scholarly journals Comparison of Vitek MS and MALDI Biotyper for Identification of Actinomycetaceae of Clinical Importance: TABLE 1

2015 ◽  
Vol 54 (3) ◽  
pp. 782-784 ◽  
Author(s):  
Janina Ferrand ◽  
Hélène Hochard ◽  
Victoria Girard ◽  
Nejla Aissa ◽  
Baptiste Bogard ◽  
...  
Keyword(s):  
Formic Acid ◽  
Acid Treatment ◽  
Clinical Importance ◽  
Species Level ◽  
Content Type ◽  
Maldi Biotyper ◽  
Level Identification ◽  
Vitek Ms

The Vitek MSin vitrodiagnostic (IVD) and MALDI Biotyper IVD systems were evaluated for the identification of 158 strains ofActinomycetaceae. Correct species-level identification rates of 60.7% and 58.2% were obtained with the Vitek MS system after direct deposit and with the MALDI Biotyper system after on-plate formic acid treatment, respectively.

scholarly journals Species-Level Identification of Actinomyces Isolates Causing Invasive Infections: Multiyear Comparison of Vitek MS (Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry) to Partial Sequencing of the 16S rRNA Gene

2016 ◽  
Vol 54 (3) ◽  
pp. 712-717 ◽  
Author(s):  
T. Lynch ◽  
D. Gregson ◽  
D. L. Church
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
16S Rrna Gene Sequencing ◽  
Species Level ◽  
Rrna Gene ◽  
Content Type ◽  
Maldi Tof ◽  
Invasive Infections ◽  
Level Identification ◽  
Vitek Ms

Actinomycesspecies are uncommon but important causes of invasive infections. The ability of our regional clinical microbiology laboratory to report species-level identification ofActinomycesrelied on molecular identification by partial sequencing of the 16S ribosomal gene prior to the implementation of the Vitek MS (matrix-assisted laser desorption ionization–time of flight mass spectrometry [MALDI-TOF MS]) system. We compared the use of the Vitek MS to that of 16S rRNA gene sequencing for reliable species-level identification of invasive infections caused byActinomycesspp. because limited data had been published for this important genera. A total of 115 cases ofActinomycesspp., either alone or as part of a polymicrobial infection, were diagnosed between 2011 and 2014.Actinomycesspp. were considered the principal pathogen in bloodstream infections (n= 17, 15%), in skin and soft tissue abscesses (n= 25, 22%), and in pulmonary (n= 26, 23%), bone (n= 27, 23%), intraabdominal (n= 16, 14%), and central nervous system (n= 4, 3%) infections. Compared to sequencing and identification from the SmartGene Integrated Database Network System (IDNS), Vitek MS identified 47/115 (41%) isolates to the correct species and 10 (9%) isolates to the correct genus. However, the Vitek MS was unable to provide identification for 43 (37%) isolates while 15 (13%) had discordant results. Phylogenetic analyses of the 16S rRNA sequences demonstrate high diversity in recoveredActinomycesspp. and provide additional information to compare/confirm discordant identifications between MALDI-TOF and 16S rRNA gene sequences. This study highlights the diversity of clinically relevantActinomycesspp. and provides an important typing comparison. Based on our analysis, 16S rRNA gene sequencing should be used to rapidly identifyActinomycesspp. until MALDI-TOF databases are optimized.

scholarly journals Antifungal Susceptibility Patterns of Opportunistic Fungi in the Genera Verruconis and Ochroconis

2014 ◽  
Vol 58 (6) ◽  
pp. 3285-3292 ◽  
Author(s):  
S. Seyedmousavi ◽  
K. Samerpitak ◽  
A. J. M. M. Rijs ◽  
W. J. G. Melchers ◽  
J. W. Mouton ◽  
...  
Keyword(s):  
Geometric Mean ◽  
Antifungal Susceptibility ◽  
Species Level ◽  
Phylogenetic Distance ◽  
Dematiaceous Fungi ◽  
Opportunistic Fungi ◽  
Content Type ◽  
Broth Microdilution Method ◽  
Susceptibility Patterns

