Methods and devices for ultrasensitive direct detection of microorganisms

Abstract

The present disclosure generally relates to the field of ultrasensitive microbial pathogen detection and identification utilizing genomic sequence recognition.

1 . A composition consisting essentially of:
 a magnesium salt;   a buffering agent;   water; and   a compound of Formula 1:   
       
         
           
           
               
               
           
         
         wherein R 1  is selected from the group consisting of optionally substituted, branched or unbranched, saturated or unsaturated C 1 -C 8  aliphatic; optionally substituted, saturated or unsaturated C 3 -C 14  carbocyclic; optionally substituted, saturated or unsaturated 3-8 membered heterocyclic; optionally substituted, branched or unbranched, saturated or unsaturated ((R a ) q —(C═O)—(R a ) q ) p ; optionally substituted C 6 -C 14  aryl; and optionally substituted 3-8 membered heteroaryl; and/or any suitable combinations thereof; 
         wherein R 2  is selected from the group consisting of hydrogen; optionally substituted, branched or unbranched, saturated or unsaturated C 1 -C 28  aliphatic; optionally substituted, branched or unbranched, saturated or unsaturated —(R b —(O—R b ) n —O—R b ) p ; optionally substituted, branched or unbranched, saturated or unsaturated —(R b —(O—R b ) n —NH—R b ) p ; optionally substituted, branched or unbranched, saturated or unsaturated —(R b —(O—R b —O) n —S—R b ) p ; optionally substituted, branched or unbranched, saturated or unsaturated —(R b —(S—R b ) n —S—R b ) p ; optionally substituted C 6 -C 14  aryl; optionally substituted 3-8 membered heteroaryl; optionally substituted, saturated or unsaturated C 3 -C 14  carbocyclic; optionally substituted, saturated or unsaturated 3-8 membered heterocyclic; optionally substituted, branched or unbranched, saturated or unsaturated —(C═O)—(R b ); optionally substituted, branched or unbranched, saturated or unsaturated —((R a ) q —O—(R a ) q ) p —; optionally substituted, branched or unbranched, saturated or unsaturated —((R a ) q —NH—(R a ) q ) p —; optionally substituted, branched or unbranched, saturated or unsaturated —((R a ) q —N(R a )—(R a ) q ) p —; and optionally substituted, branched or unbranched, saturated or unsaturated —((R a ) q —S—(R a ) q ) p —; and/or any suitable combinations thereof; 
         wherein each occurrence of R a is independently C 1 -C 8  aliphatic or C 6 -C 14  aryl; 
         wherein each occurrence of R b  is independently C 1 -C 15  aliphatic or C 6 -C 14  aryl; 
         wherein each occurrence of subscript q is independently an integer between 0 and 1, inclusive; 
         wherein each occurrence of subscript p is independently an integer between 1 and 6, inclusive; and 
         wherein each occurrence of subscript n is independently an integer between 0 and 14, inclusive. 
       
     
     
         2 . The composition of  claim 1 , further comprising blood. 
     
     
         3 . The composition of  claim 2 , wherein the composition comprises between 20% and 60%, inclusive, of the blood by volume. 
     
     
         4 . The composition of  claim 2 , wherein the blood comprises microbial cells. 
     
     
         5 . A kit, comprising:
 the composition of  claim 1 ; and   an anion-exchanger.   
     
     
         6 . The kit of  claim 5 , wherein the kit further comprises microparticles. 
     
     
         7 . The kit of  claim 5 , wherein the anion-exchanger comprises microparticles. 
     
     
         8 . The kit of  claim 5 , wherein the anion-exchanger comprises magnetizable, electro-reactive microparticles. 
     
     
         9 . The kit of  claim 5 , further comprising a composition comprising cell lysis reagents that allow for the lysis of microbial cells. 
     
     
         10 . The kit of  claim 5 , further comprising a fluidic device. 
     
     
         11 . The kit of  claim 5 , wherein the buffering agent comprises a polar small molecule and/or an inorganic salt. 
     
     
         12 . The kit of  claim 5 , wherein the magnesium salt comprises an inorganic counter ion. 
     
     
         13 . The kit of  claim 5 , wherein the magnesium salt is selected from the group consisting of MgCl 2 , MgCO 3 , MgSO 4 , and MgBr 2 . 
     
     
         14 . The kit of  claim 5 , wherein R 2  is selected from the group consisting of optionally substituted, branched or unbranched, saturated or unsaturated C 1 -C 28  aliphatic; optionally substituted, branched or unbranched, saturated or unsaturated —(R b —(O—R b ) n —O—R b ) p ; optionally substituted, branched or unbranched, saturated or unsaturated —(R b —(O—R b ) n —NH—R b ) p ; optionally substituted, branched or unbranched, saturated or unsaturated —(R b —(O—R b —O) n —S—R b ) p ; optionally substituted, branched or unbranched, saturated or unsaturated —(R b —(S—R b ) n —S—R b ) p ; optionally substituted C 6 -C 14  aryl; optionally substituted 3-8 membered heteroaryl; optionally substituted, saturated or unsaturated C 3 -C 14  carbocyclic; optionally substituted, saturated or unsaturated 3-8 membered heterocyclic; optionally substituted, branched or unbranched, saturated or unsaturated —(C═O)—(R b ); optionally substituted, branched or unbranched, saturated or unsaturated —((R a ) q —O—(R a ) q ) p —; optionally substituted, branched or unbranched, saturated or unsaturated —((R a ) q —NH—(R a ) q ) p —; optionally substituted, branched or unbranched, saturated or unsaturated —((R a ) q —N(R a )—(R a ) q ) p —; and optionally substituted, branched or unbranched, saturated or unsaturated —((R a ) q —S—(R a ) q ) p —; and/or any suitable combinations thereof;
 wherein each occurrence of R a is independently C 1 -C 8  aliphatic or C 6 -C 14  aryl; 
 wherein each occurrence of R b  is independently C 1 -C 15  aliphatic or C 6 -C 14  aryl; 
 wherein each occurrence of subscript q is independently an integer between 0 and 1, inclusive; 
 wherein each occurrence of subscript p is independently an integer between 1 and 6, inclusive; and 
 wherein each occurrence of subscript n is independently an integer between 0 and 14, inclusive. 
 
     
     
         15 . The kit of  claim 5 , wherein R 1  is independently selected from the group consisting of optionally substituted, branched or unbranched C 1 -C 8  alkyl; optionally substituted, branched or unbranched C 2 -C 8  alkenyl; and optionally substituted, branched or unbranched C 2 -C 8  alkynyl. 
     
     
         16 . The kit of  claim 5 , wherein R 1  is optionally substituted, branched or unbranched C 1 -C 8  alkyl. 
     
     
         17 . The kit of  claim 5 , wherein R 2  is independently selected from the group consisting of optionally substituted, branched or unbranched C 1 -C 28  alkyl and optionally substituted, branched or unbranched C 2 -C 28  alkenyl. 
     
     
         18 . The kit of  claim 5 , wherein the compound of Formula 1 is selected from the group consisting of: 
       
         
           
           
               
               
           
         
       
     
     
         29 . The kit of  claim 5 , wherein the compound of Formula 1 is 
       
         
           
           
               
               
           
         
       
     
     
         20 . The kit of  claim 5 , wherein the pH has a value of between 8 and 11.5, inclusive.