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Journal of Global Antimicrobial... Jun 2022Identification and classification of microorganisms is one of the most important but difficult and challenging issues in microbiology. Whole genome sequencing (WGS),...
OBJECTIVES
Identification and classification of microorganisms is one of the most important but difficult and challenging issues in microbiology. Whole genome sequencing (WGS), which can give a thorough understanding for the genome of bacteria strain, has been universally used for studying bacterial classification, evolution, and drug-related resistant genes. We in this study aimed to identify a Gram-positive, microaerophilic, catalase-negative cocci strain named AV208, which has shown resistance to vancomycin, by whole genome's average nucleotide identity (ANI) and high-throughput sequencing technology.
METHODS
The AV208 strain was identified by following commercially available identification systems, including API 20 Strep system and Vitek 2 Compact Gram-positive identification system for biochemical phenotypic test. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS) and 16S rRNA gene sequencing were used for confirmation identification. The whole genome of AV208 was sequenced by using high throughput sequencing technology and ANI between AV208, and its phylogenetic neighbours were analysed by the Orthologous Average Nucleotide Identity Tool (OAT) software. Polymerase chain reaction (PCR) and DNA sequencing were used to investigate the potential molecular mechanism for vancomycin resistance.
RESULTS
The AV208 strain was isolated from an ascites sample from a patient with chronic kidney disease who showed extensive resistance to the drugs detected, such as vancomycin with MIC >256 μg/mL. With combination of biochemical phenotypic test, MALDI-TOF-MS and 16S rRNA gene sequencing, the AV208 strain was tentatively identified as an Aercoccus viridans. By using complete genome sequence, we found a 96.24% ANI between strain AV208 and Aerococcus urinaeequi CCUG 28094, which was higher than that with A. viridans CCUG4311 (94.9%). The consistency of 16S rRNA sequence of strain AV208 was 100% with A. urinaeequi CCUG 28094 and 99.9% with A. viridans CCUG4311, with only one base difference between them. PCR and sequencing for van genes revealed that AV208 was positive for the vanA gene. A Tn1546 transposon-like structure with vanA gene was found in the genome, which was predicted locating in plasmid, causing vancomycin resistance phenotypes.
CONCLUSION
Average nucleotide identity analysis based on whole genome sequence is an accurate and effective method for identification of bacteria, especially for strains that are not discernible by existing methods such as Aerococcus.
Topics: Aerococcus; Bacterial Typing Techniques; Humans; Nucleotides; Phylogeny; RNA, Ribosomal, 16S; Vancomycin; Whole Genome Sequencing
PubMed: 35477007
DOI: 10.1016/j.jgar.2022.04.013 -
Biochemistry Insights 2019() and () are gram-positive bacteria belonging to the family Aerococcaceae and colonize the human immunocompromised and catheterized urinary tract. We identified both...
() and () are gram-positive bacteria belonging to the family Aerococcaceae and colonize the human immunocompromised and catheterized urinary tract. We identified both pathogens in polymicrobial urethral catheter biofilms (CBs) with a combination of 16S rDNA sequencing, proteomic analyses, and microbial cultures. Longitudinal sampling of biofilms from serially replaced catheters revealed that each species persisted in the urinary tract of a patient in cohabitation with 1 or more gram-negative uropathogens. The and proteomes revealed active glycolytic, heterolactic fermentation, and peptide catabolic energy metabolism pathways in an anaerobic milieu. A few phosphotransferase system (PTS)-based sugar uptake and oligopeptide ABC transport systems were highly expressed, indicating adaptations to the supply of nutrients in urine and from exfoliating squamous epithelial and urothelial cells. Differences in the vs metabolisms pertained to citrate lyase and utilization and storage of glycogen (evident only in proteomes) and to the enzyme Xfp that degrades d-xylulose-5'-phosphate and the biosynthetic pathways for 2 protein cofactors, pyridoxal 6'-phosphate and 4'-phosphopantothenate (expressed only in proteomes). A predicted ZnuA-like transition metal ion uptake system was identified for while expressed 2 LPXTG-anchored surface proteins, one of which had a predicted pilin D adhesion motif. While these proteins may contribute to fitness and virulence in the human host, it cannot be ruled out that and fill a niche in polymicrobial biofilms without being the direct cause of injury in urothelial tissues.
