Tag Archives: Frequency

Microbiology

Study identifies key genetic mechanism of drug resistance in the deadliest malaria parasites

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Reviewed by Emily Henderson, B.Sc.May 11 2023

An important genetic mechanism of drug resistance in one of the deadliest human malaria parasites has been identified in a new study published in Nature Microbiology.

A second key gene, pfaat1, responsible for encoding a protein that transports amino acids in the membrane of Plasmodium falciparum, is involved in its resistance to the major anti-malaria drug, chloroquine.

The findings may have implications for the ongoing battle against malaria, which infects an estimated 247 million people worldwide and kills more than 619,000 each year, most of which are young children.

Chloroquine is a major antimalaria drug, however in recent years, resistance has emerged in malaria parasites, first spreading through Southeast Asia and then through Africa in the 1970s and 1980s. Although alternative antimalarial drugs have been developed, resistance to chloroquine remains a big challenge.

Since its discovery in 2000, only one gene has been believed to have been responsible for resistance to chloroquine – the resistance transporter pfcrt which helps the malaria parasite transport the drug out of a key region in their cells, subsequently rendering it ineffective.

In this study, researchers from the Medical Research Council (MRC) Unit The Gambia at the London School of Hygiene & Tropical Medicine (LSHTM) analysed more than 600 genomes of P. falciparum that were collected in The Gambia over a period of 30 years. The team found that mutant variants of  a second gene, pfaat1, which encodes an amino acid transporter, increased in frequency from undetectable to very high levels between 1984 and 2014. Importantly, their genome-wide population analyses also indicated long term co-selection on this gene alongside the previously-known resistance gene pfcrt.

In the laboratory, a further team of researchers including from Texas Biomed, University of Notre Dame and Seattle Children’s Research Institute found that replacing these mutations in parasite genomes using CRISPR gene-editing technology impacted drug resistance. A team from Nottingham University also found that these mutations could impact the function of pfaat1 in yeast, resulting in drug resistance.

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Complementary analysis of malaria genome datasets additionally suggested that parasites from Africa and Asia may carry different mutations in pfaat1 which could help explain differences in the evolution of drug resistance across these continents.

Alfred Amambua-Ngwa, Professor of Genetic Epidemiology at MRC Unit The Gambia at LSHTM said: “This is a very clear example of natural selection in action – these mutations were preferred and passed on with extremely high frequency in a very short amount of time, suggesting they provide a significant survival advantage.

“The mutations in pfaat1 very closely mirror the increase of pfcrt mutations. This, and other genetic analyses in the paper demonstrate that the transporter AAT1 has a major role in chloroquine resistance.”

Grappling with drug resistance, for malaria and other pathogens, requires taking a holistic approach to both drug development and pathogen surveillance. We must be aware that different genes and molecules will be working together to survive treatments. That is why looking at whole genomes and whole populations is so critical.”

David Conway, Professor of Biology, LSHTM

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Source:

London School of Hygiene & Tropical Medicine (LSHTM)

Journal reference:

Amambua-Ngwa, A., et al. (2023). Chloroquine resistance evolution in Plasmodium falciparum is mediated by the putative amino acid transporter AAT1. Nature Microbiology. doi.org/10.1038/s41564-023-01377-z.

Microbiology

Epigenome reprogramming after SARS-CoV-2 infection

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Neha MathurBy Neha MathurMar 27 2023Reviewed by Lily Ramsey, LLM

In a recent article in published in the journal Nature Microbiology, researchers in Texas, United States (US) performed a three-dimensional (3D) evaluation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected human cells to show a direct cell-autonomous effect elicited by SARS-CoV-2 on the host chromatin.

The study aimed at improving the understanding of coronavirus disease 2019 (COVID-19)-related perturbations in the genome and epigenome of a host cell.

Study: SARS-CoV-2 restructures host chromatin architecture. Image Credit:FUNFUNPHOTO/Shutterstock.com

Study: SARS-CoV-2 restructures host chromatin architecture. Image Credit:FUNFUNPHOTO/Shutterstock.com

Background

The 3D folding of chromatin in mammals, including humans, influences deoxyribonucleic acid (DNA) replication, recombination, DNA damage repair, and transcription. It is a key determinant of how human cells act and function. Viruses, including SARS-CoV-2, antagonize host defense by rewiring their chromatin architecture, which typically has several layers, e.g., A/B compartments, chromatin loops, and topological associating domains (TADs).

The A and B compartments superimpose transcriptionally active euchromatin and relatively inactive heterochromatin, respectively. However, studies have barely investigated these effects.

In addition, epigenetic alterations impact gene expression and resulting phenotypes in the long term. Thus, a sneak peek into the interactions between the virus, host chromatin, and epigenome could help find novel methods to fight SARS-CoV-2 in the acute phase. In addition, it could unravel the molecular basis of post-acute SARS-CoV-2 sequelae or long COVID and subsequently mitigate it.

