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Test ID: GNRG Gram-Negative Bacillus Antimicrobial Resistance Genes, PCR Panel, Varies

Biohazard Infectious

Useful For

Characterizing the molecular mechanisms of antimicrobial resistance in Gram-negative bacilli to explain unusual phenotypic susceptibility profiles or for epidemiologic purposes.

 

This panel detects the following beta-lactamase enzyme producing genes:

Carbapenemase Genes:

GES (Carbapenemase)

GIM

IMP

KPC

NDM

OXA-23 like

OXA-24 like

OXA-48 like

OXA-58 like

SPM

VIM

 

ESBL Genes:

BEL

CTX-M1 Group

CTX-M2 Group

CTX-M9 Group

CTX-M8/25 Group

GES (ESBL)

PER

SHV

TEM

VEB

 

AmpC Genes:

ACC

ACT/MIR

CMY MOX

CMYII

DHA

FOX

 

Colistin/Polymyxin B Resistance Genes

MCR-1

MCR-2

Method Name

Multiplex Polymerase Chain Reaction (PCR) with Microarray Detection of Amplified Products

Reporting Name

Gram-Negative Resistance Genes, PCR

Specimen Type

Varies


Additional Testing Requirements


1. Organism identification must be provided. If organism identification is unknown, concomitantly order IDENT / Organism Referred for Identification, Aerobic Bacteria.

2. If susceptibility testing is needed; also order ZMMLS / Antimicrobial Susceptibility, Aerobic Bacteria, MIC.



Shipping Instructions


1. See Infectious Specimen Shipping Guidelines in Special Instructions for shipping information.

2. Place specimen in a large infectious container (T146) and label as an etiologic agent/infectious substance.



Necessary Information


Organism identification and specimen source are required.



Specimen Required


Supplies: Infectious Container, Large (T146)

Collection Container/Tube: Slant

Specimen Volume: Isolate

Collection Instructions:

1. Isolate infecting bacteria.

2. Organism must be in pure culture, actively growing. Do not submit mixed cultures.

Additional Information: Relevant susceptibility results may be provided (eg, meropenem resistant, cefepime resistant, colistin resistant).


Specimen Stability Information

Specimen Type Temperature Time Special Container
Varies Ambient (preferred)
  Refrigerated 

Clinical Information

The Check-MDR CT103XL panel, which is performed on bacterial isolates, detects 29 genes associated with antimicrobial resistance in Gram-negative bacilli.

 

Antibiotic resistance is evolving as a result of use and overuse of antibacterial agents. Characterizing the molecular mechanisms of antimicrobial resistance can be helpful to explain unusual phenotypic susceptibility profiles or for epidemiologic purposes. A myriad of beta-lactamase enzymes may be found in Gram-negative bacteria; these enzymes hydrolyze (break down) the beta-lactam ring of beta-lactam antibiotics, destroying their antibacterial activity. A single bacterial isolate may carry 1 or more genes that code for the production of a beta-lactamase enzyme. Beta-lactamases can be on the chromosome or on plasmids and may be classified as extended-spectrum beta-lactamases (ESBLs), AmpCs, and carbapenemases, among other types. Resistance to polymixins can occur through plasmid-encoded MCR-1 and MCR-2. MCR-1 and MCR-2 are phosphoethanolamine transferases that modify lipid A, a component of lipopolysaccharide (LPS) located in the outer membrane of Gram-negative bacteria. This modification reduces the ability of polymixins to bind to LPS and disrupt bacterial membranes, rendering the antibiotics ineffective.

 

ESBL are beta-lactamases with an expanded substrate profile and are typically plasmid-borne. They are capable of hydrolyzing first-, second-, third- and fourth-generation cephalosporins, penicillins, and monobactams. TEM, SHV, and CTX-M genes are the most clinically prevalent.

-TEM and SHV subtypes are derived from the parental sequences by point mutations resulting in amino acid substitutions, which allow the enzymes to hydrolyze a wide range of beta-lactam antibiotics.

-CTX-M genes originate from Kluyvera species and can be separated into 5 different groups based on their amino acid sequence: CTX-M-1, CTX-M-2, CTX-M-9, CTX-M-8, and CTX-M-25.

-VEB, PER, BEL, and GES genes are less common.

 

AmpC cephalosporinases hydrolyze almost all beta-lactam antibiotics including penicillins, cephalosporins, and monobactams and may be chromosomally or plasmid encoded. Several Enterobacteriaceae carry a chromosomal copy of an AmpC gene.

 

AmpC Gene

Origin of Chromosomal Gene

CMY II

Citrobacter freundii

DHA

Morganella morganii

FOX

Aeromonas caviae

ACC

Hafnia alvei

ACT/MIR

Enterobacter cloacae and Enterobacter asburiae

CMY I/MOX

Aeromonas hydrophilia

 

-Plasmid-encoded AmpC genes may be shared among bacteria. Plasmid-encoded AmpC genes may produce a higher amount of beta-lactamase as compared to chromosomally encoded AmpC genes; knowing the mechanism may be useful in assessing treatment. An AmpC gene detected in a species that does not have a chromosomal AmpC (see table above) suggests that the gene is plasmid -encoded.

 

Carbapenemases show general resistance to all beta-lactam antibiotics including the beta-lactam-beta-lactamase inhibitor combinations and elevated or complete resistance against carbapenem antibiotics. In addition, isolates harboring carbapenemases often have additional beta-lactamase genes and genes for resistance to quinolones and aminoglycosides.

-Klebsiella pneumoniae carbapenemase (KPC) is a plasmid-encoded carbapenemase first identified in Klebsiella pneumoniae isolates in North America. KPC has since spread to many parts of the world and can be found in several species of the Enterobacteriaceae.

