Microbiota analysis in the hemodialysis population - Focusing on Enterobacteriaceae.

BACKGROUND: Infection is a recognized risk factor for mortality among hemodialysis (HD) population, including infection caused by Enterobacteriaceae. We aimed to investigate Enterobacteriaceae in gut microbiota among HD patients and to analyze associations between microbiota and clinical parameters. METHODS: This prospective study of microbiota analysis in HD patients was conducted in April-May 2019. A control group without recent antibiotic use or hospitalization was used for comparison. Stool samples underwent 16S rRNA sequencing, using Greengenes 16S rRNA database for microbiota analysis. RESULTS: Among 96 hemodialysis (HD) patients, mean age was 61.9 ± 0.8 years and mean duration of HD was 6.5 ± 0.7 years. No significant differences were found in alpha diversity between HD and control groups (HD group 949.5, controls 898; p = 0.16) although significant between-group differences were found in beta diversity (p < 0.001). At phylum level, HD group had a higher abundance of Firmicutes and Proteobacteria, but lower abundance of Bacteriodetes. At genus level, Escherichia-Shigella complex increased among HD patients who had hospitalization with 1 year (median 0.024 vs 0.004, p = 0.054) and Klebsiella was associated with emergency room visit within 1 year among HD patients (p = 0.002). CONCLUSIONS: Alpha diversity in HD patients is not lower than that in healthy controls but significant between-group differences are found in microbiota composition according to beta diversity, due to decreased Bacteriodetes and increased Firmicutes and Proteobacteria. Deeper microbiota analyses for Enterobacteriaceae are necessary. Whether change in dietary components can help to decrease mortality among dialysis population warrants further research.

Klebsiella pneumoniae bacteremia revisited: Comparison between 2007 and 2017 prospective cohorts at a medical center in Taiwan.

BACKGROUND: Community onset K. pneumoniae bacteremia (KPB) is a major problem in Taiwan for decades. We aimed to revisit the role of virulent genotype K1/K2 and possible predisposing factors, compared to our published 2007 cohort. METHODS: All adult patients with monomicrobial KPB during 2017 at a medical center in Taiwan were prospectively enrolled. We genotyped the major K types of K. pneumoniae strains, and analyzed the role of prior use of antibiotic or proton pump inhibitor (PPI). RESULTS: A total of 213 cases were enrolled. Compared to our previous 2007 study (n = 231), there was a higher percentage of patients with community onset bacteremia (75% vs. 60%, p = 0.003). The overall mortality rate was lower in 2017 (23% vs. 32%, p = 0.02), while the rates of antimicrobial resistance (all classes) were higher in 2017. There were 40 cases of liver abscesses in 2017 (19%), with an overall mortality rate of 7.5%. The prevalence of K1 was similar (16% in 2017 vs. 19% in 2007), but the prevalence of K2 decreased significantly (7% in 2017 vs. 17% in 2007, p = 0.001). After excluding 39 cases without data of recent medication use, 48 of 174 (28%) of patients had received a PPI within 90 days. Patients with recent PPI use had more complicated underlying illnesses, higher antimicrobial resistance, and higher in-hospital mortality, but was negatively associated with liver abscess (4% vs. 24%, p = 0.002). Of patients with community-acquired bacteremia, 51% used antibiotics within 90 days. After excluding 37 patients received antibiotics within 14 days before the detection of bacteremia, patient with antibiotic use within 15-90 days had higher Pittsburgh bacteremia scores (4.5 vs. 2.7, p = 0.04), creatinine levels, and frequency of recent surgery, but was not associated with liver abscess (21% vs. 31%, p = 0.33). DISCUSSION: In summary, after a decade, community onset KPB is still prevalent (1.3 case per 1000 emergency department visit). K1 remains to be the dominant genotype. The association of prior ampicillin/amoxicillin or PPIs use for liver abscess is not confirmed.

Characterization of rifampin-resistant Staphylococcus aureus nasal carriage in patients receiving rifampin-containing regimens for tuberculosis.