About the study

At 24 hours post-infection (24 hpi), human A549 cells expressing angiotensin-converting enzyme 2 (ACE2), infected with SARS-CoV-2 at a multiplicity of infection (MOI) of 0.1, had high levels of infection. This was shown by ribonucleic acid-sequencing (RNA-seq). Immunofluorescence of the SARS-CoV-2 spike (S) glycoprotein also substantiated an elevated infection ratio.

So, in the present study, researchers used an improved version of in situ Hi-C high-throughput chromosome conformation capture (Hi-C) 3.0 to study host chromatin changes in these cells at 24 hpi and mock-infected cells (Mock).

In addition, the team evaluated the epigenetic features of the altered chromatin regions to understand the vulnerability to compartmental changes due to infection. To this end, they used chromatin immunoprecipitation (ChIP-seq) methods to generate data on representative histone markers and polymerase II (Pol2) in A549-ACE2 cells. This analysis covered four histone markers, viz., H3K27ac, H3K4me3, H3K9me3, and H3K27me3.

It helped them examine the epigenetic features of these six categories of bins. They ranked E1-score changes for each genomic bin to sort bins. They dubbed bins showing E1-score increase and decrease as ‘A-ing’ and ‘B-ing’ bins, respectively.

Results

The Hi-C analysis showed extensive alterations in the hosts’ 3D genome after SARS-CoV-2 infection. The researchers also plotted a Pearson correlation map of their Hi-C analysis that reaffirmed these changes alongside indicating modified chromatin compartmentalization.

A focused view of the ~0.7 Mb region showed a weakening of the rectangle-shaped chromatin domains and deregulation of chromatin loops. While SARS-CoV-2 prompted a global decline in near-diagonal short-range chromatin contacts (<560 kilobases), as seen in a P(s) curve, chromatin contacts far-separated from the diagonal (>28 megabases) were often deregulated.

Further, a P(s) curve showed that SARS-CoV-2 elicited modest and enhanced interactions in middle-to-long-distance contacts (~560 kb to 8.9 Mb) and far-positioned regions, respectively.

Fold changes in inter-chromosomal interactions or trans-vs-cis contact ratios also depicted the effect of SARS-CoV-2 infection on inter-chromosomal contacts. The enhancement of inter- and intra-chromosomal interactions indicated changes in chromatin compartmentalization. Consequently, principal component analysis (PCA) of a 100-kb bin on Hi-C background showed noticeable defects of chromatin compartmentalization in virus-infected cells.

The total PCA E1 scores quantifying E1 changes in ~30% of genomic regions showed a widespread diminishing of the A compartment, A-to-B switching, or strengthening of the B compartment post-SARS-CoV-2 infection.

Among all, A to weaker A changes were the most common and occurred in ~18% of the genome, which indicated that SARS-CoV-2 extensively weakened the host euchromatin.

Further analysis showed that the ‘B-ing’ and ‘A-ing’ genomic regions were historically enriched in active chromatin markers (e.g., H3K27ac) and repressive histone markers, especially H3K27me3. Unexpectedly, SARS-CoV-2 infection selectively modified the H3K4me3 marker of phytochrome interacting factors (PIF) gene promoters, suggesting unappreciated mechanisms at these promoters that confer deviating inflammation in COVID-19.

A flawed chromatin compartmentalization likely caused the historically well-partitioned A or B compartments to lose their identity. A saddle plot illustrating inter-compartment chromatin interactions across the genome showed these global changes.

The authors also noted weakened compartmentalization between chromosomes. For instance, in chromosomes 17 & 18, while A–B interactions were amplified, A–A/B–B homotypic interactions appeared to have become compromised.

Moreover, SARS-CoV-2 infection mechanistically depleted the cohesin complex in a pervasive but selective manner from intra-TAD regions. These changes provided a molecular explanation for the weakening of intra-TAD interactions.

It supported the notion that defective cohesin loop extrusion inside TADs releases this chromatin to engage in long-distance associations. Intriguingly, chromatin in SARS-CoV-2-infected cells exhibited a higher frequency of long-distance intra-chromosomal and inter-chromosomal interactions.

Conclusions

SARS-CoV-2 infection markedly restructured 3D host chromatin, featuring widespread compartment A weakening and A–B mixing and global reduction in intra-TAD chromatin contacts.

However, it is still unknown exactly how SARS-COV-2 infection restructures host chromatin. Likely, open reading frame 8 (ORF8) disrupts the host epigenome, suggesting that some viral factors are involved in host chromatin rewiring.

It also altered the host epigenome, including a global reduction in active chromatin mark H3K27ac and a specific increase in H3K4me3 at pro-inflammatory gene promoters. Intriguingly, all these host chromatin alterations were unique to SARS-CoV-2 infection, and other common-cold coronaviruses or immune stimuli did not elicit these changes.

Journal reference:
Microbiology

New study focuses on genetic diversity of E. coli bacteria in hospitalized patients

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Reviewed by Emily Henderson, B.Sc.Mar 13 2023

The human intestine is an environment inhabited by many bacteria and other microorganisms collectively known as the gut microbiome, gut microbiota or intestinal flora. In most people, it contributes to wellness. A healthy gut indicates a stronger immune system, improved metabolism, and a healthy brain and heart, among other functions.

