Sunday, 1 March 2015

Culture reference strains

Examples of reference strains

Here is a handy list of reference strains for different microbiological tests.

Test
Example Reference Strain
Aesculin Hydrolysis Test
Positive control
Negative control
Enterococcus faecalis NCTC 12697
Streptococcus agalactiae NCTC 8181
Agglutination Test
Positive control
Negative control
N/A
Bile Solubility Test
Positive control
Negative control
Streptococcus pneumoniae NCTC 12977
Streptococcus mitis NCTC 10712
Catalase Test
Positive control
Negative control
Staphylococcus aureus NCTC 6571
Streptococcus mitis NCTC 10712
Coagulase Test
Positive control
Negative control
Staphylococcus aureus NCTC 6571
Staphylococcus haemolyticus NCTC 11042
Deoxyribonuclease Test
Positive control
Negative control
Staphylococcus aureus NCTC 6571
Staphylococcus haemolyticus NCTC 11042
Indole Test
Positive control
Negative control
Escherichia coli NCTC 10418
Proteus mirabilis NCTC 10975
Motility Test
Positive control
Negative control
Proteus mirabilis NCTC 10975
Acinetobacter lwoffii NCTC 5866
Nagler Test
Positive control
Negative control
Clostridium perfringens NCTC 8359*
Clostridium difficile NCTC 11204*
ONPG (ß-Galactosidase) Test (for
Enterobacteriaceae)
Positive control
Negative control
Escherichia coli NCTC 10418
Proteus mirabilis NCTC 10975
ONPG (ß-Galactosidase) Test (for Neisseria species
Positive control
Negative control
Neisseria lactamica NCTC 10617
Neisseria gonorrhoeae NCTC 8375
Optochin Test
Positive control
Negative control
Streptococcus pneumoniae NCTC 12977
Streptococcus mitis NCTC 10712
Oxidase Test
Positive control
Negative control
Pseudomonas aeruginosa NCTC 10662
Escherichia coli NCTC 10418
Oxidation/Fermentation of Glucose Test
(Gram negative rods)
Oxidation:
Positive control
Negative control
Pseudomonas aeruginosa NCTC 10662
Acinetobacter Iwoffii NCTC 5866
Oxidation/Fermentation of Glucose Test
(Gram positive cocci)
Oxidation:
Positive control
Negative control
Micrococcus luteus NCTC 2665
OF basal medium without carbohydrate
Porphyrin synthesis (ALA) Test
Positive control
Negative control
Haemophilus parainfluenzae NCTC 10665
Haemophilus influenzae NCTC 11931
Potassium Hydroxide Test
Positive control
Negative control
Escherichia coli NCTC 10418
Staphylococcus aureus NCTC 6571
Changing the Phase of Salmonella
Positive control
Negative control
N/A
Thermonuclease Test
Positive control
Negative control
Staphylococcus aureus NCTC 6571
Staphylococcus haemolyticus NCTC 11042
Urease Test
Positive control
Negative control
Proteus mirabilis NCTC 10975
Escherichia coli NCTC 10418
X and V factor Test
X and V factor
Haemophilus influenzae NCTC 11931
V factor only
Haemophilus parainfluenzae NCTC 10665
X factor only
Haemophilus haemoglobinophilus NCTC 8540*


Source: Public health England

Posted by Tim Sandle

Saturday, 28 February 2015

New USP #38

USP38-NF33

Official 01 May 2015

The USP–NF is a single–volume combination of two official compendia, the United States Pharmacopeia (USP) and the National Formulary (NF). Monographs for drug substances and preparations are featured in the USP. Excipient monographs are in the NF

Listed are items in which changes have been made to existing official text.

