Tuesday, 4 February 2020

Microbiology in Forensic Medicine

Microbial forensics is the study area that applies knowledge on microbiology to the challenges of forensic medicine, resulting promising but far from universal acceptance. Notwithstanding, this relatively novel sub-domain of medicinal forensics has laid grounds for an encouraging partnership that, due to its short existence, is in need of globalised methodological standardisation (1, 2). Once a consistent globally accepted set of guidelines emerge, its associated tools and paradigms will become as ubiquitous as microorganisms themselves. Microorganisms will then be providing reliable traceable evidence, crucial in the investigational process, be it in the course of a crime enquiry (3, 4), as an attempt to control the widespread of an epidemic (e.g., the recent tracking of coronavirus outbreak to patient zero and its point source), or even as pointers towards the most adequate treatment response when time is a constraint (5).

It is undeniable that microorganisms are becoming increasingly relevant in Forensic Medicine as professionals in the area build a more robust understanding of the intrinsic specificities of microbiomes, particularly due to the present capabilities of the biomolecular technologies at their disposal (6). Polymerase chain reaction (PCR), quantitative PCR (qPCR), fluorescent dyes and genetic probes, etc, individually or combined, empower the investigator, even when samples are minute or almost inexistent (7).

But what exactly makes the case for microbial forensics as a reputed science? The answer is simple and it is known by field experts as ‘predictable ecologies’ (8, 9). In simple terms this is defined by the application of undoubtful standardised methodologies that go from analysing a multicomplex ‘microbiome’ to ultimately relate it to an individualised ecology. Ergo, helping to accurately determine racial traits, geographical origin and other physiological singularities (6), link dynamic bodily fluids (e.g., vaginal, salivary, etc.) to specific individuals (10), generate exclusion hypothesis (11) supported by mathematical algorithms and predictive in silica models that greatly reduce apparent biological confounders (e.g., as with human twins), efficiently identify individual differences based on behavioural aspects and environmental exposure (12), analyse post-mortem, bodily decay and the agonal period (3), predict efficient medical approaches upstream to the infection cascade (13) and so forth.

[1] Aggarwal P, Chopra A, Gupte S, Sandhu S (2011). "Microbial forensics - An upcoming investigative discipline". Journal of Indian Academy of Forensic Medicine; 33.
[2] Fernandez-Rodriguez A, Cohen M, Lucena J, Van de Voorde W, Angelini A, Ziyade N, et al. (2015). "How to optimise the yield of forensic and clinical post-mortem microbiology with an adequate sampling: a proposal for standardisation". European Journal of Clinical Microbiology; 34.
[3] Metcalf J, Carter D, Knight R (2016). "Microbiology of death". Current biology : CB; 26:R561-R563.
[4] Metcalf JL (2019). "Estimating the postmortem interval using microbes: Knowledge gaps and a path to technology adoption". Forensic Science International: Genetics; 38:211-218.
[5] Engstrom-Melnyk J, Rodriguez PL, Peraud O, Hein RC. Chapter 5 - Clinical Applications of Quantitative Real-Time PCR in Virology. In: Sails A, Tang Y-W, editors. Methods in Microbiology. 42: Academic Press; 2015. p. 161-197.
[6] Hampton-Marcell J, Lopez J, Jack G (2017). "The human microbiome: an emerging tool in forensics". Microbial Biotechnology; 10:228-230.
[7] Kuiper I (2016). "Microbial forensics: next-generation sequencing as catalyst". EMBO reports; 17(8):1085-1087.
[8. Riedel S (2014). "The Value of Postmortem Microbiology Cultures". Journal of Clinical Microbiology; 52(4):1028.
9. Gunn A, Pitt S (2012). "Microbes as forensic indicators". Tropical biomedicine; 29:1-20.
10. Leake SL, Pagni M, Falquet L, Taroni F, Greub G (2016). "The salivary microbiome for differentiating individuals: proof of principle". Microbes and Infection; 18(6):399-405.
11. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R (2009). "Bacterial Community Variation in Human Body Habitats Across Space and Time". Science; 326(5960):1694.
12. Wu H, Zeng B, Li B, Ren B, Zhao J, Li M, et al. (2018). "Research on oral microbiota of monozygotic twins with discordant caries experience - in vitro and in vivo study". Scientific Reports; 8(1):7267.
13. Hemarajata P, Baghdadi JD, Hoffman R, Humphries RM (2016). "<span class="named-content genus-species" id="named-content-1">Burkholderia pseudomallei</span>: Challenges for the Clinical Microbiology Laboratory". Journal of Clinical Microbiology; 54(12):2866.