Escherichia coli is one of the bacteria found in practically everyone’s gut microbiota, where it performs important functions, such as producing certain vitamins.

But there’s a vast amount of genetic diversity in the species. Some of its members are pathogenic and can cause diseases such as urinary tract infections. E. coli is the main agent of this type of infection among both healthy people and hospitalized patients or users of healthcare services.”

Tânia Gomes do Amaral, Head of the Experimental Enterobacterial Pathogenicity Laboratory (LEPE), Federal University of São Paulo’s Medical School (EPM-UNIFESP), Brazil

Amaral is first author of an article published in the journal Pathogens on the virulence of these bacteria and their resistance to antibiotics in hospitalized patients.

“Our study focused on hospitalized patients because patients who stay in hospital for a long period are more likely to undergo various procedures, such as urine catheter insertion or venous access. Although these procedures are performed to assure life support, they may facilitate the entry of bacteria into the organism and cause an infection,” Amaral explained.

She earned a PhD in microbiology from EPM-UNIFESP in 1988, conducting part of her research at New York University Medical School and the Center for Vaccine Development at the University of Maryland, Baltimore (UMB) in the United States.

The article reports the findings of a broader study led by Amaral, with 12 co-authors who are researchers and graduate students, on the virulence and drug resistance of E. coli strains associated with urinary tract infections. The study was supported by FAPESP via three projects (18/17353-7, 19/21685-8 and 17/14821-7).

The main aim of this part of the study, described in the master’s dissertation of José Francisco Santos Neto, was to evaluate the diversity and drug resistance of pathogenic E. coli strains isolated from the gut microbiota of inpatients, and to analyze the frequency of endogenous infection (caused by bacteria from the patient’s own microbiota).

The UNIFESP group first investigated the genetic diversity and drug resistance of E. coli strains isolated from the gut microbiota of hospitalized patients, sequencing these strains as well as others isolated from their urine and comparing the results in order to evaluate dissemination of the bacteria in the hospital environment.

“We also compared the genomes of these strains with those of E. coli strains isolated in different parts of the world in order to see if any globally disseminated pathogenic bacteria were present in the study sample,” said Ana Carolina de Mello Santos, a postdoctoral researcher working on the LEPE team.

Urinary tract infections proved to be endogenous for the vast majority of the patients in the study (more than 70%). The results also showed that the patients’ gut microbiota contained at least two genetically different populations of E. coli and that about 30% were colonized by non-lactose-fermenting E. coli strains, which are less common, with some of the patients studied having only such strains in their gut microbiota.

“This finding is most interesting because previous research conducted in other countries to analyze the composition of human gut microbiota didn’t investigate non-lactose-fermenting E. coli,” Santos said.

The authors also note the presence of bacteria with all the genetic markers required for classification as pathogenic and the detection of pathogenic bacteria in the gut microbiota of all patients that had not yet developed an infection. “Hospitalized patients are more susceptible to infection because by definition they are already unwell. Colonization by pathogens is the first step in the spread of hospital-acquired infections now so frequent worldwide,” Santos said.

With regard to antibiotics and other antimicrobials, the authors stress that drug resistance is also a growing global problem, and enterobacterial resistance to third-generation cephalosporins as well as colistin is critical. In all patients whose gut microbiota was colonized by drug-resistant bacteria, the same bacteria also caused endogenous urinary tract infections. In other words, the multidrug-resistant bacteria colonized the gut and traveled to the urinary tract, where they caused an infection.

“In light of these findings, early assessment of gut microbiota in hospitalized patients, at least in cases of E. coli infection, can facilitate and guide their treatment, while also identifying patients who risk progressing to extra-intestinal diseases such as urinary tract infections, which were part of the focus for our study,” Amaral said. “We don’t yet know whether the findings also apply to other bacteria found in gut microbiota, such as the genera Klebsiella, Enterobacter, Pseudomonas and others that can cause infections when they travel to extra-intestinal sites.”

These bacterial genera tend to be even more drug-resistant than E. coli, representing a major public health problem in the hospital environment. As the researchers noted, the World Health Organization (WHO) considers E. coli strains resistant to cephalosporin and colistin to be a critical global health threat. “The presence in human gut microbiota of drug-resistant bacteria associated with severe infectious disease is a matter of great concern, not least because they could spread to people outside the hospital environment,” Amaral said.

Another point raised by the study is the importance of finding out when colonization of the patient’s gut by drug-resistant virulent bacteria occurred. The authors of the article were unable to determine whether the bacteria resistant to cephalosporins and colistin colonized the patients before or after they were hospitalized.

By analyzing the genomes of the strains, however, the researchers were able to identify global risk clones that can cause severe disease and are associated with antimicrobial resistance. “One such clone found in the gut microbiota of two patients was identical to others isolated from urinary tract infections in Londrina, Paraná [a state in South Brazil], and in the United States, as well as European and Asian countries. This shows that some strains found in the study are clones generally associated with infections in all regions of the world,” Amaral said.

