scholarly journals Genomic and phenotypic diversity of Enterococcus faecalis isolated from endophthalmitis

2020 ◽  
Author(s):  
Gayatri Shankar Chilambi ◽  
Hayley R. Nordstrom ◽  
Daniel R. Evans ◽  
Regis P. Kowalski ◽  
Deepinder K. Dhaliwal ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Enterococcus Faecalis ◽  
Biofilm Formation ◽  
Phenotypic Diversity ◽  
Medical Center ◽  
Phenotypic Variability ◽  
Comparative Genomic ◽  
Mismatch Repair Gene ◽  
Ocular Infection ◽  
First Case

ABSTRACTEnterococcus faecalis are hospital-associated opportunistic pathogens and also causative agents of post-operative endophthalmitis. Patients with enterococcal endophthalmitis often have poor visual outcomes, despite appropriate antibiotic therapy. Here we investigated the genomic and phenotypic characteristics of E. faecalis isolates collected from 13 patients treated at the University of Pittsburgh Medical Center Eye Center over 19 years. Comparative genomic analysis indicated that patients were infected with E. faecalis of diverse multi-locus sequence types (STs) previously associated with clinical, commensal, and environmental sources. We identified known E. faecalis virulence factors and antibiotic resistance genes in each genome, including genes conferring resistance to aminoglycosides, erythromycin, and tetracyclines. We assessed all isolates for their cytolysin production, biofilm formation, and antibiotic susceptibility, and observed phenotypic differences between isolates. Fluoroquinolone and cephalosporin susceptibilities were particularly variable, as were biofilm formation and cytolysin production. In addition, we found evidence of E. faecalis adaptation during recurrent endophthalmitis by identifying genetic variants that arose in sequential isolates sampled over eight-months from the same patient. We identified a mutation in the DNA mismatch repair gene mutS that was associated with a hypermutator phenotype in the final isolate from the patient, which was also more resistant to ceftazidime. Overall this study documents the genomic and phenotypic variability among E. faecalis causing endophthalmitis, as well as possible adaptive mechanisms underlying bacterial persistence during recurrent ocular infection.IMPORTANCEBacterial endophthalmitis is a sight-threatening infection of the inside of the eye. Enterococcus faecalis cause endophthalmitis occasionally, but when they do the infections are often severe. Here we investigated the genomes, antibiotic susceptibilities, and virulence-associated traits among E. faecalis collected from 13 patients with post-operative endophthalmitis. We wondered whether there were common bacterial factors that might explain why enterococcal endophthalmitis is so destructive to ocular tissues. Instead we found that E. feacalis isolated from endophthalmitis were genetically and phenotypically diverse; isolates belonged to a variety of genetic lineages and showed varying levels of antibiotic resistance and biofilm formation. We also undertook further characterization of three closely related E. faecalis isolates from a patient with recurrent endophthalmitis, and found that a hypermutator strain emerged during persistent infection. Hypermutators have been found in a variety of other infection contexts; here we describe what we believe is the first case of a hypermutator arising during ocular infection.

scholarly journals Genomic and phenotypic diversity of Enterococcus faecalis isolated from endophthalmitis

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250084
Author(s):  
Gayatri Shankar Chilambi ◽  
Hayley R. Nordstrom ◽  
Daniel R. Evans ◽  
Regis P. Kowalski ◽  
Deepinder K. Dhaliwal ◽  
...  
Keyword(s):  
Enterococcus Faecalis ◽  
Biofilm Formation ◽  
Phenotypic Diversity ◽  
Medical Center ◽  
Phenotypic Variability ◽  
Spontaneous Mutation ◽  
Comparative Genomic ◽  
Mismatch Repair Gene ◽  
Ocular Infection ◽  
Repair Gene

Enterococcus faecalis are hospital-associated opportunistic pathogens and also causative agents of post-operative endophthalmitis. Patients with enterococcal endophthalmitis often have poor visual outcomes, despite appropriate antibiotic therapy. Here we investigated the genomic and phenotypic characteristics of E. faecalis isolates collected from 13 patients treated at the University of Pittsburgh Medical Center Eye Center over 19 years. Comparative genomic analysis indicated that patients were infected with E. faecalis belonging to diverse multi-locus sequence types (STs) and resembled E. faecalis sampled from clinical, commensal, and environmental sources. We identified known E. faecalis virulence factors and antibiotic resistance genes in each genome, including genes conferring resistance to aminoglycosides, erythromycin, and tetracyclines. We assessed all isolates for their cytolysin production, biofilm formation, and antibiotic susceptibility, and observed phenotypic differences between isolates. Fluoroquinolone and cephalosporin susceptibilities were particularly variable between isolates, as were biofilm formation and cytolysin production. In addition, we found evidence of E. faecalis adaptation during recurrent endophthalmitis by identifying genetic variants that arose in sequential isolates sampled over eight months from the same patient. We identified a mutation in the DNA mismatch repair gene mutS that was associated with an increased rate of spontaneous mutation in the final isolate from the patient. Overall this study documents the genomic and phenotypic variability among E. faecalis causing endophthalmitis, as well as possible adaptive mechanisms underlying bacterial persistence during recurrent ocular infection.