Post image by Hannah Gibbs on Unsplash

Wednesday, 8 January 2020

On the management of Paediatric Vesicoureteral Reflux

For any parent/carer dealing with a child diagnosed with Vesicoureteral Reflux, the state of alarm is constant, and consequently a certain emotional burden can be identified. For having all possible variables that infer in the child's quality of life, under perfect control, can be time-consuming and quite tricky. Nevertheless, it is primordial to first have a complete understanding of the disease basics, so whoever is caring for the affected child can understand that there are clinical responses addressing the problem and that the issue itself is characterised by grey areas where agreements had to be made between experts in the area. Why? Due to lack of consensus. 

Vesicoureteral Reflux is not immediately an easily describable succession of rigid events, there are underlying little aspects that can confuse the diagnostic and bring personal opinions from clinicians to the debate table. 

What is Vesicoureteral Reflux?
This relates to a flow of urine that is contrary to normal motion. Going from the bladder into the ureter and, sometimes/eventually, depositing into the renal system (e.g., kidney). 

Can it happen to any child?
For most subjects this type of reflux derives from an existing physiological anomaly of the ureterovesical junction occurring from birth (congenital anomaly), but it can also emerge from other origins such as: 

a) from high-pressure passing urine from secondary to posterior urethral valves
b) due to a neuropathic bladder (where associated peripheral nerves are dysfunctional),
c) due to a voiding dysfunction (incapacity to urinate as normally expected). 

How many are affected?
About forty percent of children experiencing a urinary tract infection (UTI) show signs of reflux according to [1], thus, considering that two to five percent of girls and one to two percent of boys experience a urinary tract infection before reaching puberty [2] the numbers and their underlying inference speak for itself. 

UTIs are the commonest bacterial disease present in the first three 3 months of life in humans, according to [3]; tolling to about over 10% of reported serious febrile events of bacterial origin in infants 2 to 6 months of age [4]; reflux nephropathy is a liability factor when considering inflammation of the lining of renal pelvis and parenchyma, resulting in injury to the kidney and scarring (lesions that are irreversible and that in case of progressive kidney disease can cause kidney failure). In that sense, reflux nephropathy can result in extremely nefarious consequences such as renal insufficiency or end-stage renal disease (that when moderate to severe can then trigger renin-mediated hypertension) [5].

How is the management of disease approached?
The very first objective in the management of vesicoureteral reflux in children is to avoid pyelonephritis [a], renal injury and other complications derived from the impact of reflux in the urinary system.

Clinicians do know that vesicoureteral reflux is common, but presently there is very little consensus to the best way to manage the disease (even among clinical experts) [6]. It is exactly because of the lack of consensus in regard to how this medical issue should be treated that the American Urological Association (AUA) gathered a group of experts to produce a treatment guide directed to children diagnosed with vesicoureteral reflux, with scope on vesicoureteral reflux in children diagnosed following a urinary tract infection [7]. If you happen to visit the document online bear in mind that it is preconditioned to children aged 10 years and younger with unilateral or bilateral reflux with or without scarring. In addition, it also entails that treatment recommendations are to be made jointly with the parents of the sick child. I suspect that is because of individual behavioural patterns of the patient, day-to-day habits and the different spaces the child might be involved in. All this can impact tremendously in the practical outcome.

As stated in the document "Only a few recommendations can be derived purely from scientific evidence of a beneficial effect on health outcomes [...] Evidence of the efficacy of medical management on health outcomes is available only for Grades I–IV reflux".