This type of information is important when patients are hospitalized. Knowledge of bacterial virulence and drug resistance can be used to prevent infection in parts of the organism outside the intestine and stop the bacteria from spreading to other patients in the same hospital.

Source:

São Paulo Research Foundation (FAPESP)

Journal reference:

Santos-Neto, J.F., et al. (2023) Virulence Profile, Antibiotic Resistance, and Phylogenetic Relationships among Escherichia coli Strains Isolated from the Feces and Urine of Hospitalized Patients. Pathogens. doi.org/10.3390/pathogens11121528.

Microbiology

UTHSC researchers secure $308,000 grant from Department of Defense for dementia study

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Reviewed by Emily Henderson, B.Sc.Feb 19 2023

Repeated traumatic brain injuries (TBI) in soldiers and military personnel can cause behavioral, neurological, and cognitive effects and lead to dementia. There is currently no treatment for that type of dementia, but a $308,000 grant from the United States Department of Defense aims to help researchers at the University of Tennessee Health Science Center find one.

TBI can lead to the development of frontotemporal degeneration (FTD), a progressive process marked by atrophy of the frontal and temporal lobes. FTD is one of the most common causes of dementia in people under the age of 65.

Principal investigator Mohammad Moshahid Khan, PhD, associate professor in the Department of Neurology, and co-investigator Tayebeh Pourmotabbed, PhD, professor in the Department of Microbiology, Immunology, and Biochemistry, are working on a project to find the first therapeutic intervention to prevent frontotemporal dementia or slow its progression in a mouse model linked with the condition.

The team is aiming to use a novel gene therapy called DNAzymes to target pathological tau aggregates, which cause frontotemporal dementia and its resulting cognitive impairment and progressive neuropathological symptoms. The team is examining the effective dose, frequency, and duration of treatment as well as its potential in reducing neurodegeneration and behavioral deficits in mice.

Our preliminary data suggest that DNAzyme is a novel therapeutic approach and has a great potential for preventing the accumulation of pathological tau. The results of this proposal would be foundational for future studies examining the clinical use of DNAzyme for other neurological diseases associated with traumatic brain injury and other tauopathies.”

Dr. Mohammad Moshahid Khan, PhD, associate professor in the Department of Neurology

“DNAzyme is a powerful gene therapy technique that can be used to prevent production of proteins associated with diseases, like tau protein in Alzheimer’s disease and dementia,” Dr. Pourmotabbed said. “We have used DNAzyme as a potential therapy for breast cancer, glioma, and Huntington’s disease in preclinical animal models with great success. Hopefully, with the use of DNAzyme technology, we would be able to reduce the risk of dementia after traumatic brain injury in veterans and other individuals that deal with this debilitating disease.”

Source:

University of Tennessee Health Science Center

Microbiology

Differences in gut microbiome diversity attributed to dietary patterns in children with obesity

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Dr. Chinta SidharthanBy Dr. Chinta SidharthanFeb 16 2023Reviewed by Benedette Cuffari, M.Sc.

In a recent study published in Microbiology Spectrum, researchers found that differences in the dietary patterns of children with normal weight and those who were overweight or obese contributed to variations in the gut microbiome diversity, virulence factors of gut bacteria, and metabolic function.

Study: Virulence factors of the gut microbiome are associated with BMI and metabolic blood parameters in children with obesity. Image Credit: Africa Studio / Shutterstock.com

Study: Virulence factors of the gut microbiome are associated with BMI and metabolic blood parameters in children with obesity. Image Credit: Africa Studio / Shutterstock.com

Background

A growing body of evidence indicates that gut microbiota has a significant role in various aspects of host metabolism, including digestion, harvesting of energy, and induction of low-grade inflammation. In addition, the genetic factors of the host, as well as other characteristics such as age, diet, immunity, and gender, influence the gut microbiome composition.

Research shows that bacterial diversity in the gut and the individual’s functional capacity vary between those with normal weight and obese individuals. Gut microbiome profile variations have also been linked to metabolic disorders, lipid accumulation, and inflammation.

Lipogenesis in the liver and the regulation of appetite through hormones are also associated with gut microbiome genes.

Aside from its role in adipogenesis, superoxide reduction, and the metabolism of vitamins, gut microbiota also regulates innate immunity and the systemic, low-grade inflammatory state that can contribute to fat deposition and obesity. Therefore, Dysbiosis, which is the imbalance of gut microbiota, combined with diet, likely has a significant role in the development of obesity.

About the study

In the present study, researchers conducted a cross-sectional analysis of data from 45 children between the ages of six and 12 to determine the association between gut microbiota and obesity.

Questionnaires were used to obtain information on dietary frequencies, gender, age, and body mass index (BMI). Based on the World Health Organization (WHO) z-scores, in which BMI is adjusted for gender and age, the children were classified into two categories of overweight and obese (OWOB) and normal weight (NW).

