bluuebunny/crossref_metadata_2025_split huggingface dataset:
Citrobacter
spp. and
Enterobacter
spp. as reservoirs of carbapenemase
bla
NDM
and
bla
KPC
resistance genes in hospital wastewater
Authors: Duran-Bedolla Josefina , Téllez-Sosa Juan , Bocanegra-Ibarias Paola , Schilmann Astrid , Bravo-Romero Sugey , Reyna-Flores Fernando , Villa-Reyes Tania , Barrios-Camacho Humberto 
Published: July 2024

ABSTRACT

Antibiotic resistance has emerged as a global threat to public health, generating a growing interest in investigating the presence of antibiotic-resistant bacteria in environments influenced by anthropogenic activities. Wastewater treatment plants in hospital serve as significant reservoirs of antimicrobial-resistant bacteria, where a favorable environment is established, promoting the proliferation and transfer of resistance genes among different bacterial species. In our study, we isolated a total of 243 strains from 5 hospital wastewater sites in Mexico, belonging to 21 distinct Gram-negative bacterial species. The presence of β-lactamase was detected in 46.9% (114/243) of the isolates, which belonging to the
Enterobacteriaceae
family. We identified a total of 169 β-lactamase genes;
bla
TEM
in 33.1%,
bla
CTX-M
in 25.4%,
bla
KPC
in 25.4%,
bla
NDM
8.8%,
bla
SHV
in 5.3%, and
bla
OXA-48
in 1.1% distributed in 12 different bacteria species. Among the 114 of the isolates, 50.8% were found to harbor at least one carbapenemase and were discharged into the environment. The carbapenemase
bla
KPC
was found in six
Citrobacter
spp. and
E. coli
, while
bla
NDM
was detected in two distinct
Enterobacter
spp. and
E. coli
. Notably,
bla
NDM-1
was identified in a 110 Kb IncFII conjugative plasmid in
E. cloacae
,
E. xiangfangensis,
and
E. coli
within the same hospital wastewater. In conclusion, hospital wastewater showed the presence of
Enterobacteriaceae
carrying a high frequency of carbapenemase
bla
KPC
and
bla
NDM
. We propose that hospital wastewater serves as reservoirs for resistance mechanism within bacterial communities and creates an optimal environment for the exchange of this resistance mechanism among different bacterial strains.

IMPORTANCE

The significance of this study lies in its findings regarding the prevalence and diversity of antibiotic-resistant bacteria and genes identified in hospital wastewater in Mexico. The research underscores the urgent need for enhanced surveillance and prevention strategies to tackle the escalating challenge of antibiotic resistance, particularly evident through the elevated frequencies of carbapenemase genes such as
bla
KPC
and
bla
NDM
within the
Enterobacteriaceae
family. Moreover, the identification of these resistance genes on conjugative plasmids highlights the potential for widespread transmission via horizontal gene transfer. Understanding the mechanisms of antibiotic resistance in hospital wastewater is crucial for developing targeted interventions aimed at reducing transmission, thereby safeguarding public health and preserving the efficacy of antimicrobial therapies.
Highly sensitive wastewater surveillance of SARS-CoV-2 variants by targeted next-generation amplicon sequencing provides early warning of incursion in Victoria, Australia
Authors: Merrett James E. , Nolan Monica , Hartman Leon , John Nijoy , Flynn Brianna , Baker Louise , Schang Christelle , McCarthy David , Lister David , Cheng Ngai Ning , Crosbie Nick , Poon Rachael , Jex Aaron 
Published: July 2024

ABSTRACT

The future of the COVID pandemic and its public health and societal impact will be determined by the profile and spread of emerging variants and the timely identification and response to them. Wastewater surveillance of SARS-CoV-2 has been widely adopted in many countries across the globe and has played an important role in tracking infection levels and providing useful epidemiological information that cannot be adequately captured by clinical testing alone. However, novel variants can emerge rapidly, spread globally, and markedly alter the trajectory of the pandemic, as exemplified by the Delta and Omicron variants. Most mutations linked to the emergence of new SARS-CoV-2 variants are found within variable regions of the SARS-CoV-2 Spike protein. We have developed a duplex hemi-nested PCR method that, coupled with short amplicon sequencing, allows simultaneous typing of two of the most highly variable and informative regions of the Spike gene: the N-terminal domain and the receptor binding motif. Using this method in an operationalized public health program, we identified the first known incursion of Omicron BA.1 into Victoria, Australia and demonstrated how sensitive amplicon sequencing methods can be combined with wastewater surveillance as a relatively low-cost solution for early warning of variant incursion and spread.

