Latest microbiology research

A trusted home for your microbiology research The scientific community has been deep in conversation about microbiology this summer, from microbial health to mechanism discovery, and the momentum should keep going. Whether you're looking to share your latest findings or explore what's being published at the forefront of the field, now is the perfect time to engage. ESCMID is at the forefront of microbial science, with the flagship journal Clinical Microbiology and Infection and the fully open access CMI Communications publishing peer-reviewed microbiology research. Learn more: Clinical Microbiology and Infection Learn more: CMI Communications

Take a look at our recent articles Diagnostic accuracy of Mucorales PCR testing in bronchoalveolar lavage fluid samples: a retrospective analysis of a prospectively collected cohort Prattes et al. | Clinical Microbiology and Infection Improving Bordetella pertussis isolation from PCR-positive samples: impact of modified Regan-Lowe agar, sample Ct value and transport time on culture positivity Klugherz et al. | CMI Communications Emergence of cefiderocol resistance mediated by blaAFM-1 overexpression and FptA mutations in clinical carbapenem-resistant Pseudomonas aeruginosa isolates Xiao et al. | Clinical Microbiology and Infection Vaginal dysbiosis is associated with urinary symptoms and urinary tract infection: A case–control study Wild et al. | CMI Communications

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Evolution of Pseudomonas aeruginosa

 

Two hundred years ago, give or take the odd decade, Pseudomonas aeruginosa was an environmental bacterium (1), apparently not one, as far as medical records in the pre-microbiology days can be discerned, associated as a human pathogen (2).

Today, P. aeruginosa is associated with a high number of multidrug-resistant infections (3), many of which are nosocomial. Those especially vulnerable to the bacterium are people with underlying lung conditions.

It is estimated that P. aeruginosa is responsible for communicable diseases leading to over 500,000 deaths per year around the world, of which over 300,000 are associated with antimicrobial resistance (AMR). People who are immunocompromised as a result of conditions such as COPD (smoking-related lung damage), cystic fibrosis (CF), and non-CF bronchiectasis, are particularly susceptible.

This week’s article looks at the bacterium and also highlights some new research that charts how the organism evolved rapidly and then proceeded to spread globally over the last 200 years. At the heart of this are changes in human behavior. 

See: https://www.linkedin.com/pulse/200-year-old-problem-evolution-multi-drug-resistant-tim-lqn4e/  

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

New class of antibiotics to fight resistant bacteria

 

Researchers have modified the chemical structure of naturally occurring peptides to develop antimicrobial molecules that bind to novel targets in the bacteria's metabolism.

 

The University of Zurich and the company Spexis have modified the chemical structure of naturally occurring peptides to develop antimicrobial molecules that bind to novel targets in the bacteria's metabolism. This has led to a new class of antibiotics that fight Gram-negative bacteria in a novel way. This includes carbapenem-resistant enterobacteria.

 

The starting point for the researchers' study was a naturally occurring peptide called thanatin, which insects use to fend off infections. Thanatin disrupts an important lipopolysaccharide transport bridge between the outer and inner membrane of Gram-negative bacteria. As a result, these metabolites build up inside the cells, and the bacteria perish. 

 

Antimicrobial peptides (AMPs) possess great potential for combating drug-resistant bacteria. Thanatin is a pathogen-inducible single-disulfide-bond.

 

However, thanatin is not suitable for use as an antibiotic drug, among other things due to its low effectiveness and because bacteria quickly become resistant to it.

 

The researchers therefore modified the chemical structure of thanatin to enhance the peptide's characteristics. Here, the scientists synthetically assembled the various components of the bacterial transport bridge and then used nuclear magnetic resonance (NMR) to visualize where and how thanatin binds to and disrupts the transport bridge.

 

Using this information, researchers from Spexis AG planned the chemical modifications that were necessary to boost the peptide's antibacterial effects. Further mutations were made to increase the molecule's stability, among other things.

 

The synthetic peptides were then tested in mice with bacterial infections -- and yielded good results, being effective against carbapenem-resistant enterobacteria.