What is recommended?
To maintain information as reliable as possible in regard to what is postulated in the original document, and because the document is quite long (I had to read it over the course of several weeks, see HERE). I decided to copy directly from the original. However, this is purely a summary of very important information that requires interpreting by involved clinicians. The present information is only for informative purposes to empower parents towards a more informed conversation with their children's doctors. It should not be interpreted as a priori direct medical advice towards a certain decision. Because consensus, as already discussed, is difficult in this area, even among experts, treatment options are the result of a selection by 8 out of 9 panel members and are, therefore, categorised as guidelines. As expected, treatment is advised by the panel based on a number of conditions, for example, nature of injury, grading of injury (I to IV, see end of post) and age. 

Having said all this, the available approaches are:

(1) No treatment (including intermittent antibiotic therapy); 
(2) Bladder training
(3) Continuous antibiotic prophylaxis
(4) Antibiotic prophylaxis and bladder training
(5) Antibiotic therapy, bladder training and anticholinergics (drugs that block the action of the neurotransmitter acetylcholine); 
(6) Open surgical repair: "although proven to cure reflux in 90–98 percent of patients, has not been demonstrated to improve health outcomes other than pyelonephritis; for this outcome, the evidence suggests that children with Grade III or IV reflux receiving continuous antibiotic prophylaxis are 2.5 times more likely to develop pyelonephritis than children who have undergone successful antireflux surgery" [...] Thus, evidence-based recommendations provide limited practical guidance for the clinician.
(7) Endoscopic repair.

"These modalities are described in Chapter 1. The recommendations assume that the patient has uncomplicated reflux (e.g., no breakthrough UTI, voiding dysfunction, duplex systems [where the ureter with the ureterocele can drain the top half of the kidney whereas the other ureter drains the lower half resulting in frequent UTIs, possibly reflux, and if not treated potential kidney damage], or other comorbid conditions); [...]

An important variable in the scope of treatment is the presence of concurrent voiding dysfunction, a common occurrence among children with reflux. Because resolution of voiding dysfunction may be accompanied by resolution or diminution of reflux such children may require more aggressive treatment with antibiotics, anticholinergics, and bladder training (e.g., timed voiding, biofeedback, parental monitoring of voided volumes). Surgical repair of reflux is less successful in children with voiding dysfunction, and thus a higher threshold is necessary before surgery is recommended in such patients. Children with reflux should therefore be assessed for voiding dysfunction as part of their initial evaluation.


[1] Bourchier, D., Abbott, G. D., Maling, T. M. (1984). "Radiological abnormalities in infants with urinary tract infections". Arch Dis Childv, 59(7); pp. 620–624.

[2] Jodal, U. and Winberg, J. (1987). "Management of children with unobstructed urinary tract infection". Practical Pediatric Nephrology, 1, pp. 647–656(1987). 

[3] Krober, M. S., Bass, J. W., Powell, J. M., Smith, F. R., Seto, D. S. (1985). "Bacterial and viral pathogens causing fever in infants less than 3 months old". Am J Dis Child, 139(9):, pp. 89-92.

[4] Allen, L. H., Lei, C., Douglas, B. (2006). "Incidence and Predictors of Serious Bacterial Infections Among 57- to 180-Day-Old Infants". Pediatrics, 117 (5), pp. 1695-1701.

[5] Martínez-Maldonado, M., (1998). "Hypertension in end-stage renal disease". Kidney International, 54(68), pp. S67-S72.

[6] Elder, Snyder, Peters, et al., 1992; International Reflux Study Committee, 1981.

[7] Management and Screening of Primary Vesicoureteral Reflux in Children (2010, amended 2017), American Urological Association, [https://www.auanet.org/guidelines/vesicoureteral-reflux-guideline], last visited on the 8th of January 2020, Last update in 2017. 

[8] Image kindly taken from Radiopaedia, [https://radiopaedia.org/cases/illustration-vesicoureteric-reflux-grading].

[a] Inflammation of both the lining of the renal pelvis and the parenchyma of the kidney especially due to bacterial infection, as per the Merriam-Webster dictionary.

Post Photo by Robina Weermeijer on Unsplash.