PubMed: 31555049
DOI: 10.1177/1178626419875089 -
Journal of Clinical Microbiology Nov 2011Aerococcus urinae has been described as resistant to trimethoprim-sulfamethoxazole (SXT), but the test medium may affect this observation. Twenty-seven clinical isolates...
Aerococcus urinae has been described as resistant to trimethoprim-sulfamethoxazole (SXT), but the test medium may affect this observation. Twenty-seven clinical isolates of A. urinae tested susceptible to SXT in cation-adjusted Mueller-Hinton broth (CAMHB) plus lysed horse blood and resistant in CAMHB plus lysed sheep blood.
Topics: Aerococcus; Animals; Anti-Bacterial Agents; Culture Media; Drug Combinations; Gram-Positive Bacterial Infections; Hemolysis; Horses; Humans; Microbial Sensitivity Tests; Sheep; Trimethoprim, Sulfamethoxazole Drug Combination
PubMed: 21918023
DOI: 10.1128/JCM.05535-11 -
PloS One 2020The diagnosis of infective endocarditis (IE) remains a challenge. One of the rare bacterial species recently associated with biofilms and negative cultures in infective...
The diagnosis of infective endocarditis (IE) remains a challenge. One of the rare bacterial species recently associated with biofilms and negative cultures in infective endocarditis is Aerococcus urinae. Whether the low number of reported cases might be due to lack of awareness and misidentification, mainly as streptococci, is currently being discussed. To verify the relevance and biofilm potential of Aerococcus in endocarditis, we used fluorescence in situ hybridization to visualize the microorganisms within the heart valve tissue. We designed and optimized a specific FISH probe (AURI) for in situ visualization and identification of A. urinae in sections of heart valves from two IE patients whose 16S rRNA gene sequencing had deteced A. urinae. Both patients had a history of urinary tract infections. FISH visualized impressive in vivo grown biofilms in IE, thus confirming the potential of A. urinae as a biofilm pathogen. In both cases, FISH/PCR was the only method to unequivocally identify A. urinae as the only causative pathogen for IE. The specific FISH assay for A. urinae is now available for further application in research and diagnostics. A. urinae should be considered in endocarditis patients with a history of urinary tract infections. These findings support the biofilm potential of A. urinae as a virulence factor and are meant to raise the awareness of this pathogen.
Topics: Aerococcus; Aged; Aged, 80 and over; Biofilms; Endocarditis, Bacterial; Female; Heart Valves; Humans; In Situ Hybridization, Fluorescence; Male; Urinary Tract Infections
PubMed: 32325482
DOI: 10.1371/journal.pone.0231827 -
Antimicrobial Agents and Chemotherapy Sep 2021and species are fastidious organisms, representing the causative agents of ∼1% to 3% of cases of infective endocarditis (IE). Little is known about the optimal...
and species are fastidious organisms, representing the causative agents of ∼1% to 3% of cases of infective endocarditis (IE). Little is known about the optimal antibiotic treatment for these species, and daptomycin has been suggested as a therapeutic option. We describe the antimicrobial profiles of and IE isolates, investigate high-level daptomycin resistance (HLDR) development, and evaluate daptomycin activity in combination therapy. studies with 16 IE strains (6 Abiotrophia defectiva strains, 9 Granulicatella adiacens strains, and 1 G. elegans strain) were performed using microdilution to determine MICs and time-kill methodology to evaluate combination therapy. Daptomycin nonsusceptibility (DNS) (MIC ≥ 2 mg/liter) and HLDR (MIC ≥ 256 mg/liter) were based on existing Clinical and Laboratory Standards Institute (CLSI) breakpoints for viridans group streptococci. All isolates were susceptible to vancomycin: G. adiacens was more susceptible to penicillin and ampicillin than A. defectiva (22% versus 0% and 67% versus 33%) but less susceptible to ceftriaxone and daptomycin (56% versus 83% and 11% versus 50%). HLDR developed in both A. defectiva (33%) and (78%) after 24 h of exposure to daptomycin. Combination therapy did not prevent the development of daptomycin resistance with ampicillin (2/3 strains), gentamicin (2/3 strains), ceftriaxone (2/3 strains), or ceftaroline (2/3 strains). Once developed, HLDR was stable for a prolonged time (>3 weeks) in , whereas in A. defectiva, HLDR reversed to the baseline MIC at day 10. This study is the first to demonstrate rapid HLDR development in and species . Resistance was stable, and most combination therapies did not prevent it.
