Clinical Infectious Diseases - Science topic

Ido From

The best way of end-point amplification of target region using RNA directly extracted from tracheal/cloacal swabs is making complementary DNA (Step 1) and amplify target region from complementary DNA (Step 2).

One-step RT-PCR system can lead to lower yields or efficiency, more complicated to troubleshoot, and does not provide a stock of cDNA for future use. Since RNAs are unstable so, you can reverse transcribe them immediately and perform PCR later (Two-step PCR System).

Still if you want to use One-Step RT-PCR system, you may use following kits;

1. QIAGEN OneStep RT-PCR Kit, https://www.qiagen.com/us/products/discovery-and-translational-research/pcr-qpcr-dpcr/pcr-enzymes-and-kits/one-step-rt-pcr/qiagen-onestep-rt-pcr-kit/

2. SuperScript™ III One-Step RT-PCR System with Platinum™ Taq DNA Polymerase (you mentioned).

Globally, Candida albicans is the most prevalent species associated with invasive candidiasis; however, the distribution of non-albicans Candida spp

Dear Alina,

Very very pertinent discussion.

I think it will not be clear to get any conclusion by the case study of two countries only.

In India, there is less death rate in comparison to USA.

The case of Italy, Germany, UK, Spain , France and many other European countries suffered a lot.

The death rate and affected people is different in different countries and even different in different zones of a Country.

So, the conclusion is very tough.

Only one thing that I think , may not be correct, is the "IMMUNITY".

The more sophisticated lives are more sensitive .

So, the fighting power of less sophisticated people is comparatively high.

I think , the people who work hard and lead live with nature are , though affected by COVID-19, were recovered naturally.

Thanks

N Das

Establishing the relationship of Double J stent Catheters with the episodes of CAUTI and CRBSI and subsequently link its prolonged exposure leading to bacterial translocation as a risk factor for the development of the sepsis.

Hi. Mostly aphthous ulcers, can be a result of stress, certain vitamin deficiency, hormonal fluctuations and even unintended mouth injuries.

Yes, I am interested @Giovanni

https://www.ijidonline.com/article/S1201-9712(06)00016-6/fulltext

Dear Diana Rodríguez Hurtado , This is an important and interesting article

Can you provide additional information e.g. Gram stain, colony morphology in other culture medium?

Good luck

Dear Monem 

thanks for valuable suggestion.

Thank you for your answers! :)

You might find this article of interest.

http://www.health.gov.au/internet/main/publishing.nsf/Content/cda-cdi4101l.htm Shigellosis reported from every jurisdiction in Australia.

If an infection becomes manifest 48 hrs or later after admission, a nosocomial infection is likely. A nosocomial infection. however, does not necessarily mean that the pathogen has been transmitted during hospital stay. A hospital acquired infection may be caused by endogenous flora or by exogenous flora (i.e. transmitted to the patient in whatsoever way).

Pointing towards the pathogens itself it means, if you isolate a pathogen within the first 48 hrs after admission, and the patient has had no previous hospitalization or health care stay (nursing home, ...) than it is pretty much likely a community and not a hospital acquired pathogen. A pathogen, isolated later during hospital stay can be reliably categorized as hospital acquired (i.e. nosocomial acquired) only, if you can rule out that the patient was not colonized upon admission. (Make sure to discriminate between colonization and infection; a patient may acquire MRSA in a hospital without getting sick – i.e. he becomes colonized. A patient without MRSA colonization upon admission may get a wound infection with MRSA after surgery – he acquires a nosocomial infection.)

asymptomatic throat carriers of beta hemolytic streptococci & healthy children should not be treated with antibiotics. 

Thank you, Omar Okasha.

I have seen the Weinberger paper because I also have a side interest in modeling changes to invasive pneumococcal disease following vaccine introduction using carriage data. I am not sure this model would directly apply to the incidence of resistant IPD following carriage of resistant pneumococci but it is an interesting question to tackle if the data to do so is available.

