scholarly journals Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to Other Enterobacter Species in Patients with Bloodstream Infection

2020 ◽  
Vol 58 (9) ◽  
Author(s):  
Austin Wesevich ◽  
Granger Sutton ◽  
Felicia Ruffin ◽  
Lawrence P. Park ◽  
Derrick E. Fouts ◽  
...  
Keyword(s):  
Clinical Outcome ◽  
Hospital Mortality ◽  
Clinical Outcomes ◽  
Genome Analysis ◽  
Enterobacter Aerogenes ◽  
Genomic Islands ◽  
Klebsiella Aerogenes ◽  
Poor Clinical Outcome ◽  
Content Type ◽  
Pan Genome

ABSTRACT Enterobacter aerogenes was recently renamed Klebsiella aerogenes. This study aimed to identify differences in clinical characteristics, outcomes, and bacterial genetics among patients with K. aerogenes versus Enterobacter species bloodstream infections (BSI). We prospectively enrolled patients with K. aerogenes or Enterobacter cloacae complex (Ecc) BSI from 2002 to 2015. We performed whole-genome sequencing (WGS) and pan-genome analysis on all bacteria. Overall, 150 patients with K. aerogenes (46/150 [31%]) or Ecc (104/150 [69%]) BSI were enrolled. The two groups had similar baseline characteristics. Neither total in-hospital mortality (13/46 [28%] versus 22/104 [21%]; P = 0.3) nor attributable in-hospital mortality (9/46 [20%] versus 13/104 [12%]; P = 0.3) differed between patients with K. aerogenes versus Ecc BSI, respectively. However, poor clinical outcome (death before discharge, recurrent BSI, and/or BSI complication) was higher for K. aerogenes than Ecc BSI (32/46 [70%] versus 42/104 [40%]; P = 0.001). In a multivariable regression model, K. aerogenes BSI, relative to Ecc BSI, was predictive of poor clinical outcome (odds ratio 3.3; 95% confidence interval 1.4 to 8.1; P = 0.008). Pan-genome analysis revealed 983 genes in 323 genomic islands unique to K. aerogenes isolates, including putative virulence genes involved in iron acquisition (n = 67), fimbriae/pili/flagella production (n = 117), and metal homeostasis (n = 34). Antibiotic resistance was largely found in Ecc lineage 1, which had a higher rate of multidrug resistant phenotype (23/54 [43%]) relative to all other bacterial isolates (23/96 [24%]; P = 0.03). K. aerogenes BSI was associated with poor clinical outcomes relative to Ecc BSI. Putative virulence factors in K. aerogenes may account for these differences.

scholarly journals Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12

2020 ◽  
Vol 6 (12) ◽  
Author(s):  
Lin Zhao ◽  
Hongyou Chen ◽  
Xavier Didelot ◽  
Zhenpeng Li ◽  
Yinghui Li ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Vibrio Parahaemolyticus ◽  
Type Species ◽  
Genomic Islands ◽  
Content Type ◽  
Pan Genome ◽  
Link Type ◽  
Gene Segregation ◽  
Strain Collection ◽  
The Usa

Vibrio parahaemolyticus is an important cause of foodborne gastroenteritis globally. Thermostable direct haemolysin (TDH) and the TDH-related haemolysin are the two key virulence factors in V. parahaemolyticus. Vibrio pathogenicity islands harbour the genes encoding these two haemolysins. The serotyping of V. parahaemolyticus is based on the combination of O and K antigens. Frequent recombination has been observed in V. parahaemolyticus , including in the genomic regions encoding the O and K antigens. V. parahaemolyticus serotype O4:K12 has caused gastroenteritis outbreaks in the USA and Spain. Recently, outbreaks caused by this serotype of V. parahaemolyticus have been reported in China. However, the relationships among this serotype of V. parahaemolyticus strains isolated in different regions have not been addressed. Here, we investigated the genome variation of the V. parahaemolyticus serotype O4:K12 using the whole-genome sequences of 29 isolates. We determined five distinct lineages in this strain collection. We observed frequent recombination among different lineages. In contrast, little recombination was observed within each individual lineage. We showed that the lineage of this serotype of V. parahaemolyticus isolated in America was different from those isolated in Asia and identified genes that exclusively existed in the strains isolated in America. Pan-genome analysis showed that strain-specific and cluster-specific genes were mostly located in the genomic islands. Pan-genome analysis also showed that the vast majority of the accessory genes in the O4:K12 serotype of V. parahaemolyticus were acquired from within the genus Vibrio . Hence, we have shown that multiple distinct lineages exist in V. parahaemolyticus serotype O4:K12 and have provided more evidence about the gene segregation found in V. parahaemolyticus isolated in different continents.

