MicrobiologyBytes

Cystic fibrosis is caused by mutations in the CFTR gene leading to a disrupted chloride channel. It is well established that the greatest contributor to patient morbidity and mortality is chronic lung disease, caused by a constant cycle of infection and inflammation throughout the patient’s life. The CFTR mutation leads to defective regulation of chloride and sodium, resulting in increased water absorption, depletion of airway surface liquid and dehydrated mucous. Consequently, the purulent sputum and mucus plugs together with an ineffective inflammatory response, all contribute to the chronic infections that are central to CF lung disease. From early childhood, CF patients experience recurrent pulmonary infections from a range of pathogens.

In spite of intensive antibiotic therapy, certain organisms persist, leading to pulmonary exacerbations, hospitalizations and patient death. These include Pseudomonas aeruginosa, Burkholderia cepacia complex (Bcc) and Achromobacter xylosoxidans, with Bcc being the most problematic. It was recently demonstrated that chronic colonisation by Bcc resulted in a greater lung function decline than by the other two pathogens. CF patients are also susceptible to colonisation by other pathogens, including Staphylococcus aureus (both methicillin-resistant and sensitive), genus Pandoraea, Stenotrophomonas maltophilia and non-tuberculous Mycobacteria, although the role of these latter four pathogens in CF lung disease is unclear. Furthermore, the identification of high levels of anaerobic organisms in CF sputum has added to the complex microbial population in the CF lung. These CF-associated anaerobes were not susceptible to antibiotics with known efficacy against anaerobes and the clinical significance of anaerobes in CF is not yet fully understood.

Bacterial host interactions in cystic fibrosis. Curr Opin Microbiol. Dec 1 2011
Chronic infection is a hallmark of cystic fibrosis (CF) and the main contributor to morbidity. Microbial infection in CF is complex, due to the number of different species that colonise the CF lung. Their colonisation is facilitated by a host response that is impaired or compromised by highly viscous mucous, zones of hypoxia and the lack of the cystic fibrosis transmembrane regulator (CFTR). Successful dominant CF pathogens combine an effective arsenal to establish infection and counter-attack the host response, together with an ability to adapt readily to an unfavourable environment. Hypermutability is common among CF pathogens facilitating adaptation and as the host response persists, progressive destruction of the normal architecture of lung tissue ensues with catastrophic consequences for the host.

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Prion diseases are transmissible, progressive and invariably fatal neurodegenerative conditions associated with misfolding and aggregation of a host-encoded cellular prion protein, PrPC. They have occurred in a wide range of mammalian species including human. Human prion diseases can arise sporadically, be hereditary or be acquired. Sporadic human prion diseases include Cruetzfeldt-Jacob disease (CJD), fatal insomnia and variably protease-sensitive prionopathy. Genetic or familial prion diseases are caused by autosomal dominantly inherited mutations in the gene encoding for PrPC and include familial or genetic CJD, fatal familial insomnia and Gerstmann-Straussler-Scheinker syndrome. Acquired human prion diseases account for only 5% of cases of human prion disease. They include kuru, iatrogenic CJD and a new variant form of CJD that was transmitted to humans from affected cattle via meat consumption especially brain. This review presents information on the epidemiology, etiology, clinical assessment, neuropathology and public health concerns of human prion diseases. The role of the PrP encoding gene (PRNP) in conferring susceptibility to human prion diseases is also discussed.

An overview of human prion diseases. (2011) Virology Journal 8: 559 doi:10.1186/1743-422X-8-559

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DNA fragments encoding enzymes, transcriptional regulators and virulence factors are fluxing through bacterial taxonomic walls by horizontal gene transfer. These elements often endow environmental and clinical strains of bacteria with new properties, including an enhanced virulence. Lateral genetic exchange, particularly of drug tolerance genes has been recognized for a long time; however, our understanding of this phenomenon is limited. Ontology and phylogeny of laterally transferred genetic elements are difficult to investigate, let alone the predictions of their insertion sites in hosts chromosomes.

An outbreak of the lethal Escherichia coli in Europe in 2011 highlighted the shortcoming of our knowledge on the basic principles of evolutionary trends of new pathogens. The outbreak first occurred in Germany in May 2011 where a rare enterohemorrhagic strain Escherichia coli O104:H4 caused haemolytic-uremic syndrome. The infection spread fast through many other European countries and sickened thousands of people. The level of lethality associated with the production of Shiga toxin by the strain and its resistance against many antibiotics was significant. A number of isolates from this outbreak have been sequenced and annotated. Based on the unique combination of genomic features these strains were suggested to represent a new pathotype Entero-Aggregative-Haemorrhagic E. coli (EAHEC).