Topics: Abiotrophia; Anti-Bacterial Agents; Carnobacteriaceae; Daptomycin; Endocarditis, Bacterial; Humans
PubMed: 34252304
DOI: 10.1128/AAC.02522-20 -
European Journal of Clinical... May 2022Our objective was to assess the incidence of bacteraemic Aerococcus urinae cases at Helsinki metropolitan area, Finland, from a 6-year study period (2013 to 2018) and to...
Our objective was to assess the incidence of bacteraemic Aerococcus urinae cases at Helsinki metropolitan area, Finland, from a 6-year study period (2013 to 2018) and to further characterize available cases. The study evaluates the outcome of commonly used cefuroxime treatment and determinate a set of A. urinae in vitro antimicrobial susceptibilities for benzylpenicillin, cefuroxime, and ceftriaxone. Clinical records of A. urinae bacteraemic patients were reviewed retrospectively. Antimicrobial susceptibility testing was performed by disk diffusion, gradient test, and broth microdilution for 139-141 clinical A. urinae isolates. Clinical data of 72/77 patients were combined with the in vitro susceptibilities. We found an increasing number of bacteraemic A. urinae cases within 6-year study period (p = 0.01). The patients were mainly elderly males, and all suffered from underlying conditions. A total of 27.3% of cases (21/77) showed polymicrobial blood cultures. Thirty-day mortality was 22.1%. Cefuroxime was the initial empiric antimicrobial agent given for 66/76 of the patients and treatment outcome was favorable for 20/22 patients who received cefuroxime at least up to day 5. All isolates were susceptible to benzylpenicillin and cefuroxime interpreted by EUCAST breakpoints for Aerococci and PK-PD breakpoints, respectively. MIC determinations gave variable results for ceftriaxone, 2.1-2.9% of the isolates were resistant. To conclude, it seems that the number of bacteraemic Aerococcus urinae cases is increasing at Helsinki metropolitan area, Finland, reflecting the growing blood culture sampling. Clinical A. urinae isolates were susceptible to cefuroxime in vitro. Treatment data indicate that empirical cefuroxime started for possibly urinary tract -derived community-acquired bacteraemia covers A. urinae.
Topics: Aerococcus; Aged; Anti-Bacterial Agents; Bacteremia; Ceftriaxone; Cefuroxime; Disease Susceptibility; Finland; Gram-Positive Bacterial Infections; Humans; Male; Microbial Sensitivity Tests; Retrospective Studies
PubMed: 35257275
DOI: 10.1007/s10096-022-04415-6 -
Emerging Infectious Diseases Aug 2023We report a novel Globicatella species causing extensive soft tissue infection in a man bitten by a stray domestic cat in the United Kingdom. We identified this...
We report a novel Globicatella species causing extensive soft tissue infection in a man bitten by a stray domestic cat in the United Kingdom. We identified this bacterium by 16S rRNA gene sequencing, whole-genome sequencing, and biochemical profiling and determined antimicrobial drug susceptibility.
Topics: Animals; Cats; Gram-Positive Bacterial Infections; RNA, Ribosomal, 16S; Soft Tissue Infections; Aerococcaceae; Bacteria
PubMed: 37486350
DOI: 10.3201/eid2908.221770 -
Oral microbiota distinguishes acute lymphoblastic leukemia pediatric hosts from healthy populations.PloS One 2014In leukemia, oral manifestations indicate aberrations in oral microbiota. Microbiota structure is determined by both host and environmental factors. In human hosts, how...
In leukemia, oral manifestations indicate aberrations in oral microbiota. Microbiota structure is determined by both host and environmental factors. In human hosts, how health status shapes the composition of oral microbiota is largely unknown. Taking advantage of advances in high-throughput sequencing, we compared the composition of supragingival plaque microbiota of acute lymphoblastic leukemia (ALL) pediatric patients with healthy controls. The oral microbiota of leukemia patients had lower richness and less diversity compared to healthy controls. Microbial samples clustered into two major groups, one of ALL patients and another of healthy children, with different structure and composition. Abundance changes of certain taxa including the Phylum Firmicutes, the Class Bacilli, the Order Lactobacillales, the Family Aerococcaceae and Carnobacteriaceae, as well as the Genus Abiotrophia and Granulicatella were associated with leukemia status. ALL patients demonstrated a structural imbalance of the oral microbiota, characterized by reduced diversity and abundance alterations, possibly involved in systemic infections, indicating the importance of immune status in shaping the structure of oral microbiota.