Data from food frequency questionnaires were used to classify the dietary habits of children into two nutritional patterns. To this end, Pattern 1 was characterized by complex carbohydrates and proteins, whereas Pattern 2 comprised simple carbohydrates and saturated fats.

Shotgun metagenomics was used to assess the taxonomic diversity of the gut microbiota and metabolic capacity from genomic deoxyribonucleic acid (DNA) extracted from fecal samples. Clade-specific markers were used for the taxonomic and functional assessment of the gut bacteria. Additionally, reverse Simpson and Shannon diversity indices were calculated.

The virulence factor database was used to screen for virulence factor genes, whereas multivariate linear modeling was used to determine the association between the taxa, virulence factors, and function of gut microbes and covariates of diet, serology, and anthropometric measurements.

Study findings

Significant differences between the alpha and beta diversity of the gut microbiota were observed between the children in the NW and OWOB groups, thus suggesting that specific phyla of bacteria contribute to higher levels of energy harvest.

Furthermore, species such as Ruminococcus species, Victivallis vadensis, Mitsuokella multacida, Alistipes species, Clostridium species, and Acinetobacter johnsonii were linked to healthier metabolic parameters.

In contrast, an increase in the abundance of bacteria such as Veillonellaceae, Lactococcus, Fusicatenibacter saccharivorans, Fusicatenibacter prausnitzii, Eubacterium, Roseburia, Dialister, Coprococcus catus, Bifidobacterium, and Bilophila was identified in children with pro-inflammatory conditions and obesity.

Bacteria such as Citrobacter europaeus, Citrobacter youngae, Klebsiella variicola, Enterococcus mundtii, Gemella morbillorum, and Citrobacter portucalensis were associated with higher lipid and sugar intake, as well as higher blood biochemistry values and anthropometric measurements.

Diets high in fats and simple carbohydrates have been associated with the abundance of Citrobacter and Klebsiella species in the gut. Moreover, previous studies have indicated that these bacterial species are potential markers of inflammation, obesity, and an increase in fasting glucose.

The metabolism of menaquinones and gamma-glutamyl was negatively associated with BMI. Furthermore, the microbiomes of children in the NW group preserved a more consistent alpha diversity of virulence factors, while OWOB microbiomes exhibited a dominance of virulence factors.

Differences in the metabolic capacities pertaining to biosynthesis pathways of vitamins, carriers, amino acids, nucleotides, nucleosides, amines, and polyamines, as well as the degradation of nucleotides, nucleosides, and carbohydrate-sugars, were also found between the NW and OWOB groups.

Conclusions

Dietary profiles and the diversity of gut microbiota were found to be interconnected and associated with changes in metabolic parameters, the dominance of virulence factors, and obesity. Changes in gut microbiome diversity and relative abundance have been linked to obesity, inflammatory responses, and metabolic disorders.

Taken together, the study findings suggested that the prevalence of virulence factors, as well as the metabolic and genetic roles of gut microbiota in increasing inflammation, can help identify individuals at an increased risk of childhood obesity.

Journal reference:
  • Murga-Garrido, S. M., Ulloa-Pérez, E. J., Díaz-Benítez, C. E., et al. (2023). Virulence factors of the gut microbiome are associated with BMI and metabolic blood parameters in children with obesity. Microbiology Spectrum. doi:10.1128/spectrum.03382-22
Microbiology

Genes encoding T cell receptors vary greatly between persons and populations, study reveals

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Reviewed by Emily Henderson, B.Sc.Feb 16 2023

Researchers from Karolinska Institutet have discovered that the genes encoding our T cell receptors vary greatly between persons and populations, which may explain why we respond differently to for example infections. The findings, presented in the journal Immunity, also demonstrate that some gene variants are inherited from Neanderthals.

T-cells that are part of our immune system are central in the protection against infections and cancer. With the help of TCRs, the cells recognize foreign invaders and tumor cells.

“It was previously unknown how variable human TCR genes are”, says Gunilla Karlsson Hedestam, professor at the department of microbiology, tumor and cell biology at Karolinska Institutet and the study’s lead author.

Using deep sequencing of blood samples, the researchers examined TCR genes in 45 people originating from sub-Saharan Africa, East Asia, South Asia and Europe. The researchers showed that these genes vary greatly between different persons and population groups. The results were confirmed by analyses of several thousand additional cases from the 1000 Genomes project.

We found that every individual, other than identical twins, has a unique set of TCR gene variants. These differences reveal possible mechanisms underlying the wide range of responses to infections and vaccines that we observe at the population level.”

Martin Corcoran, first author of the study

“We discovered 175 new gene variants, which doubles the number of known TCR gene variants. An unexpected and surprising finding is that certain gene variants originate from Neanderthals and one of these is present in up to 20% of modern humans in Europe and Asia.”

Gunilla Karlsson Hedestam explains that the variation in these genes cannot be detected with the standard methods used in whole genome sequencing, but with the development of specialized deep sequencing methods and analysis software that allow highly precise definition of B- and T-cell receptor genes, this is now possible.