 

Journal Reference:

 

Matthias Schuster, Emile Brabet, Kathryn K. Oi, et al. Peptidomimetic antibiotics disrupt the lipopolysaccharide transport bridge of drug-resistant Enterobacteriaceae. Science Advances, 2023; 9 (21) DOI: 10.1126/sciadv.adg3683

 

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

Virulence profiles of Pseudomonas aeruginosa clinical isolates and their association with polymicrobial infections

Pseudomonas aeruginosa is an opportunistic pathogen that can cause a variety of diseases especially in the hospital environment. However, this pathogen also exhibits antimicrobial activity against Gram-positive bacteria and fungi. This study aimed to characterize different virulence factors, secreted metabolites and to study their role in the suppression of Candida growth. Fifteen P. aeruginosa isolates were tested for their anticandidal activity against 3 different Candida spp. by the cross-streak method. The effect on hyphae production was tested microscopically using light and scanning electron microscopy (SEM). Polymerase chain reaction was used in the detection of some virulence genes. Lipopolysaccharide profile was performed using SDS-polyacrylamide gel stained with silver. Fatty acids were analyzed by GC-MS as methyl ester derivatives. It was found that 5 P. aeruginosa isolates inhibited all tested Candida spp. (50–100% inhibition), one isolate inhibited C. glabrata only and 3 isolates showed no activity against the tested Candida spp.

The P. aeruginosa isolates inhibiting all Candida spp. were positive for all virulence genes. GC-Ms analysis revealed that isolates with high anticandidal activity showed spectra for several compounds, each known for their antifungal activity in comparison to those with low or no anticandidal activity. Hence, clinical isolates of P. aeruginosa showed Candida species-specific interactions by different means, giving rise to the importance of studying microbial interaction in polymicrobial infections and their contribution to causing disease.

See:

Abd El-Baky RM, Mandour SA, Ahmed EF, Hashem ZS, Sandle T., Safwat, D. (2020) Virulence profiles of some Pseudomonas aeruginosa clinical isolates and their association with the suppression of Candida growth in polymicrobial infections, PLOS ONE 15(12): e0243418. https://doi.org/10.1371/journal.pone.0243418

Posted by Dr. Tim Sandle, Pharmaceutical Microbiology Resources (http://www.pharmamicroresources.com/)

New assay for bioterrorism threat

Researchers in Spain are using RPA as the foundation for a highly sensitive and specific solid-phase optical assay that can detect the potential biowarfare agent, Y. pestis, in less than an hour. The enzyme-linked oligonucleotide assay (ELONA) approach developed by Ioanis Katakis and Ciara K. O’Sullivan, at the Universitat Rovira i Virgili’s Interfibio Research Group, and the ICREA (Catalan Institution for Research and Advanced Studies), uses conventional PCR primers to amplify both single- and double-stranded Y. pestis DNA. Their work provides proof of concept for applying RPA in a heterogeneous format, with one primer immobilized onto a solid surface. The researchers aim to further develop the technology into an integrated, portable lateral flow-type test device for the rapid amplification and detection of Y. pestis in resource limited and field settings.

For further details see:

New National Quality Standard for Healthcare Associated Infection (QS 113)

A new standard has been issued for U.K. health services. This quality standard covers organisational factors in preventing and controlling healthcare-associated infections in secondary care settings.

Organisational factors include management arrangements, policies, procedures, monitoring, evaluation, audit and accountability.

Secondary care settings include hospital buildings and grounds; inpatient, day case and outpatient facilities and services; elective and emergency care facilities; and hospital maternity units and services.

For further details on the revised standard, see NICE.



Posted by Dr. Tim Sandle

Microbe Menaces Emerging Infectious Diseases

Infection Control Today have a free digital issue on the subject “Microbe Menaces Emerging Infectious Diseases, Hospital Pathogens Remain an Ongoing Challenge”.

The article can be accessed here.

This publication explores disease caused by emerging infectious threats as well as hospital pathogens, and the interventions – such as hand hygiene, contact precautions and environmental cleaning – that can be used to control and prevent infection transmission.



 Posted by Dr. Tim Sandle

Tuberculosis Is Coming Back – Here’s Why

Tuberculosis is a disease caused by bacteria that infects the lungs. It is highly contagious and can potentially be fatal, but until recently it was on the way out.

A special report by Megan Ray Nichols.

During the last 20 years, overuse of antibiotics has helped to create drug-resistant strains of the bacterium that have turned tuberculosis from a Victorian-era disease that was often romanticized into something that needs to be feared and respected once again.

Concentration in Cases

While the overall number of tuberculosis cases in the U.S. is dropping, a number of population subsets are increasingly affected by the disease.

A number of factors put individuals at risk for contracting TB, including weakened immune systems or medical professionals pass on the infection after treating infected patients. A 2014 report by the CDC revealed some worrisome trends, including the fact that more than 50 percent of TB cases are concentrated in four states: Florida, New York, Texas and Florida.

