Therapeutic drug monitoring (TDM) of antibiotics has been practiced for more than half a century, but it is still not widely applied for infected patients. It has a traditional focus on limiting ...toxicity of specific classes of antibiotics such as aminoglycosides and vancomycin. With more patients in critical care with higher levels of sickness severity and immunosuppression as well as an increasingly obese and ageing population, an increasing risk of suboptimal antibiotic exposure continues to escalate. As such, the value of TDM continues to expand, especially for beta-lactams which constitute the most frequently used antibiotic class. To date, the minimum inhibitory concentration (MIC) of infectious microbes rather than classification in terms of susceptible and resistant can be reported. In parallel, increasingly sophisticated TDM technology is becoming available ensuring that TDM is feasible and can deliver personalized antibiotic dosing schemes. There is an obvious need for extensive studies that will quantify the improvements in clinical outcome of individual TDM-guided dosing. We suggest that a broad diagnostic and medical investigation of the TDM arena, including market analyses and analytical technology assessment, is a current priority.
The two main pillars of clinical microbiological diagnostics are the identification of potentially pathogenic microorganisms from patient samples and the testing for antibiotic susceptibility (AST) ...to allow efficient treatment with active antimicrobial agents. While routine microbial species identification is increasingly performed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routine AST still largely relies on conventional and molecular techniques such as broth microdilution or disk and gradient diffusion tests, PCR and automated variants thereof. However, shortly after the introduction of MALDI-TOF MS based routine identification, first attempts to perform AST on the same instruments were reported. Today, a number of different approaches to perform AST with MALDI-TOF MS and other MS techniques have been proposed, some restricted to particular microbial taxa and resistance mechanisms while others being more generic. Further, while some of the methods are in a stage of proof of principles, others are already commercialized. In this review we discuss the different principal approaches of mass spectrometry based AST and evaluate the advantages and disadvantages compared to conventional and molecular techniques. At present, the possibility that MS will soon become a routine tool for AST seems unlikely - still, the same was true for routine microbial identification a mere 15 years ago.
spp. are primary pathogens of diarrhea in children worldwide. Emergence of resistance to fluoroquinolones and third-generation cephalosporins is crucial in the management of pediatric shigellosis. We ...determined the prevalence and the antibiotic resistance patterns of
species isolated from pediatric patients in central Iran.
Pediatric diarrhea samples (n=230) were cultured on MacConkey and XLD agar media and in GN broth. Genus-specific PCR for
was also used for detection directly from fecal specimens. Antibiotic resistance and the frequency of ESBL and AmpC genes were determined.
Out of the 230 samples, 19 (8.2%) cases of
spp. were identified using culture. Twenty-six samples were positive by PCR (11.3%),
(4/19; 21%) and
(15/19; 78.9%) being the most detected. The highest antibiotic resistance rates were found for cotrimoxazole (19/19; 100%), ampicillin (16/19; 84.2%), cefixime (13/19; 68.4%) and ceftriaxone (12/19; 63.1%). Ten cases showed phenotypic ESBL presence and all these strains were positive for
,
, and
. Three strains were AmpC positive, all of which harbored
and two contained
. Of the 19
isolates 5 (26.3%), 2 (10.5%), and 1 (5.2%) were phenotypically resistant to nalidixic acid, ciprofloxacin, and norfloxacin, respectively. Class 1 integron was found in 18 (94.7%) isolates whereas class 2 integron was found in 19 (100%) strains.
We found a considerable presence of
species with elevated antibiotic resistance levels. In particular, the resistance to third-generation cephalosporins (ESBL) and ciprofloxacin must be taken seriously.
is an opportunistic pathogen of animals and humans that is capable of both colonizing and infecting its eukaryotic host. It is frequently detected in the clinical microbiology routine laboratory.
is ...capable of acquiring antibiotic resistance traits with ease and, given its rapid global dissemination, resistance to meticillin in
has received extensive coverage in the popular and medical press. The detection of meticillin-resistant versus meticillin-susceptible
(MRSA and MSSA) is of significant clinical importance. Detection of meticillin resistance is relatively straightforward since it is defined by a single determinant, penicillin-binding protein 2a', which exists in a limited number of genetic variants carried on various Staphylococcal Cassette Chromosomes
. Diagnosis of MRSA and MSSA has evolved significantly over the past decades and there has been a strong shift from culture-based, phenotypic methods toward molecular detection, especially given the close correlation between the presence of the
genes and phenotypic resistance. This brief review summarizes the current state of affairs concerning the mostly polymerase chain reaction-mediated detection of MRSA and MSSA in either the classical laboratory setting or at the point of care. The potential diagnostic impact of the currently emerging whole genome sequencing (WGS) technology will be discussed against a background of diagnostic, surveillance, and infection control parameters. Adequate detection of MSSA and MRSA is at the basis of any subsequent, more generic antibiotic susceptibility testing, epidemiological characterization, and detection of virulence factors, whether performed with classical technology or WGS analyses.