OBJECTIVES: This study investigated molecular characteristics of rifampin (RIF)-resistant (RIF-R) Staphylococcus aureus isolates recovered from patients receiving RIF-containing regimens for tuberculosis (TB). PATIENTS AND METHODS: Patients with TB who received RIF-containing regimens from November 2009 to May 2011 at a medical center were enrolled. Nasal swabs for S. aureus culture were obtained at the time of enrollment, and then every two months until two months after RIF treatment had been completed. Genetic relatedness of the isolates was determined using pulsed-field gel electrophoresis, multilocus sequence typing, and gene typing of spa and SCCmec. The presence of RIF resistance-associated mutations in rpoB, and fusidic acid resistance genes fusB and fusC in the S. aureus isolates were analyzed. RESULTS: Among the 200 patients enrolled in this study, 152 completed follow-ups during treatment, and 114 completed two months of follow-up after discontinuing use of RIF. At enrollment, ten patients (5%) had nasal colonization with S. aureus, namely eight with methicillin-susceptible S. aureus (MSSA), and two with methicillin-resistant S. aureus (MRSA, ST59-SCCmecIV-RIF-susceptible). All these patients were decolonized after RIF usage. Two patients with MSSA colonization at enrollment showed recolonization with genetically unrelated MSSA strains two months after completion of RIF treatment. There were five ST45-SCCmecVT-RIF-R strains from two patients isolated during RIF exposure. Sequencing of rpoB in the RIF-R S. aureus isolates revealed different mutation sites between the MSSA and MRSA isolates. CONCLUSION: RIF-R S. aureus strains are more likely to result in persistent nasal carriage in TB patients receiving RIF treatment. Monitoring of emergence and possible dissemination of the MRSA ST45 strains among TB patients treated with RIF in Taiwan is warranted.

Emergence of multidrug-resistant sequence type 45 strains among mecA-positive borderline oxacillin-resistant Staphylococcus aureus causing bacteraemia in a medical centre in Taiwan.

Clinical data related to bacteraemia caused by mecA-positive borderline oxacillin-resistant Staphylococcus aureus (BORSA) isolates [minimum inhibitory concentrations (MICs) of 0.5-4 mg/L] are limited. Patients aged ≥15 years with bacteraemia due to BORSA who were admitted to the emergency department of a Taiwanese tertiary hospital between January 2001 and December 2015 were evaluated. Clinical characteristics of patients with bacteraemia caused by BORSA, methicillin-susceptible S. aureus and methicillin-resistant S. aureus (MRSA) were compared. MICs of 12 antibiotics were determined by agar dilution. Genetic characteristics of 64 available BORSA isolates were analysed by detection of the SCCmec gene, the mecA promoter region sequence and multilocus sequence typing (MLST). Pulsed-field gel electrophoresis (PFGE) was performed to identify the clonality of the emerging ST isolates. The quinolone resistance genes were analysed for the emerging ciprofloxacin-resistant ST45 clone isolates. Among the 65 BORSA bacteraemic patients, in-hospital mortality was 24.6%, significantly lower than that of MRSA patients (38.5%) (P = 0.03). Underlying conditions were similar between BORSA and MRSA patients, but with less dialysis in the former (P = 0.01). Multivariate analysis revealed that septic shock [odds ratio (OR) = 15.95] and bacteraemia originating from lower respiratory tract infection (OR = 5.78) were two independent risk factors for 30-day mortality. The ST45 clone with high-level ciprofloxacin resistance (MICs of 8-128 mg/L) replaced ST59 as the predominant clone since 2012, although no major clustering was detected. In conclusion, the emerging multidrug-resistant ST45 clone has replaced ST59 as the most common among BORSA isolates.

The prevalence of rectal carriage of Klebsiella pneumoniae amongst diabetic patients and their clinical relevance in Taiwan: A five-year prospective study.

BACKGROUND/PURPOSE: Pyogenic liver abscess (PLA) and bacteremia caused by Klebsiella pneumoniae is a common complication among patients with diabetes mellitus (DM). The aim of this study is to investigate the prevalence of rectal carriage and serotype distribution of K. pneumoniae amongst DM patients and their clinical relevance. METHODS: We prospectively collected rectal swabs for K. pneumoniae culture in asymptomatic DM patients from March 2008 to June 2009. Seven capsular serotypes that were commonly associated with PLA were determined by capsular polysaccharide synthesis (cps) genotyping. Microbiologically confirmed bacterial infections were evaluated 1 and 5 years after initial enrolment of the patients. RESULTS: A total of 100 male and 62 female patients (mean age, 56.6 years) were enrolled. Of these, 77 (47.5%) had rectal K. pneumoniae colonization. Colonizers were older than non-colonizers (p = 0.03). Sex, fasting blood glucose, and initial HbA1C were not statistically different (p = 0.26, 0.18, and 0.31, respectively). Among the 65 available isolates, 22 (33.8%) belonged to the seven main serotypes. During the 5-year's follow-up, 21 patients developed microbiologically documented bacterial infections but none of them developed PLA and bacteremia. Risk factors for bacterial infection within 5 years included initial glycosylated hemoglobin (HbA1C) > 10% or first-year average HbA1C > 10%. CONCLUSION: Although nearly half of asymptomatic DM patients had rectal carriage of K. pneumoniae and one-third of them colonized by isolates belonging to the seven serotypes related to PLA, none of them subsequently developed PLA and colonized patients did not have higher risk of microbiologically confirmed bacterial infections.

