scholarly journals Genomic Diversity of Azole-Resistant Aspergillus fumigatus in the United States

mBio ◽  
2021 ◽  
Author(s):  
Kizee A. Etienne ◽  
Elizabeth L. Berkow ◽  
Lalitha Gade ◽  
Natalie Nunnally ◽  
Shawn R. Lockhart ◽  
...  

Aspergillus fumigatus is one of the most common causes of invasive mold infections in patients with immune deficiencies and has also been reported in patients with severe influenza and severe acute respiratory syndrome coronavirus 2 (SARs-CoV-2). Triazole drugs are the first line of therapy for this infection; however, their efficacy has been compromised by the emergence of azole resistance in A. fumigatus , which was proposed to be selected for by exposure to azole fungicides in the environment [P.

mBio ◽  
2018 ◽  
Vol 9 (4) ◽  
Author(s):  
Edward W. Davis ◽  
Javier F. Tabima ◽  
Alexandra J. Weisberg ◽  
Lucas Dantas Lopes ◽  
Michele S. Wiseman ◽  
...  

ABSTRACTRathayibacter toxicusis a species of Gram-positive, corynetoxin-producing bacteria that causes annual ryegrass toxicity, a disease often fatal to grazing animals. A phylogenomic approach was employed to model the evolution ofR. toxicusto explain the low genetic diversity observed among isolates collected during a 30-year period of sampling in three regions of Australia, gain insight into the taxonomy ofRathayibacter, and provide a framework for studying these bacteria. Analyses of a data set of more than 100 sequencedRathayibactergenomes indicated thatRathayibacterforms nine species-level groups.R. toxicusis the most genetically distant, and evidence suggested that this species experienced a dramatic event in its evolution. Its genome is significantly reduced in size but is colinear to those of sister species. Moreover,R. toxicushas low intergroup genomic diversity and almost no intragroup genomic diversity between ecologically separated isolates.R. toxicusis the only species of the genus that encodes a clustered regularly interspaced short palindromic repeat (CRISPR) locus and that is known to host a bacteriophage parasite. The spacers, which represent a chronological history of infections, were characterized for information on past events. We propose a three-stage process that emphasizes the importance of the bacteriophage and CRISPR in the genome reduction and low genetic diversity of theR. toxicusspecies.IMPORTANCERathayibacter toxicusis a toxin-producing species found in Australia and is often fatal to grazing animals. The threat of introduction of the species into the United States led to its inclusion in the Federal Select Agent Program, which makesR. toxicusa highly regulated species. This work provides novel insights into the evolution ofR. toxicus.R. toxicusis the only species in the genus to have acquired a CRISPR adaptive immune system to protect against bacteriophages. Results suggest that coexistence with the bacteriophage NCPPB3778 led to the massive shrinkage of theR. toxicusgenome, species divergence, and the maintenance of low genetic diversity in extant bacterial groups. This work contributes to an understanding of the evolution and ecology of an agriculturally important species of bacteria.


2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e17589-e17589 ◽  
Author(s):  
Ronda Copher ◽  
Oluwakayode Adejoro ◽  
Stacey DaCosta Byfield ◽  
Mary DuCharme ◽  
Debanjana Chatterjee ◽  
...  

e17589 Background: Describe the treatment patterns of patients initiated on NCCN-recommended small molecular kinase inhibitors (SMKIs) for radioiodine-refractory differentiated thyroid cancer (DTC) approved in the United States. Methods: A large national US claims database was used to identify adult patients diagnosed with thyroid cancer (≥2 non-DX medical claims, ≥ 30 days apart) from 1/1/2006 - 6/30/2016 (study period) with claims for SMKIs from 1/1/2010 - 5/31/2016. Continuous enrollment required participation in a commercial or Medicare Advantage health plan ≥3 months before and ≥1 month following index date (date of first pharmacy claim for SMKI). Line of therapy (LOT) periods were defined by receipt and timing of SMKIs. Patient follow up was earliest disenrollment, death or end of the study period. Patient characteristics and SMKI treatment patterns were described. Results: A total of 217 DTC patients were identified; 63% commercially insured and 37% Medicare Advantage. Almost half were male (48%); mean age was 61.2 years (standard deviation SD 12.5 years) and mean follow-up period was 499 days (SD 414 days). In the study period, 35% (n = 77) of patients had ≥2 LOTs and 18% (n = 39) had ≥3 LOTs. Mean treatment duration was 5.4 months (SD 6.7 mos) for LOT1, 4.9 months (SD 3.8 mos) for LOT2, and 4.2 months (SD 4.9 mo) for LOT3. During the full study period, the most used regimens were Sorafenib for both LOT1 (37%) and LOT2 (25%), pazopanib (18%) and sunitinib (18%) in LOT3. Also, in the study period, 33 patients had sorafenib in LOT1 of which 16 were treated with sorafenib again (48%) in LOT2. Post FDA approval in 2015, Lenvatinib became the predominant first-line regimen (47%, n = 29) during study period. Across all first line therapies, for those patients with ≥12 months of follow-up, 53% (n = 60) initiated LOT2. Conclusions: Sorafenib was the most common first line of therapy for DTC, with Lenvatinib adoption increasing as first-line therapy since the drug’s approval in 2015. Depending on the period evaluated, almost half to 2/3 of patients are not receiving a second line of treatment, efficacious and patient appropriate therapy is of importance in treating this rare cancer.


