Talk:Antibiotic sensitivity testing

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Improvements directed toward WP:GA status

Hi Graham Beards, great to work with you. Would you have any interest in bringing this article up to GA status with me? I've made some further edits and thought we could discuss the article here so that we don't end up editing at crossways. Cheers --Tom (LT) (talk) 01:00, 5 July 2020 (UTC)

Hi Tom, Sorry I'm too busy in real life (controlling a pandemic). I have made a few more edits and corrections today. I'll keep the article on my watchlist. Best wishes, Graham Beards (talk) 09:43, 5 July 2020 (UTC)

• @Graham Beards would it be better to rename this article to antimicrobial sensitivity testing, which seems to be the current and more commonly used name, and in addition covers the use of similar methods for fungi. I'm in two minds about this; an alternative at a future date may be to expand the antimicrobial sensitivity testing article with some content from here, but include additional sections relating to virus / bacteria / fungal methods. Thoughts? --Tom (LT) (talk) 02:13, 7 July 2020 (UTC)

I think anti-viral susceptibility testing is best left to a separate article - the techniques are quite different. I am not fussed about the name change at this stage.Graham Beards (talk) 06:53, 7 July 2020 (UTC)

Tom (LT), would it be okay if I start reviewing this right away or would you like some more time to polish the article before the GA review? I know that you might have been expecting a months-long wait. I'm just very excited to see someone besides myself working on improving medical laboratory articles. :) Spicy (talk) 00:33, 8 July 2020 (UTC)

@Spicy woah! Yes I was expecting to wait some months. Did you change your username by the way? I think the article is at GA standard but I still have some planned edits. Happy if you want to take up the review but if you could put it on hold for a week or so that would be much appreciated. --Tom (LT) (talk) 00:43, 8 July 2020 (UTC)

Yup, I thought it was time for a change. :) I don't mind giving you a few days to work on it. Happy editing, Spicy (talk) 00:44, 8 July 2020 (UTC)

Probably best to address this before starting the GA review proper - I'm concerned by the article's reliance on an MDPI journal. MDPI does not have a great reputation and this particular journal is not MEDLINE indexed, so it's questionable if it meets MEDRS. Spicy (talk) 15:57, 9 July 2020 (UTC)

That's a real pity Spicy, because it's an excellent and comprehensive review that contains some basic information that many listed journals might think is too obvious to include. I'll keep searching for a good replacement but this really will take a while. --Tom (LT) (talk) 06:14, 16 July 2020 (UTC)

IMO textbooks are the best sources for articles like this, they tend to cover the obvious stuff more than journals do. Spicy (talk) 15:18, 16 July 2020 (UTC)

@Spicy I've replaced and removed I think all the complex or controversial claims from this source. The rest are used to either cite things that I don't think are controversial, or things that are to do with history where I really can't find an equivalent source (and I think to which MEDRS doesn't apply). --Tom (LT) (talk) 07:25, 9 August 2020 (UTC)

Thanks - are you ready to start the GA review then? I am a bit busy with other things at the moment but I can see what I can do. Spicy (talk) 10:07, 9 August 2020 (UTC)

@Spicy, no rush, things are pretty busy for me too. Happy to wait until you're ready or, if someone else reviews in the meantime, will ping you so that you're aware. --Tom (LT) (talk) 07:29, 10 August 2020 (UTC)

GA Review

This review is transcluded from Talk:Antibiotic sensitivity testing/GA1. The edit link for this section can be used to add comments to the review.

Reviewer: Larry Hockett (talk · contribs) 21:41, 22 August 2020 (UTC)

I'm happy to review this entry. I'll leave some initial feedback in the next few hours. Thanks to the nominator for the work that has gone into this article. Larry Hockett (Talk) 21:41, 22 August 2020 (UTC)

To start off, the article appears well-sourced and neutral, and it was run through Earwig's Copyvio Detector, which turned up no significant copyright issues. The article has appropriate images with the necessary license information.

Here is some section-by-section feedback. Most of it should just involve some rewording for clarity. Not all of these items are going to be essential for promotion to GA, so let me know if you disagree with any of these items.

