77 research outputs found
Genetic Profiles and Antimicrobial Resistance Patterns of Salmonella Infantis Strains Isolated in Italy in the Food Chain of Broiler Meat Production
This work aimed to evaluate the antimicrobial susceptibility of 87 Salmonella Infantis strains isolated in Italy from 2016 to 2019 along the food chain of broiler meat production and in humans and to determine the genetic profiles of the strains in order to establish a possible correlation with the antimicrobial pattern. All isolates were tested by the disk diffusion method to evaluate antimicrobial susceptibility toward sixteen antimicrobials, and the broth microdilution method was used to confirm extended spectrum β-lactamase (ESBL) production. PCR and pulsed field gel electrophoresis (PFGE) were applied to characterize ESBL-encoding and AmpC β-lactamase genes and to analyze the S. Infantis strains genetic profiles respectively. S. Infantis isolates showed high prevalence of resistance, in particular toward nalidixic acid (97.7%), tetracycline (96.5%), sulphamethoxazole/trimethoprim (91%) and cefepime (72.4%). The 80.5% of isolates were ESBL, cefotaxime-resistant, carrying the blaCTX-M1 gene. The most prevalent PFGE profile was XbaI.0126 (35.6%). The remaining strains had a genetic homology from 81% to 97% with the XbaI.0126 profile. The strains belonging to these profiles were isolated from different matrices collected along the broiler food chain independently on the year and from the region and there was no correlation between the PFGE profiles and resistance patterns. We found two ESBL-producing S. Infantis strains with the same XbaI.2621 profile isolated from humans and from poultry feces, not yet reported in Italy. Our findings confirmed the diffusion of ESBL-multi drug resistant (MDR) S. Infantis along the broiler food chain and in humans and underlined the importance of continuous monitoring to control and to reduce the prevalence of this bacterium, applying a global One Health approach. © 2020 by the authors. Licensee MDPI, Basel, Switzerlan
Genetic diagnosis of autoinflammatory disease patients using clinical exome sequencing
Autoinflammatory diseases comprise a wide range of syndromes caused by dysregulation of the innate immune response. They are difficult to diagnose due to their phenotypic heterogeneity and variable expressivity. Thus, the genetic origin of the disease remains undetermined for an important proportion of patients. We aim to identify causal genetic variants in patients with suspected autoinflammatory disease and to test the advantages and limitations of the clinical exome gene panels for molecular diagnosis. Twenty-two unrelated patients with clinical features of autoinflammatory diseases were analyzed using clinical exome sequencing (~4800 genes), followed by bioinformatic analyses to detect likely pathogenic variants. By integrating genetic and clinical information, we found a likely causative heterozygous genetic variant in NFKBIA (p.D31N) in a North-African patient with a clinical picture resembling the deficiency of interleukin-1 receptor antagonist, and a heterozygous variant in DNASE2 (p.G322D) in a Spanish patient with a suspected lupus-like monogenic disorder. We also found variants likely to increase the susceptibility to autoinflammatory diseases in three additional Spanish patients: one with an initial diagnosis of juvenile idiopathic arthritis who carries two heterozygous UNC13D variants (p.R727Q and p.A59T), and two with early-onset inflammatory bowel disease harbouring NOD2 variants (p.L221R and p.A728V respectively). Our results show a similar proportion of molecular diagnosis to other studies using whole exome or targeted resequencing in primary immunodeficiencies. Thus, despite its main limitation of not including all candidate genes, clinical exome targeted sequencing can be an appropriate approach to detect likely causative variants in autoinflammatory diseases
Interplay between Basic Residues of Hepatitis C Virus Glycoprotein E2 with Vi ral Receptors Neutralizing Antibodies and Lipoproteins.
