bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nosocomial transmission of fluconazole-resistant
Candida glabrata
bloodstream isolates revealed by whole-genome sequencing
Authors: Hwang In Ji , Kwon Yong Jun , Lim Ha Jin , Hong Ki Ho , Lee Hyukmin , Yong Dongeun , Won Eun Jeong , Byun Seung A. , Lee Ga Yeong , Kim Soo Hyun , Song Eun Song , Shin Jong Hee 
Published: August 2024

ABSTRACT

The clonal transmission of fluconazole-resistant
Candida glabrata
isolates within hospitals has seldom been analyzed by whole-genome sequencing (WGS). We performed WGS on 79
C
.
glabrata
isolates, comprising 31 isolates from three premature infants with persistent
C. glabrata
bloodstream infection despite antifungal treatment in the same neonatal intensive care unit (NICU) in 2022 and 48 (27 fluconazole-resistant and 21 fluconazole-susceptible dose-dependent) bloodstream isolates from 48 patients in 15 South Korean hospitals from 2010 to 2022. Phylogenetic analysis based on WGS single-nucleotide polymorphisms (SNPs) distinguished the 79 isolates according to multilocus sequence typing (MLST) (17 sequence type [ST]3, 13 ST7, two ST22, 41 ST26, four ST55, and two ST59 isolates) and unveiled two possible clusters of nosocomial transmission among ST26 isolates. One cluster from two premature infants with overlapping NICU hospitalizations in 2022 encompassed 15 fluconazole-resistant isolates harboring pleiotropic drug-resistance transcription factor (Pdr1p) P258L (13 isolates) or N1086I (two isolates), together with 10 fluconazole-susceptible dose-dependent isolates lacking Pdr1p SNPs. The other cluster indicated unforeseen clonal transmission of fluconazole-resistant bloodstream isolates among five patients (four post-lung transplantation and one with diffuse interstitial lung disease) in the same hospital over 8 months. Among these five isolates, four obtained after exposure to azole antifungals harbored distinct Pdr1p SNPs (N1091D, E388Q, K365E, and R376Q). The findings reveal the transmission patterns of clonal bloodstream isolates of
C. glabrata
among patients undergoing antifungal treatment, exhibiting different levels of fluconazole susceptibility or distinct Pdr1p SNP profiles.

IMPORTANCE

The prevalence of fluconazole-resistant bloodstream infections caused by
Candida glabrata
is increasing globally, but the transmission of these resistant strains within hospitals has rarely been documented. Through whole-genome sequencing and epidemiological analyses, this study identified two potential clusters of
C. glabrata
bloodstream infections within the same hospital, revealing the transmission of clonal
C. glabrata
strains with different levels of fluconazole susceptibility or distinct transcription factor pleiotropic drug resistance protein 1 (Pdr1p) single-nucleotide polymorphism profiles among patients receiving antifungal therapy.
Hetero-antagonism of avibactam and sulbactam with cefiderocol in carbapenem-resistant
Acinetobacter
spp.
Authors: Wong Olivia , Mezcord Vyanka , Lopez Christina , Traglia German Matias , Pasteran Fernando , Tuttobene Marisel R. , Corso Alejandra , Tolmasky Marcelo E. , Bonomo Robert A. , Ramirez María Soledad 
Published: August 2024

ABSTRACT

Cefiderocol, a siderophore-cephalosporine conjugate antibiotic, shows promise as a therapeutic option for carbapenem-resistant (CR)
Acinetobacter
infections. While resistance has already been reported in
A. baumannii
, combination therapies with avibactam or sulbactam reduce MICs of cefiderocol, extending its efficacy. However, careful consideration is necessary when using these combinations. In our experiments, exposure of
A. baumannii
and
A. lwoffii
to cefiderocol and sulbactam or avibactam led to the selection of cefiderocol-resistant strains. Three of those were subjected to whole genome sequencing and transcriptomic analysis. The strains all possessed synonymous and non-synonymous substitutions and short deletions. The most significant mutations affected efflux pumps, transcriptional regulators, and iron homeostasis genes. Transcriptomics showed significant alterations in expression levels of outer membrane proteins, iron homeostasis, and β-lactamases, suggesting adaptive responses to selective pressure. This study underscores the importance of carefully assessing drug synergies, as they may inadvertently foster the selection of resistant variants and complicate the management of CR
Acinetobacter
infections.