scholarly journals The Role of Biofilm Formation in Antibiotic Resistance of Bacteria Isolated from Saliva of Patients with Dental Caries

2021 ◽  
pp. 40-49
Author(s):  
Merriam Ghadhanfar Alwan ◽  
Hadeel Adil Al Rubaye ◽  
Noor Adil Abood ◽  
Hind Tahseen Ibrahem ◽  
Hamiza Bt Hamidon ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Antibiotic Resistance ◽  
Dental Caries ◽  
Antimicrobial Resistance ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Enterococcus Faecalis ◽  
Biofilm Formation ◽  
Rrna Gene ◽  
Tissue Culture Plate

Objectives: This study aim to determine the bacterial diversity, biofilm forming ability and the antimicrobial resistance of bacteria isolated from saliva of patients with dental caries conditions with the using of 16S rRNA gene sequencing technique for identification of the most virulent isolates. Methods: Isolation and identification of microorganisms were done employing standard bacteriologic techniques, followed by biofilm detection using tissue culture plate method. The strong biofilm forming isolates were selected for antibiotic susceptibility test against selected antibiotics using disk diffusion technique. In order to identify the selected isolates. The genomic DNA obtained following the extraction process were used for the amplification of the bacterial 16S rRNA gene. Results: A total of 137 bacterial isolates were obtained and identified as belonging to 21 genera. Tissue culture plate (TCP) method were employed for screening the isolates according to its biofilm forming ability, its showed that 55 (40.1%) of the total isolates were strong, 57 (41.6%) were moderate and 25 (18.3%) were weak biofilm producers. The antimicrobial susceptibility test showed the multi antibiotics resistance of the strong biofilm former isolates to the conventional antibiotics. Enterococcus faecalis isolates showed the highest biofilm formation and antibiotic resistance. The 16S rRNA gene for two of these isolates have been amplified using PCR and the product sequenced, analyzed and registered in the National Center for Biotechnology Information (NCBI) as UKMS1 and UKMS2 and the accession numbers KX960104.1 and KX960105.1 respectively. Conclusion: The study has revealed that antimicrobial resistance of bacteria isolates from saliva of patients with dental caries conditions is associated with biofilm formation. Other uncommon pathogenic bacteria were also isolated in this study as a result of the use of non-selective enrichment medium for culturing. Enterococcus faecalis isolates indicated the highest biofilm formation and antibiotic resistance.

scholarly journals Antibiotic Resistance and Biofilm Formation of Enterococcus faecalis in Patient and Environmental Samples

2015 ◽  
Vol 8 (10) ◽  
Author(s):  
Malihe Talebi ◽  
Nastaran Asghari Moghadam ◽  
Zeynab Mamooii ◽  
Mohsen Enayati ◽  
Mahnaz Saifi ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Enterococcus Faecalis ◽  
Biofilm Formation ◽  
Environmental Samples

In vitro biofilm formation and antimicrobial susceptibility patterns of bacteria isolated from suspected external ocular infected patients attending Jimma University Medical Center eye clinic, southwest Ethiopia

2019 ◽  
Author(s):  
Kuma Diriba ◽  
Tesfaye Kassa ◽  
Yared Alemu ◽  
Sisay Bekele
Keyword(s):  
Antimicrobial Susceptibility ◽  
Biofilm Formation ◽  
Medical Center ◽  
Ocular Infection ◽  
Bacterial Isolates ◽  
Susceptibility Pattern ◽  
Southwest Ethiopia ◽  
Antimicrobial Susceptibility Pattern ◽  
Ocular Infections ◽  
Jimma University

