Blood stream infection (BSI),a blood-borne disease caused by microorganisms such as bacteria,fungi,and viruses,can lead to bacteremia,sepsis,and infectious shock,posing a serious threat to human life and health.Identifying the pathogen is central to the precise treatment of BSI.Traditional blood culture is the gold standard for pathogen identification,while it has limitations in clinical practice due to the long time consumption,production of false negative results,etc.Nanopore sequencing,as a new generation of sequencing technology,can rapidly detect pathogens,drug resistance genes,and virulence genes for the optimization of clinical treatment.This paper reviews the current status of nanopore sequencing technology in the diagnosis of BSI.
Humans ; Nanopore Sequencing ; Sepsis/diagnosis* ; Bacteremia/microbiology* ; Bacteria ; Blood Culture/methods*

BACKGROUND: We evaluated the performance of the BD MAX StaphSR Assay (SR assay; BD, USA) for direct detection of Staphylococcus aureus and methicillin resistance not only in S. aureus but also in coagulase-negative Staphylococci (CNS) from positive blood cultures. METHODS: From 228 blood culture bottles, 103 S. aureus [45 methicillin-resistant S. aureus (MRSA), 55 methicillin-susceptible S. aureus (MSSA), 3 mixed infections (1 MRSA+Enterococcus faecalis, 1 MSSA+MRCNS, 1 MSSA+MSCNS)], and 125 CNS (102 MRCNS, 23 MSCNS) were identified by Vitek 2. For further analysis, we obtained the cycle threshold (Ct) values from the BD MAX system software to determine an appropriate cutoff value. For discrepancy analysis, conventional mecA/mecC PCR and oxacillin minimum inhibitory concentrations (MICs) were determined. RESULTS: Compared to Vitek 2, the SR assay identified all 103 S. aureus isolates correctly but failed to detect methicillin resistance in three MRSA isolates. All 55 MSSA isolates were correctly identified by the SR assay. In the concordant cases, the highest Ct values for nuc, mecA, and mec right-extremity junction (MREJ) were 25.6, 22, and 22.2, respectively. Therefore, we selected Ct values from 0-27 as a range of positivity, and applying this cutoff, the sensitivity/specificity of the SR assay were 100%/100% for detecting S. aureus, and 97.9%/98.1% and 99.0%/95.8% for detecting methicillin resistance in S. aureus and CNS, respectively. CONCLUSIONS: We propose a Ct cutoff value for nuc/mec assay without considering MREJ because mixed cultures of MSSA and MRCNS were very rare (0.4%) in the positive blood cultures.
Anti-Bacterial Agents/pharmacology ; Bacteremia/diagnosis/microbiology ; Coagulase/metabolism ; Humans ; Methicillin-Resistant Staphylococcus aureus/drug effects/genetics/*isolation & purification ; Microbial Sensitivity Tests ; Oxacillin/pharmacology ; Reagent Kits, Diagnostic ; Staphylococcus/drug effects/enzymology/genetics/isolation & purification ; Staphylococcus aureus/drug effects/genetics/*isolation & purification

No abstract available.
Anti-Bacterial Agents/*pharmacology ; Bacteremia/*diagnosis/microbiology ; Colistin/*pharmacology ; Drug Resistance, Bacterial ; Escherichia coli/*drug effects/isolation & purification ; Humans ; Microbial Sensitivity Tests ; Republic of Korea