2015 ◽  
Vol 54 (1) ◽  
pp. 168-171 ◽  
Author(s):  
Nathan P. Wiederhold ◽  
Veronica Garcia Gil ◽  
Felipe Gutierrez ◽  
Jonathan R. Lindner ◽  
Mohammad T. Albataineh ◽  
...  

Azole resistance inAspergillus fumigatusis an increasing problem. The TR34 L98H and TR46 Y121F T289A mutations that can occur in patients without previous azole exposure have been reported in Europe, Asia, the Middle East, Africa, and Australia. Here, we report the detection of both the TR34 L98H and TR46 Y121F T289A mutations in confirmedA. fumigatusisolates collected in institutions in the United States. These mutations, other mutations known to cause azole resistance, and azole MICs are reported here.


2015 ◽  
Vol 60 (2) ◽  
pp. 1129-1133 ◽  
Author(s):  
Jose A. Vazquez ◽  
Elias K. Manavathu

ABSTRACTMolecular characterization ofcyp51Afrom the azole-resistantAspergillus fumigatusisolate 50593 from a lung transplant patient showed Y121F/T289A changes coupled with a 46-bp tandem repeat (TR46) on the promoter, whereascyp51Afrom the pretherapy isolate,A. fumigatus47381, showed no changes. This is the first reported case ofA. fumigatusazole resistance due to Y121F/T289A/TR46 in the United States, suggesting that multiple mutational alterations ofcyp51Aresulting in high-level azole resistance could occur during prolonged antifungal therapy.


2014 ◽  
Vol 81 (2) ◽  
pp. 569-577 ◽  
Author(s):  
Lydia V. Rump ◽  
Narjol Gonzalez-Escalona ◽  
Wenting Ju ◽  
Fei Wang ◽  
Guojie Cao ◽  
...  

ABSTRACTEscherichia coliO157:H7 is, to date, the majorE. coliserotype causing food-borne human disease worldwide. Strains of O157 with other H antigens also have been recovered. We analyzed a collection of historic O157 strains (n= 400) isolated in the late 1980s to early 1990s in the United States. Strains were predominantly serotype O157:H7 (55%), and various O157:non-H7 (41%) serotypes were not previously reported regarding their pathogenic potential. Although lacking Shiga toxin (stx) andeaegenes, serotypes O157:H1, O157:H2, O157:H11, O157:H42, and O157:H43 carried several virulence factors (iha,terD, andhlyA) also found in virulent serotypeE. coliO157:H7. Pulsed-field gel electrophoresis (PFGE) showed the O157 serogroup was diverse, with strains with the same H type clustering together closely. Among non-H7 isolates, serotype O157:H43 was highly prevalent (65%) and carried important enterohemorrhagicE. coli(EHEC) virulence markers (iha,terD,hlyA, andespP). Isolates from two particular H types, H2 and H11, among the most commonly found non-O157 EHEC serotypes (O26:H11, O111:H11, O103:H2/H11, and O45:H2), unexpectedly clustered more closely with O157:H7 than other H types and carried several virulence genes. This suggests an early divergence of the O157 serogroup to clades with different pathogenic potentials. The appearance of important EHEC virulence markers in closely related H types suggests their virulence potential and suggests further monitoring of those serotypes not implicated in severe illness thus far.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 4787-4787 ◽  
Author(s):  
Brandon Arnieri ◽  
Coen Bernaards ◽  
Kenneth Wilhelm ◽  
James Black ◽  
Ceri Hirst ◽  
...  

