Let’s get things in perspective

Chromobacterium While the current outbreak of Ebola virus in West Africa is very serious, in the current panic people have forgotten that malaria kills thousands of times more people than Ebola each year. In spite of decades of effort, we are still struggling with malaria vaccines, so attention is starting to switch to a new strategy, targeting the mosquitoes that spread malaria.

Just like those of humans, insect guts are full of microbes, and this microbiota can influence the insect’s ability to transmit diseases. A new study reports that a bacterium (Chromobacterium Csp_P) isolated from the gut of an Aedes mosquito can reduce infection of mosquitoes by malaria parasites and dengue virus. The bacterium can also directly inhibit these pathogens in the test tube, and shorten the life span of the mosquitoes that transmit both diseases.

Chromobacterium Csp_P can effectively colonize the midguts of Anopheles gambiae and Aedes aegypti mosquitoes and can, when ingested by the mosquito, significantly reduce the mosquito’s susceptibility to infection with the malaria parasite and dengue virus. We also show that exposure to, and ingestion of, Csp_P can reduce the lifespan of larval and adult mosquitoes. Csp_P has anti-Plasmodium and anti-dengue activity independent of the mosquito, suggesting that the bacterium secretes metabolites that could potentially be exploited to prevent disease transmission or to treat infection.

This comes on top of earlier work involving the use of Wolbachia to attack mosquitoes. We may be some way away from an effective malaria vaccine, but the development of novel control strategies for vector-borne diseases is gaining ground rapidly.


Chromobacterium Csp_P Reduces Malaria and Dengue Infection in Vector Mosquitoes and Has Entomopathogenic and In Vitro Anti-pathogen Activities. (2014) PLoS Pathog 10(10): e1004398. doi: 10.1371/journal.ppat.1004398
Plasmodium and dengue virus, the causative agents of the two most devastating vector-borne diseases, malaria and dengue, are transmitted by the two most important mosquito vectors, Anopheles gambiae and Aedes aegypti, respectively. Insect-bacteria associations have been shown to influence vector competence for human pathogens through multi-faceted actions that include the elicitation of the insect immune system, pathogen sequestration by microbes, and bacteria- produced anti-pathogenic factors. These influences make the mosquito microbiota highly interesting from a disease control perspective. Here we present a bacterium of the genus Chromobacterium (Csp_P), which was isolated from the midgut of field-caught Aedes aegypti. Csp_P can effectively colonize the mosquito midgut when introduced through an artificial nectar meal, and it also inhibits the growth of other members of the midgut microbiota. Csp_P colonization of the midgut tissue activates mosquito immune responses, and Csp_P exposure dramatically reduces the survival of both the larval and adult stages. Ingestion of Csp_P by the mosquito significantly reduces its susceptibility to Plasmodium falciparum and dengue virus infection, thereby compromising the mosquito’s vector competence. This bacterium also exerts in vitro anti-Plasmodium and anti-dengue activities, which appear to be mediated through Csp_P-produced stable bioactive factors with transmission-blocking and therapeutic potential. The anti-pathogen and entomopathogenic properties of Csp_P render it a potential candidate for the development of malaria and dengue control strategies.

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How to stop the spread of Ebola [video]

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HCMV I’m a little out of date with my cytomegalovirus (CMV) knowledge. As I currently have a student working on a project on virus infections in pregnancy, this short review – focussing on new treatment options for cytomegalovirus infection, recent clinical trials and bone marrow transplantation, congenital infections and interventions during pregnancy – is most welcome.

Cytomegalovirus. Curr Opin Infect Dis. 08 Oct 2014. doi: 10.1097/QCO.0000000000000107
Three double-blind randomized placebo-controlled phase 2 proof-of-concept studies have each identified a novel antiviral drug with activity against CMV infection in bone marrow transplant patients. One of these (brincidofovir) inhibits the DNA polymerase that is the target of the currently licensed drug ganciclovir. Another new drug (maribavir) inhibits a protein kinase which, coincidentally, is the enzyme responsible for activating ganciclovir through phosphorylation. The third drug (letermovir) inhibits the terminase enzyme complex responsible for packaging unit length DNA into assembling virions.In addition, in a double-blind randomized placebo-controlled trial in neonates with symptomatic congenital CMV infection, a 6-month course of valganciclovir was superior to the standard 6-week course of the same drug. In pregnant women with primary CMV infection, administration of hyperimmune immunoglobulin did not significantly reduce transmission of CMV across the placenta. The ability to diagnose CMV infections reliably in different clinical settings through application of molecular laboratory methods has ushered in new ways of evaluating potential new treatments for CMV. Several of these may help control the diseases caused by this important human pathogen.

