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Article ; Online: Bacteriophages: Status quo and emerging trends toward one health approach.

Samson, Rachel / Dharne, Mahesh / Khairnar, Krishna

2023 Volume 908, Page(s) 168461

Abstract: The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, ... ...

Abstract	The alarming rise in antimicrobial resistance (AMR) among the drug-resistant pathogens has been attributed to the ESKAPEE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumanii, Pseudomonas aeruginosa, Enterobacter sp., and Escherichia coli). Recently, these AMR microbes have become difficult to treat, as they have rendered the existing therapeutics ineffective. Thus, there is an urgent need for effective alternatives to lessen or eliminate the current infections and limit the spread of emerging diseases under the "One Health" framework. Bacteriophages (phages) are naturally occurring biological resources with extraordinary potential for biomedical, agriculture/food safety, environmental protection, and energy production. Specific unique properties of phages, such as their bactericidal activity, host specificity, potency, and biocompatibility, make them desirable candidates in therapeutics. The recent biotechnological advancement has broadened the repertoire of phage applications in nanoscience, material science, physical chemistry, and soft-matter research. Herein, we present a comprehensive review, coupling the substantial aspects of phages with their applicability status and emerging opportunities in several interdependent areas under one health concept. Consolidating the recent state-of-the-art studies that integrate human, animal, plant, and environment health, the following points have been highlighted: (i) The biomedical and pharmacological advantages of phages and their antimicrobial derivatives with particular emphasis on in-vivo and clinical studies. (ii) The remarkable potential of phages to be altered, improved, and applied for drug delivery, biosensors, biomedical imaging, tissue engineering, energy, and catalysis. (iii) Resurgence of phages in biocontrol of plant, food, and animal-borne pathogens. (iv) Commercialization of phage-based products, current challenges, and perspectives.
MeSH term(s)	Animals ; Humans ; One Health ; Bacteriophages ; Staphylococcal Infections ; Klebsiella pneumoniae ; Escherichia coli ; Anti-Infective Agents ; Anti-Bacterial Agents/pharmacology
Chemical Substances	Anti-Infective Agents ; Anti-Bacterial Agents
Language	English
Publishing date	2023-11-13
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.168461
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Article: COVID-19 associated mucormycosis: evolving technologies for early and rapid diagnosis

Samson, Rachel / Dharne, Mahesh

3 Biotech. 2022 Jan., v. 12, no. 1

2022

Abstract: The post-coronavirus disease (COVID-19) mucormycosis is a deadly addition to the pandemic spectrum. Although it’s a rare, aggressive, and opportunistic disease, the associated morbidity and mortality are significant. The complex interplay of factors ... ...

Abstract	The post-coronavirus disease (COVID-19) mucormycosis is a deadly addition to the pandemic spectrum. Although it’s a rare, aggressive, and opportunistic disease, the associated morbidity and mortality are significant. The complex interplay of factors aggravating CAM is uncontrolled diabetes, irrational and excessive use of antibiotics, steroids, and an impaired immune system. Recently, India has been witnessing a rapid surge in the cases of coronavirus disease-associated mucormycosis (CAM), since the second wave of COVID-19. The devastating and lethal implications of CAM had now become a matter of global attention. A delayed diagnosis is often associated with a poor prognosis. Therefore, the rapid and early diagnosis of infection would be life-saving. Prevention and effective management of mucormycosis depend upon its early and accurate diagnosis followed by a multimodal therapeutic approach. The current review summarizes an array of detection methods and highlights certain evolving technologies for early and rapid diagnosis of CAM. Furthermore, several potential management strategies have also been discussed, which would aid in tackling the neglected yet fatal crisis of mucormycosis associated with COVID-19.
Keywords	COVID-19 infection ; diabetes ; early diagnosis ; immune system ; morbidity ; mortality ; pandemic ; prognosis ; therapeutics ; zygomycosis ; India
Language	English
Dates of publication	2022-01
Size	p. 6.
Publishing place	Springer International Publishing
Document type	Article
Note	Review
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-021-03080-4
Database	NAL-Catalogue (AGRICOLA)

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Article: COVID-19 associated mucormycosis: evolving technologies for early and rapid diagnosis.