General Tests and Assays:

General Requirements for Tests and Assays

Chapter 1       Injections

Chapter 7       Labelling [NEW]

Apparatus for Tests and Assays

Chapter 41      Balances

Chemical Tests and Assays

Chapter 231    Heavy Metals [deleted]

Chapter 251    Lead

Physical Tests and Determinations

Chapter 659    Packaging and Storage Requirements - Introduction (deleted), Packing, General Definitions, Injection Packaging (added), and Storage Conditions

Chapter 660    Containers - Glass

Description, Specific Tests, and Functionality

Chapter 697 Container Content for Injections [NEW]

Chapter 852    Atomic Absorption Spectroscopy [NEW]

Chapter 853    Fluorescence Spectroscopy [NEW]

Chapter 854    Mid-Infrared Spectroscopy [NEW]

Chapter 857    Ultraviolet-Visible Spectroscopy [NEW]

Chapter 911    Viscosity-Capillary Viscometer Methods

Chapter 787    Measurement of Subvisible Particulate Matter in Therapeutic Protein Injections [NEW]

Chapter 1852  Atomic Absorption Spectroscopy – Theory and Practice [NEW]

Chapter 1853  Fluorescence Spectroscopy - Theory and Practice [NEW]

Chapter 1854  Mid-Infrared Spectroscopy - Theory and Practice [NEW]

Chapter 1857  Ultraviolet-Visible Spectroscopy - Theory and Practice [NEW]

Posted by Tim Sandle

Friday, 27 February 2015

Oxidase Test – an introduction

The oxidase test is used to determine if an organism possesses the cytochrome oxidase enzyme. The test is used as an aid for the differentiation of Neisseria, Moraxella, Campylobacter and Pasteurella species (oxidase positive). It is also used to differentiate pseudomonads from related species.

Oxidase positive bacteria possess cytochrome oxidase or indophenol oxidase (an iron containing haemoprotein). Both of these catalyse the transport of electrons from donor compounds (NADH) to electron acceptors (usually oxygen).

The test reagent, N, N, N’, N’-tetramethyl-p-phenylenediamine dihydrochloride acts as an artificial electron acceptor for the enzyme oxidase. The oxidised reagent forms the coloured compound indophenol blue.

The cytochrome system is usually only present in aerobic organisms which are capable of utilising oxygen as the final hydrogen receptor. The end product of this metabolism is either water or hydrogen peroxide (broken down by catalase).

There are many method variations to the oxidase test. These include, but are not limited to, the filter paper test, direct plate method, swab method, impregnated oxidase test strip method and test tube method. All times and concentrations are based upon the original recommendations.

Positive Result
Development of a deep purple-blue/blue colour indicates oxidase production.

Negative Result
No purple-blue colour/No colour change.

In relation to the oxidase test, Public Health England has issued a technical report, including safety information. The report can be accessed here.

  Posted by Tim Sandle

Thursday, 26 February 2015

Establishing a Cleanroom Safety Plan

There are many similarities with establishing and maintaining quality and safety cultures. Successful quality and safety cultures are top management driven using defined procedures and protocols based on Federal regulations, industry standards, and best management practices. A cleanroom safety program may be established, implemented, and maintained.

Jan Eudy has written an interesting article for Controlled Environments on the importance of cleanroom safety.

For instance:

‘The plan should define how personal protective equipment or cleanroom garments are worn to enhance operator safety. Safety criteria should include information on how to properly wear hoods, masks, goggles/safety glasses, coveralls, and boots/shoe covers.’

To view the article, see Controlled Environments.

Posted by Tim Sandle

Wednesday, 25 February 2015

Preparing for an Effective Lab Safety Inspection

The laboratory environment can be a hazardous place to work. Laboratory workers are exposed to numerous potential hazards including chemical, biological, physical and radioactive hazards, as well as musculoskeletal stresses.

The typical research facility contains a multitude of hazards. Most facilities will have a mix of research laboratories, instrument rooms, chemical storage areas, waste handling areas, and busy receiving/loading docks. The focus of this column will be on conducting safety audits in research laboratories, but the steps and the process can be applied to all the different areas of the facility.

‘Prior to entering the lab, make note of any signs, hazard indicators, and warnings. Lab entrances should have appropriate signage to alert those preparing to enter about the hazards present. Most important, emergency contact information for after-hours incidents should be listed. Double-check this again when exiting to note if all hazards are represented and that any newer ones have been added.’

This is the basis of a useful article in Lab Manager magazine. The article can be accessed on-line.

Posted by Tim Sandle

Tuesday, 24 February 2015

Are Bacteria as Individual as People?

