Thank you a lot. ... View more

Thank you Tom ... View more

Hi Tom, Thank you for the response. For the second code, I tried it because I had the errors in the first code, I was trying to match on Patient_Name only. ... View more

Thank you PaigeMiller.    Here's the proc contents of AllData   And the proc contents of Death: Please let me know if I'm missing any other information.       ... View more

I had this in my proc contents for both datasets. I can't find any discrepancies. As I mentioned before, DOB seems to cause the issue but I'm not sure how!       ... View more

Thank you mkeintz, how can I export it to an Excel worksheet? ... View more

Thank you Tom,   This was very helpful. I can see that the first 4 rows are related to the same note since it has 4 organisms listed as below: SPECIMEN NOTES:Collection Method ID: Transport MediaNTE:Heavy Growth Carbapenem Resistant Klebsiella pneumoniae Heavy Growth Multi-Drug Resistant Acinetobacter baumannii complex Moderate Growth ESBL Proteus mirabilis Moderate Growth Morganella morganii What if we want only the first organism listed and discard the rest, or just the one with heavy growth? Wonder if we can add any option in the "findw"? Thank you  ... View more

Hi Tom, This worked for the most part. But for #3, #4, and #5 it picked Acinetobacter baumannii complex, Proteus mirabilis, and Morganella morganii instead of Klebsiella pneumoniae. Is there an explanation for that? Below are the data used:   data Organisms; length Organism $250; infile datalines dsd truncover; input Organism $; datalines4; Klebsiella pneumoniae Acinetobacter baumannii complex Proteus mirabilis Morganella morganii Providencia stuartii Citrobacter freundii ESCHERICHIA COLI Klebsiella pneumoniae Citrobacter brakii Klebsiella aerogenes ;;;; run; data have; length Notes $256; infile datalines dsd truncover; input Notes $; datalines4; SPECIMEN NOTES:Collection Method ID: Transport MediaNTE:Heavy Growth Carbapenem Resistant Klebsiella pneumoniae Heavy Growth Multi-Drug Resistant Acinetobacter baumannii complex Moderate Growth ESBL Proteus mirabilis Moderate Growth Morganella morganii Providencia stuartii SPECIMEN NOTES:Collection Method NTE:75 --99 cfu/ml Citrobacter freundii This CRE isolate demonstrates carbapenemase-producing SPECIMEN NOTES:119334006 Sputum specimen SPUTUM 1NTE:=4+ CARBAPENEM RESISTANT ESCHERICHIA COLI NTE:=2+ Klebsiella pneumoniae Carbapenemase-producing Enterobacteriaceae Positivefor Carbapenemase: KPC COLISTIN 2 INTERMEDIATE- Klebsiella pneumoniae to organism column and KPC to Gene-mechanism SPECIMEN NOTES:Collection Method ID: TMOT - Transport MediaNTE:70 cfu/ml Citrobacter brakii CRE (carbapenem-resistant Enterobacteriaceae) Targeted carbapenemase producing genes NOT detectedOther-Citrobacter brakii to organism, yes to carbapenem-resistant and no to carbapenemase-producing SPECIMEN NOTES: URC Urine clean catch HL70487 2.5 Urine clean catch SPECIMEN NOTES:Collection Method ID: TMOT - Transport MediaNTE:Recovered Klebsiella aerogenes ***This CRE isolate demonstrates carbapenemase production.** Positive for NDM gene for carbapenemase production by PCR.Carbapenem resistant organism. ;;;; run; proc sql; create table want as select a.notes , b.organism from have a left join Organisms b on findw(a.notes,trim(b.organism)) ; quit;   Thank you ... View more

Thank you Tom. I'll try using this function and see if it works. ... View more

Yes, Tom. That's why I created a list of all possible organisms but I'm not sure how I can use this list to pick them from the string! What code? method?   ... View more