Abstract Introduction: Approximately 18,960 new cases of CLL and 4,660 deaths from CLL are estimated in the US in 2016, with an overall estimated 5-year survival rate of 82%. Despite this, CLL patients with unfavorable genetic features such as 17p deletion have relatively poor outcomes when treated with conventional chemoimmunotherapy (e.g. fludarabine and cyclophosphamide, or bendamustine plus rituximab); however, several new treatments have been approved by the FDA for the treatment of previously untreated CLL in the past 3 years, including obinutuzumab with chlorambucil and ibrutinib. The aim of this analysis was to assess demographics and treatment patterns in patients with previously untreated CLL since the introduction of new treatment options using a novel oncology electronic health record (EHR) database. Methods: A cohort of CLL patients was selected by identifying patients within Flatiron's real-world oncology database. The Flatiron provider network comprises 230 clinics, 2,000 clinicians, and more than 1 million cancer patients throughout the United States (US). Patients included in the cohort were required to meet the following criteria: ≥2 clinic encounters on different days occurring on or after January 1, 2011; ≥1 medication order for an antineoplastic occurring on or after January 1, 2013; physician documentation of CLL; and, evidence in unstructured documents (ie, information not organized in a pre-existing data model, such as free text from a physician note/lab report) of having been treated specifically for CLL. The latter two criteria were assessed based on technology-enabled abstraction of unstructured data (e.g., pathology reports, clinician notes). Patients who lacked unstructured documents, absence of evidence of first-line treatment, or received CLL treatment at a practice outside of the Flatiron network were excluded. The cohort included patients of all ages treated between 2011 and 2015 from all 50 states of the US. The index date was defined as the date of the patient's CLL treatment initiation. Start of first-line therapy after January 1, 2011, was defined as the first episode of an eligible therapy given after or up to 14 days before the date of the patient's CLL treatment initiation. Line of therapy was the first eligible drug episode plus other eligible drugs given within 28 days. Therapies eligible for inclusion in lines of therapy were systemic treatment, as evidenced by an order or administration of an antineoplastic agent recorded in the EHR; radiotherapy and surgery were not included. For patients with documented transformation of CLL, the abstracted date of transformation ended any active line of therapy, and the patient was not considered eligible for any subsequent CLL lines of therapy. Any treatment that occurred after the date of transformation was not included as a CLL line of therapy (steroids were not included in the definition of CLL lines of therapy). Results: As of June 2016, the cohort consisted of 766 eligible CLL patients with a median age of 71 years, and 64% were male (Table 1). While distribution of first-line therapies initiated in 2011 to 2013 remained relatively constant by year, changes were observed during 2014 and 2015 following the introduction of obinutuzumab and ibrutinib (Figure 1); obinutuzumab monotherapy as first-line therapy increased from 8.2% in 2014 to 14.5% in 2015, and ibrutinib monotherapy or ibrutinib + rituximab increased from 10.5% in 2014 to 13.6% in 2015. Of note, fludarabine containing regimens declined from 19.8% in 2012 to 8.8% in 2015. Decreases were also observed with rituximab monotherapy from 21.0% to 16.2%, bendamustine + rituximab (BR) from 36.1% to 31.6%, and rituximab + fludarabine + cyclophosphamide (RFC) from 11.0% to 8.8%. Factors associated with chlorambucil treatment (as monotherapy or in combination) vs. chemoimmunotherapy included older age (75.9 years vs. 68.7 years and 62.6 years for BR and RFC, respectively) and Rai stage (78.1% of patients treated with chlorambucil had Rai stage 0-I disease vs. 70.1% and 71.7% treated with BR and RFC, respectively). A fifth of patients with 17p deletion were treated with ibrutinib. Updated data inclusive of 2016 treatments will be presented. Conclusion: Using a novel EHR database, the marked change in CLL treatments from 2011 to 2015 shows increased utilization of newer agents. Further follow-up and analysis will contrast treatment patterns beyond RCT data in a real-world setting. Disclosures Arnieri: F. Hoffmann La-Roche Ltd: Employment. Bernaards:F. Hoffmann La-Roche Ltd: Employment. Wilhelm:Roche: Equity Ownership; Genentech: Employment. Black:F. Hoffmann La-Roche Ltd: Employment. Hirst:F. Hoffmann La-Roche Ltd: Employment; AstraZeneca: Other: Previous employment . Taylor:F. Hoffmann La-Roche Ltd: Employment. Lambert:F. Hoffmann La-Roche Ltd: Employment. Green:F. Hoffmann La-Roche Ltd: Employment. Lu:F. Hoffmann La-Roche Ltd: Employment. Humphrey:Genentech, Inc.: Employment.


2018 ◽  
Vol 62 (8) ◽  
Author(s):  
Yubhisha Dabas ◽  
Immaculata Xess ◽  
Sameer Bakshi ◽  
Manoranjan Mahapatra ◽  
Rachna Seth

ABSTRACT This prospective study shows that the rate of azole-resistant Aspergillus fumigatus (ARAF) in an immunocompromised Indian patient population with invasive aspergillosis (IA) is low, 6/706 (0.8%). This low rate supports the continued use of voriconazole as the first line of treatment. However, the ARAF isolates from India in this study exhibited three kinds of unreported cyp51A mutations, of which two were at hot spots, G54R and P216L, while one was at codon Y431C.