IMPORTANCE
This study offers a rapid, cost-effective, and sensitive approach for monitoring SARS-CoV-2 variants in wastewater. The method’s flexibility permits timely modifications, enabling the integration of emerging variants and adaptations to evolving SARS-CoV-2 genetics. Of particular significance for low- and middle-income regions with limited surveillance capabilities, this technique can potentially be utilized to study a range of pathogens or viruses that possess diverse genetic sequences, similar to influenza.
AhR ligands from
LGG
metabolites promote piglet intestinal ILC3 activation and IL-22 secretion to inhibit PEDV infection
Authors: Wang Junhong , Zhao Yibo , Cui Tong , Bao Hongyu , Gao Ming , Cheng Mingyang , Sun Yu , Lu Yiyuan , Guan Jiayao , Zhang Di , Jiang Yanlong , Huang Haibin , Shi Chunwei , Wang Jianzhong , Wang Nan , Hu Jingtao , Yang Wentao , Qian Hongxi , Jiang Qingrong , Yang Guilian , Zeng Yan , Wang Chunfeng , Cao Xin 
Published: July 2024

ABSTRACT

In maintaining organismal homeostasis, gut immunity plays a crucial role. The coordination between the microbiota and the immune system through bidirectional interactions regulates the impact of microorganisms on the host. Our research focused on understanding the relationships between substantial changes in jejunal intestinal flora and metabolites and intestinal immunity during porcine epidemic diarrhea virus (PEDV) infection in piglets. We discovered that
Lactobacillus rhamnosus GG
(
LGG
) could effectively prevent PEDV infection in piglets. Further investigation revealed that
LGG
metabolites interact with type 3 innate lymphoid cells (ILC3s) in the jejunum of piglets through the aryl hydrocarbon receptor (AhR). This interaction promotes the activation of ILC3s and the production of interleukin-22 (IL-22). Subsequently, IL-22 facilitates the proliferation of IPEC-J2 cells and activates the STAT3 signaling pathway, thereby preventing PEDV infection. Moreover, the AhR receptor influences various cell types within organoids, including intestinal stem cells (ISCs), Paneth cells, and enterocytes, to promote their growth and development, suggesting that AhR has a broad impact on intestinal health. In conclusion, our study demonstrated the ability of
LGG
to modulate intestinal immunity and effectively prevent PEDV infection in piglets. These findings highlight the potential application of
LGG
as a preventive measure against viral infections in livestock.

IMPORTANCE

We observed high expression of the AhR receptor on pig and human ILC3s, although its expression was negligible in mouse ILC3s. ILC3s are closely related to the gut microbiota, particularly the secretion of IL-22 stimulated by microbial signals, which plays a crucial regulatory role in intestinal immunity. In our study, we found that metabolites produced by beneficial gut bacteria interact with ILC3s through AhR, thereby maintaining intestinal immune homeostasis in pigs. Moreover,
LGG
feeding can enhance the activation of ILC3s and promote IL-22 secretion in the intestines of piglets, ultimately preventing PEDV infection.
Delayed treatment of cynomolgus macaques with a FVM04/CA45 monoclonal antibody cocktail provides complete protection against lethal Sudan virus infection
Authors: Chan Mable , Warner Bryce M. , Audet Jonathan , Barker Douglas , Tailor Nikesh , Vendramelli Robert , Truong Thang , Tierney Kevin , Boese Amrit S. , Qiu Honguy , Holtsberg Frederick W. , Aman Javad , Kodihalli Shantha , Kobasa Darwyn 
Published: July 2024