Genome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or detailed assessment of marker effect. Recently, alignment-free ...methods based on k-mer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are sometimes hard to interpret. Here we introduce DBGWAS, an extended k-mer-based GWAS method producing interpretable genetic variants associated with distinct phenotypes. Relying on compacted De Bruijn graphs (cDBG), our method gathers cDBG nodes, identified by the association model, into subgraphs defined from their neighbourhood in the initial cDBG. DBGWAS is alignment-free and only requires a set of contigs and phenotypes. In particular, it does not require prior annotation or reference genomes. It produces subgraphs representing phenotype-associated genetic variants such as local polymorphisms and mobile genetic elements (MGE). It offers a graphical framework which helps interpret GWAS results. Importantly it is also computationally efficient-experiments took one hour and a half on average. We validated our method using antibiotic resistance phenotypes for three bacterial species. DBGWAS recovered known resistance determinants such as mutations in core genes in Mycobacterium tuberculosis, and genes acquired by horizontal transfer in Staphylococcus aureus and Pseudomonas aeruginosa-along with their MGE context. It also enabled us to formulate new hypotheses involving genetic variants not yet described in the antibiotic resistance literature. An open-source tool implementing DBGWAS is available at https://gitlab.com/leoisl/dbgwas.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Diarrheagenic
(DEC) is a significant cause of gastroenteritis and a major public health problem. This study investigates the prevalence and the antibiotic resistance patterns of DEC that were ...isolated from infectious diarrhea samples of pediatric patients from central Iran.
Pediatric diarrhea samples were collected from 230 pediatric patients visiting the hospital.
pathotypes were diagnosed by using conventional culture methods and PCR. Antibiotic resistance profiles, the frequency of multi-drug resistance (MDR), and the phenotypic and genotypic characteristics of extended spectrum-β-lactamase (ESBL), AmpC and integron-associated genes were analyzed.
Of the 230 samples of infectious diarrhea, 91 (39.5%) produced
isolates. Of these, 32 cases (35.1%) were identified as DEC by culture and PCR. The frequency of the
pathotypes obtained was as follows: EAEC 11/32 (34.3%), EPEC 9/32 (28.1%), ETEC 6/32 (18.7%), EIEC 3/32 (9.3%), and EHEC 3/32 (9.3%). The antibiotic resistance rates were greater for nalidixic acid (30/32; 93.7%), ampicillin (29/32; 90.6%), and tetracycline (25/32; 78.1%) than for any of the other tested antibiotics. High levels of MDR (25/32; 78.1%) and the presence of ESBL (18/32; 56.2%) and AmpC (9/32; 28.1%) were observed in the DEC isolates. The isolates showed a higher frequency of the ESBL genes
(18/18; 100%),
(17/18; 94.4%), and AmpC
(4/9; 44.4%) and
(4/9; 44.4%) than of the other ESBL and AmpC genes.
Compared to the previous study, DEC appeared to be the second-most abundant agent of diarrhea in pediatric patients after
, with frequent MDR and ESBL presence.
Abstract
Background
Recent years have witnessed the development of several k-mer–based approaches aiming to predict phenotypic traits of bacteria on the basis of their whole-genome sequences. While ...often convincing in terms of predictive performance, the underlying models are in general not straightforward to interpret, the interplay between the actual genetic determinant and its translation as k-mers being generally hard to decipher.
Results
We propose a simple and computationally efficient strategy allowing one to cope with the high correlation inherent to k-mer–based representations in supervised machine learning models, leading to concise and easily interpretable signatures. We demonstrate the benefit of this approach on the task of predicting the antibiotic resistance profile of a Klebsiella pneumoniae strain from its genome, where our method leads to signatures defined as weighted linear combinations of genetic elements that can easily be identified as genuine antibiotic resistance determinants, with state-of-the-art predictive performance.
Conclusions
By enhancing the interpretability of genomic k-mer–based antibiotic resistance prediction models, our approach improves their clinical utility and hence will facilitate their adoption in routine diagnostics by clinicians and microbiologists. While antibiotic resistance was the motivating application, the method is generic and can be transposed to any other bacterial trait. An R package implementing our method is available at https://gitlab.com/biomerieux-data-science/clustlasso.
Staphylococcus aureus permanently colonizes the vestibulum nasi of one-fifth of the human population, which is a risk factor for autoinfection. The precise mechanisms whereby S. aureus colonizes the ...nose are still unknown. The staphylococcal cell-wall protein clumping factor B (ClfB) promotes adhesion to squamous epithelial cells in vitro and might be a physiologically relevant colonization factor.
We define the role of the staphylococcal cytokeratin-binding protein ClfB in the colonization process by artificial inoculation of human volunteers with a wild-type strain and its single locus ClfB knock-out mutant. The wild-type strain adhered to immobilized recombinant human cytokeratin 10 (CK10) in a dose-dependent manner, whereas the ClfB(-) mutant did not. The wild-type strain, when grown to the stationary phase in a poor growth medium, adhered better to CK10, than when the same strain was grown in a nutrient-rich environment. Nasal cultures show that the mutant strain is eliminated from the nares significantly faster than the wild-type strain, with a median of 3 +/- 1 d versus 7 +/- 4 d (p = 0.006). Furthermore, the wild-type strain was still present in the nares of 3/16 volunteers at the end of follow-up, and the mutant strain was not.
The human colonization model, in combination with in vitro data, shows that the ClfB protein is a major determinant of nasal-persistent S. aureus carriage and is a candidate target molecule for decolonization strategies.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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