Thanks Larry Hockett, I appreciate you taking up this review. I unfortunately have only enough mental bandwith to respond to one nomination at a time, so I will try and address some small concerns below but will have to leave the rest until Prostate has been attended to. --Tom (LT) (talk) 00:12, 23 August 2020 (UTC)

Ping also to Spicy who was planning on contributing and has some expertise in the area, so that he knows this review is open. --Tom (LT) (talk) 00:12, 23 August 2020 (UTC)

Sorry about that. I try to check for that issue before starting a review but I overlooked it this time. There is no hurry. Larry Hockett (Talk) 00:17, 23 August 2020 (UTC)

Comments by Larry

Lead

• The last sentence of the first paragraph is a little convoluted. I wonder if we could say "Sensitivity testing results often allow a clinician to prescribe directed therapy rather than empiric therapy."
  •  Done
• "culture methods that exposure bacteria" - I haven't seen exposure as a verb. I'm assuming it's expose.
  •  Done
• In the image at the top, the first two words are bolded. It's probably not a sticking point, but I don't think I've seen bold text used that way.
  •  Done

Uses

• "exposure to with antibiotics"
  •  Done

• "information about what antibiotics" --> information about which antibiotics
  •  Done

• ""and are used in this context" --> and is used (is agrees with antibiotic sensitivity testing)
  •  Done

• "Methicillin-resistant Staphylococcus aureus" - lowercase M since methicillin is not a proper noun; there is one more issue with that (Vancomycin-resistant enterococci) in the last section of the article.
  •  Done

Methods

• need source for the qualitative and quantitative methods explanation; I think the van Belkum source might mention it; not sure if there is much explanation given
  •  Done

• disc diffusion - in the literature, it looks like the preferred spelling is disk with a K
  •  Not done I think this is an issue of WP:ENGVAR
    • Just a suggestion, you might want to put one of the ENGVAR templates on the article so people don't get confused. I actually have no idea what English variant this article is written in - hopefully my edits haven't messed anything up! Spicy (talk) 00:12, 7 September 2020 (UTC)
      • Good point -  Done--Tom (LT) (talk) 23:07, 7 September 2020 (UTC)

• "This is also called the Kirby-Bauer method, although modified methods are also used" - Do you mean that the Kirby-Bauer method is a modified form of the disk diffusion method? Or that these two methods are the same thing and there are other, separate modified methods besides that?
  •  Done
• "It is considered the cheapest and most simple of the methods" - Are you referring to the disk diffusion method in general here, or specifically to the use of Mueller-Hinton agar?
  •  Done
• In this section, you have two paragraphs that begin with what look like headings, but they are not formatted like our typical headings (Gradient methods and Agar and broth dilution methods). I know that kind of formatting is used in journals, but I'm wondering if it wouldn't be easier to either make them level 4 headings or just make them part of the prose ("Gradient methods, such as the Etest...")
  •  Done

• Matrix-Assisted Laser Desorption Ionisation-Time of Flight Mass Spectrometry - lowercase, unless I'm missing something.
  •  Done

• Under genetic methods you used only the acronym PCR on the first mention, then used the full term and the acronym on the second mention (MOS:ACRO).
  •  Done

Reporting

• The wording of the information on MIC values is almost identical to the wording in the Jacobs source. The age of the source makes me wonder whether these are still the accepted values.
  •  Done

• "empirical treatment, to a more custom-tailored" - no comma
  •  Done changed second part of sentence

• beta lactamase - usually hyphenated, I think
  •  Done

Clinical practice

• The Burnett source is used a few times in the entry. Is there a more recent edition of it?
  •  Partly done I'm removing these as I see them when other sources are more suitable, but per Spicy's comment I will leave the remainder as I have enough on my plate for the moment and most of what they state is not too controversial :).

• Why not link clinical laboratory much higher than this, such as in the Methods section? (says laboratory setting there right now)
  •  Done

• "This is done through collecting samples from affected body sites" --> Samples are collected from...
  •  Done

• There is a little redundancy in this section, unless I am misreading it. It talks about collecting samples, then starting empirical treatment, then collecting samples before you do that.
  •  Done Have trimmed a whole paragraph and inserted what I think are some useful additional pieces of information, which I'll now need to cite. Let me know what you think.