No ...since there are a lot of commensial niesseria which may add to confusion on gram stain. so culture or molecular dtetection is necessary

How can PBS-BSA be called as a preservative Buffer? And presence of antibiotics in any buffer can be a very short term solution. Phil is right in pointing out at Isothiazolinone. It will take care of bacteria, fungi, algae everything.

  The chocolate agar is a complete media rich in nutrients for growth and any bacteria will grow.

Antibodies elicited during earlier time points post-infection could be trapped in immune complexes. This would preclude detection of both antigen and antibody.

I don't personally have experience in the hospital setting....BUT regardless of your field you should be able to break down your team (should be a team) brainstorm session into a standard "Fish Bone" format. Look to the internet for a simple fish bone diagram. On each point of the "fish bone" you have a key feature.Most common used in a lot of fields I've been in might work for you. The headers would be - Man/Machine/Environment/Method/Material. Anything that relates to the key point your trying to solve R.C. goes up on the board under 1 of those categories. No matter how unlikely the reason is you still put it up there. This empowers your team to speak up and can open your eyes to other issues that are not even part of this current issue.

After all your ideas from the team are on the Fish bone, you go through as a team and circle the most likely 5 it could be by group vote. Take those 3 and do a visual for the team. Show that issue followed by what should it be/what is normal/what is standard.....once you establish that, now go back and find out what the condition was of that specific topic in your case your trying to solve. If it was the realm of your "standard" its less likely the cause (but still could be) and if it wasn't in standard/spec/etc. Then that is a big flag to take to the next step.

At  this point grab any of the ones that were not standard/normal/in spec....and write them in a column. For each one use the 5 WHY process to get to root cause. Example below

Issue- The car failed to start today-

 Direct cause #1 Light in the car was left on over night

Why #1 The light was left on because the door was not closed all the way

Why #2 The door wasn't closed all the way because the seat belt got stuck in the door closure

Why #3 The seat belt got stuck because the belt tension spring didn't retracted it after it was unlatched.

Why #4 The spring in the belt needs replacing because it can't function as needed anymore

In this example most would stop at the Direct Cause but in realty it could happen again because the door light was a contributing factor to the light staying on but what really happen was the seat belt got stuck in the door not letting it close because the spring needs repair.

"It s a very simple example for demonstrating purposes only"

The key is to always push past 3 Why's for each of your, team agreed, Direct Causes. Go until they dont make much sense to push father or start to sound silly  (example why is the belt spring bad....we don't do a force test on our belt system and spring in our car each time we drive- No one does this and is unrealistic to expect also.

Once you have your Root Cause now go and test it out. List your action items on how to solve the problem, and in this case the problem was a bad spring. When you complete your action items to solve the problem, compare the current issues happening vs what it was like before the fixes. If you can improve the results you did it.

Remember you can make progress and still not find all the issues. sometimes several attempts are made to find all aspects that didn't pop up the first go around.

Lastly its good to get people involved in the process/task and those that don't know your process. An outside set of eyes has asked the simple questions or brought the over-looked idea to the table more than once to teams I've lead on solving this.

Remember that in the brainstorming stage NO IDEA is bad as long as it can be tied to the problem. Let it get voted out later. If not you will cause people to not take the exercise seriously.

I typed this while doing some other tasks so please excuse any grammar or spelling issues but I wanted to get this to you to start with something

There is an interesting and applicable commentary in Lancet Infectious Disease this week.

Barnini, S., Ghelardi, E., Brucculeri, V., Morici, P., and Lupetti, A. (2015). Rapid and reliable identification of Gram-negative bacteria and Gram-positive cocci by deposition of bacteria harvested from blood cultures onto the MALDI-TOF plate. BMC microbiology 15, 124.

Carbonnelle, E., Mesquita, C., Bille, E., Day, N., Dauphin, B., Beretti, J.-L., Ferroni, A., Gutmann, L., and Nassif, X. (2011). MALDI-TOF mass spectrometry tools for bacterial identification in clinical microbiology laboratory. Clin Biochem 44, 104-109.