ABSTRACT

Sudan ebolavirus (SUDV) is a member of the genus
Ebolavirus
(Family
Filoviridae
) and has caused sporadic outbreaks of Ebola disease (EBOD), or more specifically Sudan virus disease (SVD), with high mortality rates in Africa. Current vaccines and therapies that have been developed for filoviruses are almost all specific for Ebola virus (EBOV; of the species
Zaire ebolavirus
), and there is a current lack of therapeutics specific for SUDV. The recent SUDV outbreak in Uganda, which was distributed across multiple districts, including Kampala, a densely populated urban center, highlights the critical need for the development of novel SUDV-specific or pan-Ebola virus therapeutics. Previous work has characterized two monoclonal antibodies, FVM04 and CA45, which have neutralization capabilities against both EBOV and SUDV and have shown protective efficacy in animal challenge studies. Here, we expand upon this work, showing that treatment with a monoclonal antibody cocktail consisting of FVM04 and CA45 provides full protection against lethal SUDV infection in cynomolgus macaques. Studies that evaluate outcomes at late time points after infection, once clinical signs of illness are apparent, are vital for assessing the therapeutic efficacy of antibody therapeutics. We have shown that when treatment is initiated as late as 5 days after infection, with a second dose given on day 8, that treated groups showed few clinical signs or morbidity, with complete survival. This work provides further evidence that FVM04 and CA45 have strong therapeutic potential against SUDV and their development as a pan-Ebola virus therapeutic should be pursued.

IMPORTANCE
There are currently no approved vaccines or therapeutics for Sudan virus, a filovirus which is highly related to Ebola virus and causes similar disease and outbreaks. In this study, a cocktail of two potent monoclonal antibodies that effectively neutralize Sudan virus was tested in a nonhuman primate model of Sudan virus disease. Treatment was highly effective, even when initiated as late as 5 days after infection, when clinical signs of infection were already evident. All treated animals showed complete recovery from infection, with little evidence of disease, while all animals that received a control treatment succumbed to infection within 8 days. The study further demonstrated the strong therapeutic potential of the antibody treatment and supported further development for use in Sudan virus outbreaks.
Comparative genomics and stable isotope analysis reveal the saprotrophic-pathogenic lifestyle of a neotropical fungus
Authors: Ribeiro Tomé Luiz Marcelo , Quintanilha-Peixoto Gabriel , Costa-Rezende Diogo Henrique , Salvador-Montoya Carlos A. , Cardoso Domingos , S. Araújo Daniel , Freitas Jorge Marcelo , Bielefeld Nardoto Gabriela , Alves-Silva Genivaldo , Drechsler-Santos Elisandro Ricardo , Góes-Neto Aristóteles 
Published: July 2024

ABSTRACT

In terrestrial forested ecosystems, fungi may interact with trees in at least three distinct ways: (i) associated with roots as symbionts; (ii) as pathogens in roots, trunks, leaves, flowers, and fruits; or (iii) decomposing dead tree tissues on soil or even on dead tissues in living trees. Distinguishing the latter two nutrition modes is rather difficult in Hymenochaetaceae (Basidiomycota) species. Herein, we have used an integrative approach of comparative genomics, stable isotopes, host tree association, and bioclimatic data to investigate the lifestyle ecology of the scarcely known neotropical genus
Phellinotus
, focusing on the unique species
Phellinotus piptadeniae
. This species is strongly associated with living
Piptadenia gonoacantha
(Fabaceae) trees in the Atlantic Forest domain on a relatively high precipitation gradient. Phylogenomics resolved
P. piptadeniae
in a clade that also includes both plant pathogens and typical wood saprotrophs. Furthermore, both genome-predicted Carbohydrate-Active Enzymes (CAZy) and stable isotopes (δ
13
C and δ
15
N) revealed a rather flexible lifestyle for the species. Altogether, our findings suggest that
P. piptadeniae
has been undergoing a pathotrophic specialization in a particular tree species while maintaining all the metabolic repertoire of a wood saprothroph.

IMPORTANCE

This is the first genomic description for
Phellinotus piptadeniae
. This basidiomycete is found across a broad range of climates and ecosystems in South America, including regions threatened by extensive agriculture. This fungus is also relevant considering its pathotrophic-saprotrophic association with
Piptadenia goanocantha
, which we began to understand with these new results that locate this species among biotrophic and necrotrophic fungi.
Complete genome sequence of
Lactococcus garvieae
isolated from a greater amberjack (
Seriola dumerili
) farmed in Japan in 2022
Authors: Salif Maiga , Ogawa Riku , Mikami Aguri , Daibata Masanori , Imajoh Masayuki 
Published: July 2024

ABSTRACT

The complete genome sequence of
Lactococcus garvieae
KN22525, isolated in May 2022 from a diseased greater amberjack (
Seriola dumerili
) with a gross indication of body surface redness in Nomi Bay, Japan, was determined. Multilocus sequencing typing revealed that KN22525’s genotype was sequence type ST95.
Draft genome sequences for a
Staphylococcus aureus
and a
Staphylococcus haemolyticus
isolate from nasal swab samples from healthy females
Authors: Jablonska Sandra , Brown Hannah , Appleberry Helen , Putonti Catherine , Kula Alex 
Published: July 2024