• The last paragraph of the section sort of sends mixed messages; the word useful is used twice. From the first mention of the word, I get the impression that this will yield helpful data, and on the second mention it seems more measured - "often" high enough for the test to be clinically useful. Could you clarify?
  •  Done

History

• consider linking Alexander Fleming
  •  Done

• "was a diffusion method, involved an antibiotic that" - missing a conjunction here?
  •  Done

Further research

• I think the reader may wonder why we used three numbers in the range of 12-48 hours to five days. Is the 12- to 48-hour range different technology than the one that takes five days?
  •  Done clarified

• "As well as the duration it takes to report of phenotypic methods" - not sure about "report of" here. May be less awkward to open this sentence with the subject ("Phenotypic methods are slow, labor-intensive...).
  •  Done

• "resistance diagnostics was: - I'd use "were" here.
  •  Done

• In the microfluidics bit, "tiny fluid" is a little awkward and it seems redundant to say that not much fluid is required.
  •  Done

• "This are labelled proteins"
  •  Done

• "the use of bioluminescent enzymes that demonstrate bacterial growth to make changes more easily visible" - it sounds like the enzymes demonstrate bacterial growth in order to make changes visible.
  •  Done

Thanks for your work on this. I particularly appreciate how accessible the language is for the lay public, especially in the beginning of the entry. I anticipate that it will pass easily once these things are addressed. Larry Hockett (Talk) 23:46, 22 August 2020 (UTC)

Larry Hockett I think I have addressed all your concerns. Please let me know what you think or if I've missed any. I also appreciate your generalist take on the article. If you have time after this and want another mammoth task, Anatomical terms of location is waiting, waiting for you...--Tom (LT) (talk) 05:51, 3 September 2020 (UTC)

Tom (LT) Thank you for your work. I'll sit down and look at the changes this week. Larry Hockett (Talk) 16:31, 3 September 2020 (UTC)

Comments by Spicy

As I was pinged by the nom I'll add my suggestions as well. Some of this may go a bit beyond what the GA criteria require so feel free to disregard if you don't think certain things are necessary. Just listing off what jumped out at me while reading.

Thanks Spicy, I've responded to all your concerns save for (I think) two. Let me know what you think. I look forward to your responses. --Tom (LT) (talk) 05:51, 3 September 2020 (UTC)

Lead

• I think it is important to explain empiric therapy and directed therapy in the lead. Most lay readers will not be familiar with these important terms and many people don't read the body of the article.
  •  Done

• "Culture methods often involve measuring the diameter of the zones of inhibition on agar culture dishes" - I would define "zones of inhibition" and link [[Agar plate|agar culture dishes]]
• "The lowest amount of the antibiotic that stops the growth of bacteria..." - rather than using an easter egg link, I would write something like "The lowest amount of the antibiotic that stops the growth of bacteria, which is termed the minimum inhibitory concentration, can be determined from this."
  •  Done

• History should be mentioned in the lead - per WP:LEAD the lead should summarize all main points of the article
  •  Done

Uses

• "In clinical medicine, antibiotics are most frequently prescribed on the basis of a person's symptoms and general guidelines, called empiric therapy." - no clear referent for "called empiric therapy". Are we saying that the symptoms or the guidelines are called empiric therapy - obviously not but a lay reader might read it that way. I think it would be more clear that we're referring to the whole process if the sentence is changed to "... antibiotics are most frequently prescribed on the basis of a person's symptoms and general guidelines. This is called empiric therapy."
  •  Done
    • I've revised this a bit more for clarity Spicy (talk) 21:44, 4 September 2020 (UTC)
      • Thanks. --Tom (LT) (talk) 23:07, 7 September 2020 (UTC)

• "based around" - maybe this is an ENGVAR thing but this sounds very informal to me, could this be changed to "based on"?
  •  Done

• "This resistance might be because of the type of bacteria" - should clarify that this is because some species have inherent resistance to certain antibiotics (I assume that's what you were going for)
  •  Done

• Antibiotic sensitivity testing provides information about what antibiotics are more likely to be successful and are used in this context to provide information about what antibiotics should be used - confusing sentence structure. Could this be changed to something like "Antibiotic sensitivity testing provides information about what antibiotics are more likely to be successful and should therefore be used to treat the infection"?
  •  Done