scholarly journals A Novel Approach to Helicobacter pylori Pan-Genome Analysis for Identification of Genomic Islands

PLoS ONE ◽  
2016 ◽  
Vol 11 (8) ◽  
pp. e0159419 ◽  
Author(s):  
Ikuo Uchiyama ◽  
Jacob Albritton ◽  
Masaki Fukuyo ◽  
Kenji K. Kojima ◽  
Koji Yahara ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Genome Analysis ◽  
Genomic Islands ◽  
Pan Genome ◽  
Novel Approach

From Pan-genome to the Genomic Context of the Two Integrons of ST-111 Pseudomonas Aeruginosa AG1: A VIM-2-carrying Old-acquaintance and a Novel Imp-18-carrying Integron

2020 ◽  
Author(s):  
Jose Arturo Molina-Mora ◽  
Raquel García Batán ◽  
Fernando García
Keyword(s):  
Pseudomonas Aeruginosa ◽  
High Risk ◽  
Genome Analysis ◽  
Genomic Region ◽  
Genomic Islands ◽  
Comparative Genomic ◽  
Genomic Context ◽  
Intrinsic Resistance ◽  
Pan Genome ◽  
Genomic Regions

Abstract Background Pseudomonas aeruginosa is an opportunist and versatile organism responsible for infections among immunocompromised hosts. This pathogen has high intrinsic resistance to most antimicrobials, including critical strains due to resistance to carbapenems, a last-resort antibiotic. P. aeruginosa AG1 (PaeAG1) is a Costa Rican high-risk ST-111 strain with resistance to multiple antibiotics, including carbapenems due to the activity of both VIM-2 and IMP-18 metallo-β-lactamases (MBLs). These genes are harbored in two class 1 integrons, belonging to one out of the 57 PaeAG1 genomic islands. However, the genomic context related to these determinants in PaeAG1 and other P. aeruginosa strains is unclear. Thus, we implemented a comparative genomic approach to define and up-date the phylogenetic relationship among complete P. aeruginosa genomes using a pan-genome analysis. We also studied the PaeAG1 genomic islands content in other strains and the architecture of genomic regions around the VIM-2- and IMP-18-carrying integrons. Results With 211 strains, the up-dated P. aeruginosa pan-genome revealed that complete genome sequences are able to separate clones by MLST profile (ST), including a clear ST-111 cluster with PaeAG1. The PaeAG1 genomic islands were found to define a diverse presence/absence pattern among related genomes, but content was related to phylogenetic relationships. Finally, landscape reconstruction of specific genomic regions showed that VIM-2-carrying integron (In59-like) is an old-acquaintance element harbored in a known genomic region completely found in other two ST-111 strains. In addition, PaeAG1 has an exclusive genomic region containing a novel IMP-18-carrying integron (registered as In1666), with an arrangement never reported before. Conclusions We provide new insights about the genomic determinants associated with the resistance to carbapenems in the high-risk PaeAG1 using comparative genomics. With the pan-genome analysis and the comparison of PaeAG1 genomic islands in other strains, it was possible to describe the genomic landscape of the two MBLs-carrying integrons, including an old-acquaintance element carrying VIM-2 and a new IMP-18-carrying integron.

scholarly journals Draft Genome Sequences of bla KPC -Containing Enterobacter aerogenes , Citrobacter freundii , and Citrobacter koseri Strains

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
Tracy H. Hazen ◽  
Roberta T. Mettus ◽  
Christi L. McElheny ◽  
Sarah L. Bowler ◽  
Yohei Doi ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Enterobacter Aerogenes ◽  
Draft Genome Sequence ◽  
Klebsiella Aerogenes ◽  
Citrobacter Freundii ◽  
Genome Sequences ◽  
Content Type