Positively-charged amino acids are located at specific positions in the envelope glycoprotein E2 of the hepatitis C virus (HCV): two histidines (H) and four arginines (R) in two conserved WHY and one RGERCDLEDRDR motifs, respectively. Additionally, the E2 hypervariable region 1 (HVR1) is rich in basic amino acids. To investigate the role(s) of these residues in HCV entry, we subjected to comparative infection and sedimentation analysis cell culture-produced (HCVcc, genotype 2a) wild type virus, a panel of alanine single-site mutants and a HVR1-deletion variant. Initially, we analyzed the effects of these mutations on E2-heparan sulfate (HS) interactions. The positive milieu of the HVR1, formulated by its basic amino acids (key residues the conserved H386 and R408), and the two highly conserved basic residues H488 and R648 contributed to E2-HS interactions. Mutations in these residues did not alter the HCVcc-CD81 entry, but they modified the HCVcc-scavenger receptor class B type I (SR-BI) dependent entry and the neutralization by anti-E2 or patients IgG. Finally, separation by density gradients revealed that mutant viruses abolished partially or completely the infectivity of low density particles, which are believed to be associated with lipoproteins. This study shows that there exists a complex interplay between the basic amino acids located in HVR1 and other conserved E2 motifs with the HS, the SR-BI, and neutralizing antibodies and suggests that HCV-associated lipoproteins are implicated in these interactions
Differences in tetracycline resistance determinant carriage among Shigella flexneri and Shigella sonnei are not related to different plasmid Inc-type carriage
Objectives: The aim of this study was to establish the prevalence of the most common molecular mechanisms involved in tetracycline resistance as well as their relationship with plasmid incompatibility (Inc) groups in a collection of Shigella spp. causing traveller’s diarrhoea.
Methods: Tetracycline susceptibility was established in 187 Shigella spp. (74 Shigella flexneri and 113 Shigella sonnei), of which 153 isolates were recovered as a confirmed cause of traveller’s diarrhoea. The prevalence of the tet(A), tet(B) and tet(G) genes was analysed by PCR. Eighteen plasmid Inc groups was determined in a subset of 59 isolates.
Results: Among 154 tetracycline-resistant isolates, 122 (79.2%) harboured at least tet(A) or tet(B). The tet(B) gene was the most frequently detected, being present in 70 isolates (45.5%), whilst tet(A) was detected in 57 isolates (37.0%). The tet(G) gene was present in only 11 (7.2%) isolates. Moreover, the tet(A) gene was more frequent in S. sonnei (P = 0.0007), whilst the tet(B) gene was more frequent in S. flexneri (P < 0.0001). Plasmids belonging to Inc group B (P < 0.05) were significantly more frequent among S. flexneri, whilst those belonging to groups K, FIC and FIIA (P < 0.05) were preferentially detected among S. sonnei.
Conclusion: The prevalence of the tet(A) and tet(B) genes differed between S. sonnei and S. flexneri. Moreover, the prevalence of plasmid Inc groups in S. flexneri and S. sonnei differed. However, no relationship was found between the two phenomena
Rapid Diagnosis of Staphylococcal Catheter-Related Bacteraemia in Direct Blood Samples by Real-Time PCR
Catheter-related bacteremia (CRB) is an important cause of
morbidity and mortality among hospitalized patients, being
staphylococci the main etiologic agents. The objective of this
study was to assess the use of a PCR-based assay for detection
of staphylococci directly from blood obtained through the
catheter to diagnose CRB caused by these microorganisms and to
perform a cost-effectiveness analysis. A total of 92 patients
with suspected CRB were included in the study. Samples were
obtained through the catheter. Paired blood cultures were
processed by standard culture methods and 4 ml blood samples
were processed by GeneXpert-MRSA assay for the detection of
methicillin-susceptible (MSSA) or methicillin-resistant (MRSA)
Staphylococcus aureus, and methicillin-resistant
coagulase-negative staphylococci (MR-CoNS). Sixteen CRB caused
by staphylococci were diagnosed among 92 suspected patients.
GeneXpert detected 14 out of 16 cases (87.5%), including 4 MSSA
and 10 MR-CoNS in approximately 1 hour after specimen receipt.
The sensitivity and specificity of GeneXpert were 87.5% (CI 95%:
60.4-97.8) and 92.1% (CI 95%: 83-96.7), respectively, compared
with standard culture methods. The sensitivity of GeneXpert for
S. aureus was 100%. Regarding a cost-effectiveness analysis, the
incremental cost of using GeneXpert was of 31.1euro per patient
while the incremental cost-effectiveness ratio of GeneXpert
compared with blood culture alones was about 180euro per life
year gained. In conclusion, GeneXpert can be used directly with
blood samples obtained through infected catheters to detect S.