Methods

• Once a bacterium has been identified after microbiological culture testing - I would add a link here, either [[Microbial culture|microbiological culture]] or [[Medical microbiology|microbiological culture testing]]
  •  Done

• The disc diffusion method involves selecting a strain of bacteria, and placing it in a growth medium. This is also called the Kirby-Bauer method, - this makes it sound like the disk diffusion method is defined as "selecting a strain of bacteria, and placing it in a growth medium" which obviously is not the case as that applies to all AST methods except MALDI-TOF and genetic testing.
  •  Done clarified
• The "selecting a strain of bacteria and placing it in a growth medium" bit is confusing. It makes it sound as if the bacteria are placed in a secondary medium to enrich growth after being cultured from patient samples and before being inoculated onto the MH agar, which isn't the case.
  •  Question: is this better now?
• The preparation of bacterial suspensions based on McFarland standards needs to be mentioned as it is a critical step in the process
  •  Done mentioned
• "Mueller-Hinton agar is frequently used in this antibiotic susceptibility test" - might want to mention situations in which other agar is used, e.g. MH blood agar for streptococci. but maybe not necessary for GA
  •  Not done can't find any recent reliable sources for this, and I don't have access to a microbiology textbook
    • This should be in Mahon but like I said it may not be necessary for GA status so I'm not too concerned if this is left out. Spicy (talk) 18:55, 4 September 2020 (UTC)
• I would mention how the E-test is read, since it differs from the KB test; and that it provides an MIC directly while KB results don't
  •  Done I have mentioned the eTest relates to MIC
• "bacteria is placed in multiple small tubes, alongside different dilutions of antibiotics." - they're placed in the antibiotic suspensions, not next to them
  •  Done good pickup
• "Automated systems exist that replicate manual processes, for example, by using pictures and software analysis to report the zone of inhibition in diffusion testing or dispensing samples and determining results in dilutional testing." - the latter, I think, deserves more coverage. Many labs do a large volume of routine AST using systems like the BD Phoenix and Vitek AST. IIRC Textbook of Diagnostic Microbiology by Connie R. Mahon (2018) has some good information on this - will verify tomorrow
  • It does - I can send you an email if you don't have access to this text
    • Thanks, could you send it to me via email?
      • Tom (LT) done. I'll try to respond to your other comments later today. Spicy (talk) 14:27, 3 September 2020 (UTC)
• Might want to mention the nitrocefin disk test for beta-lactamase (again might be outside GA scope)
• "However, resistance genes detected do not always match whether a bacterium has resistance on a phenotypic method." - could this be simplified to "the results of genetic testing do not always correlate with phenotypic testing"?
  •  Done clarified
• To satisfy the broadness criterion I think there should be some discussion of quality control procedures and factors that can lead to incorrect results - even if only a sentence or two
  •  Question: could you give me some pointers on what actually goes on in practice here :)... --Tom (LT) (talk) 05:51, 3 September 2020 (UTC)

Clinical practice

• "Empirical treatment is often started before laboratory microbiological reports are available when treatment should not be delayed due to the seriousness of the disease" - makes it sound like that's the only case in which empirical treatment is used; many minor infections such as uncomplicated UTIs and otitis media are often treated empirically
  •  Done

• "This is done through collecting samples from affected body sites, preferably before antibiotics are given. For example, a person in an intensive care unit may develop a hospital-acquired pneumonia. There is a chance the causal bacteria may be different to community-acquired pneumonia." - the last two sentences seem out of place. We switch from talking about collecting a specimen to discussing different types of infections. And it's introduced with "For example," - what in the preceding sentences is this an example of?
  •  Done

• "a blood culture sample when bacteria possibly have invaded the bloodstream, a sputum sample in the case of a ventilator associated pneumonia, and a urine sample in the case of a urinary tract infection." - the use of "and" here made me do a double take, at first it sounds like a urine sample would be collected along with the other samples - suggest changing to "or"
  •  Done

• " a sputum sample in the case of a ventilator associated pneumonia" - or any other type of pneumonia
  •  Done

• "Microscopy is not useful for all samples because often the normal bacterial flora cannot be distinguished from pathogens" - This is a bit vague. I think you are trying to say that the direct Gram stain isn't always helpful because it can't tell the difference, for instance, between S. aureus and a coag negative staph. But you should clarify that this is relevant to empiric vs. directed therapy because the direct Gram stain is done before the culture and sensitivity results are available.
  •  Done