ABSTRACT

Staphylococcus aureus
and
Staphylococcus haemolyticus
are common members of the human microbiota, but they are also opportunistic pathogens. To identify antibiotic resistance in healthy individuals, we present the genome sequences of
S. aureus
139 N-1 and
S. haemolyticus
173 N-3, both isolated from nasal swab samples from asymptomatic female participants.
Genome sequences of four bacterial strains isolated from organofluorine enrichment cultures
Authors: Goff Jennifer L. , Hahn Chris , Ingrassia Rebecca A. , Tiyapun Chanistha , Waldschmidt Gray G. , Smith Emma R. , Marini Miranda N. , Shevchenko Olga , Maresca Julia A. 
Published: July 2024

ABSTRACT

Because fluorinated organic compounds are broadly used and highly persistent, microbes isolated from wastewater may be able to degrade these contaminants. Here, we report the genome sequences of
Flavobacterium
sp. str. WV_118_3,
Nocardioides
sp. str. WV_118_6,
Ochrobactrum anthropi
str. WV_118_8, and
Sphingomonas
sp. str. VL_57B, isolated from wastewater.
Evolution and strain diversity advance exploration of
Candida albicans
biology
Authors: Anderson Matthew Z. , Dietz Siobhan M. 
Published: July 2024

ABSTRACT

Fungi were some of the earliest organismal systems used to explore mutational processes and its phenotypic consequences on members of a species. Yeasts that cause significant human disease were quickly incorporated into these investigations to define the genetic and phenotypic drivers of virulence. Among
Candida
species,
Candida albicans
has emerged as a model for studying genomic processes of evolution because of its clinical relevance, relatively small genome, and ability to tolerate complex chromosomal changes. Here, we describe major recent findings that used evolution of strains from defined genetic backgrounds to delineate mutational and adaptative processes and include how nascent exploration into naturally occurring variation is contributing to these conceptual frameworks. Ultimately, efforts to discern adaptive mechanisms used by
C. albicans
will continue to divulge new biology and can better inform treatment regimens for the increasing prevalence of fungal disease.
A newly identified IncY plasmid from multi-drug-resistant
Escherichia coli
isolated from dairy cattle feces in Poland
Authors: Zalewska Magdalena , Błażejewska Aleksandra , Gawor Jan , Adamska Dorota , Goryca Krzysztof , Szeląg Michał , Kalinowski Patryk , Popowska Magdalena 
Published: July 2024

ABSTRACT

Comprehensive whole-genome sequencing was performed on two multi-drug-resistant
Escherichia coli
strains isolated from cattle manure from a typical dairy farm in Poland in 2020. The identified strains are resistant to beta-lactams, aminoglycosides, tetracyclines, trimethoprim/sulfamethoxazole, and fluoroquinolones. The complete sequences of the harbored plasmids revealed antibiotic-resistance genes located within many mobile genetic elements (e.g., insertional sequences or transposons) and genes facilitating conjugal transfer or promoting horizontal gene transfer. These plasmids are hitherto undescribed. Similar plasmids have been identified, but not in Poland. The identified plasmids carried resistance genes, including the tetracycline resistance gene
tet(A
), aph family aminoglycoside resistance genes
aph(3
″)
-lb
and
aph (6)-ld
, beta-lactam resistance genes
bla
TEM-1
and

bla
CTX-M-15

, sulfonamide resistance gene
sul2
, fluoroquinolone resistance gene
qnrS1
, and the trimethoprim resistance gene
dfrA14
. The characterized resistance plasmids were categorized into the IncY incompatibility group, indicating a high possibility for dissemination among the
Enterobacteriaceae
. While similar plasmids (99% identity) have been found in environmental and clinical samples, none have been identified in farm animals. These findings are significant within the One Health framework, as they underline the potential for antimicrobial-resistant
E. coli
from livestock and food sources to be transmitted to humans and
vice versa
. It highlights the need for careful monitoring and strategies to limit the spread of antibiotic resistance in the One Health approach.