Mainstreams of Horizontal Gene Exchange in Enterobacteria: Consideration of the Outbreak of Enterohemorrhagic E. coli O104:H4 in Germany in 2011. (2011) PLoS ONE 6(10): e25702. doi:10.1371/journal.pone.0025702
Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods. The study revealed oscillations of gene exchange in enterobacteria, which originated from marine γ-Proteobacteria. These mobile genetic elements have become recombination hotspots and effective ‘vehicles’ ensuring a wide distribution of successful combinations of fitness and virulence genes among enterobacteria. Two remarkable peculiarities of the strain TY-2482 and its relatives were observed: i) retaining the genetic primitiveness by these strains as they somehow avoided the main fluxes of horizontal gene transfer which effectively penetrated other enetrobacteria; ii) acquisition of antibiotic resistance genes in a plasmid genomic island of β-Proteobacteria origin which ontologically is unrelated to the predominant genomic islands of enterobacteria. Oscillations of horizontal gene exchange activity were reported which result from a counterbalance between the acquired resistance of bacteria towards existing mobile vectors and the generation of new vectors in the environmental microflora. We hypothesized that TY-2482 may originate from a genetically primitive lineage of E. coli that has evolved in confined geographical areas and brought by human migration or cattle trade onto an intersection of several independent streams of horizontal gene exchange. Development of a system for monitoring the new and most active gene exchange events was proposed. Tweet

It was my privilege to work with Phil Minor during my PhD. 25 years later (gulp), Phil looks back and forward to the polio endgame.

The Polio-Eradication programme and issues of the end game. J Gen Virol. Nov 29 2011
Poliovirus causes paralytic poliomyelitis, an ancient disease of humans that became a major public health issue in the 20th century. The primary site of infection is the gut where virus replication is entirely harmless; the two very effective vaccines developed in the 1950s (Oral Polio Vaccine, or OPV and Inactivated Polio Vaccine, or IPV) induce humoral immunity which prevents viraemic spread and disease. The success of vaccination in developing countries and in middle income countries encouraged the World Health Organization to commit itself to an eradication programme which has made great advances. The features of the infection including its largely silent nature and the ability of the live vaccine (OPV) to evolve and change in vaccine recipients and their contacts make eradication particularly challenging. Understanding the pathogenesis and virology of the infections is of major significance as the programme reaches its conclusion.

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The delightful NCBI ROFL carried this item recently. Certainly something to think about over the “festive” season.

Scent Recognition of Infected Status in Humans. J Sex Med. Dec 6 2011. doi: 10.1111/j.1743-6109.2011.02562.x
There is a body of experimental evidence that mice and rats use chemical signals to avoid sexual contact with infected conspecifics. In contrast to animals, body scent of sick humans is employed only in medical diagnostics. A modification of human body odor, due to an infection, has not been studied as a potential signal for choice of a sexual partner. It might, however, be especially important for sexually transmitted infections (STI) because many such infections have no obvious external manifestations.
Aim: In this study, we have investigated odor pleasantness of young men infected with gonorrhea, Neisseria gonorrhoeae.
Methods:We collected armpit sweat and saliva from young men (17-25 years old) belonging to three groups: healthy persons (N=16), young men infected with gonorrhea, Neisseria gonorrhoeae (N=13), and persons recovered due to specific therapy (N=5). The sweat samples odor was then assessed by healthy young women (17-20 years old). Concentrations of cortisol, testosterone, immunoglobulin A (IgA), and immunoglobulin G (IgG) were measured in saliva by means of enzyme-linked immunosorbent assay.
Main Outcome Measures: Subjective rates of odor pleasantness, association of scent of armpit sweat with odor descriptors, stepwise regression of odor pleasantness and salivary cortisol, testosterone, IgA, and IgG. Results: The odor from infected individuals was reported as less pleasant in comparison with the odor of healthy and recovered young men. The scent of infected men was more frequently associated by raters with the descriptor “putrid.” Odor pleasantness of the male sweat correlated negatively with concentration of the nonspecific salivary IgA and IgG, which was measured as an indicator of current immunoenhancement.
Conclusion: Perhaps, the immune-dependent reduction of the scent pleasantness in the acute phase of STI is part of an evolutionary mechanism ensuring, unconsciously, avoidance of a risky romantic partner.

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Methicillin-resistant Staphylococcus aureus (MRSA), first identified in the 1960s, was initially considered to be a nosocomial pathogen (hospital acquired infection). Beginning in the late 20th century, a specific clone of MRSA known as USA300 emerged as a leading cause of community-acquired infection, but doubts remain as to where many cases of MRSA infection originate, and how to break the transmission of this dangerous strain.

