Annual Report of Method Tracking

Form Approved OMB Control No.: 0920-1310 Expiration date: XX/XX/XXXX

­Annual Report of Method Tracking

1. Record ID (label as State_monthyear, ex: AK_032021)

2. Jurisdiction

3. Date of entry

4. Which organisms are you performing identification on?

5. Please list which "other" organism(s) ID is performed on

6. Which organisms are you performing antimicrobial susceptibility testing (AST) on?

7. Please list which "other" organism(s) AST is performed on

8. Which organisms are you performing phenotypic testing on?

9. Please list which "other" organism(s) phenotypic testing is performed on

10. Which organisms are you performing molecular mechanism testing on?

11. Please list which "other" organism(s) molecular mechanism testing is being performed on

12. Which AR Lab Network methods are CLIA validated and reported for patient treatment?

13. Organism identification method (select all that apply)

14. If other, please specify

15. If using a MALDI-TOF, which system?

16. Which MALDI-TOF databases are utilized? Please list.

17. Does your lab utilize CDC's MicrobeNet?

18. Antimicrobial susceptibility testing (AST) method (select all that apply)

19. If other AST method, please specify

20. Please explain why your laboratory is not performing AST on HAI isolates.

21. If BMD, which platform(s) do you use?

22. If other BMD platform, please specify

23. Which Sensititre panel(s) do you test?

24. If custom, please share which drugs are tested on your panel

25. If other, please share which panel you use and what drugs are included

26. If performing BMD with Sensititre, what transfer inoculum do you use?

27. If other Sensititre transfer inoculum used, please specify

28. If performing BMD with Sensititre, what incubation method do you use?

29. If performing BMD with Sensititre, what read method do you use?

30. If ATI, which instrument(s) do you use?

31. If ATI, which panel(s) do you test?

32. If using Microscan, what inoculation method do you use?

33. If other Microscan inoculation method, please specify

34. If using Microscan, what read method do you use?

35. If using Microscan, what incubation method do you use?

36. Are all drugs on the panel(s) tested validated?

37. If not all drugs on a panel are validated, please list which drugs are NOT currently validated on your panel(s)

38. List of drugs (and the manufacturer) tested and reported by your laboratory

39. If no, please describe the decision tree for AST in your lab

40. Alternatively, if no, you may upload any decision trees or workflow for AST in your lab

41. Phenotypic carbapenemase production testing method (select all that apply)

42. ATI instrument brand used for phenotypic carbapenemase testing (select all that apply)

43. If other carbapenemase detection method, please specify

44. If using more than one method for phenotypic carbapenemase detection, please describe workflow. (Example, CarbaNP is performed on isolates testing intermediate via mCIM.)

45. MBL screen method (select all that apply)

46. If other MBL method, please specify

47. Carbapenemase gene identification method (select all that apply)

48. If using an immunochromatography test, which brand are you using?

49. If other, please specify

50. Please select all activities for which your GeneXpert detection is utilized

51. What extraction method do you use?

52. If other, please specify

53. What PCR equipment do you use for rt-PCR?

54. If other, please specify

55. What Master Mix (catalog number) do you use?

56. If other, please specify

57. Which mechanisms do you have molecular detection validated/verified?

58. If other was selected, what other mechanisms do you perform molecular detection for?

59. Is your PCR multiplex or singleplex?

60. If multiplex, which targets are multiplexed?

61. If other, please specify

62. Please list any "new" instrumentation or assays undergoing evaluation or validation/verification in your laboratory

63. What laboratory information management system (LIMS) is your laboratory using?

64. Are instruments used for testing ARLN isolates integrated to report results in your Laboratory Information Management System (LIMS)?

65. If yes, please describe which instruments are integrated to report results in your Laboratory Information Management System (LIMS)

66. Please describe the CURRENT "life of an isolate" within your lab--from receipt to reporting of results (i.e. Day 1 subculture, Day 2 mCIM/CP production, Day 3 PCR/AST, etc).

67. Alternatively, please upload any SOP or visual workflow of an isolate in your lab--from receipt to reporting of results

68. Are you performing whole genome sequencing (WGS)?

69. Are your WGS protocols validated and verified under CLIA standards?

70. Is this WGS work currently funded, at least in part, by CDC?

71. If yes, by which mechanisms? (select all that apply)

72. What short-read sequencing platform do you use? (select all that apply)

73. Number of iSeq instruments available for use

74. Number of MiSeq instruments available for use

75. Number of HiSeq instruments available for use

76. Number of NextSeq instruments available for use

77. Number of NovaSeq instruments available for use

78. Number of ClearLabs instruments available for use

79. Please specify other short-read platforms you are using and the number of each

80. What long-read sequencing platform do you use? (select all that apply)

81. Number of MinION instruments available for use

82. Number of GridION instruments available for use

83. Number of PromethION instruments available for use

84. Number of PacBio RSII instruments available for use

85. Number of PacBio Sequel instruments available for use

86. Please specify other long-read platforms you are using and the number of each

87. What type of DNA extraction is your lab utilizing?

88. What kit(s) and/or instrument(s) are used for DNA extraction?

89. What type of library prep does your lab do?

90. What kit(s) and/or instrument(s) are used for library prep?

91. What instrument(s) are used to assess DNA quantity and quality and fragment size?

92. What type of platform do you use to run your bioinformatic analysis?" (check all that apply). If you send isolates to a regional lab for analysis, please select "other" and report which state samples are sent to.

93. Report which state WGS samples are sent to for bioinformatic analysis.

94. What bioinformatic pipeline(s) do you use for taxa ID and AR gene detection? (Check all that apply). If you send isolates to a regional lab for analysis, please select "other" and report which state samples are sent to.

95. Report which state samples are sent to for WGS analysis.

96. What barriers are keeping your lab from analyzing your own WGS data? (Check all that apply).

97. Describe "other" barriers keeping your lab from analyzing your own WGS data.

98. Are you performing culture-based colonization screenings?

99. If yes, please share which anatomical sites are validated and which are RUO (and if organism specific, please specify)

100. If yes, please upload your culture-based screening methods

101. Alternatively, if you don't want to upload methods, please describe your culture-based screening methods

102. Have you validated gram-positive organism colonization screening methods?

103. Please list which Gram positive organisms your lab performs screening for

104. If yes, please upload your gram-positive colonization screening methods

105. Who within your jurisdiction does the reporting for CPOs? (Select all that apply)

106. Which antibiotic resistance organisms are reportable within your jurisdiction? (Check all that apply)

107. Please list "other" reportable antibiotic resistant organisms within your jurisdiction.

108. Does your jurisdiction restrict reporting requirement to specific organisms (e.g., E. coli, K. pneumoniae, E. cloacae, etc.)?

109. List the specific organism your jurisdiction restricts reporting to.

110. How are isolates submitted to the PHL in your jurisdiction?

111. Which organisms are required or requested to be submitted within your jurisdiction? (Select all that apply).

112. POC(s) for G2 project (please provide names and email addresses for any staff that should be involved in communications and meeting invites)

Public reporting burden of this collection of information is estimated to average 120 minutes per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing the collection of information.  An agency may not conduct or sponsor, and a person is not required to respond to a collection of information unless it displays a currently valid OMB Control Number.  Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to CDC/ATSDR Reports Clearance Officer, 1600 Clifton Road NE, MS D-74, Atlanta, Georgia 30333; ATTN: PRA 0920-1310