ABSTRACTSpecies ofVerruconisand species ofOchroconisare dematiaceous fungi generally found in the environment but having the ability to infect humans, dogs, cats, poultry, and fish. This study presents the antifungal susceptibility patterns of these fungi at the species level. Forty strains originating from clinical and environmental sources were phylogenetically identified at the species level by using sequences of the ribosomal DNA internal transcribed spacer (rDNA ITS).In vitroantifungal susceptibility testing was performed against eight antifungals, using the Clinical and Laboratory Standards Institute (CLSI) broth microdilution method. The geometric mean MICs for amphotericin B (AMB), flucytosine (5FC), fluconazole (FLC), itraconazole (ITC), voriconazole (VRC), and posaconazole (POS) and minimum effective concentrations (MECs) for caspofungin (CAS) and anidulafungin (AFG) across theOchroconisandVerruconisspecies were as follows, in increasing order. ForVerruconisspecies, the values (μg/ml) were as follows: AFG, 0.04; POS, 0.25; ITC, 0.37; AMB, 0.50; CAS, 0.65; VRC, 0.96; 5FC, 10.45; and FLC, 47.25. ForOchroconisspecies, the values (μg/ml) were as follows: AFG, 0.06; POS, 0.11; CAS, 0.67; VRC, 2.76; ITC, 3.94; AMB, 5.68; 5FC, 34.48; and FLC, 61.33. Antifungal susceptibility ofOchroconisandVerruconiswas linked with phylogenetic distance and thermotolerance. Echinocandins and POS showed the greatestin vitroactivity, providing possible treatment options forOchroconisandVerruconisinfections.

scholarly journals Antimicrobial Susceptibilities of Abiotrophia defectiva, Granulicatella adiacens, and Granulicatella elegans

2015 ◽  
Vol 60 (3) ◽  
pp. 1411-1420 ◽  
Author(s):  
Michael O. Alberti ◽  
Janet A. Hindler ◽  
Romney M. Humphries
Keyword(s):  
Antimicrobial Susceptibility ◽  
Susceptibility Testing ◽  
16S Rrna Gene Sequencing ◽  
Species Level ◽  
Rrna Gene ◽  
Content Type ◽  
Susceptibility Data ◽  
Abiotrophia Defectiva ◽  
Granulicatella Adiacens ◽  
Level Identification

Nutritionally variant streptococci (NVS) are fastidious Gram-positive cocci comprised of the speciesAbiotrophia defectiva,Granulicatella adiacens, andGranulicatella elegans. NVS are an important cause of bacteremia and infective endocarditis (IE) associated with significant morbidity and mortality. Antimicrobial susceptibility testing (AST) was performed for 14 antimicrobials using the broth microdilution MIC method described in the Clinical and Laboratory Standards Institute (CLSI) M45 guideline. A total of 132 clinical NVS blood isolates collected from 2008 to 2014 were tested. Species level identification of NVS isolates was achieved by 16S rRNA gene sequencing and/or matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). Ninety isolates were identified asG. adiacens, 37 asA. defectiva, and 5 asG. elegans. All isolates were susceptible to vancomycin (MIC90= 1 μg/ml), and none displayed high-level resistance to aminoglycosides.G. adiacenswas considerably more susceptible to penicillin thanA. defectiva(38.9% versus 10.8% of isolates susceptible) but was less susceptible to cephalosporins than wasA. defectiva(43.3% versus 100% of isolates susceptible to ceftriaxone). Several isolates were resistant to levofloxacin (6%), erythromycin (51%), and clindamycin (10%). The MIC90for daptomycin was ≥4 μg/ml forG. adiacensandA. defectiva.G. elegansisolates were 100% susceptible to all antimicrobials tested, with the exception of erythromycin, to which only 20% were susceptible. This study provides antimicrobial susceptibility data for a recent collection of NVS and demonstrates important NVS species-related differences with respect to susceptibility to penicillin, cephalosporins, carbapenems, and daptomycin. Species-level identification of NVS organisms when susceptibility testing is not readily available may aid in treatment decisions.

