bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of malate on the activity of ciprofloxacin against
Pseudomonas aeruginosa
in different
in vivo
and
in vivo
-like infection models
Authors: Bao Xuerui , Goeteyn Ellen , Crabbé Aurélie , Coenye Tom 
Published: October 2023

ABSTRACT

The clinical significance of
Pseudomonas aeruginosa
infections and the tolerance of this opportunistic pathogen to antibiotic therapy makes the development of novel antimicrobial strategies an urgent need. We previously found that D,L-malic acid potentiates the activity of ciprofloxacin against
P. aeruginosa
biofilms grown in a synthetic cystic fibrosis sputum medium by increasing metabolic activity and tricarboxylic acid cycle activity. This suggested a potential new strategy to improve antibiotic therapy in
P. aeruginosa
infections. Considering the importance of the microenvironment on microbial antibiotic susceptibility, the present study aims to further investigate the effect of D,L-malate on ciprofloxacin activity against
P. aeruginosa
in physiologically relevant infection models, aiming to mimic the infection environment more closely. We used
Caenorhabditis elegans
nematodes,
Galleria mellonella
larvae, and a 3-D lung epithelial cell model to assess the effect of D,L-malate on ciprofloxacin activity against
P. aeruginosa
. D,L-malate was able to significantly enhance ciprofloxacin activity against
P. aeruginosa
in both
G. mellonella
larvae and the 3-D lung epithelial cell model. In addition, ciprofloxacin combined with D,L-malate significantly improved the survival of infected 3-D cells compared to ciprofloxacin alone. No significant effect of D,L-malate on ciprofloxacin activity against
P. aeruginosa
in
C. elegans
nematodes was observed. Overall, these data indicate that the outcome of the experiment is influenced by the model system used which emphasizes the importance of using models that reflect the
in vivo
environment as closely as possible. Nevertheless, this study confirms the potential of D,L-malate to enhance ciprofloxacin activity against
P. aeru
ginosa-associated infections.
Competitive interactions facilitate resistance development against antimicrobials
Authors: Svet Luka , Parijs Ilse , Isphording Simon , Lories Bram , Marchal Kathleen , Steenackers Hans P. 
Published: October 2023

ABSTRACT

While the evolution of antimicrobial resistance is well studied in free-living bacteria, information on resistance development in dense and diverse biofilm communities is largely lacking. Therefore, we explored how the social interactions in a duo-species biofilm composed of the brewery isolates
Pseudomonas rhodesiae
and
Raoultella terrigena
influence the adaptation to the broad-spectrum antimicrobial sulfathiazole. Previously, we showed that the competition between these brewery isolates enhances the antimicrobial tolerance of
P. rhodesiae
. Here, we found that this enhanced tolerance in duo-species biofilms is associated with a strongly increased antimicrobial resistance development in
P. rhodesiae
. Whereas
P. rhodesiae
was not able to evolve resistance against sulfathiazole in monospecies conditions, it rapidly evolved resistance in the majority of the duo-species communities. Although the initial presence of
R. terrigena
was thus required for
P. rhodesiae
to acquire resistance, the resistance mechanisms did not depend on the presence of
R. terrigena
. Whole genome sequencing of resistant
P. rhodesiae
clones showed no clear mutational hot spots. This indicates that the acquired resistance phenotype depends on complex interactions between low-frequency mutations in the genetic background of the strains. We hypothesize that the increased tolerance in duo-species conditions promotes resistance by enhancing the selection of partially resistant mutants and opening up novel evolutionary trajectories that enable such genetic interactions. This hypothesis is reinforced by experimentally excluding potential effects of increased initial population size, enhanced mutation rate, and horizontal gene transfer. Altogether, our observations suggest that the community mode of life and the social interactions therein strongly affect the accessible evolutionary pathways toward antimicrobial resistance.

IMPORTANCE
Antimicrobial resistance is one of the most studied bacterial properties due to its enormous clinical and industrial relevance; however, most research focuses on resistance development of a single species in isolation. In the present study, we showed that resistance evolution of brewery isolates can differ greatly between single- and mixed-species conditions. Specifically, we observed that the development of antimicrobial resistance in certain species can be significantly enhanced in co-culture as compared to the single-species conditions. Overall, the current study emphasizes the need of considering the within bacterial interactions in microbial communities when evaluating antimicrobial treatments and resistance evolution.
Rapid phenotypic antimicrobial susceptibility testing of Gram-negative rods directly from positive blood cultures using the novel Q-linea ASTar system
Authors: Esse Jan , Träger Johannes , Valenza Giuseppe , Bogdan Christian , Held Jürgen 
Published: October 2023