Samson, Rachel / Dharne, Mahesh

3 Biotech

2021 Volume 12, Issue 1, Page(s) 6

Abstract: The post-coronavirus disease (COVID-19) mucormycosis is a deadly addition to the pandemic spectrum. Although it's a rare, aggressive, and opportunistic disease, the associated morbidity and mortality are significant. The complex interplay of factors ... ...

Abstract	The post-coronavirus disease (COVID-19) mucormycosis is a deadly addition to the pandemic spectrum. Although it's a rare, aggressive, and opportunistic disease, the associated morbidity and mortality are significant. The complex interplay of factors aggravating CAM is uncontrolled diabetes, irrational and excessive use of antibiotics, steroids, and an impaired immune system. Recently, India has been witnessing a rapid surge in the cases of coronavirus disease-associated mucormycosis (CAM), since the second wave of COVID-19. The devastating and lethal implications of CAM had now become a matter of global attention. A delayed diagnosis is often associated with a poor prognosis. Therefore, the rapid and early diagnosis of infection would be life-saving. Prevention and effective management of mucormycosis depend upon its early and accurate diagnosis followed by a multimodal therapeutic approach. The current review summarizes an array of detection methods and highlights certain evolving technologies for early and rapid diagnosis of CAM. Furthermore, several potential management strategies have also been discussed, which would aid in tackling the neglected yet fatal crisis of mucormycosis associated with COVID-19.
Language	English
Publishing date	2021-12-06
Publishing country	Germany
Document type	Journal Article ; Review
ZDB-ID	2600522-0
ISSN	2190-5738 ; 2190-572X
ISSN (online)	2190-5738
ISSN	2190-572X
DOI	10.1007/s13205-021-03080-4
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Article ; Online: Capturing chromosome conformation in Crenarchaea.

Pilatowski-Herzing, Elyza / Samson, Rachel Y / Takemata, Naomichi / Badel, Catherine / Bohall, Peter B / Bell, Stephen D

Molecular microbiology

2024

Abstract: While there is a considerable body of knowledge regarding the molecular and structural biology and biochemistry of archaeal information processing machineries, far less is known about the nature of the substrate for these machineries-the archaeal ... ...

Abstract	While there is a considerable body of knowledge regarding the molecular and structural biology and biochemistry of archaeal information processing machineries, far less is known about the nature of the substrate for these machineries-the archaeal nucleoid. In this article, we will describe recent advances in our understanding of the three-dimensional organization of the chromosomes of model organisms in the crenarchaeal phylum.
Language	English
Publishing date	2024-02-25
Publishing country	England
Document type	Journal Article
ZDB-ID	619315-8
ISSN	1365-2958 ; 0950-382X
ISSN (online)	1365-2958
ISSN	0950-382X
DOI	10.1111/mmi.15245
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Article ; Online: Chromosome organization affects genome evolution in Sulfolobus archaea.

Badel, Catherine / Samson, Rachel Y / Bell, Stephen D

Nature microbiology

2022 Volume 7, Issue 6, Page(s) 820–830

Abstract: In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this ... ...

Abstract	In all organisms, the DNA sequence and the structural organization of chromosomes affect gene expression. The extremely thermophilic crenarchaeon Sulfolobus has one circular chromosome with three origins of replication. We previously revealed that this chromosome has defined A and B compartments that have high and low gene expression, respectively. As well as higher levels of gene expression, the A compartment contains the origins of replication. To evaluate the impact of three-dimensional organization on genome evolution, we characterized the effect of replication origins and compartmentalization on primary sequence evolution in eleven Sulfolobus species. Using single-nucleotide polymorphism analyses, we found that distance from an origin of replication was associated with increased mutation rates in the B but not in the A compartment. The enhanced polymorphisms distal to replication origins suggest that replication termination may have a causal role in their generation. Further mutational analyses revealed that the sequences in the A compartment are less likely to be mutated, and that there is stronger purifying selection than in the B compartment. Finally, we applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) to show that the B compartment is less accessible than the A compartment. Taken together, our data suggest that compartmentalization of chromosomal DNA can influence chromosome evolution in Sulfolobus. We propose that the A compartment serves as a haven for stable maintenance of gene sequences, while sequences in the B compartment can be diversified.
MeSH term(s)	Archaea/genetics ; Chromosomes ; Evolution, Molecular ; Replication Origin ; Sulfolobus/genetics
Language	English
Publishing date	2022-05-26
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	2058-5276
ISSN (online)	2058-5276
DOI	10.1038/s41564-022-01127-7
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Article: Reply to van der Pluijm et al. Comment on "Weitzman et al. Resistance to Antimalarial Monotherapy Is Cyclic.