IMPORTANCE

The emergence of carbapenem-resistant
Acinetobacter
strains as a serious global health threat underscores the urgent need for effective treatment options. Although few drugs show promise against CR
Acinetobacter
infections, resistance to both drugs has been reported. In this study, the molecular characterization of spontaneous cefiderocol-resistant variants, a CR
A. baumannii
strain with antagonism to sulbactam, and an
A. lwoffii
strain with antagonism to avibactam, provides valuable insights into the mechanisms of resistance to cefiderocol. Some mechanisms observed are associated with mutations affecting efflux pumps, regulators, and iron homeostasis genes. These findings highlight the importance of understanding resistance mechanisms to optimize treatment options. They also emphasize the importance of early evaluation of drug synergies to address the challenges of antimicrobial resistance in
Acinetobacter
infections.
Enterohemorrhagic
Escherichia coli
(EHEC) disrupts intestinal barrier integrity in translational canine stem cell-derived monolayers
Authors: Nagao Itsuma , Kawasaki Minae , Goyama Takashi , Kim Hyun Jung , Call Douglas R. , Ambrosini Yoko M. 
Published: August 2024

ABSTRACT

This study addresses the gap in translatable
in vitro
models for investigating Enterohemorrhagic
E. coli
(EHEC) infections, particularly relevant to both canine and human health. EHEC is known to induce acute colitis in dogs, leading to symptoms like hemorrhagic diarrhea and hemolytic uremic syndrome, similar to those observed in humans. However, understanding the pathophysiology and developing treatment strategies have been challenging due to the lack of effective models that replicate the clinical disease caused by EHEC in both species. Our approach involved the development of colonoid-derived monolayers using intestinal tissues from healthy, client-owned dogs. These monolayers were exposed to EHEC, and the impact of EHEC was assessed through several techniques, including trans-epithelial electrical resistance (TEER) measurement, immunofluorescence staining for junction proteins and mucus, and scanning electron microscopy for morphological analysis. Modified culture with saline, which was intended to prevent bacterial overgrowth, maintained barrier integrity and cell differentiation. EHEC infection led to significant decreases in TEER and ZO-1 expression, but not in E-cadherin levels or mucus production. In addition, EHEC elicited a notable increase in tumor necrosis factor-alpha production, highlighting its distinct impact on canine intestinal epithelial cells compared to non-pathogenic
E. coli
. These findings closely replicate
in vivo
observations in dogs and humans with EHEC enteropathy, validating the canine colonoid-derived monolayer system as a translational model to study host-pathogen interactions in EHEC and potentially other clinically significant enteric pathogens.

IMPORTANCE

This study develops a new model to better understand Enterohemorrhagic
E. coli
(EHEC) infections, a serious bacterial disease affecting both dogs and humans, characterized by symptoms such as hemorrhagic diarrhea and hemolytic uremic syndrome. Traditional research models have fallen short of mimicking how this disease manifests in patients. Our research used intestinal tissues from healthy dogs to create layers of cells, known as colonoid-derived monolayers, which we then exposed to EHEC. We assessed the damage caused by the bacteria using several techniques, observing significant changes similar to those seen in actual cases of the disease. The model proved effective in replicating the interaction between the host and the pathogen, marking an important step toward understanding EHEC’s effects and developing treatments. This canine colonoid-derived monolayer system not only bridges a crucial gap in current research but also offers a promising platform for studying other enteric pathogens affecting both canine and human health.
Performance of common primary and chromogenic culture media for MALDI-TOF MS identification of clinically relevant yeasts
Authors: Lévesque Simon , Brown Nathalie , Dufresne Philippe J. , Allard Catherine 
Published: August 2024

ABSTRACT

Timely and accurate identification of yeasts is essential for adequate treatment, considering the increase in antifungal resistance of some species, particularly for
C. auris
. Current matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) manufacturer’s protocol for identification of yeasts requires 24- to 72-h cultivation on Sabouraud dextrose media (SAB), but not some of the mainstay primary culture media used in mycology such as inhibitory mold agar (IMA), Mycosel, CHROMagar Candida Plus, and CHROMagar Candida. As culture media can influence MALDI-TOF MS identification results, this study evaluated the accuracy and performance of identification of clinically relevant yeasts on these first-line media using the VITEK-MS MALDI-TOF MS system.

