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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 -
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 -
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 -
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 -
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 -
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 -
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 -
Journal of Dairy Science May 2021The objective of this prospective cohort study was to explore associations between intramammary infection (IMI) in late-lactation cows and postcalving udder health and...
Postcalving udder health and productivity in cows approaching dry-off with intramammary infections caused by non-aureus Staphylococcus, Aerococcus, Enterococcus, Lactococcus, and Streptococcus species.
The objective of this prospective cohort study was to explore associations between intramammary infection (IMI) in late-lactation cows and postcalving udder health and productivity. Cows (n = 2,763) from 74 US dairy herds were recruited as part of a previously published cross-sectional study of bedding management and IMI in late-lactation cows. Each herd was visited twice for sampling. At each visit, aseptic quarter milk samples were collected from 20 cows approaching dry-off (>180 d pregnant), which were cultured using standard bacteriological methods and MALDI-TOF for identification of isolates. Quarter-level culture results were used to establish cow-level IMI status at enrollment. Cows were followed from enrollment until 120 d in milk (DIM) in the subsequent lactation. Herd records were used to establish whether subjects experienced clinical mastitis or removal from the herd, and DHIA test-day data were used to record subclinical mastitis events (somatic cell count >200,000 cells/mL) and milk yield (kg/d) during the follow-up period. Cox regression and generalized estimating equations were used to evaluate the associations between IMI and the outcome of interest. The presence of late-lactation IMI caused by major pathogens was positively associated with postcalving clinical mastitis [hazard ratio = 1.5, 95% confidence interval (CI): 1.2, 2.0] and subclinical mastitis (risk ratio = 1.5, 95% CI: 1.3, 1.9). Species within the non-aureus Staphylococcus (NAS) group varied in their associations with postcalving udder health, with some species being associated with increases in clinical and subclinical mastitis in the subsequent lactation. Late-lactation IMI caused by Streptococcus and Streptococcus (Strep)-like organisms, other than Aerococcus spp. (i.e., Enterococcus, Lactococcus, and Streptococcus spp.) were associated with increases in postcalving clinical and subclinical mastitis. Test-day milk yield from 1 to 120 DIM was lower (-0.9 kg, 95% CI: -1.6, -0.3) in late-lactation cows with any IMI compared with cows without IMI. No associations were detected between IMI in late lactation and risk for postcalving removal from the herd within the first 120 DIM. Effect estimates reported in this study may be less than the underlying quarter-level effect size for IMI at dry-off and postcalving clinical and subclinical mastitis, because of the use of late-lactation IMI as a proxy for IMI at dry-off and the use of cow-level exposure and outcome measurements. Furthermore, the large number of models run in this study (n = 94) increases the chance of identifying chance associations. Therefore, confirmatory studies should be conducted. We conclude that IMI in late lactation may increase risk of clinical and subclinical mastitis in the subsequent lactation. The relationship between IMI and postcalving health and productivity is likely to vary among pathogens, with Staphylococcus aureus, Streptococcus spp., Enterococcus spp., and Lactococcus spp. being the most important pathogens identified in the current study.
Topics: Aerococcus; Animals; Cattle; Cattle Diseases; Cell Count; Cross-Sectional Studies; Enterococcus; Female; Lactation; Lactococcus; Mammary Glands, Animal; Mastitis, Bovine; Milk; Pregnancy; Prospective Studies; Staphylococcus; Streptococcus
PubMed: 33685704
DOI: 10.3168/jds.2020-19288 -
Biology Open Aug 2021In recent years, the clinical significance of Aerococcus urinae has been increasingly recognized. A. urinae has been implicated in cases of urinary tract infection (UTI;...
In recent years, the clinical significance of Aerococcus urinae has been increasingly recognized. A. urinae has been implicated in cases of urinary tract infection (UTI; acute cystitis and pyelonephritis) in both male and female patients, ranging from children to older adults. Aerococcus urinae can also be invasive, causing urosepsis, endocarditis, and musculoskeletal infections. Mechanisms of pathogenesis in A. urinae infections are poorly understood, largely due to the lack of an animal model system. In response to this gap, we developed a model of A. urinae urinary tract infection in mice. We compared A. urinae UTI in female C3H/HeN and C57BL/6 mice and compared four clinical isolates of A. urinae isolated from patients with UTI, urgency urinary incontinence, and overactive bladder. Our data demonstrate that host genetic background modulates A. urinae UTI. Female C57BL/6 female mice rapidly cleared the infection. Female C3H/HeN mice, which have inherent vesicoureteral reflux that flushes urine from the bladder up into the kidneys, were susceptible to prolonged bacteriuria. This result is consistent with the fact that A. urinae infections most frequently occur in patients with underlying urinary tract abnormalities or disorders that make them susceptible to bacterial infection. Unlike uropathogens such as E. coli, which cause infection and inflammation both of the bladder and kidneys in C3H/HeN mice, A. urinae displayed tropism for the kidney, persisting in kidney tissue even after clearance of bacteria from the bladder. Aerococcus urinae strains from different genetic clades displayed varying propensities to cause persistent kidney infection. Aerococcus urinae infected kidneys displayed histological inflammation, neutrophil recruitment and increased pro-inflammatory cytokines. These results set the stage for future research that interrogates host-pathogen interactions between A. urinae and the urinary tract.
Topics: Aerococcus; Animals; Disease Models, Animal; Disease Susceptibility; Genetic Background; Genome, Bacterial; Genomics; Gram-Positive Bacterial Infections; Host-Pathogen Interactions; Mice; Mice, Inbred C3H; Mice, Inbred C57BL; Phylogeny; Urinary Tract Infections
PubMed: 34387311
DOI: 10.1242/bio.058931 -
Analytical Chemistry Nov 2019Currently, there is a severe shortage of donor kidneys that are fit for transplantation, due in part to a lack of adequate viability assessment tools for transplant...
Currently, there is a severe shortage of donor kidneys that are fit for transplantation, due in part to a lack of adequate viability assessment tools for transplant organs. This work presents the integration of a novel wireless two-channel amperometric potentiostat with microneedle-based glucose and lactate biosensors housed in a 3D printed chip to create a microfluidic biosensing system that is genuinely portable. The wireless potentiostat transmits data via Bluetooth to an Android app running on a tablet. The whole miniaturized system is fully enclosed and can be integrated with microdialysis to allow continuous monitoring of tissue metabolite levels in real time. We have also developed a wireless portable automated calibration platform so that biosensors can be calibrated away from the laboratory and in transit. As a proof of concept, we have demonstrated the use of this portable analysis system to monitor porcine kidneys for the first time from organ retrieval, through warm ischemia, transportation on ice, right through to cold preservation and reperfusion. The portable system is robust and reliable in the challenging conditions of the abattoir and during kidney transportation and can detect clear physiological changes in the organ associated with clinical interventions.
Topics: Aerococcus; Animals; Aspergillus niger; Bacterial Proteins; Biosensing Techniques; Dialysis Solutions; Fungal Proteins; Glucose; Glucose Oxidase; Kidney; Lab-On-A-Chip Devices; Lactic Acid; Microdialysis; Microfluidic Analytical Techniques; Mixed Function Oxygenases; Monitoring, Physiologic; Proof of Concept Study; Swine
PubMed: 31647870
DOI: 10.1021/acs.analchem.9b03774