Calfon-Peretz, Ortal / Weitzman, Rachel / Amitay, Moshe / Samson, Abraham O

Journal of clinical medicine

2022 Volume 11, Issue 11

Abstract: Thank you for the opportunity to respond to comments gracefully raised by van der Pluijm et al. [ ... ]. ...

Abstract	Thank you for the opportunity to respond to comments gracefully raised by van der Pluijm et al. [...].
Language	English
Publishing date	2022-05-25
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm11112972
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Article ; Online: Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India

Samson, Rachel / Rajput, Vinay / Yadav, Rakeshkumar / Shah, Manan / Dastager, Syed / Khairnar, Krishna / Dharne, Mahesh

Science of the Total Environment. 2023, p.162125-

2023 , Page(s) 162125–

Abstract: Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated ... ...

Abstract	Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.
Keywords	Burkholderia ; Pseudomonas ; anthropogenic activities ; antibiotic resistance genes ; bacteriophages ; community structure ; copper ; cross infection ; environment ; fosmidomycin ; metagenomics ; metal tolerance ; microbial communities ; microbiome ; multiple drug resistance ; nanopores ; riparian areas ; rivers ; tetracycline ; zinc ; Ganges River ; India ; River Ganges ; Antibiotics (ARGs) ; Heavy metals (MRGs)
Language	English
Publishing place	Elsevier B.V.
Document type	Article ; Online
Note	Pre-press version
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.162125
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India.

Samson, Rachel / Rajput, Vinay / Yadav, Rakeshkumar / Shah, Manan / Dastager, Syed / Khairnar, Krishna / Dharne, Mahesh

The Science of the total environment

2023 Volume 872, Page(s) 162125

Abstract	Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.
MeSH term(s)	Genes, Bacterial ; Rivers/chemistry ; Bacteria/genetics ; Microbiota ; India ; Metals ; Anti-Bacterial Agents
Chemical Substances	Metals ; Anti-Bacterial Agents
Language	English
Publishing date	2023-02-10
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2023.162125
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Article ; Online: Reply to van der Pluijm et al. Comment on “Weitzman et al. Resistance to Antimalarial Monotherapy Is Cyclic. J. Clin. Med. 2022, 11 , 781”

Ortal Calfon-Peretz / Rachel Weitzman / Moshe Amitay / Abraham O. Samson

Journal of Clinical Medicine, Vol 11, Iss 2972, p

2022 Volume 2972

Abstract: Thank you for the opportunity to respond to comments gracefully raised by van der Pluijm et al. [.] ...

Abstract	Thank you for the opportunity to respond to comments gracefully raised by van der Pluijm et al. [.]
Keywords	n/a ; Medicine ; R
Language	English
Publishing date	2022-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction: "We know about schistosomiasis but we know nothing about FGS": A qualitative assessment of knowledge gaps about female genital schistosomiasis among communities living in Schistosoma haematobium endemic districts of Zanzibar and Northwestern Tanzania.

Mazigo, Humphrey D / Samson, Anna / Lambert, Valencia J / Kosia, Agnes L / Ngoma, Deogratias D / Murphy, Rachel / Matungwa, Dunstan J

PLoS neglected tropical diseases

2023 Volume 17, Issue 1, Page(s) e0011099

Abstract: This corrects the article DOI: 10.1371/journal.pntd.0009789.]. ...

Abstract	[This corrects the article DOI: 10.1371/journal.pntd.0009789.].
Language	English
Publishing date	2023-01-26
Publishing country	United States
Document type	Published Erratum
ZDB-ID	2429704-5
ISSN	1935-2735 ; 1935-2735
ISSN (online)	1935-2735
ISSN	1935-2735
DOI	10.1371/journal.pntd.0011099
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