Topics: Biodiversity; Case-Control Studies; Child; Child, Preschool; Cluster Analysis; Female; Healthy Volunteers; Humans; Male; Metagenome; Microbiota; Mouth; Precursor Cell Lymphoblastic Leukemia-Lymphoma; Risk Factors
PubMed: 25025462
DOI: 10.1371/journal.pone.0102116 -
Gastroenterology Report 2022Severe alcohol-associated hepatitis (SAH) patients with infections have a high short-term mortality rate. Gut microbiota dysbiosis plays an important role in the...
Clinical outcomes and gut microbiota analysis of severe alcohol-associated hepatitis patients undergoing healthy donor fecal transplant or pentoxifylline therapy: single-center experience from Kerala.
BACKGROUND
Severe alcohol-associated hepatitis (SAH) patients with infections have a high short-term mortality rate. Gut microbiota dysbiosis plays an important role in the pathogenesis of SAH. Preliminary studies have demonstrated long-term benefits with healthy donor fecal microbiota transplantation (FMT). Data on FMT compared with pentoxifylline for SAH and relevant gut microbial changes are lacking in literature.
METHODS
From January 2019 to February 2021, retrospective analysis of a single hospital's records revealed 47 SAH patients undergoing FMT (100 mL/day via nasoduodenal tube for 7 days) and 25 matched patients receiving pentoxifylline (400 mg/8 h for 28 days). The primary end point was a 6-month survival rate. Secondary end points included incidence of ascites, hepatic encephalopathy, infections, acute kidney injury, and gut microbiota changes between post-therapy groups. Biomarker discovery and network analysis were also performed to identify significant taxa of gut microbiota in post-treatment groups in retrospectively stored stool samples.
RESULTS
All were males. The 6-month survival rate was higher in the patients undergoing FMT than in patients receiving pentoxifylline (83.0% vs 56.0%, =0.012). At the end of 6-month follow-up, the incidences of clinically significant ascites (56.0% vs 25.5%, =0.011), hepatic encephalopathy (40.0% vs 10.6%, =0.003), and critical infections (52.0% vs 14.9%, <0.001) in patients administered pentoxifylline were significantly higher than those in patients treated with FMT. At 3 months, biomarker analysis revealed a significant abundance of and in the FMT group and the pentoxifylline group, respectively. At 6 months, in the FMT group and pathogenic in the pentoxifylline group were notable. Network analysis showed beneficial taxa () as a central influencer in those undergoing FMT at 6 months.
CONCLUSIONS
Healthy donor FMT improved survival rate and reduced liver-related complications compared with pentoxifylline. These clinical benefits were associated with favorable modulation of intestinal bacterial communities. Difficult-to-treat SAH patients may be safely bridged to transplantation using FMT. Controlled trials evaluating long-term outcomes are an unmet need.
PubMed: 36479155
DOI: 10.1093/gastro/goac074 -
Annals of Clinical Microbiology and... Feb 2022Pyelonephritis is one of the most serious bacterial illnesses during childhood. Gram-negative organisms account for up to 90% of the cases. Gram-positive bacteria are... (Review)
Review
BACKGROUND
Pyelonephritis is one of the most serious bacterial illnesses during childhood. Gram-negative organisms account for up to 90% of the cases. Gram-positive bacteria are uncommon causes of urinary tract infections, and only a few cases caused by Facklamia hominis have been reported in the literature.
CASE PRESENTATION
A five-year-old girl with tracheostomy and gastrostomy and past medical history of congenital lymphangioma presented with a two-week history of with intermittent fever, frequent urination, and vesical tenesmus. Diagnosis of pyelonephritis was made. Urine culture reported colonies with alpha-hemolysis in blood agar at 48-h of incubation and Facklamia hominis was identified by MALDI-TOF. The patient was successfully treated with gentamicin.
CONCLUSIONS
This is the first reported case of pyelonephritis by Facklamia hominis in a child, and the second involving infection in a pediatric patient. Although this pathogen is uncommon, current treatment of F. hominis is a challenge for physicians. This case illustrates the requirement to standardize identification and treatment of care to avoid treatment failure and antimicrobial resistance.
Topics: Aerococcaceae; Anti-Bacterial Agents; Child, Preschool; Female; Fever; Gentamicins; Humans; Pyelonephritis; Treatment Outcome; Urinary Tract Infections
PubMed: 35151319
DOI: 10.1186/s12941-022-00497-4