scholarly journals Effects of Formic Acid on Amblyomma americanum (Ixodida: Ixodidae) Larvae and Nymphs

2020 ◽  
Vol 57 (4) ◽  
pp. 1184-1192
Author(s):  
Allan T Showler ◽  
Bailee N Dorsey ◽  
Ryan M Caesar
Keyword(s):  
Formic Acid ◽  
Varroa Destructor ◽  
Direct Contact ◽  
Acid Treatment ◽  
Blood Feeding ◽  
Amblyomma Americanum ◽  
Alternative Control ◽  
Temporary Immersion ◽  
Varroa Mites

Abstract Ixodids are blood-feeding ectoparasitic vectors of many disease agents that infect humans, livestock, and wild animals. As ixodid resistance to conventional synthetic acaricides becomes increasingly problematic, natural products are receiving greater attention as possible alternative control tactics. Formic acid, produced by ants, is a commercially available product for fumigating varroa mites, Varroa destructor Anderson & Trueman, infesting honey bee, Apis mellifera L., hives, and it has been reported to repel ixodids. Lone star tick, Amblyomma americanum (L.), larvae and nymphs were used as a model ixodid to investigate deterrent, repellent, and lethal effects of formic acid as a fumigant and contact toxin in vitro in the laboratory. Although formic acid failed to deter or repel A. americanum, it was highly toxic as a fumigant to larvae at a 1% concentration even when exposure was limited to 5 min. Contact by crawling on wet, moist, and dry treated substrates under ventilated conditions causes >90% mortality to larvae in 5% formic acid concentration treatments within 30–120 min, and temporary immersion killed ≈60% of the larvae by 24 h after they were removed from the 5% formic acid treatment solution. Substantial nymphal mortality occurred after 1–1.5 h following exposure to substrate treated with the 10% concentration and immersion killed ≈45% of the nymphs. It appears that formic acid volatiles are more lethal to A. americanum immatures than direct contact with the external integument.

scholarly journals The Persistence-Inducing Toxin HokB Forms Dynamic Pores That Cause ATP Leakage

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Dorien Wilmaerts ◽  
Mariam Bayoumi ◽  
Liselot Dewachter ◽  
Wouter Knapen ◽  
Jacek T. Mika ◽  
...  
Keyword(s):  
Membrane Potential ◽  
Lipid Bilayers ◽  
Channel Blocker ◽  
Clinical Importance ◽  
Chronic Infections ◽  
Persister Cells ◽  
Bacterial Populations ◽  
Content Type ◽  
Intracellular Atp

ABSTRACTBacterial populations harbor a small fraction of cells that display transient multidrug tolerance. These so-called persister cells are extremely difficult to eradicate and contribute to the recalcitrance of chronic infections. Several signaling pathways leading to persistence have been identified. However, it is poorly understood how the effectors of these pathways function at the molecular level. In a previous study, we reported that the conserved GTPase Obg induces persistence inEscherichia colivia transcriptional upregulation of the toxin HokB. In the present study, we demonstrate that HokB inserts in the cytoplasmic membrane where it forms pores. The pore-forming capacity of the HokB peptide is demonstrated byin vitroconductance measurements on synthetic and natural lipid bilayers, revealing an asymmetrical conductance profile. Pore formation is directly linked to persistence and results in leakage of intracellular ATP. HokB-induced persistence is strongly impeded in the presence of a channel blocker, thereby providing a direct link between pore functioning and persistence. Furthermore, the activity of HokB pores is sensitive to the membrane potential. This sensitivity presumably results from the formation of either intermediate or mature pore types depending on the membrane potential. Taken together, these results provide a detailed view on the mechanistic basis of persister formation through the effector HokB.IMPORTANCEThere is increasing awareness of the clinical importance of persistence. Indeed, persistence is linked to the recalcitrance of chronic infections, and evidence is accumulating that persister cells constitute a pool of viable cells from which resistant mutants can emerge. Unfortunately, persistence is a poorly understood process at the mechanistic level. In this study, we unraveled the pore-forming activity of HokB inE. coliand discovered that these pores lead to leakage of intracellular ATP, which is correlated with the induction of persistence. Moreover, we established a link between persistence and pore activity, as the number of HokB-induced persister cells was strongly reduced using a channel blocker. The latter opens opportunities to reduce the number of persister cells in a clinical setting.