Bacteria are as individual as people, according to new research by Professor Peter Young and his team in the Department of Biology at the University of York. Bacteria are essential to health, agriculture and the environment, and new research tools are starting to shed more light on them.

The York team dug up a square meter of roadside verge on the University’s campus in search of a bacterium called Rhizobium leguminosarum. The name means "root dweller of the legumes," and these bacteria are natural fertilizer factories that extract nitrogen from the air and make it available to peas, beans, clover and their wild relatives.

In the laboratory, the team extracted the bacteria from the plant roots and established 72 separate strains. They determined the DNA sequence of the genome of each strain. Their research, published in Open Biology, shows that each of those 72 strains is unique -- each has different genes and is capable of growing on different food sources.

People are unique because each of us inherits half our genes from our mother and half from our father, but bacteria reproduce by binary fission, making two identical daughters. What bacteria are good at, though, is passing packages of genes from one cell to another. It is this process of horizontal gene transfer that made every rhizobium unique.

"We can think of the bacterial genome as having two parts," says Professor Young. "The core genome does the basic housekeeping and is much the same in all members of the species, while the accessory genome has packages of genes that are not essential to the operation of the cell, but can be very useful in coping with aspects of the real world.

"Bacteria are like smartphones. Each phone comes out of the factory with standard hardware and operating system (core genome), but gains a unique combination of capabilities through apps (accessory genes) downloaded through the internet (by horizontal gene transfer)."
We increasingly recognize the vital roles played by bacterial communities, such as those in our gut or on the roots of plants. Many researchers have used variation in a standard core gene to draw up lists of the species in a community, but the new research shows that a list of names is not sufficient.

"There may be 300 people called Baker in your city, but you can't assume that there are 300 people baking bread," explains Professor Young.

It is possible, with more sequencing effort, to look at all the genes in a bacterial community -- an approach called "metagenomics" -- but to understand how they are functioning, we also need to know which genes occur together in the same bacterium. This new study helps us to understand the way in which bacterial genomes are assembled.

Story Source: University of York.

Journal Reference:
Nitin Kumar, Ganesh Lad, Elisa Giuntini, Maria E. Kaye, Piyachat Udomwong, N. Jannah Shamsani, J. Peter W. Young, Xavier Bailly. Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biology, January 2015 DOI: 10.1098/rsob.140133

Posted by Tim Sandle

Monday, 23 February 2015

Dracunculiasis and the Long Decline of an Ancient Disease


The disease dracunculiasis has ravaged human populations for thousands of years (reference to the disease is documented in the Egyptian medical Ebers Papyrus, dating from around 1550 BC.) Current indications suggest that global incidences of the disease have been rapidly declining due to the concerted efforts of national and international health agencies. Here, only 148 dracunculiasis cases were reported worldwide in 2013 (which represents the lowest annual total ever recorded) and only four endemic countries remain: Chad, Ethiopia, Mali and South Sudan. With these countries, the majority of the cases occur in South Sudan. Nonetheless across these regions the number of endemic villages has declined from the peak of 23,735 in 1991 to 79 in 2013.

The disease is the basis of a new editorial by Tim Sandle. The reference is:

Sandle, T. (2015) Dracunculiasis and the Long Decline of an Ancient Disease, Journal of Ancient Diseases & Preventive Remedies, 2 (3): 1-2

For a copy, please contact Tim Sandle

Posted by Tim Sandle

Sunday, 22 February 2015

How bacteria control their size

New work shows that bacteria (and probably other cells as well) don't double in mass before dividing. Instead they add a constant volume (or mass) no matter what their initial size. A small cell adds the same volume as a large cell. By following this rule a cell population quickly converges on a common size.

A new study has found that found that rather than doubling in size every generation, each cell added the same volume (or mass; the term reflects the measurement technique). Importantly a cell that was small added the same volume as a cell that was large.

