MONITORING AND MANAGING A FACILITY MICROBIOME

• US 20170081707A1
• Filed: 05/06/2015
• Published: 03/23/2017
• Est. Priority Date: 05/06/2014
• Status: Abandoned Application

• Current Assignee: Phylagen, Inc.
• Original Assignee: Phylagen, Inc.
• Inventors: Dillon, Harrison, Meadow, James
• Application Number:
  US15/308,971
• Publication Number:
  US 20170081707A1
• Time in Patent Office: Days
• CPC Class Codes: C12Q 1/689 for bacteria

Abstract

Facilities operations can be conducted more safely, efficiently, and cost-effectively by monitoring changes in the facility microbiome and intervening when those changes indicate the likelihood of a deleterious effect there-from.

Claims

1. A method for improving the performance of a facility, said method comprising (i) correlating a facility microbiome with one or more facility operation parameters to identify changes in the facility microbiome that contribute positively or negatively to a facility performance indicator;

(ii) identifying changes in the microbiome that correlate with facility operation parameters, wherein said changes can be prevented or caused by altering a changeable facility condition; and

(iii) altering one or more changeable facility conditions to effectuate the desired change in one or more facility performance indicators.

2. The method of claim 1, wherein the one or more alterations to the changeable facility conditions comprises an alteration that preferentially induces or reduces proliferation or dissemination of one or more microbes, biological activities, or operational taxonomic units over another.

3. The method of claim 2, wherein the one or more alterations preferentially induce proliferation or dissemination of one or more microbes, biological activities, or operational taxonomic units distinct from those of the group consisting of Streptococcus pneumonia, Klebsiella, Staphylococcus aureus, Candida albicans, Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia, E. coli O157:

H7, Clostridium difficile, Mycobacterium tuberculosis, Enterococcus, Legionella pneumophila and Streptococcus pyogenes.

4. The method of claim 1, wherein the one or more alterations to the changeable facility conditions comprises an alteration that preferentially induces or reduces proliferation or dissemination of biochemical activities that are correlated with facility performance, the biochemical activities being measured using the presence and relative abundance of DNA or RNA molecules that impart the activity.

5. The method of claim 1, wherein the one or more alterations to changeable facility conditions comprises an alteration that preferentially reduces viability or proliferation of one or more microbes, biological activities, or operational taxonomic units.

6. The method of claim 5, wherein the one or more alterations preferentially reduces viability or proliferation of one or more microbes, biological activities, or operational taxonomic units of the group consisting of species or genera of Streptococcus pneumonia, Klebsiella, Staphylococcus aureus, Candida albicans, Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia, E. coli O157:

H7, Clostridium difficile, Mycobacterium tuberculosis, Enterococcus, Legionella pneumophila and Streptococcus pyogenes.

7. The method of claim 1, wherein the one or more alterations to changeable facility conditions comprises an alteration that reduces dissemination of one or more microbes, biological activities, or operational taxonomic units within the facility.

8. The method of claim 1, wherein the one or more alterations to changeable facility conditions comprises an alteration that reduces virulence of one or more one or more microbes, biological activities, or operational taxonomic units.

9. The method of claim 8, wherein the one or more alterations reduces virulence of one or more microbes, biological activities, or operational taxonomic units of the group consisting of Streptococcus pneumonia, Klebsiella, Staphylococcus aureus, Candida albicans, Pseudomonas aeruginosa, Acinetobacter baumannii, Stenotrophomonas maltophilia, E. coli O157:

H7, Clostridium difficile, Mycobacterium tuberculosis, Enterococcus, Legionella pneumophila and Streptococcus pyogenes.

10. The method of claim 1, wherein changes in the facility microbiome are detected by nucleic acid sequencing of microbial DNA in samples taken from said facility, and said sequencing occurs simultaneously or within 15 minutes (real time) or within 15 minutes to within one day (near real-time), and said altering step occurs within 15 minutes to within one day of said sequencing.

11. The method of claim 10, wherein said sequencing is metagenomic.

12. The method of claim 1, wherein data for said facility operation parameters are displayed on a computer screen together with information characterizing said facility microbiome or changes therein, and information relating to facility performance indicators.