ABSTRACT
Adequate and timely antibiotic therapy is crucial for the treatment of sepsis. Innovative systems, like the Q-linea ASTar, have been developed to perform rapid antimicrobial susceptibility testing (AST) directly from positive blood cultures (BCs). We conducted a prospective study to evaluate ASTar under real-life conditions with a focus on time-to-result and impact on antimicrobial therapy. Over 2 months, all positive BCs that showed Gram-negative rods upon microscopy were tested with the ASTar and our standard procedure (VITEK 2 from short-term culture). Additionally, we included multidrug-resistant Gram-negative bacteria from our archive. Both methods were compared to broth microdilution. In total, 78 bacterial strains (51 prospective and 27 archived) were tested. ASTar covered 94% of the species encountered. The categorical and essential agreement was 95.6% and 90.7%, respectively. ASTar caused 2.4% minor, 2.0% major, and 2.4% very major errors. The categorical agreement was similar to standard procedure. The average time between BC sampling and the availability of the antibiogram for the attending physician was 28 h 49 min for ASTar and 44 h 18 min for standard procedure. ASTar correctly identified all patients who required an escalation of antimicrobial therapy and 75% of those who were eligible for de-escalation. In conclusion, ASTar provided reliable AST results and significantly shortened the time to obtain an antibiogram. However, the percentage of patients that will profit from ASTar in a low-resistance setting is limited, and it is currently unclear if a change of therapy 29 h after BC sampling will have a significant impact on the patient’s prognosis.
A CRISPR-based system to investigate HBV cccDNA biology
Authors: Seeger Christoph 
Published: October 2023

ABSTRACT
Chronic hepatitis B virus (HBV) infections affect over 250 million people worldwide, and over 800,000 are expected to die yearly from complications including cirrhosis and primary hepatocellular carcinoma. While clinically available nucleoside analog-based antiviral therapies inhibit virus production, they cannot cure infections due to the persistence of covalently closed circular (cccDNA) in the nuclei of infected hepatocytes. Hence, the goals of future curative antiviral therapies for chronic hepatitis B are to either eliminate or permanently silence transcription from cccDNA. Novel antiviral approaches building on a better understanding of the mechanisms underlying transcriptional regulation and the stability of HBV cccDNA will be necessary to accomplish such goals. To advance our understanding of cccDNA biology, we have employed a CRISPR/Cas9-based system to produce extrachromosomal circular (ec) DNA from plasmid DNA integrated into the host genome originally developed by Moller et al. [Nucleic Acid Research 46:(22) e131, 2018]. We modified the enhanced green fluorescent protein (EGFP) reporter system to include portions of the HBV genome encoding wild-type and inactive hepatitis B virus X (HBx) proteins on ecDNA to mimic cccDNA. We demonstrated that expression of EGFP is inhibited by the SMC5/6 complex, as is cccDNA, and that HBx expression can reverse transcriptional silencing of ecDNA. Moreover, we demonstrated that ecDNA is lost during cell division. The system described in this report permits investigations on ecDNA and enables large-scale screening of compound libraries for small molecules targeting host factors involved in ecDNA and, by inference, cccDNA transcription, maintenance, and loss during cell division.

IMPORTANCE
Hepatitis B virus cccDNA is the key target for the necessary development of antiviral therapies aimed at curing chronic hepatitis B. The CRISPR-based system to produce covalently closed circular (cccDNA)-like extrachromosomal DNAs described in this report enables large-scale screens of chemical libraries to identify drug candidates with the potential to permanently inactivate cccDNA. Moreover, this approach permits investigations on unresolved problems as described in this report concerning cccDNA biology including mechanisms of SMC5/6-dependent transcriptional silencing and the contributions of the SMC5/6 complex to cccDNA stability in resting and dividing hepatocytes.
The neuraminidase activity of influenza A virus determines the strain-specific sensitivity to neutralization by respiratory mucus
Authors: Iseli Alena N. , Pohl Marie O. , Glas Irina , Gaggioli Elisabeth , Martínez-Barragán Patricia , David Shannon C. , Schaub Aline , Luo Beiping , Klein Liviana K. , Bluvshtein Nir , Violaki Kalliopi , Motos Ghislain , Hugentobler Walter , Nenes Athanasios , Krieger Ulrich K. , Peter Thomas , Kohn Tamar , Stertz Silke 
Published: October 2023