This study was performed to measure early changes in the serotype distribution of pneumococci isolated from children with invasive disease during the 3-year period following the introduction of 10- and 13-valent pneumococcal conjugate vaccines (PCVs) in Korea. From January 2011 to December 2013 at 25 hospitals located throughout Korea, pneumococci were isolated among children who had invasive pneumococcal disease (IPD). Serotypes were determined using the Quellung reaction, and the change in serotype distribution was analyzed. Seventy-five cases of IPD were included. Eighty percent of patients were aged 3-59 months, and 32% had a comorbidity that increased the risk of pneumococcal infection. The most common serotypes were 19A (32.0%), 10A (8.0%), and 15C (6.7%). The PCV7 serotypes (4, 6B, 9V, 14, 18C, 19F, 23F, and 6A) accounted for 14.7% of the total isolates and the PCV13 minus PCV7 types (1, 3, 5, 7F and 19A) accounted for 32.0% of the total isolates. Serotype 19A was the only serotype in the PCV13 minus PCV7 group. The proportion of serotype 19A showed decreasing tendency from 37.5% in 2011 to 22.2% in 2013 (P = 0.309), while the proportion of non-PCV13 types showed increasing tendency from 45.8% in 2011 to 72.2% in 2013 (P = 0.108). Shortly after the introduction of extended-valent PCVs in Korea, serotype 19A continued to be the most common serotype causing IPD in children. Subsequently, the proportion of 19A decreased, and non-vaccine serotypes emerged as an important cause of IPD. The impact of extended-valent vaccines must be continuously monitored.
Adolescent ; Bacteremia/complications/diagnosis ; Child ; Child, Preschool ; Female ; Hospitals ; Humans ; Infant ; Male ; Pneumococcal Infections/microbiology/*prevention & control ; Pneumococcal Vaccines/*immunology ; Republic of Korea ; Serotyping ; Streptococcus pneumoniae/*classification/isolation & purification ; Vaccines, Conjugate/*immunology

No abstract available.
Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteremia/*diagnosis/drug therapy/microbiology ; Clostridium tertium/drug effects/isolation & purification/*metabolism ; Humans ; Male ; Microbial Sensitivity Tests ; Middle Aged ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

No abstract available.
Aged ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteremia/blood/*diagnosis/microbiology ; C-Reactive Protein/analysis ; Cholecystitis/blood/cerebrospinal fluid/microbiology ; Electrophoresis, Gel, Pulsed-Field ; Enterococcus faecium/drug effects/isolation & purification/metabolism ; Humans ; Male ; Microbial Sensitivity Tests ; Microscopy, Electron, Scanning ; Ochrobactrum/drug effects/isolation & purification/*metabolism ; RNA, Ribosomal, 16S/analysis/genetics/metabolism ; Sequence Analysis, DNA ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

The incidence and mortality of infective endocarditis (IE) in patients with severe burn remain high, which are attributed to invasive procedures, bacteremia, and wound infection after burns. Clinical clues for IE in burns are usually masked by burn-related manifestations, so the diagnosis of IE may be delayed or missed. For burned patients with persistent bacteremia of unknown source, especially Staphylococcus aureus-induced bacteremia, the diagnosis of IE should be considered according to the Duke criteria, and early echocardiography performance is particularly important. Antibiotic therapy is the mainstay initial management, and early surgical intervention is strongly recommended once IE is clearly diagnosed in patients with burns. In order to lower the incidence and mortality of IE in burns, it is very important to take prophylactic procedures along with the whole course of burn management.
Bacteremia ; epidemiology ; Burn Units ; Burns ; complications ; mortality ; surgery ; Endocarditis, Bacterial ; complications ; diagnosis ; microbiology ; mortality ; Humans ; Incidence ; Severity of Illness Index ; Staphylococcal Infections ; complications ; diagnosis ; Staphylococcus aureus ; isolation & purification ; Surgery, Plastic ; Wound Infection ; etiology ; mortality