Deak, E., Charlton, C.L., Bobenchik, A.M., Miller, S.A., Pollett, S., McHardy, I.H., Wu, M.T., and Garner, O.B. (2015). Comparison of the Vitek MS and Bruker Microflex LT MALDI-TOF MS platforms for routine identification of commonly isolated bacteria and yeast in the clinical microbiology laboratory. Diagn Microbiol Infect Dis 81, 27-33.

Kohlmann, R., Hoffmann, A., Geis, G., and Gatermann, S. (2015). MALDI-TOF mass spectrometry following short incubation on a solid medium is a valuable tool for rapid pathogen identification from positive blood cultures. Int J Med Microbiol 305, 469-479.

Schneiderhan, W., Grundt, A., Wörner, S., Findeisen, P., and Neumaier, M. (2013). Work flow analysis of around-the-clock processing of blood culture samples and integrated MALDI-TOF mass spectrometry analysis for the diagnosis of bloodstream infections. Clin Chem 59, 1649-1656.

Singhal, N., Kumar, M., Kanaujia, P.K., and Virdi, J.S. (2015). MALDI-TOF mass spectrometry: an emerging technology for microbial identification and diagnosis. Front Microbiol 6, 791.

Good morning Nabuhiro.

On could imagine at least two mechanisms that cause headache in patients with severe bacteremia:

1) The increased plasma level of inflammatory mediators that disturb the trigemino-vascular system and create various types of headache as is the case in catamenial migraine (where prostaglandins are involved) or in some thoracic pathologies like aortic dissection (see Kamtchum et al, 2015 / PMID 26082134 / attached file). Moreover, some bacterial toxins might have an intrincic potential to stimulate CNS nociceptors.

2) The activation of the sympathetic system as a part of the body response to physiologic (especially circulatory) perturbations induced by bacteremia. This activation of the sympathetic system could result in an increase in systemic blood pressure that causes headache (as seen in hypertensive encephalopathy, posterior reversible encephalopathy syndrome - PRES, eclampsia or phaeochromocytoma).

I hope this helps for your research. Good luck!

I totally agree with Dr Mohamed Elkoushy and would like to add that recommendations for pregnant women are to be screened by urine culture by the end of first trimester. If asymptomatic bacteruria detected, then antibiotic is given and further screening during whole pregnancy is recommended. If no asymptomatic bacteruria is detected by screening at then end of first trimester, then no further screening is recommended during the whole course of pregnancy.

I'm surprised that the 16s PCR is negative, as discharges are seldom sterile. However, such samples may be highly inhibitory. I would advise reanalysing the sample with a small amount (ca. 2 ng) of bacterial DNA added. If it still comes up negative, the sample is inhibitory (try further purification, or just dilute it). If it comes up positive, your sample is probably free of bacteria. 

Note however, that some bacteria may amplify poorly with the 16s primers. 

Hi Terri, I think this is possibly the first example of a new generation of more subtle diseases. The kinetics of spread are relatively slow and highly granular and this explains why these outbreaks have gone hidden for so long. Also this is not a 'silo' disease with a simple diagnosis, the effects are complex and can probably be best described as exacerbation of existing conditions. Hence it hides behind other recognisable diseases. Have just submitted a big review attempting to show that something like cytomegalovirus could cause such disease types. Still many questions to be answered which was why I asked for help. Cheers

Rod

Thanks sir for your valuable information

In response to colleagues’ inquiries about any relevance to blood donors of recent MERS-CoV spread to the Korean peninsula, the following reflects what recently came from colleagues in the US and Europe. So far, there has been no evidence of parenteral transmission published. No specific intervention related to blood donors has been recommended, and there are no new recommendations related to ongoing transmission in the Middle East or the outbreak in South Korea at this time. Donors must be well on the day of donation, and in the unlikely event that a history of MERS-CoV infection is provided by a donor, they should be fully recovered before being accepted for phlebotomy.

VHF cases are certainly not always malaria positive – if that were true then there would not be cases of CCHF in Europe or northern Asia. However, this is definitely an interesting (and underresearched) area.