ABSTRACT
Respiratory mucus lining the airway epithelium constitutes an important first line of defense against infection with influenza A virus (IAV). Previous studies suggested that the inhibitory potential of mucus relies not only on the presence of decoy receptors but also on the dense meshwork blocking virus access to the epithelium independent of sialic acid. Here, we report for a panel of human and avian IAV isolates that susceptibility to neutralization by respiratory mucus varies in a strain-dependent manner. Our data reveal that viral neuraminidase (NA) activity inversely correlates with the mucus sensitivity of a given strain. As NA cleaves sialic acid from glycan chains and thus releases IAV from decoy receptor binding, our results imply that virus inhibition by mucus is mainly driven by decoy receptor binding of IAV. Other inhibitory properties of mucus, such as size exclusion, non-covalent interactions with mucus components, or the presence of immunomodulatory molecules, likely play minor roles in neutralizing IAV. Inhibition of NA activity using oseltamivir was sufficient to increase the sensitivity of a seasonal IAV strain to mucus during infection in a cell-based neutralization assay and in differentiated primary human airway epithelial cultures. Overall, our data highlight the importance of NA for the initiation of virus infection besides its major function in release, especially in overcoming the host defense mechanism of mucociliary clearance in the airway epithelium. Furthermore, strain-specific differences in the ability to penetrate respiratory mucus may be the result of host adaptation and can have consequences for the transmissibility and infectivity of circulating viruses.

IMPORTANCE
The respiratory tract of humans is constantly exposed to potentially harmful agents, such as small particles or pathogens, and thus requires protective measures. Respiratory mucus that lines the airway epithelia plays a major role in the prevention of viral infections by limiting the mobility of viruses, allowing subsequent mucociliary clearance. Understanding the interplay between respiratory mucus and viruses can help elucidate host and virus characteristics that enable the initiation of infection. Here, we tested a panel of primary influenza A viruses of avian or human origin for their sensitivity to mucus derived from primary human airway cultures and found that differences between virus strains can be mapped to viral neuraminidase activity. We also show that binding of influenza A viruses to decoy receptors on highly glycosylated mucus components constitutes the major inhibitory function of mucus against influenza A viruses.
Establishment of tongue microbiota by 18 months of age and determinants of its microbial profile
Authors: Kageyama Shinya , Ma Jiale , Furuta Michiko , Takeshita Toru , Asakawa Mikari , Okabe Yuka , Yamashita Yoshihisa 
Published: October 2023

ABSTRACT

Acquisition of oral bacteria early in life is considered to have an important role in the establishment of oral microbiota. In this study, we examined tongue swab samples collected from 216 infants at the 18-month checkup, along with samples collected from them and from their mothers at the 4-month checkup. The bacterial composition of each sample was determined using PacBio single-molecule long-read sequencing of the full-length 16S rRNA gene and amplicon sequence variant (ASV) analysis. At 18 months of age, the tongue microbiota was dominated by
Streptococcus salivarius
,
Neisseria perflava
, and
Granulicatella adiacens
; and the overall bacterial composition was more similar to that of the mothers than at 4 months of age. The bacterial composition at 18 months of age was classified into three microbiota profiles:
S. salivarius
-dominant,
Neisseria
-dominant, and infant profile dominated by 4 months specific ASVs such as
S. salivarius
,
Streptococcus lactarius
, and
Streptococcus peroris
. Those with infant profiles exhibited significantly higher rates of current breastfeeding, dental caries or white spot lesions, and dental plaque accumulation compared to infants with the other profiles. Comparison between the
S. salivarius
- and
Neisseria
-dominant profiles showed that incomplete weaning, low intake of fruits, and frequent intake of sweetened beverages or sweet snacks were significantly associated with the
S. salivarius
-dominant profile. Our findings, based on a high-resolution profiling approach, demonstrate that the foundation of the adult tongue microbiota is established by 18 months of age, and the bacterial profile is possibly determined by dietary habits during this period.

IMPORTANCE

Understanding the development of oral microbiota early in life and the factors that influence it is important for preventing the establishment of dysbiotic oral microbiota later in life. This study demonstrates that the tongue microbiota undergoes early development from 4 to 18 months of age and converges into two types of microbiota showing indications of adult characteristics, with either
S. salivarius
or
Neisseria
-dominance. Interestingly, their divergence was strongly determined by their weaning status and the dietary frequencies of sweetened beverages, snacks, and fruits, suggesting that dietary habits during this period might influence the establishment of the oral microbiota. These findings may contribute to the development of novel preventive strategies against oral microbiota-related diseases.
Genome sequences of
bla
NDM-1
producing
Acinetobacter lactucae
isolated from immunocompromised patients in India
Authors: Amar Ashutosh Kumar , Sawant Ajit Ramesh , Manoharan Meerabai , Tomar Archana , Sistla Sujatha , Prashanth K 
Published: October 2023