IMPORTANCE

In this study, a panel of 140 strains (21 species) was used to assess the performance of the selected media. Although not in the manufacturer’s list of accepted media, IMA and chromogenic media are suitable for the identification of yeasts on the VITEK-MS systems. CHROMagar Candida Plus allowed the identification of 135/140 isolates tested after 24-h incubation similar to SAB reference media (137/140). Yeast isolates that grew on Mycosel selective media were also reliably identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. VITEK-MS system with IVD database V3.2 correctly identified
C. auris
strains to the species level on CHROMagar Candida Plus alleviating the need for subcultivation and reduced turnaround time (24–72 h) to identification for patient screening.
Emergence of a novel sequence type carbapenem-resistant hypervirulent
Klebsiella pneumoniae
ST6417 harboring
bla
NDM-5
on the lncX3 plasmid
Authors: Liu Junnian , Yuan Sue , Xuan Luhan , Sun Yu , Zhang Xinyu , Qiao Lu , Du Xuefei 
Published: August 2024

ABSTRACT

Carbapenem-resistant hypervirulent
Klebsiella pneumoniae
(CR-hvKP) is a significant pathogen causing major public health problems worldwide. This study characterized a novel sequence type 6417 (ST6471) CR-hvKP strain recovered from the blood of a male patient with septicemia. Strain CR2021 is not susceptible to carbapenems, cephalosporin, sulfonamides, quinolones, or levofloxacin and is susceptible to amikacin and tigecycline. Molecular typing indicated that ST6417 is derived from the most dominant hypervirulent
K. pneumoniae
(hvKP) clone in China, ST23, with a single-locus variation in
tonB
. The genomic characterization of CR2021, which contains three plasmids, was performed through whole-genome sequencing. The plasmid pCR2021_IncFII contains 12 antibiotic resistance genes [
bla
CTX-M-3
,
bla
TEM-1B
,
bla
DHA-1
,
aac (3)-Ild
,
aadA16
,
sul1
,
sul2
,
qnrB4
,
ARR-3
,
dfrA27
,
qacE
,
merACDE
], all of which are associated with genetic elements. The plasmid pCR2021_IncFIB carries crucial virulence-related genes, while the plasmid pCR2021_IncX3 only harbors the
bla
NDM-5
resistance gene and exhibits 99% similarity with two other
bla
NDM-5
-carrying IncX3 plasmids (pSHX180-NDM5, pNDM-K725), with coverage of 87% and 100%, respectively. The
bla
NDM-5
genetic region contains an additional IS26-Tn3 genetic module. Serum killing and anti-human neutrophil phagocytosis tests indicated that CR2021 exhibits high virulence, which was further confirmed in a
Galleria mellonella
larvae infection model. CR-hvKP is becoming more prevalent in China; however, the majority have evolved from the multidrug resistance clone ST11 and its variants by acquiring virulence factors. Conversely, CR-hvKP derived from hvKP, such as the clone ST23, remains relatively rare. Therefore, the discovery of ST6417 underscores the need for further research into the genetic characteristics and evolution of bacteria.

IMPORTANCE

ST11 and its variants, which often exhibit drug resistance, represent popular clones of carbapenem-resistant hypervirulent
Klebsiella pneumoniae
(CR-hvKP) in China, often leading to high morbidity and mortality rates owing to their high virulence and robust drug resistance. Conversely, CR-hvKP, originating from the high-virulence sequence type ST23, remains rarely reported. In this study, we identified a novel ST6417 CR-hvKP strain derived from ST23, carrying
bla
NDM-5
on an IncX3 plasmid conferring resistance to carbapenems. In addition, we elucidate its virulence, resistance to drugs, and genetic characteristics. The discovery of ST6417 highlights the diverse pathways in the evolution of CR-hvKP, warranting increased attention.
In vitro
small molecule screening to inform novel candidates for use in fluconazole combination therapy
in vivo
against
Coccidioides
Authors: Mead Heather L. , Valentine Michael , Yin Holly , Thompson III George R. , Keim Paul , Engelthaler David M. , Barker Bridget M. 
Published: August 2024