For further details see:

Sattar Taheri-Araghi, Serena Bradde, John T. Sauls, Norbert S. Hill, Petra Anne Levin, Johan Paulsson, Massimo Vergassola, Suckjoon Jun. Cell-Size Control and Homeostasis in Bacteria. Current Biology, 2014; DOI: 10.1016/j.cub.2014.12.009

  Posted by Tim Sandle

Saturday, 21 February 2015

Skin microbes trigger specific immune responses

The immune system in the skin develops distinct responses to the various microbes that naturally colonize the skin, referred to as commensals, new research in mice shows. A research team found that each type of microbe triggers unique aspects of the immune system, suggesting that immune cells found in the skin can rapidly sense and respond to changes in microbial communities.

The research showed that colonizing the skin of mice with S. epidermidis increased the number of CD8+ T immune cells, which produced the chemical messenger IL-17A. Dendritic cells, another type of immune cell, played a key role in generating this specific, non-inflammatory response.

For further details, see:

Shruti Naik, Nicolas Bouladoux, Jonathan L. Linehan, Seong-Ji Han, Oliver J. Harrison, Christoph Wilhelm, Sean Conlan, Sarah Himmelfarb, Allyson L. Byrd, Clayton Deming, Mariam Quinones, Jason M. Brenchley, Heidi H. Kong, Roxanne Tussiwand, Kenneth M. Murphy, Miriam Merad, Julia A. Segre, Yasmine Belkaid. Commensal%u2013dendritic-cell interaction specifies a unique protective skin immune signature. Nature, 2015; DOI: 10.1038/nature14052

Posted by Tim Sandle

Friday, 20 February 2015

GMP Data Integrity Definitions and Guidance

The MHRA has published a guidance document headed “GMP Data Integrity Definitions and Guidance.” The document has been issued due to concerns from European inspectors about the storage, handling and traceability of data, especially data contained within computerised systems.

Data integrity: The extent to which all data are complete, consistent and accurate throughout the data lifecycle.

The introduction to the document reads:

“Data integrity is fundamental in a pharmaceutical quality system which ensures that medicines are of the required quality. This document provides MHRA guidance on GMP data integrity expectations for the pharmaceutical industry. This guidance is intended to complement existing EU GMP, and should be read in conjunction with national medicines legislation and the GMP standards published in Eudralex volume 4.

The data governance system should be integral to the pharmaceutical quality system described in EU GMP chapter 1. The effort and resource assigned to data governance should be commensurate with the risk to product quality, and should also be balanced with other quality assurance resource demands. As such, manufacturers and analytical laboratories are not expected to implement a forensic approach to data checking, but instead design and operate a system which provides an acceptable state of control based on the data integrity risk, and which is fully documented with supporting rationale.

Data integrity requirements apply equally to manual (paper) and electronic data. Manufacturers and analytical laboratories should be aware that reverting from automated / computerised to manual / paper-based systems will not in itself remove the need for data integrity controls. This may also constitute a failure to comply with Article 23 of Directive 2001/83/EC, which requires an authorisation holder to take account of scientific and technical progress and enable the medicinal product to be manufactured and checked by means of generally accepted scientific methods.”

The document can be accessed via the MHRA here.

Posted by Tim Sandle

Thursday, 19 February 2015

TB Alliance Advances Next-Generation TB Drug Candidate into Clinical Testing


TBA-354 is the first potential tuberculosis drug to advance to Phase 1 trial in six years

TB Alliance has announced the start of the first human trial of a new tuberculosis (TB) drug candidate, designated TBA-354. It is the first new TB drug candidate to begin a Phase 1 clinical trial since 2009.

“There is a critical gap of new compounds for TB,” said Mel Spigelman, MD, President and CEO of TB Alliance. “The advancement of TBA-354 into clinical testing is a major milestone, not only because of the potential it shows for improving TB treatment, but because it is the first new TB drug candidate to begin a Phase 1 clinical trial in six years.”

TBA-354 comes from the nitroimidazole class of chemicals, known for being effective against drug-sensitive and drug-resistant tuberculosis. The class also includes the experimental TB drug pretomanid (formerly PA-824), which is being tested as a component of other novel regimens in multiple clinical trials.

TBA-354 emerged from studies designed to identify a next generation nitroimidazole for TB. TB Alliance conducted the studies in collaboration with the University of Auckland and University of Illinois-Chicago. Once identified, TB Alliance further advanced TBA-354 through pre-clinical development and is now the sponsor of the Phase 1 study.