aureus and MR-CoNS in approximately 1h after sampling. In
addition, it is cost-effective especially in areas with high
prevalence of staphylococcal CRB
Risk factors for mortality in patients with acute leukemia and bloodstream infections in the era of multiresistance
Objectives: We assess the epidemiology and risk factors for mortality of bloodstream infection (BSI) in patients with acute leukemia (AL). Methods:
Prospectively collected data of a cohort study from July 2004 to February 2016. Multivariate analyses were performed. Results: 589 episodes of BSI were documented in 357 AL patients, 55% caused by gram-positive bacteria (coagulase-negative staphylococci 35.7%, Enterococcus spp 10.8%) and 43.5% by gram-negative bacteria (E. coli 21%, PA 12%). We identified 110 (18.7%) multidrug-resistant (MDR) microorganisms, especially MDR-Pseudomonas aeruginosa (7%) and extended-spectrum beta-lactamase producing Enterobacteriaceae (7%). The 30-day mortality was 14.8%. Age (OR 3.1; 95% CI 1.7–5.7); chronic lung disease (4.8; 1.1–21.8); fatal prognosis according to McCabe index (13.9; 6.4–30.3); shock (3.8; 1.9–7.7); pulmonary infection (3.6; 1.3–9.9); and MDR-PA infections with inappropriate treatment (12.8; 4.1–40.5) were related to mortality. MDR-PA BSI was associated to prior antipseudomonal cephalosporin use (9.31; 4.38–19.79); current use of betalactams (2.01; 1.01–4.3); shock (2.63; 1.03–6.7) and pulmonary source of infection (9.6; 3.4–27.21). Conclusions: MDR organisms were commonly isolated in BSI in AL. Inappropriate empiric antibiotic treatment for MDR-PA is the primary factor related to mortality that can be changed. New treatment strategies to improve the coverage of MDR-PA BSI should be considered in those patients with risk factors for this infection
Time-to-positivity, type of culture media and oxidase test performed on positive blood culture vials to predict Pseudomonas aeruginosa in patients with Gram-negative bacilli bacteraemia
OBJECTIVE: The aim of this study was to determine the usefulness of oxidase test and time-to-positivity (TTP) in aerobic and anaerobic blood culture vials to detect the presence of Pseudomonas aeruginosa in patients with Gram-negative bacilli (GNB) bacteraemia. METHODS: TTP was recorded for each aerobic and anaerobic blood culture vial of monomicrobial bacteraemia due to GNB. Oxidase test was performed in a pellet of the centrifuged content of the positive blood culture. An algorithm was developed in order to perform the oxidase test efficiently taking into account TTP and type of vial. RESULTS: A total of 341 episodes of GNB bacteraemia were analysed. Sensitivity, specificity, positive predictive value and negative predictive value of the oxidase test performed on positive vials with GNB to predict P. aeruginosa were 95%, 99%, 91%, and 99%, respectively. When growth was first or exclusively detected in anaerobic vials, P. aeruginosa was never identified hence the performance of the oxidase test could be avoided. When growth was only or first detected in aerobic vials, a TTP≥8h predicted P. aeruginosa in 37% or cases (63 of 169), therefore oxidase test is highly recommended. CONCLUSIONS: Oxidase test performed onto positive blood culture vials previously selected by TTP and type of vials is an easy and inexpensive way to predict P. aeruginosa. In most cases, this can lead to optimization of treatment in less than 24 hours
Evaluation of a Mixing versus a Cycling Strategy of Antibiotic Use in Critically-Ill Medical Patients: Impact on Acquisition of Resistant Microorganisms and Clinical Outcomes
OBJECTIVE: To compare the effect of two strategies of antibiotic
use (mixing vs. cycling) on the acquisition of resistant
microorganisms, infections and other clinical outcomes. METHODS:
Prospective cohort study in an 8-bed intensive care unit during
35- months in which a mixing-cycling policy of antipseudomonal
beta-lactams (meropenem, ceftazidime/piperacillin-tazobactam)
and fluoroquinolones was operative. Nasopharyngeal and rectal
swabs and respiratory secretions were obtained within 48h of
admission and thrice weekly thereafter. Target microorganisms
included methicillin-resistant S. aureus, vancomycin-resistant
enterococci, third-generation cephalosporin-resistant
Enterobacteriaceae and non-fermenters. RESULTS: A total of 409
(42%) patients were included in mixing and 560 (58%) in cycling.