Tuesday, 12 November 2019

"Vaping nearly killed me, says British teenager", by BBC News

I thought it would be pertinent to share this brand new story that came out published online today in the BBC News website. I had already posted some information on the topic concerning the dangers associated to vaping and vaporisers, but more and more reports are coming out that show detrimental effects on lung tissue caused by vaping fumes/toxicants. The truth is that people have been now using these for a while and even though the so called long-term studies aren't still available, the first real-world data is starting to come out... and it doesn't look good.

If you'd like to revisit my post access HERE. For the BBC News story entitled "Vaping nearly killed me, says British teenager" please access HERE

Friday, 11 October 2019

Is it safe to fridge-store food in metal container pots?

One of the most long standing myths or undeniable truths that my mother has always reinforced at home was to avoid putting cooking pans, metal pots and the like, in the fridge. From her 'limited' toxicology knowledge metals would leak out of the pot to the food stored in it, hence contaminating the food and consequently the organism of the person eating it/from it. I was a little child when I started hearing her go on about that, but where most of the times it's a hear-say stigma, dragged on through generations and multiplied by the satisfaction of empirical knowledge without consubstantiation by any kind of proven science, other times life has shown me that there is something there to learn from and apply, for the sake of our health and our safety.

Because of all these myths and empirical structuralism of undoubted 'truths' The Toxicologist Today blog was born back in 2010 - 9 years ago!! Today I will once again attempt to unveil the real toxicology facts that lie dormant in this idea that metal pans in fridges is definitely A BIG NO NO!


Since food is cooked in pans of all sorts, the first concerns that would emerge from placing a room temperature food-containing lid-covered pan in the fridge would be, in my humble opinion:

- Danger of Corrosion,

- Reactivity between food and container,

- Temperature exposure.

Pardon me for what can be interpreted as a blunt assumption, but from where my common sense stands I can see no other immediate possibilities, but I am well open to contribution (use the comments section down below). However, bear in mind I am not discussing food contamination by bacteria. This is purely related to the putative linking to metal contamination of food when stored in the fridge in a metal pan/container! 

I guess the best way to address the question is:

Can food be contaminated by metals present in food-storing containers when at a temperature equal or below 4 degrees Celsius?

The first thing we can assume is that if the food-storing containers (let's call them FSC for the sake of simplicity) are without lid, exposure to air will (allegedly) dissolute and more rapidly encourage transferring of metals to food that is in contact with [1] - simple oxireduction chemistry. The recommended maximum permissible levels of tin in food are described in Blunden and Wallace (2003)'s review [1] as of typically 250 mg/kg (200 mg/kg UK) for solid foods and 150 mg/kg for beverages. The authors of this review additionally state that based on published data there is only small and almost unintentionally cherry-picked evidence suggesting that the consumption of food or beverages containing tin at concentrations at or below 200 ppm has allegedly caused adverse gastrointestinal side effects in a small fraction of those exposed to it. They say allegedly because this is based on evidence from reports of adverse side effects anterior to follow-up studying of these cases, therefore with "limited", "incomplete" data of "uncertain veracity". Moreover, they have provided numbers on clinical studies reflecting on the same matter, and these refer 700 ppm or above as the concentration relates to adverse gastrointestinal side effects, but they also imply that the observations at higher concentrations lacked uniformity and linearity. Thus, concluding that there is little evidence for a link between "consumption of food containing tin at concentrations up to 200 ppm and significant acute adverse gastrointestinal effects" based on the available studies.

Moreover, and as a matter of additional protection when there are concerns that the metal might corrode, food tins are usually coated internally with lacquer. Lacquer is "a thermosetting resin polymerised on the surface of the tin" . There is a French study showing that such layer provides an approximately 24-fold increased protection in comparison to other tins without said coating (check [2] for references). Over the years this protection might be insufficient, especially in cases where acidic food is stored within, however for the sake of this post I am not considering food stored in fridges for longer than a couple of months.

Conor Reilly (2002) [2] considers that many factors can be involved and must be studied in relation to metal corrosion and metal transferring from containers to food, such as, the "presence of nitrate" in food that can increase the solubility of metals, "storage temperatures, length of storage time, presence of oxidising and reducing agents in the food". But he also states that after lead has been abandoned, the new lead-free containers have reduced tremendously the number of reported cases of metal-contaminated food in developed countries. 