20. The facility system of claim 19 that is capable of performing a method of claim 1.

13. A method of modulating one or more target biochemical activities, microbes, or OTUs within a built environment facility, comprising:

(a) collecting one or more samples from locations in said facility;

(ii) subjecting the samples to DNA sequence analysis;

(iii) quantifying the target biochemical activity by determining the number of sequences that fall within a predetermined sequence identity definition characterizing said biochemical activity(ies), microbes, or OTUs; and

(iv) modifying at least one facility operation parameter that alters the number of sequences in the facility that fall within the predetermined sequence identity definition in a subsequent sampling.

14. The method of claim 13, further comprising a step of correlating a facility performance parameter with the facility operation parameter modification.

15. The method of claim 13, wherein the target biochemical activity is selected from the group consisting of allergenicity, antibiotic resistance, volatile organic compound production, volatile organic compound degradation, bacterial toxicity, fungal toxicity, bacterial sporulation, building material degradation and viral infectivity.

16. The method of claim 13, wherein the facility operation parameter involves the ventilation system of the facility.

17. The method of claim 16, wherein the facility performance parameter is lung function of occupants.

18. The method of claim 15, wherein the target biochemical activity is antibiotic resistance, and the activity is resistance to one or more of the following antibiotics:

6_n_netilmicin, acriflavin, acriflavine, amikacinaminoglycoside, apramycin, astromicin, bacitracin, beta_lactam, butirosin, carbapenem, carbenicillin, cefoxitin, ceftazidime, ceftriaxone, cephalosporin, cephamycin, chloramphenicol, ciprofloxacin, cloxacillin, deoxycholate, dibekacin, doxorubicin, e_cephalosporin, enoxacin, erythromycin, fluoramphenicol, fluoroquinolone, fosfomycin, fosmidomycin, gentamicin, glycylcycline, isepamicin, imipenem, meropenem, kanamycin, kasugamycin, lincomycin, lincosamide, lividomycin, macrolide, methicillin, monobactam, n_cephalosporin, neomycin, netilmicin, norfloxacin, paromomycin, penicillin, polymyxin, puromycin, ribostamycin, roxithromycin, sisomicin, spectinomycin, streptogramin, streptomycin, sulfonamide, t_chloride, teicoplanin, tetracenomycin, tetracycline, thiostrepton, tigecycline, tobramycin, trimethoprim, vancomycin, erythromycin, clindamycin, doxycycline and minocycline, and the facility performance parameter is selected from the group consisting of number, frequency and/or outcome of infections of patients or occupants, and health or growth of animals.

19. An automated facility system comprising:

a. means for collecting and sequencing microbiome samples from the facility;

b. means for measuring facility operation parameters; and

c. means for automated modification of facility operation parameters in response to detection of nucleotide sequences that fall within a predetermined sequence identity definition;

wherein the facility operation parameters are modified to optimize facility performance on an ongoing basis as sequence data is obtained from the samples.

21. The facility system of claim 19, wherein an automated modification occurs through a system that prioritizes human or animal health over minimizing energy use and effects facility operation through changing (a) ventilation flow rates and/or (b) the ratio of indoor:

outdoor air entering the HVAC system and/or (c) the amount and type of air filtration.

22. A method of optimizing the bioburden of a surface material in a facility comprising:

(a) placing two or more distinct surface materials in an identical location within a facility or a test chamber, (b) measuring one or more facility operation parameters, (c) analyzing the microbiome of the materials, and (d) determining which materials harbor an identity and/or relative abundance of microbes and/or OTUs that are associated with improved facility performance compared to others.

23. The method of claim 22, wherein said facility is a hospital, an office building, a food preparer or a food processor, or a seaborne or airborne vessel.