What do those four states have in common? They are also the main entry points for immigrants, both legal and illegal, who are entering the United States. As of 2013, more than 64 percent of TB cases were diagnosed in foreign-born individuals who had come to the United States.

Since a standard case of TB often costs around $17,000 to treat, many people who don’t have access to health care or insurance often go untreated, spreading the disease to anyone that they may come into contact with. Drug-resistant TB can cost even more, with a full treatment reaching $134,000. Extreme drug-resistant TB, which doesn’t respond to any of the traditional treatments, can cost nearly half a million dollars and even this cost doesn’t guarantee that the patient will be cured of the disease.

What Has Been Done?

TB causes more deaths globally than any other infectious diseases. It is airborne and released when an infected patient coughs or sneezes, and can easily be caught by anyone who is in close proximity to the infected individual.

The current immigration polices both in the U.S. and in areas like London do not allow for the screening and/or treatment of potentially infected individuals. Instead, large numbers of these individuals are living together, often in small or substandard housing which creates the perfect transmission conditions for TB and other similar diseases.

The Centers for Disease Control have guidelines in place requiring medical examinations for any refugees or immigrants coming into the United States, whether they are here on a temporary visa or permanently. Unfortunately, they can only perform these exams if the individuals are entering the country legally. Individuals who carry TB and other similar diseases but are not able to be examined are carrying a disease that was nearly eradicated in many countries into fresh breeding grounds.

What Precautions Need to be Taken?

While there is a great call right now for countries to open their borders in the wake of the events in Syria that left many as refugees, the borders should be opened intelligently.

• Housing needs to be improved for refugees or immigrants so that large numbers of people are not crammed into small spaces.
• Individuals need to submit to a medical exam before being allowed to enter a country. A basic TB test usually takes less than 24 hours if the patient isn’t symptomatic. 
• Medical establishments need to be more approachable — if an individual is presenting symptoms of TB, they should be able to approach a medical establishment for treatment, if for no other reason than to prevent the disease from spreading farther. 
• The public as a whole, including refugees and immigrants, needs to be educated on the symptoms and effects of the disease. Someone might go about their day just thinking they have a bad cough while transmitting TB to everyone they meet.

These precautions might seem a bit harsh, but with many people crossing borders into countries where TB was nearly a thing of the past, heavy-handed precautionary measures may be just the thing to help us wipe out TB once and for all.

Clinical Evidence Summary Antimicrobial Chemotherapy

Human papilloma virus (HPV) is the causative agent of cervical and anogenital cancers, with the HPV16 strain responsible for up to 60% of all HPV-associated cancers. Little is known about HPV susceptibility to disinfection. Researchers, using a novel method of virus production, demonstrate how two commonly used disinfectants are unable to inactivate HPV in a liquid suspension test.

For further details, see Infection Control Today

Posted by Tim Sandle

Incidences and Treatments for Buruli Ulcer

Buruli ulcer is a bacterial disease, alternatively called Bairnsdale ulcer, Searls ulcer, or Daintree ulcer. The tropical disease causes blood clots on the skin and, when untreated, leads to severe ulceration. The infectious disease caused by a bacterium called Mycobacterium ulcerans. It is the third most common mycobacterial disease after tuberculosis and leprosy.

The current treatment option primarily involves courses of antibiotics. More serious or untreatable cases require surgical intervention. To improve current treatment regimes, scientists are investigating alternative approaches; this article assesses some of these approaches alongside current practices.

In a short article, Tim Sandle assesses the current strategies and new treatment options for the disease.

The reference is:

Sandle, T. (2015) Incidences and Treatments for Buruli Ulcer, Journal of Ancient Diseases &

Preventive Remedies, 3 (2): 1000e122 (http://dx.doi.org/10.4172/2329-8731.1000e122)

For further information or to review a copy please contact Tim Sandle



 Posted by Tim Sandle

Data concerning the incidence of respiratory pathology in different seasonal periods

At different periods of the year, the human’s body's resistance decreases. For any of the forms of respiratory diseases, is useful for patients a preliminary investigation in order to diagnose and to treat the respiratory disease.

A new article of interest:

The human body is vulnerable to different pathogens. From this point of view we can see a high incidence of diseases that are part of the respiratory pathology. At different periods of the year, the human’s body's resistance decreases. For any of the forms of respiratory diseases, is useful for patients a preliminary investigation in order to diagnose and to treat the respiratory disease.