Hi Tom, Klebsiella aerogenes was picked because it's an organism (It falls under the Organism column). It could be anywhere in the string and it doesn't have to do anything with NTE: or 2+. Citrobacter freundii, Citrobacter brakii, and other organisms fall in varied places. I created a list of all organisms (about 22) that should be picked but I'm not sure how I can tackle this.  For the second column, only 5 values can be picked (KPC, NDM, OXA, VIM, and no gene) The third column picks yes when it says carbapenem resistant dectected or positve and No for carbapenem resistant not detected or No carbapenem resistant detected. Fourth column same for 3rd but carbapenemase producing instead of carbapenem resistant. Thank you ... View more

Hi Tom, This is an example of what is needed below: data have; length Notes $256; infile datalines dsd truncover; input Notes $; datalines4; NTE:=2+ Klebsiella pneumoniae Carbapenemase-producing Enterobacteriaceae Positivefor Carbapenemase: NDM COLISTIN 2 INTERMEDIATE- Klebsiella pneumoniae to organism column and NDM to Gene-mechanism SPECIMEN NOTES:Collection Method NTE:75 --99 cfu/ml Citrobacter freundii This CRE isolate demonstrates carbapenemase-producing SPECIMEN NOTES:119334006 Sputum specimen SPUTUM 1NTE:=4+ CARBAPENEM RESISTANT ESCHERICHIA COLI NTE:=2+ Klebsiella pneumoniae Carbapenemase-producing Enterobacteriaceae Positivefor Carbapenemase: KPC COLISTIN 2 INTERMEDIATE- Klebsiella pneumoniae to organism column and KPC to Gene-mechanism SPECIMEN NOTES:Collection Method ID: TMOT - Transport MediaNTE:70 cfu/ml Citrobacter brakii CRE (carbapenem-resistant Enterobacteriaceae) Targeted carbapenemase producing genes NOT detectedOther-Citrobacter brakii to organism, yes to carbapenem-resistant and no to carbapenemase-producing NTE:INTERPRETATION: An ?Inconclusive? result cannot determine the presence or absence of blaVIM blaNDM blaKPC and blaOXA-48 associated with carbapenem non-susceptible Acineto baumannii, or Pseudo aeruginosa. SPECIMEN NOTES:Collection Method ID: CANTE:Candida aurisOther Identifiers: PI: 14310303980 PI: CCRFFLO5JXTLH SPECIMEN NOTES:Collection Method ID: TMOT - Transport MediaNTE:Recovered Klebsiella aerogenes ***This CRE isolate demonstrates carbapenemase production.** Positive for KPC gene for carbapenemase production by PCR.Carbapenem resistant organism. SPECIMEN NOTES:119334006 Sputum specimen SCT SPU SPUTUM L 20130731 v1NTE:=1+ Carbapenem resistant Klebsiella pneumonaiae POSITIVE Class A CarbapenemaseProducerOther Identifiers: CCREXRZYLDMRP SPECIMEN NOTES:Collection Method: TRACHNTE:Carbapenem-resistant Enterobacteriaceae (CRE) - Klebsiella oxytocaSusceptibility profile is consistent with a probable ESBL.Carbapenemase not detected ;;;; run; data want8; infile datalines delimiter=","; length Organism $25 Gene_Mechanism $6 Carbapenem_Resistance $6 Carbapenemase_Producing $6; input Organism $ Gene_Mechanism $ Carbapenem_Resistance $ Carbapenemase_Producing $; datalines; Klebsiella aerogenes,NDM, ,Yes Citrobacter freundii, , ,Yes ESCHERICHIA COLI, ,Yes, Klebsiella pneumoniae,KPC, ,Yes Citrobacter brakii, ,Yes,No ,unk, , Klebsiella aerogenes,KPC,Yes,Yes Candida auris, , , Klebsiella pneumonaiae, , ,Yes Klebsiella oxytoca, ,Yes,No ; run; Thank you ... View more