24. A system for improving facility performance, comprising:

multiple collectors positioned at various locations within a facility, said collectors configured to collect samples potentially containing nucleic acid;

a nucleic acid sequencer operably connected to the collectors and configured to sequence any nucleic acid therein so as to determine whether one or more indicator taxa, biochemical activity, or OTU is present in the sample and to send a signal if such nucleic acid is detected in an amount predetermined to generate the signal;

a control unit operably coupled to one or more devices of the facility, the one or more devices performing a function that is related to an operational parameter of the facility, the control unit further being operably coupled to receive a signal from the nucleic acid sequencer, the control unit comprising computer executable software for performing a step for receiving a signal that the one or more indicator taxa, biochemical activity, or OTU is present in a sample in an amount that requires adjusting a setting of the one or more devices to alter the level of the nucleic acid detected after one or more operational parameters have been changed.

25. The system of claim 24, wherein the nucleic acid sequencer sequences the one or more samples in real-time or near real-time.

26. The system of claim 24, wherein the step for receiving a signal that the one or more indicator taxa, biochemical activity, or OTU is present in a sample in an amount that requires adjusting a setting the one or more devices to alter the level of the nucleic acid detected is performed in time increments form every 15 minutes to weekly.

27. The system of claim 24, wherein the facility is a hospital.

28. The system of claim 24, wherein the facility is an office.

29. The system of claim 24, wherein the facility is a cruise ship.

30. The system of claim 24, wherein the facility is an airliner.

31. The system of claim 24, further comprising a user interface for viewing at least one of i) the sequence of the one or more indicator taxa, biochemical activity, or OTU, ii) the level of nucleic acid detected, and iii) the setting of the one or more devices.

32. The system of claim 24, wherein the one or more indicator taxa, biochemical activity, or OTU is selected from the group consisting of a pollen, a fungus, a virus, or a bacteria.

33. The system of claim 24, wherein the level of nucleic acid detected indicates the presence of one or more microbes.

34. The system of claim 24, wherein the one or more devices is an HVAC system, and the step of adjusting the setting of the HVAC system comprises adjusting (a) ventilation flow rates and/or (b) the ratio of indoor:

outdoor air entering the HVAC systems and/or (c) the amount and type of air filtration.

35. The system of claim 24, wherein the step for receiving a signal that the one or more indicator taxa, biochemical activity, or OTU is present in a sample in an amount that requires adjusting a setting the one or more devices to alter the level of the nucleic acid detected is performed at intervals determined by occupancy within the facility.

36. The system of claim 24, wherein the step for receiving a signal that the one or more indicator taxa, biochemical activity, or OTU is present in a sample in an amount that requires adjusting a setting the one or more devices to alter the level of the nucleic acid detected is performed at intervals determined by one or more environmental considerations selected from the group consisting of a season, a time of the day, a day of the week, a proximity of the facility to a source of one or more indicator taxa, and a weather event.

37. The system of claim 24, wherein level of nucleic acid detected is altered to a lower level.

38. The system of claim 24, wherein the level of nucleic acid detected is altered to a higher level.

39. The system of claim 24, wherein the operational parameter is selected from the group consisting of air flow, exposed surface composition, lighting, temperature, relative humidity, frequency of cleaning, chemicals used for cleaning, surface moisture pH, CO2 level, O2 level, NO2 level, waste container location and frequency of removal, amount of airborne particulates and particle size distribution, facility volume, heating and cooling systems, human occupancy patterns, occupant traffic patterns, and occupant diversity.

43. The system of claim 24, wherein the step for receiving a signal that the one or more indicator taxa, biochemical activity or OTU is present in a sample in at least a minimum predetermined amount activates a warning devices that audibly and/or visibly indicates that (a) an action should be taken and/or (b) an indicator taxa, biochemical activity, or OTU is present.

40. A method for improving facility performance, comprising:

collecting from a facility a sample potentially containing nucleic acid;

sequencing any nucleic acid present within the sample so as to determine whether one or more indicator taxa, biochemical activity, or OTU is present in the sample;

adjusting one or more operational parameters of the facility to alter the level of the nucleic acid detected.

41. The method of claim 40, further comprising a step for providing multiple collectors at various locations within the facility, said collectors configured to collect a plurality of samples potentially containing nucleic acid.

42. The method of claim 40, further comprising a step for adjusting a setting of one or more devices of the facility, the devices performing a function that is related to the one or more operational parameters of the facility, wherein the step of adjusting the setting of the one or more devices alters the level of the nucleic acid detected.