 Transcription Factor; Child; Female; Genetic Association Studies; Genetic Predisposition to Disease; Genetic Testing; Genotype; Humans; Infant; Infant, Newborn; Male; Mutation; Phenotype; Sacrococcygeal Region; Exome Sequencing
PubMed: 34671974
DOI: 10.1111/cge.14076