Ebola screening in West Africa at present has a malaria lateral-flow test performed concurrently - these statistics are not publically available as the malaria screen is informative rather than for diagnostic purposes. The majority of Ebola positive cases are malaria negative, but it does appear that cases of Ebola/malaria co-infection are more likely to end in a fatal outcome. If this is a genuine trend it could bias experiences of small VHF outbreaks - coinfection leads to more severe cases and severe cases are more likely to tested which would give the impression that most/all cases are both VHF and malaria positive.

It seems logical that any underlying infection that weakens the immune system will increase the likelihood of developing a symptomatic VHF infection if exposed (infectious doses + the level of asymptomatic infection are also underresearched areas for most/all VHFs) and for that infection to end in a fatal outcome, so being malaria or HIV positive when exposed to a VHF virus is not likely to end well. However, at present we do not have enough data to make firm hypotheses. I am sure that someone will analyse the association between malaria/Ebola co-infection and the change in case fatality rate when compared to Ebola only infections once the outbreak has ceased - at the present though all efforts are focused on providing assistance in the affected regions

I agree with you. But I can not follow the third explanation. Do you mean the second challenge damage the immune tissue or organs? Such as, altering the total number of T cells or subgroups. I am reasrching the effect of  influenza vaccination on cognitive function during pregnancy. And i have found A(H1N1) influenza vaccine vaccination contribute to neurogenesis in offspring and pregnant mothers. I think the mechanism links to T cells in the periphery, such as the systemic T cells were recruited to the choroid plexes.

This website may partially already cover what you were thinking of 

I am also looking at bibliometrics to go alongside my research investments (see my pubs list for the general idea) work, so am ploughing through papers related to (for the moment, pneumonia, HIV, TB and malaria) that have a UK author. Will soon have an idea of numbers across different types of science there. Not specifically highlighting the case reports, but it will cover disease areas within infection. 

Hi,

very nice reviews from Vinh, Lancet Infect Dis 11; Kuhns, DB, NEJM 2010 and Falcone Curr Opin Infect Dis 12. Watch out mainly from Gram (+) indeed but also mold infections and especially breakthrough fungi since those patients are under long-term antifungals.

See u,

Many thanks Elena! :)

Concomitant infection may be more appropriate as co-infections tend to have more in common e.g. exposure, route of infection, clinical presentation, pathology/-genesis, outcome or treatment. I guess if the there is suggestion of say a common route of infection e.g. blood transfusion then malaria and HIV could, in that context, be co-infections

Please refer to the following very good study and their Methods

If you have further questions, consider contacting the authors of this study

jgrosse4@jhmi.edu or dalmeid3@jhmi.edu.

To assess the bactericidal and sterilizing activity of the first-line regimen, we infected 223 female BALB/c mice by aerosol with M. tuberculosis strain H37Rv, achieving a mean implantation of 2.62 (SD 0.44) log 10 cfus in the lungs, with the spleens being culture-negative the day after infection.

Our objective was to establish a heavy infection with high cfu counts in the lungs and the spleens; as such, our original protocol was to initiate treatment 6 wk after infection. However, by 4 wk after infection, 12 mice had already died and all remaining mice were sick; therefore, we began treatment at 4 wk postinfection.

An additional 10 mice died during the first 4 d of treatment. To compensate for this loss of mice, we reduced the numbers of mice killed on day 0 (the day of treatment initiation) as well as at some of the relapse assessment time points (detailed in Materials and Methods).

I think fecal transplant should be arranged in this case. Meanwhile, You could try another cycle of fidaxomicine or other drugs less expensive as rifaximine, or give vancomicine a last chance (but the tappered cycle, at least 6 weeks)

Hi,

The subjects is controversial. Gastroenterologists have looked at the subject with skepticism, and cardiologists has not taken this association as a targeted clinical approach in daily practice. Publications in marginal impact factor journals indicate a potential role of H. pylori in atherosclerosis/atherogenesis. However, other publications in higher impact journals consider that the subject is still debatable. I think that current data accumulated still does not allow one either to prove or to disprove this association.