In preclinical studies,
 TBA-354 demonstrated more potent anti-bactericidal and sterilizing activity compared to pretomanidRecruitment is under way to enroll nearly 50 U.S. volunteers for the randomized, double-blind Phase 1 trial, which will evaluate the safety, tolerability, pharmacokinetics, and dosing of TBA-354.
 
The World Health Organization reported that 1.5 million people die each year from TB, and more than nine million were diagnosed with the disease. The lack of short, simple, and effective treatments is a significant obstacle to TB control. However, because there is little economic incentive to develop new tools, there are not enough promising drugs in the pipeline, which could hinder efforts to develop the appropriate treatments needed to combat the TB epidemic.

Posted by Tim Sandle

How bacteria control their size

New work shows that bacteria (and probably other cells as well) don't double in mass before dividing. Instead they add a constant volume (or mass) no matter what their initial size. A small cell adds the same volume as a large cell. By following this rule a cell population quickly converges on a common size. A new study has found that found that rather than doubling in size every generation, each cell added the same volume (or mass; the term reflects the measurement technique). Importantly a cell that was small added the same volume as a cell that was large. For further details see: Sattar Taheri-Araghi, Serena Bradde, John T. Sauls, Norbert S. Hill, Petra Anne Levin, Johan Paulsson, Massimo Vergassola, Suckjoon Jun. Cell-Size Control and Homeostasis in Bacteria. Current Biology, 2014; DOI: 10.1016/j.cub.2014.12.009
Posted by Tim Sandle

Wednesday, 18 February 2015

Skin microbes trigger specific immune responses

The immune system in the skin develops distinct responses to the various microbes that naturally colonize the skin, referred to as commensals, new research in mice shows. A research team found that each type of microbe triggers unique aspects of the immune system, suggesting that immune cells found in the skin can rapidly sense and respond to changes in microbial communities.

The research showed that colonizing the skin of mice with S. epidermidis increased the number of CD8+ T immune cells, which produced the chemical messenger IL-17A. Dendritic cells, another type of immune cell, played a key role in generating this specific, non-inflammatory response.

For further details, see:

Shruti Naik, Nicolas Bouladoux, Jonathan L. Linehan, Seong-Ji Han, Oliver J. Harrison, Christoph Wilhelm, Sean Conlan, Sarah Himmelfarb, Allyson L. Byrd, Clayton Deming, Mariam Quinones, Jason M. Brenchley, Heidi H. Kong, Roxanne Tussiwand, Kenneth M. Murphy, Miriam Merad, Julia A. Segre, Yasmine Belkaid. Commensal%u2013dendritic-cell interaction specifies a unique protective skin immune signature. Nature, 2015; DOI: 10.1038/nature14052

Posted by Tim Sandle

Tuesday, 17 February 2015

Pharmig Conference Report

A review of the recent Pharmig conference - the U.K.'s leading pharmaceutical microbiology conference.


Posted by Tim Sandle

Pharmacopeial Forum 41 (1)

The USP Pharmacopeial Forum has a new update. This is Volume 41, No.1. Of interest in the new issue is:

Chapter 21      Thermometers (Revision proposal target, USP39-NF34): It is proposed to omit this general chapter from USP.

Chapter 856    Near-Infrared Spectroscopy (Revision proposal target, USP39-NF34)

This new general chapter is being proposed as part of the broader initiative to revise the general chapters related to spectroscopy. This chapter provides calibration and qualification criteria for near-infrared (NIR) spectroscopic instrumentation as well as the acceptable procedure validation criteria

Chapter 1119 Near-Infrared Spectroscopy (Revision proposal target, USP39-NF34)

The chapter is to be re-numbered to <1856> and a change of title, Near-Infrared Spectroscopy – Theory and Practice.

Chapter 1790 Visual Inspection of Injections (Revision proposal target, USP39-NF34)

A new general chapter aimed to provide guidance on the inspection of injectable drug products for visible particles. The methods discussed are also applicable to detection of other visible defects that may affect container integrity or cosmetic appearance of the product.

 Posted by Tim Sandle