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Viroids: Survivors from the RNA World?

Viroid A new review in Annual Review of Microbiology gives an excellent introduction to viroids.


  • Introduction: Why The Need For An RNA World?
  • Viroids: Essential Features
  • Discovery of a Subviral World
  • Structure: Small Circular RNAs with Compact Folding
  • Replication: Rolling-Circle Mechanism Catalyzed by Enzymes and Ribozymes
  • Sequence Diversity
  • Viroid-Related Replicons
  • Viroid-Like Satellite RNAs
  • Retroviroid-Like Elements
  • Hepatitis δ virus
  • Why Are Viroids And Viroid-Related Replicons Regarded As Survivors Of The RNA World?
  • Early Speculations on the Origin of Viroids
  • Circular RNAs: Relics of Precellular Evolution?
  • Viroid-Related Replicons
  • Summary


Viroids: Survivors from the RNA World? (2014) Annual Review of Microbiology, 68(1): 395-414. doi: 10.1146/annurev-micro-091313-103416


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The Flawed Prokaryote

Bacterial origins There are two types of biologist – those who think that prokaryotes exist and those who don’t.

The simple binary divide between prokaryotes and eukarotes is an old (19th Century) idea. Splitting all life forms into two headings (let’s leave viruses out of this for now) is seductive. The problem is that this old idea – still trotted out in textbooks – doesn’t stand up to molecular data. Even though we only need three domains (bacteria, eukarya and archaea) to account for scientific observations, the old prokaryote-eukaryote idea just won’t die. Think about that when you’re writing your essays…


Pace, N.R. (2006) Time for a change. Nature, 441(7091), 289-289. doi:10.1038/441289a

Close Encounters of the Third Domain: The Emerging Genomic View of Archaeal Diversity and Evolution. Archaea, 2013. http://dx.doi.org/10.1155/2013/202358

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Welcome to new microbiology students

MicrobiologyBytes MicrobiologyBytes has been explaining the latest news about microbiology for nearly ten years and is read by thousands of people worldwide each month. I hope that you will become one of them. You can read MicrobiologyBytes on this website, or if you prefer, get notification of new items on Facebook or Twitter or by email (click the Follow button top right). And it’s all free and always will be.

Over the years, I have built up collections of thousands of microbiology images such as bacteria, viruses and fungi which you’re free to use as long as you remember to say where you got them from.

So whether you’re a student (or a teacher) of microbiology, welcome to MicrobiologyBytes. Remember to ask lots of questions, and most importantly – enjoy learning. And if you, like me, are not so new to microbiology, thanks for sticking around. i’d appreciate it if you left me a brief comment on how you use MicrobiologyBytes and if there’s anything else you’d lie to see here – because while the content is microbiology, MicrobiologyBytes is really all about you.


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Whole Genome Sequencing for Outbreak Detection of Salmonella enterica

Salmonella typhimurium Salmonella bacteria are a common cause of infectious disease in human and animals. Salmonella is classically divided into species S. bongori and S. enterica – which is in turn further divided into more than 2,500 different serotypes. However, only a limited number of serovars that are responsible for most infections. In Europe, the most prevalent S. enterica serovars isolated from humans are Enteritidis and Typhimurium, responsible for over 75% of the human cases of salmonellosis.

In order to understand the epidemiology and implement control programs, reliable and rapid sub-typing is essential. Different typing methods are commonly used as a central part of the detection and investigation of Salmonella outbreaks, for instance, serotyping, phage typing, pulse-field gel electrophoresis (PFGE) and multilocus variable number of tandem repeat analysis (MLVA). PFGE has become the standard for epidemiological investigations of foodborne bacterial pathogens including Salmonella. A drawback of PFGE is that it is unable to separate very closely related strains because the low rate of genetic variation does not significantly impact the electrophoretic mobility of a restriction fragment.

During recent years the cost of whole genome sequencing (WGS) has decreased dramatically and the technology becomes increasingly available for routine use around the world. The speed of sequencing is decreasing from several days or weeks to perhaps hours for a bacterial genome in the near future. This combination of low cost and high speed opens an opportunity for WGS to become very useful and practical in bacterial infection studies including the routine use in diagnostic and public health microbiology.

A new study evaluates WGS for outbreak typing of S. enterica and compares it to results obtained using the conventional typing method, PFGE. The results show that WGS alone is insufficient to determine whether strains are related or un-related to outbreaks. This still requires the combination of epidemiological data and whole genome sequencing results.