ABSTRACT We report here the draft genome sequences of four bla KPC -containing bacteria identified as Klebsiella aerogenes , Citrobacter freundii , and Citrobacter koseri . Additionally, we report the draft genome sequence of a K. aerogenes strain that did not contain a bla KPC gene but was isolated from the patient who had the bla KPC-2 -containing K. aerogenes strain.

scholarly journals Poor clinical outcomes associated with suboptimal antibiotic treatment among older long-term care facility residents with urinary tract infection: a retrospective cohort study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Haley J. Appaneal ◽  
Theresa I. Shireman ◽  
Vrishali V. Lopes ◽  
Vincent Mor ◽  
David M. Dosa ◽  
...  
Keyword(s):  
Cohort Study ◽  
Clinical Outcome ◽  
Clinical Outcomes ◽  
Antibiotic Treatment ◽  
Antibiotic Use ◽  
Poor Clinical Outcome ◽  
Dose Frequency ◽  
Term Care ◽  
Increased Risk

Abstract Background Antibiotic use is associated with several antibiotic-related harms in vulnerable, older long-term care (LTC) residents. Suboptimal antibiotic use may also be associated with harms but has not yet been investigated. The aim of this work was to compare rates of poor clinical outcomes among LTC residents with UTI receiving suboptimal versus optimal antibiotic treatment. Methods We conducted a retrospective cohort study among residents with an incident urinary tract infection (UTI) treated in Veterans Affairs LTC units (2013–2018). Potentially suboptimal antibiotic treatment was defined as use of a suboptimal initial antibiotic drug choice, dose frequency, and/or excessive treatment duration. The primary outcome was time to a composite measure of poor clinical outcome, defined as UTI recurrence, acute care hospitalization/emergency department visit, adverse drug event, Clostridioides difficile infection (CDI), or death within 30 days of antibiotic discontinuation. Shared frailty Cox proportional hazard regression models were used to compare the time-to-event between suboptimal and optimal treatment. Results Among 19,701 LTC residents with an incident UTI, 64.6% received potentially suboptimal antibiotic treatment and 35.4% experienced a poor clinical outcome. In adjusted analyses, potentially suboptimal antibiotic treatment was associated with a small increased hazard of poor clinical outcome (aHR 1.06, 95% CI 1.01–1.11) as compared with optimal treatment, driven by an increased hazard of CDI (aHR 1.94, 95% CI 1.54–2.44). Conclusion In this national cohort study, suboptimal antibiotic treatment was associated with a 6% increased risk of the composite measure of poor clinical outcomes, in particular, a 94% increased risk of CDI. Beyond the decision to use antibiotics, clinicians should also consider the potential harms of suboptimal treatment choices with regards to drug type, dose frequency, and duration used.

scholarly journals Living in an Extremely Polluted Environment: Clues from the Genome of Melanin-Producing Aeromonas salmonicida subsp. pectinolytica 34melT

2015 ◽  
Vol 81 (15) ◽  
pp. 5235-5248 ◽  
Author(s):  
María Elisa Pavan ◽  
Esteban E. Pavan ◽  
Nancy I. López ◽  
Laura Levin ◽  
M. Julia Pettinari
Keyword(s):  
Genome Analysis ◽  
Aeromonas Salmonicida ◽  
Genomic Islands ◽  
Polluted Environment ◽  
Pectin Degradation ◽  
Fish Pathogens ◽  
Melanin Production ◽  
Melanin Biosynthesis ◽  
Content Type ◽  
Metabolic Versatility

ABSTRACTAeromonas salmonicidasubsp.pectinolytica34melTcan be considered an extremophile due to the characteristics of the heavily polluted river from which it was isolated. While four subspecies ofA. salmonicidaare known fish pathogens, 34melTbelongs to the only subspecies isolated solely from the environment. Genome analysis revealed a high metabolic versatility, the capability to cope with diverse stress agents, and the lack of several virulence factors found in pathogenicAeromonas. The most relevant phenotypic characteristics of 34melTare pectin degradation, a distinctive trait ofA. salmonicidasubsp.pectinolytica, and melanin production. Genes coding for three pectate lyases were detected in a cluster, unique to this microorganism, that contains all genes needed for pectin degradation. Melanin synthesis in 34melTis hypothesized to occur through the homogentisate pathway, as no tyrosinases or laccases were detected and the homogentisate 1,2-dioxygenase gene is inactivated by a transposon insertion, leading to the accumulation of the melanin precursor homogentisate. Comparative genome analysis of other melanogenicAeromonasstrains revealed that this gene was inactivated by transposon insertions or point mutations, indicating that melanin biosynthesis inAeromonasoccurs through the homogentisate pathway. Horizontal gene transfer could have contributed to the adaptation of 34melTto a highly polluted environment, as 13 genomic islands were identified in its genome, some of them containing genes coding for fitness-related traits. Heavy metal resistance genes were also found, along with others associated with oxidative and nitrosative stresses. These characteristics, together with melanin production and the ability to use different substrates, may explain the ability of this microorganism to live in an extremely polluted environment.