“As these genes are among the most variable in our genome, the results also provide new information about how our immune system has developed over the course of history, says Martin Corcoran. We are particularly interested in uncovering the function of the TCR variants we have inherited from Neanderthal ancestors. The frequency of these variants in modern humans suggests an advantageous function in our biology and we are keen to understand this”, adds Martin Corcoran.

The findings and the new TCR gene database the researchers now publish can be of great importance in the development of new therapeutic approaches in the future.

“Understanding human genetics is fundamental for the development of targeted treatments. The methods described in the study provide new opportunities, not the least in the cancer field where T-cells are central to several promising forms of immunotherapy”, says Gunilla Karlsson Hedestam.

The results can also shed light on other areas of research.

“The findings can lead to the development of new diagnostics and therapies in a range of medical disciplines, including precision medicine”, says Gunilla Karlsson Hedestam.

What is the next step in your research?

“We are now investigating the functional significance of several of the newly discovered gene variants and how this variation impacts our T-cell responses. We are also planning extended studies involving large groups of individuals to examine the role of TCR gene variation in diseases we know involve T cells, such as infectious diseases, cancer, and autoimmune disorders”, says Gunilla Karlsson Hedestam.

Main funding for the study comes from an ERC Advanced Grant and the Swedish Research Council.

Source:

Karolinska Institutet

Journal reference:

Corcoran, M., et al. (2023) Archaic humans have contributed to large-scale variation in modern human T cell receptor genes. Immunity. doi.org/10.1016/j.immuni.2023.01.026.

Microbiology

Increase in multidrug-resistant gram-negative bacteria in German hospitals linked to patients from Ukraine

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Reviewed by Emily Henderson, B.Sc.Feb 2 2023

The pathogens reach German hospitals with refugees and war casualties. Researchers recommend precautionary screening for hospitals.

Since the outbreak of the war in Ukraine, certain hospital pathogens that are resistant to many antibiotics have been detected with striking frequency in German hospitals. Due to a combination of two enzymes, some strains of the pathogen Klebsiella pneumoniae are resistant even to carbapenems, which are classified as antibiotics of last resort. In collaboration with the Robert Koch Institute (RKI), the National Reference Centre (NRC) for multidrug-resistant Gram-negative bacteria, based at Ruhr University Bochum, has proved that many of the reported cases are associated with patients from Ukraine. The researchers therefore recommend that this group should be screened prior to hospital admission. They published their findings in the journal Eurosurveillance on 15 December 2022.

Proof of a conspicuous connection

The isolates of the bacterium Klebsiella pneumoniae, which have been detected in large numbers in samples from German hospitals since the spring of 2022, produce a combination of two different so-called carbapenemases, NDM-1 and OXA-48, which are able to cleave carbapenem antibiotics.

We noticed that many of the respective samples had a connection to Ukraine, that the corresponding patients had fled from there, for example, or had been hospitalized in Germany as war casualties.”

Dr. Niels Pfennigwerth from the NRC

Subsequent investigations proved that there was indeed a connection, which was also reflected in the surveillance data collected by the Robert Koch Institute.

“Our analyses have shown that it is very likely that outbreaks with these bacterial strains have occurred in Germany as a result of the hospitalization of Ukrainian patients,” says Niels Pfennigwerth.

The NRZ and RKI team therefore recommend precautionary screening of persons with a connection to Ukraine when admitted to German hospitals. “If the screening confirms that the person is infected with the pathogen, they will be isolated in the hospital and very strict hygiene measures will be implemented,” points out the researcher.

People who are otherwise healthy often don’t notice that they have been exposed to such pathogens. In hospitals, however, the pathogens can be transmitted to people who are severely compromised due to illness or injury, especially via the hands of the medical personnel. In this case, Klebsiella pneumoniae can cause pneumonia, wound infections or urinary tract infections, to name but a few. Due to its resistance even to antibiotics of last resort, which are reserved exclusively for severe cases that need to be treated in hospital, treatment may no longer be possible at all in the worst case scenario.

Source:

Ruhr-Universitaet-Bochum

Journal reference:

Sandfort, M., et al. (2022) Increase in NDM-1 and NDM-1/OXA-48-producing Klebsiella pneumoniae in Germany associated with the war in Ukraine. Eurosurveillance. doi.org/10.2807/1560-7917.ES.2022.27.50.2200926.

Microbiology

Enveloped viruses show greater cross-species transmission, according to new research

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Nidhi Saha, BDSBy Nidhi Saha, BDSDec 9 2022Reviewed by Aimee Molineux

A study published in PNAS Microbiology found that enveloped viruses harbor greater cross-species transmissibility and are more likely to cause zoonotic infections than nonenveloped viruses. The research suggested that viral envelopes aid these pathogens in evading host immunity.