Exposure to ceftazidime/piperacillin-tazobactam and
fluoroquinolones was significantly higher in mixing while
exposure to meropenem was higher in cycling, although overall
use of antipseudomonals was not significantly different
(37.5/100 patient-days vs. 38.1/100 patient-days). There was a
barely higher acquisition rate of microorganisms during mixing,
but this difference lost its significance when the cases due to
an exogenous Burkholderia cepacia outbreak were excluded (19.3%
vs. 15.4%, OR 0.8, CI 0.5-1.1). Acquisition of Pseudomonas
aeruginosa resistant to the intervention antibiotics or with
multiple-drug resistance was similar. There were no significant
differences between mixing and cycling in the proportion of
patients acquiring any infection (16.6% vs. 14.5%, OR 0.9, CI
0.6-1.2), any infection due to target microorganisms (5.9% vs.
5.2%, OR 0.9, CI 0.5-1.5), length of stay (median 5 d for both
groups) or mortality (13.9 vs. 14.3%, OR 1.03, CI 0.7-1.3).
CONCLUSIONS: A cycling strategy of antibiotic use with a 6-week
cycle duration is similar to mixing in terms of acquisition of
resistant microorganisms, infections, length of stay and
mortality
Methylprednisolone Pulses Plus Tacrolimus in Addition to Standard of Care vs. Standard of Care Alone in Patients With Severe COVID-19. A Randomized Controlled Trial
Introduction: Severe lung injury is triggered by both the SARS-CoV-2 infection and the subsequent host-immune response in some COVID-19 patients. Methods: We conducted a randomized, single-center, open-label, phase II trial with the aim to evaluate the efficacy and safety of methylprednisolone pulses and tacrolimus plus standard of care (SoC) vs. SoC alone, in hospitalized patients with severe COVID-19. The primary outcome was time to clinical stability within 56 days after randomization. Results: From April 1 to May 2, 2020, 55 patients were prospectively included for subsequent randomization; 27 were assigned to the experimental group and 28 to the control group. The experimental treatment was not associated with a difference in time to clinical stability (hazard ratio 0.73 [95% CI 0.39-1.37]) nor most secondary outcomes. Median methylprednisolone cumulative doses were significantly lower (360 mg [IQR 360-842] vs. 870 mg [IQR 364-1451]; p = 0.007), and administered for a shorter time (median of 4.00 days [3.00-17.5] vs. 18.5 days [3.00-53.2]; p = 0.011) in the experimental group than in the control group. Although not statistically significant, those receiving the experimental therapy showed a numerically lower all-cause mortality than those receiving SoC, especially at day 10 [2 (7.41%) vs. 5 (17.9%); OR 0.39 (95% CI 0.05-2.1); p = 0.282]. The total number of non-serious adverse events was 42 in each the two groups. Those receiving experimental treatment had a numerically higher rate of non-serious infectious adverse events [16 (38%) vs. 10 (24%)] and serious infectious adverse events [7 (35%) vs. 3 (23%)] than those receiving SoC. Conclusions: The combined use of methylprednisolone pulses plus tacrolimus, in addition to the SoC, did not significantly improve the time to clinical stability or other secondary outcomes compared with the SoC alone in severe COVID-19. Although not statistically significant, patients receiving the experimental therapy had numerically lower all-cause mortality than those receiving SoC, supporting recent non-randomized studies with calcineurin inhibitors. It is noteworthy that the present trial had a limited sample size and several other limitations. Therefore, further RCTs should be done to assess the efficacy and safety of tacrolimus to tackle the inflammatory stages of COVID-19
Bacterial co-infection at hospital admission in patients with COVID-19
Objectives: We described the current incidence and risk factors of bacterial co-infection in hospitalized patients with COVID-19. Methods: Observational cohort study was performed at the Hospital Clinic of Barcelona (February 2020-February 2021). All patients with COVID-19 who were admitted for >48 hours with microbiological sample collection and procalcitonin (PCT) determination within the first 48 hours were included. Results: A total of 1125 consecutive adults met inclusion criteria. Co-infections were microbiologically documented in 102 (9.1%) patients. Most frequent microorganisms were Streptococcus pneumoniae (79%), Staphylococcus aureus (6.8%), and Haemophilus influenzae (6.8%). Test positivity was 1% (8/803) for blood cultures, 10.1% (79/780) for pneumococcal urinary antigen test, and 11.4% (15/132) for sputum culture. Patients with PCT higher than 0.2, 0.5, 1, and 2 ng/mL had significantly more co-infections than those with lower levels (p=0.017, p=0.031, p94%
- …