ABSTRACT

Identifying improved treatments for severe and refractory coccidioidomycosis (Valley fever) is needed. This endemic fungal disease is common in North and South America, and cases have increased substantially over the last 30 years. The current standard of care, oral daily fluconazole, often fails to completely eradicate
Coccidioides
infection; however, the high cost of identifying new compounds effective in treating Valley fever is a barrier to improving treatment. Therefore, repurposing existing pharmaceutical agents in combination with fluconazole therapy is an attractive option. We screened the Library of Pharmacologically Active Compounds (LOPAC) small molecule library for compounds that inhibited fungal growth
in vitro
and determined IC
50
values for a subset of compounds. Based on these findings, we tested a small subset of these agents to validate the screen, as well as to test the performance of fluconazole in a combination therapy approach, as compared with fluconazole alone, in a murine model. We observed that combination therapy of tamoxifen:fluconazole and sertraline:fluconazole significantly reduced the burden of live fungus in the lung compared with fluconazole alone, and we observed reduced or nonexistent dissemination. These results suggest that tamoxifen and sertraline may be repurposed as adjunctive agents in the treatment of this important fungal disease.

IMPORTANCE
Developing new drugs, especially for regional orphan diseases, such as Valley Fever, is a slow and costly endeavor. However, there is a wealth of FDA-approved drugs available for repurposing, offering a more economical and expedited approach to improve treatment. Those existing compounds with antifungal properties can become novel therapies with relative ease: a considerable advantage for patients in need of alternative treatment. Despite the scope of remaining tasks, our comprehensive screening of potential candidates has revealed promising combinations for further exploration. This effort outlines a practical pipeline for Valley fever drug screening and identifies viable drug combinations that could impact patients more rapidly than single drug development pathways.
Exploring antimicrobial interactions between metal ions and quaternary ammonium compounds toward synergistic metallo-antimicrobial formulations
Authors: Lekhan Andrii , Turner Raymond J. 
Published: August 2024

ABSTRACT

Multi-target antimicrobial agents are considered a viable alternative to target-specific antibiotics, resistance to which emerged as a global threat. Used centuries before the discovery of conventional antibiotics, metal(loid)-based antimicrobials (MBAs), which target multiple biomolecules within the bacterial cell, are regaining research interest. However, there is a significant limiting factor—the balance between cost and efficiency. In this article, we utilize a checkerboard assay approach to explore antimicrobial combinations of MBAs with commonly used quaternary ammonium compound (QAC) antiseptics in order to discover novel combinations with more pronounced antimicrobial properties than would be expected from a simple sum of antimicrobial effects of initial components. This phenomenon, called synergy, was herein demonstrated for several mixtures of Al3+with cetyltrimethylammonium bromide (CTAB) and TeO32- with benzalkonium chloride (BAC) and didecyldimethylammonium bromide (DDAB) against planktonic and biofilm growth of
Pseudomonas aeruginosa
ATCC27853. Biofilm growth of
Escherichia coli
ATCC25922 was synergistically inhibited by the Cu2 +and benzalkonium chloride (BAC) mixture. Multiple additive mixtures were identified for both organisms. The current study observed unexpected species and growth state specificities for the synergistic combinations. The benefit of synergistic mixtures will be captured in economy/efficiency optimization for antimicrobial applications in which MBAs and QACs are presently used.

IMPORTANCE
We are entering the antimicrobial resistance era (AMR), where resistance to antibiotics is becoming more and more prevalent. In order to address this issue, various approaches are being explored. In this article, we explore for synergy between two very different antimicrobials, the antiseptic class of quaternary ammonium compounds and antimicrobial metals. These two antimicrobials have very different actions. Considering a OneHealth approach to the problem, finding synergistic mixtures allows for greater efficacy at lower concentrations, which would also address antimicrobial pollution issues.
Respiratory virus disease and outcomes at a large academic medical center in the United States: a retrospective observational study of the early 2023/2024 respiratory viral season
Authors: Mostafa Heba H. , Fall Amary , Norton Julie M. , Sachithanandham Jaiprasath , Yunker Madeline , Abdullah Omar , Hanlon Ann , Gluck Linda , Morris C. Paul , Pekosz Andrew , Klein Eili Y. 
Published: August 2024