Evaluation of Whole Genome Sequencing for Outbreak Detection of Salmonella enterica. (2014) PLoS ONE 9(2): e87991. doi: 10.1371/journal.pone.0087991
Salmonella enterica is a common cause of minor and large food borne outbreaks. To achieve successful and nearly ‘real-time’ monitoring and identification of outbreaks, reliable sub-typing is essential. Whole genome sequencing (WGS) shows great promises for using as a routine epidemiological typing tool. Here we evaluate WGS for typing of S. Typhimurium including different approaches for analyzing and comparing the data. A collection of 34 S. Typhimurium isolates was sequenced. This consisted of 18 isolates from six outbreaks and 16 epidemiologically unrelated background strains. In addition, 8 S. Enteritidis and 5 S. Derby were also sequenced and used for comparison. A number of different bioinformatics approaches were applied on the data; including pan-genome tree, k-mer tree, nucleotide difference tree and SNP tree. The outcome of each approach was evaluated in relation to the association of the isolates to specific outbreaks. The pan-genome tree clustered 65% of the S. Typhimurium isolates according to the pre-defined epidemiology, the k-mer tree 88%, the nucleotide difference tree 100% and the SNP tree 100% of the strains within S. Typhimurium. The resulting outcome of the four phylogenetic analyses were also compared to PFGE reveling that WGS typing achieved the greater performance than the traditional method. In conclusion, for S. Typhimurium, SNP analysis and nucleotide difference approach of WGS data seem to be the superior methods for epidemiological typing compared to other phylogenetic analytic approaches that may be used on WGS. These approaches were also superior to the more classical typing method, PFGE. Our study also indicates that WGS alone is insufficient to determine whether strains are related or un-related to outbreaks. This still requires the combination of epidemiological data and whole genome sequencing results.

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Where will Ebola strike next?

Ebola risk Since the first outbreaks of Ebola virus disease in 1976, there have been numerous other outbreaks in humans across Africa with fatality rates ranging from 50% to 90%. Humans can become infected with the Ebola virus after direct contact with blood or bodily fluids from an infected person or animal. The virus also infects and kills other primates, though fruit bats are suspected to be the most likely carriers of the virus in the wild.

The largest recorded outbreak of Ebola virus disease is ongoing in West Africa: more people have been infected in this current outbreak than in all previous outbreaks combined. The current outbreak is also the first to occur in West Africa – which is outside the previously known range of the Ebola virus. A new paper in eLife updates predictions about where in Africa wild animals may harbour the virus and where the transmission of the virus from these animals to humans is possible.

Mapping the zoonotic niche of Ebola virus disease in Africa. (2014) eLife 3:e04395 doi: 10.7554/eLife.04395
Ebola virus disease (EVD) is a complex zoonosis that is highly virulent in humans. The largest recorded outbreak of EVD is ongoing in West Africa, outside of its previously reported and predicted niche. We assembled location data on all recorded zoonotic transmission to humans and Ebola virus infection in bats and primates (1976–2014). Using species distribution models, these occurrence data were paired with environmental covariates to predict a zoonotic transmission niche covering 22 countries across Central and West Africa. Vegetation, elevation, temperature, evapotranspiration, and suspected reservoir bat distributions define this relationship. At-risk areas are inhabited by 22 million people; however, the rarity of human outbreaks emphasises the very low probability of transmission to humans. Increasing population sizes and international connectivity by air since the first detection of EVD in 1976 suggest that the dynamics of human-to-human secondary transmission in contemporary outbreaks will be very different to those of the past.

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Recent developments linking retroviruses to human breast cancer

Retrovirus replication We have known for decades that viruses =can couse breast cancer in animals (Mouse Mammary Tumour Virus – MMTV). Evidence has been accumulating that retroviruses may play a part in human breast cancers. This short review summarizes iur prsent state fo knowledge.


Recent developments linking retroviruses to human breast cancer: infectious agent, enemy within or both? J Gen Virol. 12 Sep 2014. doi: 10.1099/vir.0.070631-0
Evidence is accumulating that one or more beta-retrovirus is associated with human breast cancer. Retroviruses can exist as an infectious (exogenous) virus or as a part of the genetic information of cells due to germline integration (endogenous). An exogenous virus with a genome that is highly homologous to mouse mammary tumor virus (MMTV) is gaining acceptance as possibly being associated with human breast cancer and recently furnished evidence is discussed in this article, as is the evidence for involvement of an endogenous human beta-retrovirus, HERV-K. Modes of interaction are also reviewed and linkage to APOBEC3 suggested.


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