It is useful to consider implementing methods of public information and practical application of screening programs, for prevention, knowing a complexity of pathogens for a possible respiratory disease. Also is known the children as a vulnerable age group. Different forms belonging to the respiratory pathology are as consequence, or may occur in accordance with sinusal infections.

The reference is:

Chesca, A., Gyurka, A., and Sandle, T. (2015) Data concerning the incidence of respiratory pathology in different seasonal periods, Archives of the Balkan Medical Union, 50 (2): 208-212

If you would like a copy, please contact Tim Sandle

Posted by Tim Sandle

Reviewing the hygiene hypothesis

Exposure by infants to the typical bacteria found in the gastrointestinal tract  may protect a person, in later life, from autoimmune disease. To date, this theory is based on studies carried out using a mouse model, and this is outlined in some recent research. 

The researchers argue state that their evidence backs the 'hygiene hypothesis.' This theory puts forward the idea that the marked increase in autoimmune and inflammatory diseases since the 1950's. is the direct result from changes in our exposure to microbes which occur in childhood as a result of reduced exposure to the less than sanitary conditions.

The reference is:

Janet G. M. Markle, Daniel N. Frank, Steven Mortin-Toth, Charles E. Robertson, Leah M. Feazel, Ulrike Rolle-Kampczyk, Martin von Bergen, Kathy D. McCoy, Andrew J. Macpherson, and Jayne S. Danska. Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity. Science, January 17, 2013 DOI: 10.1126/science.1233521

Posted by Tim Sandle

Standards for Microbiology Investigations (SMI)

SMIs are a collection of recommended algorithms and procedures for clinical microbiology.

The new standards are developed and reviewed by the SMI Steering Committee, which includes Society for General Microbiology representative Professor Jodi Lindsay (St George’s University of London).

Details about recent reissued and withdrawn SMI documents can be found on this website and people can contribute to public consultations that are run to inform the development of SMIs.





Posted by Tim Sandle

Identification of Clostridium species

The genus Clostridium belongs to the family Clostridiaceae and it currently contains 203 species and 5 subspecies, with only a few species being pathogenic to humans. Of these species, 21 have been reclassified to other genera, 5 have been reclassified within the genus and 1 has been de-accessioned.

Clostridium are phylogenetically heterogeneous and are Gram positive but can decolourise easily and appear Gram negative or Gram variable, spore formers and non-spore formers, rods and cocci and anaerobic and non-anaerobic bacteria.

Medically significant Clostridium strains tend to be Gram positive rods (some are Gram variable), 0.3 – 2.0 x 1.5 – 20.0μm which are often arranged in pairs or short chains, with rounded or sometimes pointed or square ends. They are commonly pleomorphic and vary considerably in their oxygen tolerance. Some species such as Clostridium novyi type A and Clostridium haemolyticum may require extended incubation on pre-reduced or freshly prepared plates and total handling in an anaerobic chamber. Conversely, Clostridium tertium, Clostridium histolyticum and Clostridium carnis are aerotolerant and will form colonies on blood agar plates incubated in an atmosphere of air with 5-10% added CO₂.

Virtually all of the members of the genus, except Clostridium perfringens, are motile with peritrichous flagellae and form oval or spherical endospores that may distend the cell. They may be saccharolytic or proteolytic and are usually catalase negative. Many species produce potent exotoxins.

.

In 1994 the heterogeneity of this species was confirmed by 16S rRNA gene sequencing. This has been reaffirmed by the work of Yutin et al that 16S rRNA and ribosomal protein sequences are better indicators of evolutionary proximity than phenotypic traits. This genus like several others has undergone a number of revisions with the increasing availability of genomic data. An analysis of proteins from a number of members of this genus suggested another revision3. The main findings from the proposal suggested that:

The Selenomonas-Megasphaera-Sporomusa group are still members of the genus Clostridium

Clostridium difficile and its close relatives are placed within the family Peptostreptococcaceae. Under this proposal, the species Clostridium difficile would become Peptoclostridium difficile

Members of the family Ruminococcaceae belong to the genus Clostridium

It was also proposed to create six new genera to accommodate the 78 validly described species that fell outside the family Clostridiaceae. These genera are: Erysipelatoclostridium, Gottschalkia, Lachnoclostridium, Peptoclostridium, Ruminiclostridium and Tyzzerella

The type species is Clostridium butyricum.

For more about the identification of Clostridium species, see a special technical note from Public Health England.

Posted by Tim Sandle