PURPOSE: Over the last 30 years, Serratia marcescens (S. marcescens) has emerged as an important pathogen, and a common cause of nosocomial infections. The aim of this study was to identify risk factors associated with mortality in patients with S. marcescens bacteremia. MATERIALS AND METHODS: We performed a retrospective cohort study of 98 patients who had one or more blood cultures positive for S. marcescens between January 2006 and December 2012 in a tertiary care hospital in Seoul, South Korea. Multiple risk factors were compared with association with 28-day all-cause mortality. RESULTS: The 28-day mortality was 22.4% (22/98 episodes). In a univariate analysis, the onset of bacteremia during the intensive care unit stay (p=0.020), serum albumin level (p=0.011), serum C-reactive protein level (p=0.041), presence of indwelling urinary catheter (p=0.023), and Sequential Oran Failure Assessment (SOFA) score at the onset of bacteremia (p<0.001) were significantly different between patients in the fatal and non-fatal groups. In a multivariate analysis, lower serum albumin level and an elevated SOFA score were independently associated with 28-day mortality [adjusted odds ratio (OR) 0.206, 95% confidential interval (CI) 0.044-0.960, p=0.040, and adjusted OR 1.474, 95% CI 1.200-1.810, p<0.001, respectively]. CONCLUSION: Lower serum albumin level and an elevated SOFA score were significantly associated with adverse outcomes in patients with S. marcescens bacteremia.
Adult ; Aged ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/drug therapy/microbiology/*mortality ; Cross Infection/mortality ; Female ; Humans ; Intensive Care Units ; Male ; Middle Aged ; Multiple Organ Failure ; Republic of Korea/epidemiology ; Retrospective Studies ; Risk Factors ; Serratia Infections/diagnosis/drug therapy/*mortality ; Serratia marcescens/drug effects/*isolation & purification ; Severity of Illness Index ; Survival Rate ; Time Factors ; Treatment Outcome

BACKGROUND/AIMS: Providencia species frequently colonize urinary catheters and cause urinary tract infections (UTIs); however, bacteremia is uncommon and not well understood. We investigated the clinical features of Providencia bacteremia and the antibiotic susceptibility of Providencia species. METHODS: We identified cases of Providencia bacteremia from May 2001 to April 2013 at a tertiary care hospital. The medical records of pertinent patients were reviewed. RESULTS: Fourteen cases of Providencia bacteremia occurred; the incidence rate was 0.41 per 10,000 admissions. The median age of the patients was 64.5 years. Eleven cases (78.6%) were nosocomial infections and nine cases (64.3%) were polymicrobial bacteremia. The most common underlying conditions were cerebrovascular/neurologic disease (n = 10) and an indwelling urinary catheter (n = 10, 71.4%). A UTI was the most common source of bacteremia (n = 5, 35.7%). The overall mortality rate was 29% (n = 4); in each case, death occurred within 4 days of the onset of bacteremia. Primary bacteremia was more fatal than other types of bacteremia (mortality rate, 75% [3/4] vs. 10% [1/10], p = 0.041). The underlying disease severity, Acute Physiologic and Chronic Health Evaluation II scores, and Pitt bacteremia scores were significantly higher in nonsurvivors (p = 0.016, p =0.004, and p = 0.002, respectively). Susceptibility to cefepime, imipenem, and piperacillin/tazobactam was noted in 100%, 86%, and 86% of the isolates, respectively. CONCLUSIONS: Providencia bacteremia occurred frequently in elderly patients with cerebrovascular or neurologic disease. Although Providencia bacteremia is uncommon, it can be rapidly fatal and polymicrobial. These characteristics suggest that the selection of appropriate antibiotic therapy could be complicated in Providencia bacteremia.
APACHE ; Adolescent ; Adult ; Aged ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/diagnosis/drug therapy/*microbiology/mortality ; Child ; Cross Infection/diagnosis/drug therapy/*microbiology/mortality ; Cross-Sectional Studies ; Drug Resistance, Bacterial ; Enterobacteriaceae Infections/diagnosis/drug therapy/*microbiology/mortality ; Female ; Hospital Mortality ; Humans ; Incidence ; Male ; Microbial Sensitivity Tests ; Middle Aged ; Predictive Value of Tests ; Providencia/drug effects/*isolation & purification ; Republic of Korea ; Retrospective Studies ; Risk Factors ; *Tertiary Care Centers ; Treatment Outcome ; Young Adult

Bacteremia ; diagnosis ; Endoscopy ; adverse effects ; Humans ; Paranasal Sinuses ; microbiology ; surgery