Study: Enveloped viruses show increased propensity to cross-species transmission and zoonosis. Image Credit: Kateryna Kon/Shutterstock
Study: Enveloped viruses show increased propensity to cross-species transmission and zoonosis. Image Credit: Kateryna Kon/Shutterstock

Background

Zoonosis refers to the spread of infectious diseases between animals and humans (or between humans and animals). In the past few decades, the cross-species transmission of viruses from wild or domestic animals to humans (zoonoses) has led to major epidemics. Still, our understanding of this complex process remains limited.

Several well-known zoonoses include human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS), Zika, Ebola, influenza, COVID, and mpox. Therefore, understanding and predicting virus emergence has become a scientific priority. Several zoonotic risk factors exist, including biodiversity elimination and species invasions, viral host variability, interaction frequency, life cycle characteristics of reservoir hosts, wildlife trade, and host closeness to humans.

Nevertheless, prior studies have revealed that three factors have been identified as contributing to the risk of zoonotic disease spread – viral genetic material – ribonucleic acid (RNA) viruses may be more susceptible than DNA viruses; replication site – viruses that replicate in the host cytoplasm rather than the nucleus may have an advantage; and genome size – smaller genomes may be more zoonotic.

The enveloped nature of viruses is a characteristic feature that distinguishes them from other organisms. Most zoonotic viruses that have caused human disease in the past were enveloped, such as – smallpox, mpox, coronaviruses, rabies, measles, and influenza.

A virus’s genome can provide information regarding host tropism and zoonotic propensity by evaluating characteristics like codon or dinucleotide usage biases and the degree to which these biases reflect those observed in the host-gene transcripts. The fundamental features of viruses remain unknown despite these advancements in understanding cross-species transmission and zoonosis.

The study

Using a database of over 12,000 mammalian virus–host interactions, the current work explored key virological properties that influence cross-species transmissibility and zoonotic propensity to understand better which viral characteristics predominantly determine zoonosis.

Here, the researchers examined a large VIRION database containing 5,149 viruses identified through metagenomic studies. This exploratory analysis utilized the Global Virome in One Network (VIRION) database. Overall, 5,149 viruses belonging to 36 families and 1,599 host species were analyzed from 20 orders, revealing 12,888 virus-host associations. 

Following this, the fundamental characteristics of the viruses were defined based on –their genetic material; single or double-stranded; segmented or non-segmented, replicating in the cytoplasm or nucleus, enveloped or nonenveloped, and the genome size. 

For each virus, the number of natural host species was identified and recorded, excluding humans, to reduce the possibility of bias. The mammalian viruses were then examined for their potential pathogenicity, i.e., their ability for zoonosis.

The findings

The results showed that the number of host species increased more rapidly for enveloped viruses than for non-enveloped viruses, being approximately twice as high for the former type. This difference was also discernible when the envelope factor was combined with the other viral characteristics. 

All other viral characteristics examined were either not significant or marginally significant. Enveloped viruses were more likely to undergo cross-species transmission than nonenveloped viruses. 

It was noted that enveloped viruses tend to have a higher proportion of zoonotic spread than non-enveloped viruses. Using binary logistic regression with N ≥5 sequence records, zoonotic propensity was estimated to increase 2.5-fold for enveloped viruses compared to non-enveloped viruses. Thus, enveloped viruses showed a higher propensity for zoonotic spillover than non-enveloped viruses.

Meanwhile, viruses replicating in the cytoplasm were found to be more likely (1.9 times) to be zoonotic than those replicating in the nucleus. Segmented viruses heightened the chances for zoonosis slightly more than non-segmented viruses. Further, viruses with smaller genomes had a greater probability of precipitating zoonotic infection. 

The lack of significant effects of these two features on cross-species transmission meant that their impact on zoonotic propensity could either be due to human-specific factors or, more likely, to biases within the human-infectious virus datasets.

This study also provided insights into how enveloped viruses might infect hosts. It was likely that envelope proteins were structurally less constraining than capsid proteins, allowing enveloped viruses to bind cellular receptors from different host species with greater flexibility, bind to a larger number of alternative receptors, or accommodate host-switch mutations without compromising other functions. 

Another possible mechanism is an apoptotic mimicry, in which viral particles are engulfed by host cells disguised as apoptotic bodies with defined membrane lipid conformations and get introduced into the host cells. 

Conclusion

The results revealed that enveloped viruses infect more host species and are more likely to be zoonotic than non-enveloped viruses. In contrast, other viral characteristics, such as genome composition, structure, size, and the viral replication compartment, are less significant. 

According to this study, viral envelopes did not significantly impact or even reduce the zoonotic risk contrary to the prior belief, and this may help in prioritizing outbreak prevention efforts. A viral envelope may facilitate cross-species transmission by facilitating structural flexibility of the receptor-binding proteins and allowing for overcoming the viral entry barriers.

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Microbiology

SARS-CoV-2 detected in white-tailed deer in Canada

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Bhavana KunkalikarBy Bhavana KunkalikarNov 14 2022Reviewed by Aimee Molineux

In a recent study published in Nature Microbiology, researchers investigated the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in white-tailed deer.