Abstract Background: Ocular disease with its complications is a major public health problem which significantly impacts on quality of life in developing countries. An ocular infection due to microbial agents, can lead to reduced vision and blindness. This study was aimed to assess the antimicrobial susceptibility pattern and biofilm forming potential of bacteria isolated from suspected external ocular infected patients attending Jimma University Medical Center (JUMC). Method: A cross sectional facility based study was conducted on 319 suspect patients with external ocular infections from March 2017 to June 2017 at JUMC in Southwest Ethiopia. External ocular specimens were collected and standard operating procedures were followed to handle and culture throughout the study period. Antimicrobial susceptibility pattern of the isolates was determined by disk diffusion method according to CLSI 2015. Microtiter (96 wells) plate method was used to screen biofilm formation by measuring optical density at 570nm. Result: Out of 319 study participants with external ocular infection, the prevalence of bacterial pathogens was 46.1%. The predominant bacterial isolates were Coagulase negative staphylococcus (CoNS) (27.7%) followed by Staphylococcus aureus (19.7%). Among Gram negatives, Pseudomonas aeroginosa (6.8%) was the leading isolate. Increased antimicrobial resistance was observed for tetracycline (64%), erthromycin (66.7%) and penicillin (77.1%). Amoxicillin-clavulanic acid, ciprofloxacin and gentamicin were the most effective drugs for both Gram negative and Gram positive ranging from about 70 to 100% with the later two drugs for external ocular infections. Methicillin resistant S. aureus (MRSA) accounted for 13.8% of S. aureus isolates.. Multidrug resistance (MDR) accounted for 68.7%. The overall biofilm formation rate of bacterial ocular pathogens was 66.1%; with P. aeruginosa (40%), CoNS (34.1%) and S. aureus (31%) formed strong biofilm phenotype. Conclusion: The prevalence of bacterial isolates among external ocular infection was high. Almost all bacterial isolates were resistant to atleast one or more drugs. MDR pathogens were observed increasingly among biofilm formers or vice versa. Therefore, antimicrobial susceptibility testing should be practiced to guide treatment of external ocular cases and to control the emergence of drug resistant bacteria.

scholarly journals Characterization of Klebsiella sp. Strain 10982, a Colonizer of Humans That Contains Novel Antibiotic Resistance Alleles and Exhibits Genetic Similarities to Plant and Clinical Klebsiella Isolates

2014 ◽  
Vol 58 (4) ◽  
pp. 1879-1888 ◽  
Author(s):  
Tracy H. Hazen ◽  
LiCheng Zhao ◽  
Jason W. Sahl ◽  
Gwen Robinson ◽  
Anthony D. Harris ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Nitrogen Fixation ◽  
Medical Center ◽  
Genomic Analysis ◽  
Bioinformatic Analysis ◽  
Clinical Isolates ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Nitrogen Fixing ◽  
Content Type

ABSTRACTA uniqueKlebsiellaspecies strain, 10982, was cultured from a perianal swab specimen obtained from a patient in the University of Maryland Medical Center intensive care unit.Klebsiellasp. 10982 possesses a large IncA/C multidrug resistance plasmid encoding a novel FOX AmpC β-lactamase designated FOX-10. A novel variant of the LEN β-lactamase was also identified. Genome sequencing and bioinformatic analysis demonstrated that this isolate contains genes associated with nitrogen fixation, allantoin metabolism, and citrate fermentation. These three gene regions are typically present in eitherKlebsiella pneumoniaeclinical isolates orKlebsiellanitrogen-fixing endophytes but usually not in the same organism. Phylogenomic analysis ofKlebsiellasp. 10982 and sequencedKlebsiellagenomes demonstrated thatKlebsiellasp. 10982 is present on a branch that is located intermediate between the genomes of nitrogen-fixing endophytes andK. pneumoniaeclinical isolates. Metabolic features identified in the genome ofKlebsiellasp. 10982 distinguish this isolate from otherKlebsiellaclinical isolates. These features include the nitrogen fixation (nif) gene cluster, which is typically present in endophyticKlebsiellaisolates and is absent fromKlebsiellaclinical isolates. Additionally, theKlebsiellasp. 10982 genome contains genes associated with allantoin metabolism, which have been detected primarily inK. pneumoniaeisolates from liver abscesses. Comparative genomic analysis ofKlebsiellasp. 10982 demonstrated that this organism has acquired genes conferring new metabolic strategies and novel antibiotic resistance alleles, both of which may enhance its ability to colonize the human body.

scholarly journals Metabolic Capacity of Sinorhizobium (Ensifer) meliloti Strains as Determined by Phenotype MicroArray Analysis

2009 ◽  
Vol 75 (16) ◽  
pp. 5396-5404 ◽  
Author(s):  
Emanuele G. Biondi ◽  
Enrico Tatti ◽  
Diego Comparini ◽  
Elisa Giuntini ◽  
Stefano Mocali ◽  
...  
Keyword(s):  
Sinorhizobium Meliloti ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Phenotypic Variability ◽  
Natural Populations ◽  
Growth Conditions ◽  
Comparative Genomic ◽  
Sulfur Source ◽  
Phenotype Microarray ◽  
High Genetic Diversity