scholarly journals Comparison of the Vitek MS and Bruker Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems for Identification of Rhodococcus equi and Dietzia spp.

2017 ◽  
Vol 55 (7) ◽  
pp. 2255-2260 ◽  
Author(s):  
Carlos Ruiz de Alegría Puig ◽  
Lilian Pilares ◽  
Francesc Marco ◽  
Jordi Vila ◽  
Luis Martínez-Martínez ◽  
...  
Keyword(s):  
Laser Desorption ◽  
Species Level ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Desorption Ionization ◽  
Flight Mass Spectrometry ◽  
Vitek Ms ◽  
Matrix Assisted Laser ◽  
Matrix Assisted Laser Desorption

ABSTRACTRhodococcus equicauses pyogranulomatous pneumonia in domesticated animals and immunocompromised humans.Dietziaspp. are environmental bacteria that have rarely been associated with human infections.R. equiandDietziaspp. are closely related actinomycetes. Phenotypic discrimination betweenR. equiandDietziaon the basis of their Gram stain morphology and colony appearance is problematic. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) is a fast, reliable, and cost-effective method for identification of a wide variety of microorganisms. We have evaluated the performance of Bruker Biotyper versus that of Vitek MS for identification of a collection of 154 isolates identified at the source asR. equithat includes isolates belonging to the genusDietzia. PCR amplification of thechoEgene, encoding a cholesterol oxidase, and 16S rRNA sequencing were considered the reference methods forR. equiidentification. Biotyper identified 131 (85.1%) of the 154 isolates at the species level, and this figure increased to 152 (98.7%) when the species cutoff was reduced from a score of ≥2.000 to ≥1.750. Vitek MS correctly identified at the species level 130 (84.4%) isolates as long as bacteria were extracted with ethanol but only 35 (22.7%) isolates when samples were prepared by direct extraction from colonies. The two systems allowed differentiation betweenR. equiandDietziaspp., but identification of allDietziasp. isolates at the species level needed sequencing of the 16S rRNA gene.

scholarly journals Rapid Differentiation of Haemophilus influenzae and Haemophilus haemolyticus by Use of Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry with ClinProTools Mass Spectrum Analysis

2017 ◽  
Vol 55 (9) ◽  
pp. 2679-2685 ◽  
Author(s):  
Jonathan H. K. Chen ◽  
Vincent C. C. Cheng ◽  
Chun-Pong Wong ◽  
Sally C. Y. Wong ◽  
Wing-Cheong Yam ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Mass Spectrum ◽  
Bacterial Species ◽  
Species Level ◽  
Laser Desorption Ionization ◽  
Ionization Time ◽  
Content Type ◽  
Flight Mass Spectrometry ◽  
Mass Spectrum Analysis ◽  
Maldi Biotyper

ABSTRACT Haemophilus influenzae is associated with severe invasive disease, while Haemophilus haemolyticus is considered part of the commensal flora in the human respiratory tract. Although the addition of a custom mass spectrum library into the matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) system could improve identification of these two species, the establishment of such a custom database is technically complicated and requires a large amount of resources, which most clinical laboratories cannot afford. In this study, we developed a mass spectrum analysis model with 7 mass peak biomarkers for the identification of H. influenzae and H. haemolyticus using the ClinProTools software. We evaluated the diagnostic performance of this model using 408 H. influenzae and H. haemolyticus isolates from clinical respiratory specimens from 363 hospitalized patients and compared the identification results with those obtained with the Bruker IVD MALDI Biotyper. The IVD MALDI Biotyper identified only 86.9% of H. influenzae (311/358) and 98.0% of H. haemolyticus (49/50) clinical isolates to the species level. In comparison, the ClinProTools mass spectrum model could identify 100% of H. influenzae (358/358) and H. haemolyticus (50/50) clinical strains to the species level and significantly improved the species identification rate (McNemar's test, P < 0.0001). In conclusion, the use of ClinProTools demonstrated an alternative way for users lacking special expertise in mass spectrometry to handle closely related bacterial species when the proprietary spectrum library failed. This approach should be useful for the differentiation of other closely related bacterial species.