• "Additionally, when reported, a decision must be made for some bacteria such as Staphylococcus epidermidis, as to whether they are the cause of an infection, or simply commensal bacteria or contaminants." - may be helpful to clarify why this is the case, i.e. it is normal skin flora but also an opportunistic pathogen
  •  Done

Misc

• Ref 10 - [1] - not really a great source - should not be hard to find a better source for this
  •  Done
• You use "empiric" in some places and "empirical" in others - should be consistent
  •  Done

I will continue tomorrow. Spicy (talk) 04:35, 23 August 2020 (UTC)

• I am not all that concerned about the 2005 source as none of the information it supports is particularly controversial or likely to change any time soon. This isn't an area where there is a lot of cutting edge research going on - and regarding the MICs specifically, Mahon (2018) lists the same MICs for S. pneumoniae on page 281. Conversely, since this is such basic information it should not be hard to source it to a more recent textbook, which would help readers who don't know the field verify that the information is still accurate... but I don't think a few uses of an older source should keep this from becoming a GA. Spicy (talk) 01:59, 24 August 2020 (UTC)
  • Spicy - I appreciate this kind of feedback so much. This review was a little bit of a stretch for me (maybe one that I should have thought more carefully about undertaking) since I don't have a laboratory science background. Thank you for sharing your expertise. Larry Hockett (Talk) 12:16, 25 August 2020 (UTC)
  • I found a little bit about QC in Mahon and added a couple of sentences to the Methods section. From my perspective, the entry meets the GA criteria, but I thought I would give Spicy a chance to provide additional feedback before promoting it. Larry Hockett (Talk) 04:35, 8 September 2020 (UTC)
    • Promoting this to GA, as I believe it now meets the criteria. Good Articles can always be improved, especially with the involvement of subject matter experts in these technical areas, but I don't believe there is any reason to hold up promotion at this point. Thanks to the editors who collaborated here to work through this process. Larry Hockett (Talk) 13:49, 15 September 2020 (UTC)
      • Thanks for your review Larry. --Tom (LT) (talk) 07:49, 16 September 2020 (UTC)

Suitability for FA?

Hey @Spicy, SandyGeorgia, Ajpolino and Graham Beards. I am considering preparing this for a first stab at FA nomination. I haven't ever done this before, would someone be able to mentor me through it and also help advise if you think it's suitable and what changes you feel I'll need to make? Many thanks, Tom (LT) (talk) 05:53, 5 September 2021 (UTC)

Tom (LT) I don't have the time or experience to be a FA mentor, but I'd be interested in improving the article towards FA status if you are. I've read Graham Beards' comments on his talk page and agree with his points. The article relies heavily on journal articles at the moment which IMO aren't the best sources for general coverage of a broad topic like this one - some of the issues with comprehensiveness could be improved by making use of more book sources (I have added a few). I haven't looked, but I suspect there is more to say about the history. The prose will also need some work for FA status, and I'm not the best person to help with that. Spicy (talk) 01:10, 6 September 2021 (UTC)

I've been looking at this again. I think the organization of the article needs work - it's very confusing to explain how the MIC is measured at the same time as what the MIC is and why it's important. The 'Reporting' section might work better as a subsection of 'Medical uses'. Spicy (talk) 06:17, 24 September 2021 (UTC)

The article needs much more on the interpretation of the results and the "expert rules" which are employed by both EUCast and CLSI. (Sometimes these rules contradict each other). Most automated methods use these rules, which are embedded in the software and can go unnoticed in busy labs. The VITEK system allows users (with admin rights) to switch between the two and often cultures with borderline breakpoints will be reported as sensitive based on one set of rules, but resistant by the other. These rules are the essence of testing. Here, for example is what EUCast rules say about vancomycin resistant enterococci "if resistant to vancomycin, determine the MIC and report dalbavancin, oritavancin and telavancin after consulting EUCAST guidance document “What to do when there are no breakpoints”. Describing the practical methods we use in our labs will not be enough for a FA. A good rule of thumb would be that even folk who set up and run these tests everyday, should discover something in the article they did not previously know. Graham Beards (talk) 12:44, 6 September 2021 (UTC)