ABSTRACT Sinorhizobium meliloti is a soil bacterium that fixes atmospheric nitrogen in plant roots. The high genetic diversity of its natural populations has been the subject of extensive analysis. Recent genomic studies of several isolates revealed a high content of variable genes, suggesting a correspondingly large phenotypic differentiation among strains of S. meliloti. Here, using the Phenotype MicroArray (PM) system, hundreds of different growth conditions were tested in order to compare the metabolic capabilities of the laboratory reference strain Rm1021 with those of four natural S. meliloti isolates previously analyzed by comparative genomic hybridization (CGH). The results of PM analysis showed that most phenotypic differences involved carbon source utilization and tolerance to osmolytes and pH, while fewer differences were scored for nitrogen, phosphorus, and sulfur source utilization. Only the variability of the tested strain in tolerance to sodium nitrite and ammonium sulfate of pH 8 was hypothesized to be associated with the genetic polymorphisms detected by CGH analysis. Colony and cell morphologies and the ability to nodulate Medicago truncatula plants were also compared, revealing further phenotypic diversity. Overall, our results suggest that the study of functional (phenotypic) variability of S. meliloti populations is an important and complementary step in the investigation of genetic polymorphism of rhizobia and may help to elucidate rhizobial evolutionary dynamics, including adaptation to diverse environments.

scholarly journals Effects of artificially introduced Enterococcus faecalis strains in experimental necrotizing enterocolitis

2019 ◽  
Author(s):  
Patrick T. Delaplain ◽  
Brandon A. Bell ◽  
Jin Wang ◽  
Mubina Isani ◽  
Emily Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Antibiotic Resistance ◽  
Enterococcus Faecalis ◽  
Necrotizing Enterocolitis ◽  
Biofilm Formation ◽  
Opportunistic Pathogens ◽  
First Feeding ◽  
Naturally Occurring ◽  
Old Rats ◽  
Artificial Introduction

AbstractEnterococcus faecalis is a ubiquitous intestinal symbiont and common early colonizer of the neonatal gut. Although colonization with E. faecalis has been previously associated with decreased NEC pathology, these bacteria have been also implicated as opportunistic pathogens. Here we characterized 21 strains of E. faecalis, naturally occurring in 4-day-old rats, for potentially pathogenic properties and ability to colonize the neonatal gut. The strains differed in hemolysis, gelatin liquefaction, antibiotic resistance, biofilm formation, and ability to activate the pro-inflammatory transcription factor NF-κB in cultured enterocytes. Only 3 strains appreciably colonized the neonatal intestine on day 4 after artificial introduction with the first feeding. The best colonizer, strain BB70, effectively displaced maternal E. faecalis and significantly increased NEC pathology. Our results show that colonization with E. faecalis may predispose neonates to NEC.

scholarly journals Genotypic and phenotypic characterization of Streptococcus mutans strains isolated from patients with dental caries

2021 ◽  
Author(s):  
Mohammad Shahadat Hossain ◽  
Sadab Alam ◽  
Yead Morshed Nibir ◽  
Tahrima Arman Tusty ◽  
Sayyeed Mahmud Bulbul ◽  
...  
Keyword(s):  
Dental Caries ◽  
Streptococcus Mutans ◽  
Biofilm Formation ◽  
Acid Production ◽  
Phenotypic Diversity ◽  
Phenotypic Variability ◽  
Clinical Isolates ◽  
Phenotypic Characterization ◽  
Specific Gene ◽  
Polymerase Chain

Background and Objectives: The oral cavity harbors numerous Streptococcus mutans strains which display remarkable genotypic and phenotypic diversity. This study evaluated the genotypic and phenotypic diversity of 209 S. mutans strains isolated from 336 patients with dental caries and compared with the universal reference strain, UA159. Materials and Methods: Selective cultivation on mitis-salivaries-bacitracin agar and species-specific polymerase chain re- action (PCR) was carried out to isolate and identify the 209 S. mutans isolates from 336 patients with dental caries. Arbitrari- ly primed polymerase chain reaction (AP-PCR), PCR amplification of specific gene, acid production and biofilm formation capacity were performed to evaluate the genotypic and phenotypic variation. Student’s t-test and Chi-square test were used for analysis of variables and a probability (P) of <0.05 was considered as significant. Results: Our study revealed a high degree of genotypic and phenotypic variability among the clinical strains. We observed significant differences in colony morphology, generation time, biofilm formation, and acid production while growing in cul- ture medium. All the clinical isolates were able to lower pH while growing in Todd-Hewitt broth. Consistent with phenotypic variations, we also observed genotypic variation by AP-PCR and gene specific PCR. AP-PCR analysis suggested that most of the patients with dental caries have distinct type of S. mutans strains. Genes related to various two component systems were highly conserved among the isolated strains, however, bacteriocin encoding genes such as nlmAB, nlmC were absent in nearly half of the clinical isolates. Conclusion: Our results support that S. mutans clinical isolates have wide genotypic diversity and show variation in growth kinetics, acid production, acid tolerance and biofilm formation capacity and indicates the presence of diverse mechanism to initiate and establish the biofilm lifestyle which leads to tooth decay.

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