scholarly journals Insights on genomic diversity of Vibrio spp. through Pan-genome analysis

2019 ◽  
Vol 69 (13) ◽  
pp. 1547-1555
Author(s):  
Suganya Nathamuni ◽  
Ashok Kumar Jangam ◽  
Vinaya Kumar Katneni ◽  
Ashok Selvaraj ◽  
Karthic Krishnan ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Genome Analysis ◽  
Antibiotic Resistance Genes ◽  
Economic Loss ◽  
Genomic Islands ◽  
Genomic Diversity ◽  
Pan Genome ◽  
Gene Sets ◽  
Downstream Analysis ◽  
Unique Genes

Abstract Purpose The aquaculture sector is a major contributor to the economic and nutritional security for a number of countries. India’s total seafood exports for the year 2017–2018 accounted for US$ Million 7082. One of the major setbacks in this sector is the frequent outbreaks of diseases often due to bacterial pathogens. Vibriosis is one of the major diseases caused by bacteria of Vibrio spp., causing significant economic loss to the aquaculture sector. The objective of this study was to understand the genetic composition of Vibrio spp. Methods Thirty-five complete genomes were downloaded from GenBank comprising seven vibrio species, namely, Vibrio alginolyticus, V. anguillarum, V. campbellii, V. harveyi, V. furnissii, V. parahaemolyticus, and V. vulnificus. Pan-genome analysis was carried out with coding sequences (CDS) generated from all the Vibrio genomes. In addition, genomes were mined for genes coding for toxin-antitoxin systems, antibiotic resistance, genomic islands, and virulence factors. Results Results revealed an open pan-genome comprising of 2004 core, 8249 accessory, and 6780 unique genes. Downstream analysis of genomes and the identified unique genes resulted in 312 antibiotic resistance genes, 430 genes coding for toxin and antitoxin systems along with 4802, and 4825 putative virulent genes from genomic island regions and unique gene sets, respectively. Conclusion Pan-genome and other downstream analytical procedures followed in this study have the potential to predict strain-specific genes and their association with habitat and pathogenicity.

scholarly journals The value of glial fibrillary acidic protein levels in the diagnosis and prognosis of subarachnoid hemorrhage

2020 ◽  
pp. 102490792091505
Author(s):  
Ozgur Tatli ◽  
Metin Yadigaroglu ◽  
Selim Demir ◽  
Seniz Dogramaci ◽  
Mustafa Cicek ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Subarachnoid Hemorrhage ◽  
Clinical Outcome ◽  
Glial Fibrillary Acidic Protein ◽  
Clinical Outcomes ◽  
Acidic Protein ◽  
Poor Clinical Outcome ◽  
Protein Levels ◽  
Diagnosis And Prognosis ◽  
Time Of Presentation