Reinfection and relapse of recurrent bacteremia caused by Klebsiella pneumoniae in a medical center in Taiwan.

AIM: To delineate the genetic relatedness of Klebsiella pneumoniae causing recurrent bacteremia. MATERIALS & METHODS: Clinical characteristics of patients, distribution of capsular genoserotypes by capsular cps-PCR genotyping and the genetic relatedness of the paired isolates using arbitrarily primed PCR and pulsed-field gel electrophoresis were investigated. RESULTS: Of 3067 patients with K. pneumoniae bacteremia, 129 (4.2%) had recurrent bacteremia (301 episodes). Of 129 patients with recurrent bacteremia, 51 (39.5%) were reinfected by the same strains (paired isolates with identical randomly amplified polymorphic DNA patterns and closely related pulsotypes). Multivariate analysis demonstrated that diabetes mellitus (odds ratio: 5.82; p < 0.001) and infection due to serotype K2 (odds ratio: 13.93; p < 0.001) were associated with relapse in patients with recurrent bacteremia. CONCLUSION: Recurrent K. pneumoniae bacteremia could occur in patients with underlying hematological malignancies or suffering from primary bacteremia. Relapse infection is associated with serotype K2 strains and underlying diabetes mellitus.

Time to positivity in blood cultures of adults with nontyphoidal Salmonella bacteremia.

BACKGROUND: Nontyphoidal Salmonella (NTS) is an important bacterial etiology of diarrheal disease, and it causes invasive diseases in immunocompromised hosts. For bacteremia from some species, blood culture with a rapid time to positivity (TTP) is associated with greater mortality. This study investigated TTP of NTS bacteremia and its relationship to clinical parameters and prognosis. METHODS: Adult patients with NTS bacteremia who were admitted to a tertiary care facility in northern Taiwan from January 2010 to December 2012 were enrolled. Demographics, clinical and microbiological characteristics, and treatment response were reviewed. The TTP for each patient was retrieved from the automated machine. RESULTS: Sixty-six adult patients (mean age, 66.1 years; range, 27-96 years) with NTS bacteremia were identified by the following serogroup distributions: serogroup B (23.4%), serogroup C1 (1.6%), serogroup C2 (6.3%), and serogroup D (68.8%). The in-hospital mortality, 14-day mortality, and 30-day mortality were 15.2%, 7.6%, and 12.1%, respectively. The TTP ranged 6.5-41.7 hours (median: 11.5 hours). Patients with rapid TTP (less than 10 hours), compared to patients without rapid TTP, were more likely to have liver cirrhosis (31.6% vs. 6.4%, p = 0.013), endovascular lesions (21.1% vs. 4.3%, p = 0.05), higher bacteremia score, intensive care unit admission (57.9% vs. 25.5%, p = 0.021), and septic shock (63.2% vs. 12.8%, p < 0.001). There were no significant differences in the in-hospital mortality and 14-day mortality between patients with TTP <10 hours and patients with TTP ≥10 hours. CONCLUSION: The TTP of blood cultures, interpreted with a cut-off point of <10 hours, in patients with NTS bacteremia may provide useful diagnostic and prognostic information.

Klebsiella pneumoniae bacteremia and capsular serotypes, Taiwan.

Capsular serotypes of 225 Klebsiella pneumoniae isolates in Taiwan were identified by using PCR. Patients infected with K1 serotypes (41 isolates) had increased community-onset bacteremia, more nonfatal diseases and liver abscesses, lower Pittsburgh bacteremia scores and mortality rates, and fewer urinary tract infections than patients infected with non-K1/K2 serotypes (147 isolates).