ABSTRACT

Respiratory disease, attributed to influenza, respiratory syncytial virus (RSV), and SARS-CoV-2, was reported nationally during the 2023/2024 respiratory viral season. The emergence of novel SARS-CoV-2 variants was considered a significant factor contributing to the rise in COVID-19 cases. Data from the Johns Hopkins Hospital System (JHHS) showed that enterovirus/rhinovirus had also been circulating at high rates. Analyzing clinical outcomes of the most prevalent respiratory viruses is crucial for understanding the role of circulating viral genotypes. A retrospective cohort of patients who tested positive for SARS-CoV-2, influenza, RSV, or enterovirus/rhinovirus between 1 June and 31 December 2023 was included in the study. Remnant clinical samples were utilized for targeted viral whole-genome sequencing and genotyping. Patients’ metadata and outcomes following infection were studied, stratified by viral variants and genotypes. The increase of SARS-CoV-2 positivity in December was associated with the predominance of JN.1. Admissions for patients under 18 years old were primarily associated with enterovirus/rhinovirus and RSV, while older age groups were mainly linked to SARS-CoV-2 and influenza infections. SARS-CoV-2-related admissions increased with the predominance of the JN.1 variant in December. No significant difference in admissions for influenza subtypes, rhinovirus species, or SARS-CoV-2 variants was observed. RSV A was associated with slightly higher odds of admission compared with RSV B. Our data highlight the importance of systematically analyzing respiratory viral infections to inform public health strategies and clinical management, especially as SARS-CoV-2 becomes endemic. The findings highlight the value of expanded genomic surveillance in elucidating the clinical significance of viral evolution.

IMPORTANCE
The analysis of the epidemiology and clinical outcomes of multiple co-circulating respiratory viruses in the early 2023/2024 respiratory virus season highlights the emergence of the SARS-CoV-2 JN.1 variant as well as underscores the importance of enterovirus/rhinovirus in respiratory infections. Understanding these dynamics is essential for refining public health strategies and clinical management, especially as SARS-CoV-2 transitions to an endemic status. This work emphasizes the need for ongoing surveillance, robust diagnostic algorithms, and detailed genomic analyses to anticipate and mitigate the burden of respiratory viral infections, ultimately contributing to more informed decision-making in healthcare settings and better patient outcomes.
The mitochondrial protein Bcs1A regulates antifungal drug tolerance by affecting efflux pump expression in the filamentous pathogenic fungus
Aspergillus fumigatus
Authors: Yang Guorong , Shi Weiwei , He Wenlin , Wu Jing , Huang Sutao , Mo Li , Zhang Junjie , Wang Huaxue , Zhou Xiaogang 
Published: August 2024

ABSTRACT

Aspergillus fumigatus
is the predominant pathogen responsible for aspergillosis infections, with emerging drug-resistant strains complicating treatment strategies. The role of mitochondrial functionality in fungal resistance to antifungal agents is well-documented yet not fully understood. In this study, the mitochondrial protein Bcs1A, a homolog of yeast Bcs1, was found to regulate colony growth, ion homeostasis, and the response to antifungal drugs in
A. fumigatus
. Microscopic observations revealed substantial colocalization of Bcs1A-GFP fusion protein fluorescence with mitochondria. Bcs1A deletion compromised colony growth and the utilization of non-fermentable carbon sources, alongside causing abnormal mitochondrial membrane potential and reduced reactive oxygen species production. These findings underscore Bcs1A’s vital role in maintaining mitochondrial integrity. Phenotypic analysis and determinations of minimum inhibitory concentrations indicated that the Δ
bcs1A
mutant was more resistant to various antifungal agents, such as azoles, terbinafine, and simvastatin, compared to wild-type strain. RNA sequencing and RT-qPCR analysis highlighted an upregulation of multiple efflux pumps in the Δ
bcs1A
mutant. Furthermore, loss of the principal drug efflux pump, mdr1, decreased azole tolerance in the Δbcs1A mutant, suggesting that Bcs1A’s modulated of azoles response via efflux pump expression. Collectively, these results establish Bcs1A as essential for growth and antifungal drug responsiveness in
A. fumigatus
mediated through mitochondrial regulation.

IMPORTANCE

Drug resistance presents a formidable obstacle in the clinical management of aspergillosis. Mitochondria are integral to various biochemical pathways, including those involved in fungi drug response, making mitochondrial proteins promising therapeutic targets for drug therapy. This study confirms that Bcs1A, a mitochondrial respiratory chain protein, is indispensable for mitochondrial functionality and multidrug tolerance in
Aspergillus fumigatus
. Mutation of Bcs1A not only leads to a series of drug efflux pumps upregulated but also shows that loss of the primary efflux pump,
mdr1
, partial reduction in drug tolerance in the Bcs1A mutant, highlighting that Bcs1A’s significant influence on mitochondria-mediated drug resistance.