Aluminium appears to be a great food/beverage-storing option for safety/quality reasons as [2] considers that the internal coating of aluminium cans (usually with resins such as vinyl epoxy) and the thermal resistance of the metal, inhibit, to an extent, the dissolution of the metal (check [2] for references). 

In what concerns cooking utensils, there are many safe and valid options these days (e.g., stainless steel and ceramics, etc...) that not only allow rapid conductivity of heat, but represent an adequate barrier to metal degradation even in the presence of acidic foods. Classic tools based on tinned copper are made with 'impure' led-tin mixtures and some studies (check [2] for references) have shown it. On the other hand traditional cast iron pots can contribute to higher levels of iron in food, especially if cooked in low intensity combustion.  Both aluminium pots and foils have been linked to aluminium re-uptake levels, and associated, directly or indirectly, to a range of neurodegenerative diseases like Alzheimer's [3]. Aluminium is a well-established, well-studied neurotoxic agent (can trigger oxidative stress,  promote inflammation and cellular apoptosis, etc).

From this very quick investigation of the vastly available literature on this topic, I have understood that the real issue is not so much linked to whether one stores food in metal pots put in the fridge, but the exposure of food to such metal containers, that due to intrinsic properties of both food and container, associated to the different cooking processes (temperature levels, length of heat exposure, etc), can contribute to the degradation of the metal itself and their inner coating layers.

The idea, I genuinely believe, is to:

1) always follow the instructions provided by each particular company on their specific product (read food-containing pot)


2) minimise exposure and contact between food and metal container, regardless of how safe the storing temperature might appear to be.

There is an 'infinite' list of studies out there that show many external participants involved in the metal degradation process, and some of these are fairly and unequivocally invisible to our naked eyes, nevertheless determinant in terms of effects to our general health.

[1] Blunden, S. and Wallace, T. (2003). "Tin in canned food: a review and understanding of occurrence and effect - Review". Food and Chemical Toxicology, 41(12), pp. 1651-1662. 

[2] "Metal Contamination of Food: Its Significance for Food Quality and Human Health". Book from 2002 by Conor Reilly- Chapter 4.2.2 Metal pick up during canning, page 51.

[3] Maya, S., Prakash. T., Madhu, K. D., Goli, D. (2016). "Multifaceted effects of aluminium in neurodegenerative diseases: A review". Biomedicine & Pharmacotherapy, 83, pp. 746-754.

First post photo by nrd on Unsplash

Second post photo by Scott Umstattd on Unsplash

Sunday, 6 October 2019

Waragi/Moonshine - The first time a documentary left me scientifically speechless

As I watched the fourth episode of the first season of Vice's Fringe, an overwhelming feeling of anguish took over my heart and stopped my brain from thinking. I accepted the outburst of commiseration as if I was part of that community my eyes could see dragging on senseless behaviour amidst the worse type of poverty that there is - the impossibility of dreaming.

Perhaps this initial paragraph will not make much sense if you just landed on this post without watching the 35-ish minute documentary on the wave of alcoholism that affects Uganda (capital of alcoholism in Africa; and apparently since 2011 figures have only gotten worse). This African country, as any other African country victim of irresponsible and selfish colonisation in the past, is still trying to find what it is to live freedom that was never returned in healthy shape. It's a bit like South America after Bolivar dreamt and prompted the country to fight for their own freedom... there is sickness in the eugenics of the revolutionary soul that results in the syndrome of inadequate deliverance when time, opportunity and comprehension are not exactly synchronised in the clock of our human nature.

Now going back to this documentary where the Ugandans' addiction to an artisanal alcoholic beverage is analysed. Women, themselves victims of historical preconceptions of higher magnitudes, are dribbling poverty with producing a fermented drink that is strong and crafted in some dodgy ways. There are reports of some consumers going blind after drinking this 'Moonshine' drink. Reports of the drink being cut with methanol or, even though unreported, sometimes with chloroform. Well, methanol in alcoholic drinks occurs almost spontaneously and if kept within legal levels (e.g., 0.4% in the European Union) will not harness harm. But when illicit methylated drinks are manufactured containing poisonous levels of methanol (some believe it'd be about 5% (V/V):95% (V/V) ethanol) [1] different serious adverse effects emerge. Blindness, metabolic disturbances such as renal failure, neurological dysfunction and even detrimental cardiovascular impact can occur [2]. 