A new study finds that 8% of hospital outpatients carrying methicillin-resistant MRSA lived with an MRSA-positive pet. When faced with chronic and or recurrent MRSA cases, physicians should consider the possibility of household pets as MRSA source. Patients should be informed of this possibility. Unnecessary close contact should be avoided and heightened hygiene practices should be instituted. Sampling/swabbing of all the human and animals in a household seems appropriate to identify unrecognized sources and break potential cycles of reinfection especially in cases involving immunocompromised patients.

Transmission of MRSA between Companion Animals and Infected Human Patients Presenting to Outpatient Medical Care Facilities. PLoS ONE 6(11): e26978. doi:10.1371/journal.pone.0026978
Methicillin-resistant Staphylococcus aureus (MRSA) is a significant pathogen in both human and veterinary medicine. The importance of companion animals as reservoirs of human infections is currently unknown. The companion animals of 49 MRSA-infected outpatients (cases) were screened for MRSA carriage, and their bacterial isolates were compared with those of the infected patients using Pulsed-Field Gel Electrophoresis (PFGE). Rates of MRSA among the companion animals of MRSA-infected patients were compared to rates of MRSA among companion animals of pet guardians attending a “veterinary wellness clinic” (controls). MRSA was isolated from at least one companion animal in 4/49 (8.2%) households of MRSA-infected outpatients vs. none of the pets of the 50 uninfected human controls. Using PFGE, patient-pets MRSA isolates were identical for three pairs and discordant for one pair (suggested MRSA inter-specie transmission p-value = 0.1175). These results suggest that companion animals of MRSA-infected patients can be culture-positive for MRSA, representing a potential source of infection or re-infection for humans. Further studies are required to better understand the epidemiology of MRSA human-animal inter-specie transmission.

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As the incidence of type 1 diabetes in developed countries has been increasing at a rate far beyond the rate of population growth, environmental factors have been considered as likely candidates responsible for this change in disease incidence in recent decades. Of those factors, the gut microbiota have come under recent interest; supported in part by observations in both non-obese diabetic (NOD) mice and BioBreeding Diabetes Prone (BB-DP) rats where antibiotic use prevents the onset of diabetes.

To explore specific differences in the microbial communities responsible for T1D modulation, a metagenomic analysis of bacteria from susceptible rodents was performed. This revealed bacteria whose members were either positively or negatively correlated with diabetes. Lactobacillus and Bifidobacterium were more abundant in BB-DR (Diabetes Resistant) rats while Bacteroides and Clostridium were more abundant in BB-DP (Diabetes Prone) rats. Both Lactobacillus and Bifidobacterium are well known to have members with probiotic characteristics. These data suggest a model for the role of bacteria in a healthy gut. The total number of lactic acid producing and butyrate producing bacteria is higher in controls than in diabetic animals. This suggest that microbial-induced butyrate production, and subsequent mucin synthesis, with a corresponding enhancement of tight junctions may contribute to the development of autoimmunity for type 1 diabetes in humans.

Gut Microbiome Metagenomics Analysis Suggests a Functional Model for the Development of Autoimmunity for Type 1 Diabetes. (2011) PLoS ONE 6(10): e25792. doi:10.1371/journal.pone.0025792
Recent studies have suggested a bacterial role in the development of autoimmune disorders including type 1 diabetes (T1D). Over 30 billion nucleotide bases of Illumina shotgun metagenomic data were analyzed from stool samples collected from four pairs of matched T1D case-control subjects collected at the time of the development of T1D associated autoimmunity (i.e., autoantibodies). From these, approximately one million open reading frames were predicted and compared to the SEED protein database. Of the 3,849 functions identified in these samples, 144 and 797 were statistically more prevalent in cases and controls, respectively. Genes involved in carbohydrate metabolism, adhesions, motility, phages, prophages, sulfur metabolism, and stress responses were more abundant in cases while genes with roles in DNA and protein metabolism, aerobic respiration, and amino acid synthesis were more common in controls. These data suggest that increased adhesion and flagella synthesis in autoimmune subjects may be involved in triggering a T1D associated autoimmune response. Extensive differences in metabolic potential indicate that autoimmune subjects have a functionally aberrant microbiome. Mining 16S rRNA data from these datasets showed a higher proportion of butyrate-producing and mucin-degrading bacteria in controls compared to cases, while those bacteria that produce short chain fatty acids other than butyrate were higher in cases. Thus, a key rate-limiting step in butyrate synthesis is more abundant in controls. These data suggest that a consortium of lactate- and butyrate-producing bacteria in a healthy gut induce a sufficient amount of mucin synthesis to maintain gut integrity. In contrast, non-butyrate-producing lactate-utilizing bacteria prevent optimal mucin synthesis, as identified in autoimmune subjects.