Study: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Image Credit: Holly Kuchera/Shutterstock
Study: Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission. Image Credit: Holly Kuchera/Shutterstock

Background

Wildlife reservoirs of viruses with a broad host range can facilitate the emergence of human-infecting viral variants. There is phylogenomic evidence of the continuous transmission of SARS-CoV-2 from humans to Odocoileus virginianus or white-tailed deer in North America. However, there is no evidence of viral transmission from deer to humans.

About the study

In the present study, researchers determined the extent of SARS-CoV-2 infection in white-tailed deer and the chances of deer-to-human transmission of the virus.

During the yearly shooting season between 1 November and 31 December 2021, the team sampled 300 white-tailed deer in Eastern and Southwestern Ontario, Canada. Most white-tailed deer in the sample were adults, with equal proportions of males and females. Approximately 213 nose swabs and tissue samples were obtained from 294 retropharyngeal lymph nodes (RPLN). These were analyzed by reverse transcription polymerase chain reaction (RT–PCR) for SARS-CoV-2 ribonucleic acid (RNA).

Three high-quality SARS-CoV-2 consensus genomes were sequenced from five SARS-CoV-2 positive nasal swabs with a standard amplicon-based technique employed to estimate the viral lineage and perhaps deduce significant epidemiological relationships. For confirmation, each sample was extracted and sequenced individually using a capture-probe-based method.

The prevalence of mutations was evaluated in the Global Initiative on Sharing All Influenza Data (GISAID) and within animal-derived variants of concern (VOC) to recognize and contextualize essential mutations. This was achieved using five complete deer-derived sequences along with human-derived sequences.  Viral isolation was performed on Vero E6 cells that expressed human transmembrane protease serine 2 (TMPRSS2) to test the infectivity of the SARS-CoV-2 positive samples.

Results

Out of the 213 nose swabs collected, five tested positive based on the results of two independent RT-PCR analyses conducted at separate institutions. Additionally, 16 RPLNs were validated by PCR. SARS-CoV-2 RNA was found in 21 samples, which accounted for 6% of white-tailed deer harvested by hunters. All SARS-CoV-2 positive animals were adult white-tailed deer found in Southwestern Ontario, with the majority female.

Combining the sequence data obtained from the amplicon and capture-probe led to the recovery of five high-quality genomes with two incomplete genomes. Most of the non-SARS-CoV-2 reads matched that of the reference genome of the white-tailed deer, indicating that contamination with human-derived SARS-CoV-2 sequences was extremely unlikely. The team also noted that the viral genomes derived from the deer samples created a highly divergent clade in the B.1 Phylogenetic Assignment of Named Global Outbreak (PANGO) lineage/20C Nextstrain clade, which had a most recent common ancestor (MRCA).

The Ontario deer lineage constitutes a very lengthy branch having 76 conserved nucleotide mutations compared to those in the SARS-CoV-2 Wuhan Hu-1 strain and 49 as compared to their most recent common ancestor with other GISAID genomes. Human-derived sequences obtained from Michigan, US, were estimated to share an MRCA between May and August 2020 with the Ontario deer lineage. These sequences obtained from humans are closely connected to a mixed clade of mink and human sequences collected in September and October 2020 in Michigan. The white-tailed deer lineage in Ontario has been identified as PANGO lineage B.1.641.

Among the 76 mutations that were similar among the six B.1.641 sequences, nine were in the SARS-CoV-2 spike (S), while 51 were in the open-reading frame (ORF)-1ab. The six nonsynonymous mutations in S include five substitutions and a six-nucleotide deletion. These S mutations, except H49Y, evolved before the divergence of B.1.641 lineage from the MRCA shared by the Michigan samples. Furthermore, only a few S mutations were preserved throughout B.1.641, S:L1265I, and S:613H and were unique to the human sample. Three other nonsynonymous mutations were detected in either 4658 or 4662 white-tailed deer samples, while 4662S:L959 exhibited a frameshift.

The team observed that four days post-infection, four of the samples displayed that 50% or less of the cell monolayer was affected by the cytopathic effect. In comparison to the original swab consensus sequences, confirmatory sequencing revealed only small frequency variations corresponding to one or two single-nucleotide polymorphism (SNP) changes.

Unlike SARS-CoV-2 Omicron, which needed three vaccine doses to neutralize B.1.641S, sera from vaccinated patients who had received two or three doses and sera from convalescent persons effectively neutralized all B.1.641S proteins. Importantly, there was no change in the neutralizing ability of sera against SARS-CoV-2 D614G or other SARS-CoV-2 isolates from Ontario white-tailed deer. Collectively, these findings imply that mutations in the S-gene of the white-tailed deer do not have a significant antigenic effect on antigenicity.

Conclusion

Overall, the study findings highlighted a distinct SARS-CoV-2 lineage in white-tailed deer and provided evidence of host adaptability and transient transfer from deer to humans. White-tailed deer have numerous characteristics essential for a viral reservoir to be sustained, including social behavior, highly transitory populations with multiple human–deer encounters, high density, and sylvatic relationships with other animals.

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