The documentary describes addiction and toxicological effects in a fashion that brings back this modern bizarre idea of the Western civilised world taking tours of poverty tourism through the intestines of infected slums, whilst reacting in astonishment... as if suddenly what is seen is consequence of poor choice rather than the results of historical utter and inhumane exploitation through centuries of abysmal disrespect for other humans. Nevertheless, I watched it for the science, conscientious that science wasn't their immediate affliction, but the detached consequential vomiting of a reality. The consumption of Waragi (a native language mutation of the words war & gin) is the locals' favourite drink. Waragi, a war heritage from the times the natives were fighting for the crown during World War I and II. A drink so popular that has known many shapes and forms. The documentary even shows us that some have perfected or created their own flavours with, for example, fermented peeled bananas left to ripen for four days, squeezed for their juices, boiled, cut with industrial chemicals!!!! All of this taking place in pre-fabricated sheds with non-existent hygiene control of any sort or type. Suddenly quoted facts strike one numb:

"In April 2010 more than 80 people died after drinking Waragi contaminated with high amounts of methanol over a three week period in the Kambala district" it was said.

The documentary reveals us that more than 60% of those people's income is related to alcohol. Education is paid from profits directly emerging from commerce of alcohol, and that it is so rooted in their culture that in certain Ugandan communities alcohol is given to children as part of initiation rituals for I don't-know-what-purpose! In addition, and from the understanding that we are given to take, women depend on Waragi to survive financially in a nation that is still extremely male chauvinist. But this financial dependency has been officially scrutinised from so long ago that the illicit 'problem' was made an economic established legality with the Enguli Act [3] of 1965. 

However, it doesn't matter matter how many laws are made to embezzle a serious problem, be it financial or sanitary or the mix of both, if a country's structure and culture is not ready to understand the need for scientific knowledge simultaneously applied with the necessary regulations, the social fabrics will always perish amidst the inconsequential poverty and ignorance.

One thing is obvious from this documentary - The sanitary conditions involved in the process of brewing this produce are appalling! Even when we are moved from the rural areas to what is called the inner-city capital (where you expect conditions to help overcome the quality of the produce from villages) one is stunned by the fact that hygiene is basically non-existent. All this whilst one is coldly stung by the image of heavily addicted drinkers residing side by side with Waragi 'factories' as if they were crack-houses where the drug is made and served to zombies who depend on it to paradoxically function.

I was mesmerised by the self-assumption of the ridicule in some of the locals when one of them said that "[we] call it sulfuric acid flavoured with purified magnesium".

I was left speechless by so many things in this documentary, but above all, by my own incapacity to deal with the sadness that preyed on me whilst watching it. I had this article drafted for a long time, nevertheless, there was something in me that just couldn't trigger that energy to research on the toxicological aspects that actually jump out of this topic and beg dismantlement. I just couldn't do a good job writing about it. You can witness it as you read through though. The post is broken in phases that stumble on each other. I am totally aware of that. It is that it appears to me that sometimes these documentaries are not made to inform, or their immediate existence does not come from an informational view point; or the seeking of scientific validation. They often appear to be mere poverty tourism screenshots where people go sneak-peak at the bottom of human dignity to see the lengths other humans will subject themselves to, in order to just survive. 

[1] Paine, A. J.; Dayan, A. D. (2001). "Defining a tolerable concentration of methanol in alcoholic drinks". Human and Experimental Toxicology, 20(11), pp. 563-568.

[2] Jahan, K. Mahmood, D., Fahim, M. (2015). "Effects of methanol in blood pressure and heart rate in the rat". J Pharm Bioallied Sci., 7(1), pp. 60–64.

[3] Willis, J. (2007). "‘Clean Spirit’: Distilling, Modernity, and the Ugandan State, 1950–86". Joural of Eastern African Studies, 1(1), pp. 79-92.

Post image kindly taken from PEP Foru - Uganda [https://pepforumuganda.wordpress.com/2017/03/06/pep-forum-ugandas-moonshine-epidemic/].