Background: Subarachnoid hemorrhages is an important emergency condition due to its high morbidity and mortality. Early diagnosis and rapid intervention are very important to prevent poor clinical outcome of this disease. Objective: The aim of this study was to determine the value of glial fibrillary acidic protein in the diagnosis and prognosis of subarachnoid hemorrhage. Methods: Patients presenting to the emergency department and undergoing computerized tomography and/or lumbar puncture due to suspicion of subarachnoid hemorrhage were included in this prospective study. Based on the computerized tomography–lumbar puncture results, cases were divided into subarachnoid hemorrhage group and non–subarachnoid hemorrhage control group. Subarachnoid hemorrhage patients were classified on the basis of severity of subarachnoid hemorrhage and were classified as good or poor clinical outcome groups based on Glasgow Outcome Scores. Glial fibrillary acidic protein levels were then compared. Results: A total of 111 patients were evaluated due to suspicion of subarachnoid hemorrhage and diagnosed with subarachnoid hemorrhage (n = 73) or without subarachnoid hemorrhage (n = 38). Cerebrospinal fluid glial fibrillary acidic protein levels were significantly higher in the subarachnoid hemorrhage group than in the non–subarachnoid hemorrhage group (p < 0.001) (median (25%–75%): 11.62 (2.64–68.04) and 2.26 (1.5–4.83), respectively). Serum glial fibrillary acidic protein levels of the subarachnoid hemorrhage patients with poor clinical outcomes were higher than those of subarachnoid hemorrhage patients with good clinical outcomes (p = 0.003) and cerebrospinal fluid glial fibrillary acidic protein levels were similar (p = 0.379). Glial fibrillary acidic protein levels at the time of presentation exhibited a low level of correlation with Glasgow coma score, World Federation of Neurological Surgeons scale, Hunter–Hess Scale, Ogilvy–Carter Scale, Glasgow Outcome Score, and modified Rankin score. Conclusion: Cerebrospinal fluid glial fibrillary acidic protein levels may be a valuable diagnostic parameter at the time of presentation for diagnosis of subarachnoid hemorrhage. And also serum glial fibrillary acidic protein levels may be useful in predicting subarachnoid hemorrhage patients with poor clinical outcomes.

scholarly journals Epidemiology of Bloodstream Infections Caused by Acinetobacter baumannii and Impact of Drug Resistance to both Carbapenems and Ampicillin-Sulbactam on Clinical Outcomes

2013 ◽  
Vol 57 (12) ◽  
pp. 6270-6275 ◽  
Author(s):  
Teena Chopra ◽  
Dror Marchaim ◽  
Reda A. Awali ◽  
Amar Krishna ◽  
Paul Johnson ◽  
...  
Keyword(s):  
Hospital Mortality ◽  
Acinetobacter Baumannii ◽  
Clinical Outcomes ◽  
Medical Records ◽  
Independent Predictor ◽  
Medical Center ◽  
Bloodstream Infections ◽  
Content Type ◽  
Increased Risk ◽  
Prior Use

ABSTRACTAcinetobacter baumanniihas become a leading cause of bloodstream infections (BSI) in health care settings. Although the incidence of infection with carbapenem- and ampicillin-sulbactam-resistant (CASR)A. baumanniihas increased, there is a scarcity of studies which investigate BSI caused by CASRA. baumannii. A retrospective cohort study was conducted on adult patients with BSI caused byA. baumanniiand who were admitted to the Detroit Medical Center between January 2006 and April 2009. Medical records were queried for patients' demographics, antimicrobial exposures, comorbidities, hospital stay, and clinical outcomes. Bivariate analyses and logistic regression were employed in the study. Two hundred seventy-four patients with BSI caused byA. baumanniiwere included in the study: 68 (25%) caused by CASRA. baumanniiand 206 (75%) caused by non-CASRA. baumannii. In multivariate analysis, factors associated with BSI caused by CASRA. baumanniiincluded admission with a rapidly fatal condition (odds ratio [OR] = 2.83, 95% confidence interval [CI] = 1.27 to 6.32,Pvalue = 0.01) and prior use of antimicrobials (OR = 2.83, 95% CI = 1.18 to 6.78,Pvalue = 0.02). In-hospital mortality rates for BSI caused by CASRA. baumanniiwere significantly higher than those for non-CASRA. baumannii-induced BSI (43% versus 20%; OR = 3.0, 95% CI = 1.60 to 5.23,Pvalue < 0.001). However, after adjusting for potential confounders, the association between BSI caused by CASRA. baumanniiand increased risk of in-hospital mortality was not significant (OR = 1.15, 95% CI = 0.51 to 2.63,Pvalue = 0.74). This study demonstrated that CASRA. baumanniihad a distinct epidemiology compared to more susceptibleA. baumanniistrains; however, clinical outcomes were similar for the two groups. Admission with a rapidly fatal condition was an independent predictor for both CASRA. baumanniiand in-hospital mortality.

Sign in / Sign up

Export Citation Format

Share Document