scholarly journals Characterization of Virulence-Related Phenotypes in Candida Species of the CUG Clade

2015 ◽  
Vol 14 (9) ◽  
pp. 931-940 ◽  
Author(s):  
Shelby J. Priest ◽  
Michael C. Lorenz
Keyword(s):  
Fungal Pathogens ◽  
Animal Studies ◽  
Debaryomyces Hansenii ◽  
Clinical Importance ◽  
Nutrient Utilization ◽  
Incidence Rates ◽  
Content Type ◽  
Evolution Of Virulence ◽  
Invasive Infections

ABSTRACTCandidaspecies cause a variety of mucosal and invasive infections and are, collectively, the most important human fungal pathogens in the developed world. The majority of these infections result from a few related species within the “CUG clade,” so named because they use a nonstandard translation for that codon. Some members of the CUG clade, such asCandida albicans, present significant clinical problems, whereas others, such asCandida(Meyerozyma)guilliermondii, are uncommon in patients. The differences in incidence rates are imperfectly correlated with virulence in animal models of infection, but comparative analyses that might provide an explanation for why some species are effective pathogens and others are not have been rare or incomplete. To better understand the phenotypic basis for these differences, we characterized eight CUG clade species—C. albicans,C. dubliniensis,C. tropicalis,C. parapsilosis,Clavispora lusitaniae,M. guilliermondii,Debaryomyces hansenii, andLodderomyces elongisporus—for host-relevant phenotypes, including nutrient utilization, stress tolerance, morphogenesis, interactions with phagocytes, and biofilm formation. Two species deviated from expectations based on animal studies and human incidence.C. dubliniensiswas quite robust, grouping in nearly all assays with the most virulent species,C. albicansandC. tropicalis, whereasC. parapsilosiswas substantially less fit than might be expected from its clinical importance. These findings confirm the utility ofin vitromeasures of virulence and provide insight into the evolution of virulence in the CUG clade.

scholarly journals Mycoplasma pneumoniae from the Respiratory Tract and Beyond

2017 ◽  
Vol 30 (3) ◽  
pp. 747-809 ◽  
Author(s):  
Ken B. Waites ◽  
Li Xiao ◽  
Yang Liu ◽  
Mitchell F. Balish ◽  
T. Prescott Atkinson
Keyword(s):  
Respiratory Tract ◽  
Mycoplasma Pneumoniae ◽  
Clinical Importance ◽  
The United States ◽  
New Drugs ◽  
Entire Genome ◽  
Content Type ◽  
The Past ◽  
Tract Infections

SUMMARYMycoplasma pneumoniaeis an important cause of respiratory tract infections in children as well as adults that can range in severity from mild to life-threatening. Over the past several years there has been much new information published concerning infections caused by this organism. New molecular-based tests forM. pneumoniaedetection are now commercially available in the United States, and advances in molecular typing systems have enhanced understanding of the epidemiology of infections. More strains have had their entire genome sequences published, providing additional insights into pathogenic mechanisms. Clinically significant acquired macrolide resistance has emerged worldwide and is now complicating treatment.In vitrosusceptibility testing methods have been standardized, and several new drugs that may be effective against this organism are undergoing development. This review focuses on the many new developments that have occurred over the past several years that enhance our understanding of this microbe, which is among the smallest bacterial pathogens but one of great clinical importance.

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