Actually, I used to teach my medical graduate students about a potential association between H. pylori (and other infective agents such as C. pneumonie) with atherogenesis, and I still do. But this has been taken just in a conceptual background.

Although some amount of data on this subject have accumulated for more than a decade, a definite associate between H. Pylori infection, atherosclerotic plaque formation and development, and further myocardial infarction triggering still needs to be demonstrated in large randomized trials.

These few references may provide some insights into the subject. I hope they can be of aid.

1) Anderson JL, Muhlestein JB, Carlquist J, Allen A, Trehan S, Nielson C, Hall S, Brady J, Egger M, Horne B, Lim T. Randomized secondary prevention trial of azithromycin in patients with coronary artery disease and serological evidence for Chlamydia pneumoniae infection: The Azithromycin in Coronary Artery Disease: Elimination of Myocardial Infection with Chlamydia (ACADEMIC) study. Circulation. 1999 Mar 30;99(12):1540-7.

2) Kowalski M. Helicobacter pylori (H. pylori) infection in coronary artery disease: influence of H. pylori eradication on coronary artery lumen after percutaneous transluminal coronary angioplasty. The detection of H. pylori specific DNA in human coronary atherosclerotic plaque. J Physiol Pharmacol. 2001;52(1 Suppl 1):3-31.

3) Alejandra Martínez Torresa, Miguel Martínez Gaenslyb. Helicobacter pylori: a New Cardiovascular Risk Factor? Rev Esp Cardiol. 2002;55:652-656.

4) Laek B, Szklo M, McClelland RL, Ding J, Tsai MY, Bluemke DA, Tracy R, Matsushita K. The prospective association of Chlamydia pneumoniae and four other pathogens with development of coronary artery calcium: the multi-ethnic study of atherosclerosis (MESA). Atherosclerosis. 2013;230(2):268-274.

Peace and blessings.

Batts Ludwig easy to interpret.

Yes,scrub typhus is a zoonosis transmitted by the bite of infected larval tromicula mite(chigger). Wild rats, mice and voles are natural reservoirs of infection.Scrub typhus is widely distributed in eastern and western Asia.

Thanks Satwant and Jessica for reply..

while discussing with colleague and seniors,I came to know that Doctors practicing in periphery are facing problems of unexpected (Biased)results due to logistic as well as environmental interference ..

Is there any technological solution like "transportation container" available or developed to reduce such problem ?

In the clinical setting, the preliminar diagnosis is usually made through in vitro susceptibility tests to oxacillin and cefoxitin, and the can be confirmed by PCR methods.

Hi

Chris...I am Vishnu Kirthi from India, doing research in the field of Malaria control using drug delivery systems. I am sure that i can help u out in the bioassaying for the effects metal nanoparticles. If everything comes good we can go for combined publishing of co-authors...

pls contact me at bioviski@gmail.com, if interested..

Vishnu Kirthi

There are two issues worth mentioning in addition to those given. Firstly having a positive viral identification may have prognostic value - rhinovirus in a wheezy infant makes asthma more likely (either as a marker or as a potentiator), adenovirus of certain types may be associated with devastating infection, enteroviruses may cause other complications. Knowing it is "just RSV" or "just parainfluenza" can be very helpful. Secondly, parents get "it's just a virus" all the time, so much that it sounds like a mantra to pass off their concerns. If you can tell them you have identified a specific virus it actually makes a big difference to your credibility, and their confidence and assurance that that is what is going on. They are not as likely to go searching for a doctor who will prescribe a cure. Simultaneously it helps their medical understanding - if they know their child, or others, have real influenza and what that is like, as opposed to what is popularly called "the flu" (the common cold) it makes a difference to their perception of the vaccine.

I admit, however, that having the test available is a luxury, and is rarely going to save lives directly.

Thank Mr. Ghazal. Of course it is normal to have bacteria, for what I wanted to discuss was about rates up when you can say it is normal, taking into account the type of bacteria and the number of colonies.

Thanks a lot Ru-Jeng For your reply