IMPORTANCE

This study reveals the identification of new strains of antibiotic-resistant
Escherichia coli
in cattle manure from a dairy farm in Poland, offering critical insights into the spread of drug resistance. Through whole-genome sequencing, researchers discovered novel plasmids within these bacteria, which carry genes resistant to multiple antibiotics. These findings are particularly alarming, as these plasmids can transfer between different bacterial species, potentially escalating the spread of antibiotic resistance. This research underscores the vital connection between the health of humans, animals, and the environment, emphasizing the concept of One Health. It points to the critical need for global vigilance and strategies to curb the proliferation of antibiotic resistance. By showcasing the presence of these strains and their advanced resistance mechanisms, the study calls for enhanced surveillance and preventive actions in both agricultural practices and healthcare settings to address the imminent challenge of antibiotic-resistant bacteria.
Linking LRP12 CGG repeat expansion to inherited peripheral neuropathy
Authors: Hobara Takahiro , Ando Masahiro , Higuchi Yujiro , Yuan Jun-Hui , Yoshimura Akiko , Kojima Fumikazu , Noguchi Yutaka , Takei Jun , Hiramatsu Yu , Nozuma Satoshi , Nakamura Tomonori , Adachi Tadashi , Toyooka Keiko , Yamashita Toru , Sakiyama Yusuke , Hashiguchi Akihiro , Matsuura Eiji , Okamoto Yuji , Takashima Hiroshi 
Published: July 2024

BackgroundThe causative genes for over 60% of inherited peripheral neuropathy (IPN) remain unidentified. This study endeavours to enhance the genetic diagnostic rate in IPN cases by conducting screenings focused on non-coding repeat expansions.MethodsWe gathered data from 2424 unrelated Japanese patients diagnosed with IPN, among whom 1555 cases with unidentified genetic causes, as determined through comprehensive prescreening analyses, were selected for the study. Screening for CGG non-coding repeat expansions inLRP12,GIPC1andRILPL1genes was conducted using PCR and long-read sequencing technologies.ResultsWe identified CGG repeat expansions inLRP12from 44 cases, establishing it as the fourth most common aetiology in Japanese IPN. Most cases (29/37) exhibited distal limb weakness, without ptosis, ophthalmoplegia, facial muscle weakness or bulbar palsy. Neurogenic changes were frequently observed in both needle electromyography (97%) and skeletal muscle tissue (100%). In nerve conduction studies, 28 cases primarily showed impairment in motor nerves without concurrent involvement of sensory nerves, consistent with the phenotype of hereditary motor neuropathy. In seven cases, both motor and sensory nerves were affected, resembling the Charcot-Marie-Tooth (CMT) phenotype. Importantly, the mean CGG repeat number detected in the present patients was significantly shorter than that of patients withLRP12-oculopharyngodistal myopathy (p<0.0001). Additionally,GIPC1andRILPL1repeat expansions were absent in our IPN cases.ConclusionWe initially elucidateLRP12repeat expansions as a prevalent cause of CMT, highlighting the necessity for an adapted screening strategy in clinical practice, particularly when addressing patients with IPN.
Development and validity testing of the Canadian Food Scoring System (CFSS), a nutrient profile model based on the recommendations of Canada’s Food Guide 2019
Authors: Lee Jennifer J. , Mulligan Christine , L'Abbé Mary 
Published: July 2024

Canada’s food guide (CFG) 2019 provides dietary guidance for all Canadians; however, there is no tool available to help Canadians easily determine how individual foods align with CFG. Therefore, the objectives of this study were (1) to develop a nutrient profile model, Canadian Food Scoring System (CFSS), to rank the healthfulness of individual foods according to the recommendations of CFG; and (2) to assess its validity. The CFSS was developed based on CFG, leveraging existing Canadian labelling regulations to set quantitative criteria for the CFG recommendations. The CFSS included three main steps: (1) classifying foods into the nutritious food categories and assigning points based on the alignment with the recommendations of CFG; (2) deducting points based on the levels of saturated fat, sugars, and sodium using thresholds from Canadian front-of-pack labelling regulations; and (3) calculating the final score from the first two steps to classify foods into one of five categories: “very poor,” “poor,” “fair,” “good,” or “excellent” choice. Convergent validity was assessed by examining the alignment of the CFSS with Health Canada’s CFG-Food Classification System using a national food composition database and the Healthy Eating Food Index-2019 using nationally representative dietary intake survey data. The CFSS showed strong correlation with the CFG-Food Classification System (ρ = 0.782, p < 0.001) and moderate correlation with the Healthy Eating Food Index-2019 ( r = 0.636, p < 0.001), indicating good convergent validity both at the food and dietary level. The newly developed CFSS can assess the alignment of individual foods with CFG, which can be used to help Canadians more easily make healthy food choices.