2016 ◽  
Vol 54 (11) ◽  
pp. 2681-2688 ◽  
Author(s):  
S. Madison-Antenucci ◽  
R. F. Relich ◽  
L. Doyle ◽  
N. Espina ◽  
D. Fuller ◽  
...  

Common causes of chronic diarrhea among travelers worldwide include protozoan parasites. The majority of parasitic infections are caused by Giardia duodenalis , Entamoeba histolytica , Cryptosporidium parvum , and Cryptosporidium hominis . Similarly, these species cause the majority of parasitic diarrhea acquired in the United States. Detection of parasites by gold standard microscopic methods is time-consuming and requires considerable expertise; enzyme immunoassays and direct fluorescent-antibody (DFA) stains have lowered hands-on time for testing, but improvements in sensitivity and technical time may be possible with a PCR assay. We performed a clinical evaluation of a multiplex PCR panel, the enteric parasite panel (EPP), for the detection of these common parasites using the BD Max instrument, which performs automated extraction and amplification. A total of 2,495 compliant specimens were enrolled, including 2,104 (84%) specimens collected prospectively and 391 (16%) specimens collected retrospectively. Approximately equal numbers were received in 10% formalin (1,273 specimens) and unpreserved (1,222 specimens). The results from the EPP were compared to those from alternate PCR and bidirectional sequencing (APCR), as well as DFA ( G. duodenalis and C. parvum or C. hominis ) or trichrome stain ( E. histolytica ). The sensitivity and specificity for prospective and retrospective specimens combined were 98.2% and 99.5% for G. duodenalis , 95.5% and 99.6 for C. parvum or C. hominis , and 100% and 100% for E. histolytica , respectively. The performance of the FDA-approved BD Max EPP compared well to the reference methods and may be an appropriate substitute for microscopic examination or immunoassays.


2018 ◽  
Vol 62 (5) ◽  
Author(s):  
Elizabeth L. Berkow ◽  
Natalie S. Nunnally ◽  
Alex Bandea ◽  
Randall Kuykendall ◽  
Karlyn Beer ◽  
...  

ABSTRACT The emergence of azole-resistant Aspergillus fumigatus has become a clinical problem in many parts of the world. Several amino acid mutations in the azole target protein Cyp51Ap contribute to this resistance, with the most concerning being the environmentally derived TR 34 /L98H and TR 46 /Y121F/T289A mutations. Here, we performed passive surveillance to assess a sample of the A. fumigatus population in the United States for the presence of these mutations. We found 1.4% of those isolates to exhibit elevated MIC via broth microdilution, and five of those isolates harbored the TR 34 /L98H mutation.


2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 7086-7086
Author(s):  
Christopher Flowers ◽  
Charles Michael Farber ◽  
Ian Flinn ◽  
David L. Grinblatt ◽  
Neil E. Kay ◽  
...  

7086 Background: The HRQOL of patients (pts) with chronic lymphocytic leukemia (CLL) has not been adequately delineated across patient, disease and treatment characteristics. We evaluated HRQOL of CLL pts undergoing treatment in the United States (US) by age, gender and line of therapy. Methods: Data were collected in Connect CLL, a prospective observational US registry. Physicians provided data on demographics, clinical characteristics and line of therapy at enrollment. HRQOL was self-reported by pts at enrollment using the Functional Assessment of Cancer Therapy-Leukemia, an instrument that yields a leukemia-specific total HRQOL score (FACT-Leu) and a cancer-specific total HRQOL score (FACT-G). Mean total scores were analyzed by line of therapy, age and gender. Statistical significance was ascertained by ANOVA using SAS 9.2. Multivariate analyses were conducted to assess the relative association of line of therapy, age and gender with HRQOL. Results: Among 1,252 pts enrolled from 161 geographically diverse centers (90% community, 8% academic, 2% veterans/military), pts were predominantly male (63%), white (89%) with mean age 69 yrs. Pts were categorized by line of therapy at enrollment: First 61%, Second 18%, Third 11%, Higher 9%; and by age group: <65 33%, 65-74 35%, 75+ 32%. Univariate analyses suggested that the total FACT-Leu score was significantly better in men than women (P=0.004); in pts aged 65-74 vs younger or older pts (P=0.033); and in pts initiating first-line treatment vs pts receiving subsequent treatments (P=0.0002). Similar results were found with the FACT-G score except that gender differences were not statistically significant. Multivariate analysis confirmed that line of therapy (P=0.007), gender (P<0.0001), and age group (P=0.039) were each associated with significant differences in the FACT-Leu total score. Conclusions: Results from the Connect CLL Registry indicate that HRQOL is better among pts initiating first-line therapy compared to pts initiating subsequent treatments, and that this remains true when age and gender are considered. Future analyses should determine how HRQOL may change over time relative to treatment and treatment response.


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