ABSTRACT

Among the species within
Acb-
complex,
Acinetobacter lactucae
has not been frequently isolated from clinical settings, unlike
Acinetobacter baumannii
, which is an important nosocomial pathogen. We report the genomic sequences of
A. lactucae
strains (PKAL1732 and 1828C) harboring multiple-resistance determinants including metallo-β-lactamase (
bla
NDM-1
) isolated from immunocompromised patients admitted to a referral hospital in India.
Stenotrophomonas maltophilia
affects the gene expression profiles of the major pathogens
Pseudomonas aeruginosa
and
Staphylococcus aureus
in an
in vitro
multispecies biofilm model
Authors: Alio Ifey , Moll Raphael , Hoffmann Tim , Mamat Uwe , Schaible Ulrich E. , Pappenfort Kai , Alawi Malik , Schie Marcel , Thünauer Roland , Stamm Johanna , Rohde Holger , Streit Wolfgang R. 
Published: October 2023

ABSTRACT

Stenotrophomonas maltophilia
is an emerging lung pathogen. In its natural habitat, it lives together with
Pseudomonas aeruginosa
,
Staphylococcus aureus
, and other pathogens. Here, we provide the first evidence that
S. maltophilia
interferes with the metabolism and physiology of other species when co-cultivated in dual- and triple-species biofilms. CSLM analyses implied that
S. maltophilia
was in general the first to colonize the bottom layer in multispecies biofilms. Structural patterns and niche formation resulting in distinct layer formation within the biofilm were observed on a species- and strain-dependent level for
S. maltophilia
. Furthermore, gene expression profiles of
S. aureus
and
P. aeruginosa
were strongly affected by the presence of
S. maltophilia
. The
S. maltophilia
metabolism was mostly fermentative in multispecies biofilms with varying sets of cytochromes used for anaerobic respiration. One of the most striking observations was that
S. maltophilia
interfered with
P. aeruginosa
LasI-dependent expression of quorum sensing-regulated pathogenicity factors in multispecies biofilms.

IMPORTANCE

In the past, studies have focused on bacterial pathogenicity in mono-species infections, in part ignoring the clinical relevance of diseases caused by more than one pathogen (i.e., polymicrobial infections). However, it is now common knowledge that multiple bacteria species are often involved in the course of an infection. For treatment of such infections, it is absolutely important to understand the dynamics of species interactions at possible infection sites and the molecular mechanisms behind these interactions. Here, we studied the impact of
Stenotrophomonas maltophilia
on its commensals
Pseudomonas aeruginosa
and
Staphylococcus aureus
in multispecies biofilms. We analyzed the 3D structural architectures of dual- and triple-species biofilms, niche formation within the biofilms, and the interspecies interactions on a molecular level. RNAseq data identified key genes involved in multispecies biofilm formation and interaction as potential drug targets for the clinical combat of multispecies infection with these major pathogens.
Association of intestinal bacteria with immune activation in a cohort of healthy adults
Authors: Riazati Niknaz , Kable Mary E. , Stephensen Charles B. 
Published: October 2023

ABSTRACT

Interactions among intestinal bacteria and the immune system contribute to the maintenance of a functional intestinal barrier in healthy individuals, and possibly to systemic immune activity. We hypothesized that intestinal bacteria would be associated with systemic biomarkers of innate and adaptive immune responses in healthy adults. 79 immune function markers were subjected to factor analysis resulting in 17 Immune Factors (IFs), each composed of 2–10 immune variables. Bacterial taxa from stool samples were identified at the family and genus levels by 16S rRNA amplicon sequence analysis and their read counts and relative abundances were utilized in a multiple linear regression model to identify microbial taxa associated with the IFs. A total of 10 significant associations were identified between bacterial taxa and IFs. The family
Rikenellaceae
showed a positive association with innate IF5 (including 5 chemokines, 2 cytokines, 2 adhesion molecules, and the macrophage metabolite neopterin) and a negative association with adaptive IF4 (including T-cells with activation marker HLA-DR). Additionally,
Pseudomonadaceae
and its genus
Pseudomonas
showed a negative relationship with innate IF5, and adaptive IF13 (including T-cell cytokines IL-10, IL-17, and IFN-γ) was negatively associated with
Butyrivibrio
and positively associated with
Slackia
. These associations suggest ongoing interactions between gut bacteria and the systemic immune system in healthy adults. The association of these taxa with the IFs may result from specific microbial-immune system interactions that play a role in maintenance of a healthy barrier integrity in our cohort of healthy adults.

IMPORTANCE
Chronic inflammation may develop over time in healthy adults as a result of a variety of factors, such as poor diet directly affecting the composition of the intestinal microbiome, or by causing obesity, which may also affect the intestinal microbiome. These effects may trigger the activation of an immune response that could eventually lead to an inflammation-related disease, such as colon cancer. Before disease develops it may be possible to identify subclinical inflammation or immune activation attributable to specific intestinal bacteria normally found in the gut that could result in future adverse health impacts. In the present study, we examined a group of healthy men and women across a wide age range with and without obesity to determine which bacteria were associated with particular types of immune activation to identify potential preclinical markers of inflammatory disease risk. Several associations were found that may help develop dietary interventions to lower disease risk.