-New Delhi metallo-beta-lactamase (NDM) was first reported in 2009 from a patient of Indian origin in Sweden. It is prevalent in the Indian subcontinent, and has spread worldwide.

-The oxacillinase group consists of 10 members, of which OXA-48 and OXA-181 are the most prevalent variants. OXA-48 occurs predominantly in Enterobacteriaceae, originated from Shewanella species, and is most prevalent in Europe and the North African subcontinent. Another grouping of OXA-type carbapenemases is found in Acinetobacter species and consists of 3 type members, OXA-23, OXA-24, and OXA-58. Each type has several subtypes.

-VIM, a metallo-beta-lactamase, was first found in 1997 in a Pseudomonas aeruginosa isolate in Verona. It may be found in Enterobacteriaceae and includes at least 38 variants of which the DNA sequences may differ significantly.

-IMP, a metallo-beta-lactamase, was detected in Japan in 1990 (IMP-1) in Pseudomonas aeruginosa. It may be found worldwide in Enterobacteriaceae and includes at least 44 members with varying gene sequences.

-GIM-1 and SPM-1, also metallo-beta-lactamases, are less frequently found carbapenemases. GIM-1 originated in Germany and has been found in Pseudomonas aeruginosa, Enterobacteriaceae, and Acinetobacter species. SPM-1 producing Pseudomonas aeruginosa is endemic in Brazilian hospitals where it has been associated with numerous outbreaks.

-GES gene family consists of both ESBL-types and carbapenemase types.

 

MCR-1 and MCR-2 confer plasmid-mediated resistance to colistin (polymixin E) and polymixin B, which are last-resort antibiotics used to treat multidrug resistant infections. Because the mcr genes are plasmid encoded, the opportunity for polymixin resistance to spread among organisms is concerning. Enterobacteriaceae harboring mcr genes have been identified in humans and animals worldwide, including in North America.

- MCR-1 was first reported by China in 2015 in Escherichia coli. MCR-2 was subsequently identified in E coli by Belgium in 2016. Since then, mcr genes have been identified in additional Enterobacteriaceae including Klebsiella pneumoniae, Salmonella enterica, Klebsiella aerogenes, and Enterobacter cloacae.

 

Content was based on the Check-MDR CT103XL User Manual and reproduced with permission by Wouter de Levita of Check-Points, 2016.

Reference Values

Not applicable

Interpretation

A negative or positive result is reported for each gene type assayed.

 

A positive result confirms the presence of a particular beta-lactamase gene or colistin/polymyxin B resistance gene in the bacterial isolate tested.

Clinical Reference

1. Patel JB, Richter SS: Mechanisms of resistance to antibacterial agents. In Manual of Clinical Microbiology. 11th edition. Edited by JH Jorgensen, MA Pfaller, KC Carrol, et al. Washington, DC, ASM Press, 2015, section 69, pp 1212-1245

2. Abbot, AN, Fange FC: Molecular detection of antibacterial drug resistance. In Manual of Clinical Microbiology, 11th edition. Edited by JH Jorgensen, MA Pfaller, KC Carrol, et al. Washington, DC, ASM Press, 2015, section 77, pp 1379-1389

3. Cunningham SA, Vasoo S, Patel R: Evaluation of the Check-Points Check MDR CT103 and CT103 XL Microarray kits using preparatory rapid cell lysis. J Clin Microbiol 2015;54:1368-1371

4. Liu YY, Wang Y, Walsh TR, et al: Emergence of plasmid-mediated colistin resistance mechanism mcr-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect Dis 2016;16:161–168

5. Xavier BB, Lammens C, Ruhal R, et al: Identification of a novel plasmid-mediated colistin-resistance gene, mcr-2, in Escherichia coli, Belgium, June 2016. Euro Surveill 2016; 21(27):pii=30280. Available at https://doi.org/10.2807/1560-7917.ES.2016.21.27.30280

Day(s) and Time(s) Performed

Varies; Batched 1 time per week

Analytic Time

10 days

Test Classification

This test was developed and its performance characteristics determined by Mayo Clinic in a manner consistent with CLIA requirements. This test has not been cleared or approved by the U.S. Food and Drug Administration.

CPT Code Information

87150

LOINC Code Information

Test ID Test Order Name Order LOINC Value
GNRG Gram-Negative Resistance Genes, PCR 93698-9

 

Result ID Test Result Name Result LOINC Value
SRCGN Specimen Source 31208-2
ORGGN Organism Identification 78702-8
38117 GES (Carbapenemase) 85823-3
38118 GIM 85833-2
38119 IMP 85498-4
38120 KPC 49617-4
38121 NDM 73982-1
38122 OXA-23-like 85825-8
38123 OXA-24-like 85826-6
38124 OXA-48-like 85503-1
38125 OXA-58-like 85828-2
38126 SPM 85829-0
38127 VIM 85501-5
38129 BEL 85831-6
38130 CTX-M1 Group 85832-4
38131 CTX-M2 Group 85844-9
38132 CTX-M9 Group 85834-0
38133 CTX-M8/25 Group 85835-7
38134 GES (ESBL) 85836-5
38135 PER 85837-3
38136 SHV 85838-1
38137 TEM 85839-9
38138 VEB 85840-7
38140 ACC 85841-5
38141 ACT/MIR 85842-3
38142 CMY MOX 85822-5
38143 CMY II 93699-7
38144 DHA 93700-3
38145 FOX 85843-1
38148 Interpretation 59464-8
601668 MCR-1 86221-9
601669 MCR-2 93701-1

Forms

If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.

Mayo Clinic Laboratories | Microbiology and Infectious Disease Catalog Additional Information:

mml-idsurveillance