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Researchers have discovered a toxin – SElX – released by methicillin-resistant Staphylococcus aureus (MRSA) which leads the body’s immune system to go into overdrive and damage healthy cells. SElX is made by 95 per cent of S. aureus strains, making it a potential drug target to fight this hospital superbug. SElX belongs to a family of toxins known as superantigens that can invoke an extreme immune response. When it is released it triggers an over multiplication of immune cells, which can lead to high fever, toxic shock and potentially fatal lung infections looked at a strain of MRSA known as USA300 that can cause severe infections in otherwise healthy individuals. If we can find ways to target this toxin, we may be able to stop it from triggering an over-reaction of the body’s immune system and prevent severe infections.

A Novel Core Genome-Encoded Superantigen Contributes to Lethality of Community-Associated MRSA Necrotizing Pneumonia. (2011) PLoS Pathog 7(10): e1002271. doi:10.1371/journal.ppat.1002271

Other research has linked a naturally occurring mutation in the bacterium Clostridium difficile to severe and debilitating diarrhoea in hospital patients undergoing antibiotic therapy. These antibiotics destroy the “good” bacteria in the gut, which allows this “bad” bacterium to colonise the colon, where it causes bowel infections that are difficult to treat. The mutation wipes out an inbuilt disease regulator, called anti-sigma factor TcdC, producing hypervirulent strains of C. difficile that are resistant to antibiotics and which have been found to circulate in Canada, the US, UK, Europe and Australia. The results suggest that bacterial strains carrying this mutation have the potential to produce more of the harmful toxins that cause disease in susceptible individuals – commonly patients aged 65 years or over. As we now have a better understanding of these strains, we can design new strategies to prevent, control and treat these infections.

The Anti-Sigma Factor TcdC Modulates Hypervirulence in an Epidemic BI/NAP1/027 Clinical Isolate of Clostridium difficile. (2011) PLoS Pathog 7(10): e1002317. doi:10.1371/journal.ppat.1002317

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Two days ago I wrote about monkeys as an animal model for smallpox. Animal models certainly have a place in microbiology research, but here’s a rather less controversial one:

Pseudomonas aeruginosa causes serious infections in people with compromised immune systems. Individuals with cystic fibrosis and hospital patients are particularly vulnerable to P. aeruginosa infections. This bacterium does not respond to many antibiotics, making these infections difficult to treat. P. aeruginosa can grow as free-floating planktonic cells or as microcolonies known as biofilms. The ability of P. aeruginosa to form biofilms is thought to contribute to their ability to cause chronic infections. The aim of this research was to develop a simple biofilm model of infection using the fruit fly (Drosophila melanogaster). The immune system of the fruit fly has similarities with the vertebrate innate immune system. Understanding how P. aeruginosa causes infections in Drosophila will aid in understanding virulence mechanisms in mammals. This study shows that feeding P. aeruginosa to Drosophila results in a biofilm infection and biofilm infections induced expression of antimicrobial peptide immune response genes in the fly. Using fly survival as a measure of virulence it shows that biofilm infections were less virulent than non-biofilm infections. These results provide novel insight into host-pathogens interactions during P. aeruginosa infection.

Drosophila melanogaster as an Animal Model for the Study of Pseudomonas aeruginosa Biofilm Infections In Vivo. (2010) PLoS Pathog 7(10): e1002299. doi:10.1371/journal.ppat.1002299
Pseudomonas aeruginosa is an opportunistic pathogen capable of causing both acute and chronic infections in susceptible hosts. Chronic P. aeruginosa infections are thought to be caused by bacterial biofilms. Biofilms are highly structured, multicellular, microbial communities encased in an extracellular matrix that enable long-term survival in the host. The aim of this research was to develop an animal model that would allow an in vivo study of P. aeruginosa biofilm infections in a Drosophila melanogaster host. At 24 h post oral infection of Drosophila, P. aeruginosa biofilms localized to and were visualized in dissected Drosophila crops. These biofilms had a characteristic aggregate structure and an extracellular matrix composed of DNA and exopolysaccharide. P. aeruginosa cells recovered from in vivo grown biofilms had increased antibiotic resistance relative to planktonically grown cells. In vivo, biofilm formation was dependent on expression of the pel exopolysaccharide genes, as a pelB::lux mutant failed to form biofilms. The pelB::lux mutant was significantly more virulent than PAO1, while a hyperbiofilm strain (PAZHI3) demonstrated significantly less virulence than PAO1, as indicated by survival of infected flies at day 14 postinfection. Biofilm formation, by strains PAO1 and PAZHI3, in the crop was associated with induction of diptericin, cecropin A1 and drosomycin antimicrobial peptide gene expression 24 h postinfection. In contrast, infection with the non-biofilm forming strain pelB::lux resulted in decreased AMP gene expression in the fly. In summary, these results provide novel insights into host-pathogen interactions during P. aeruginosa oral infection of Drosophila and highlight the use of Drosophila as an infection model that permits the study of P. aeruginosa biofilms in vivo.

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