Carbapenemase dendogram fragment
Typing Services

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$40 / $50 for PCR service

As highlighted in a recent CDC report (1), the emergence and spread of antibiotic resistant bacteria represent major threats to the health of the American public. Major culprits are the enterobacteria (family Enterobacteriaceae, particularly KlebsiellaE. coliSalmonellaShigellaProteusEnterobacter, and Serratia species) and their distant relatives Pseudomonas and Acinetobacter species. Not surprisingly in light of their widespread use, beta-lactam antibiotics (penicillins, cephalosporins, monobactams, carbapenems) represent the major target of resistance mechanisms. In the Gram negative species noted above, the resistance mechanism typically involves plasmid-mediated acquisition of one or more beta-lactamase (bla) genes.

Since the 1980’s, many novel bla genes have emerged that confer resistance to extended spectrum beta-lactams including aztreonam and third generation cephalosporins (e.g., cefotaxime). This epidemic spread of extended spectrum beta-lactamases (ESBL) has been labelled a “serious” threat by the CDC. ESBL-expressing bacteria fortunately remain susceptible to the remaining class of beta-lactams, the carbapenems. However, recent years have seen the emergence and worldwide spread of carbapenemase genes among Gram negative pathogens. Indeed, the CDC recognizes carbapenemase-resistant Enterobacteriaceae (CRE) as an “urgent” threat. To date, carbapenemases identified in the U.S. are predominantly of the KPC type, although isolated cases involving OXA-48, VIM, IMP, and NDM group-carbapenemases have also been reported.

One of the four core actions in the CDC plan to address these multiple threats is “tracking resistant bacteria”. Of course, this tracking remains heavily dependent on conventional antimicrobial susceptibility testing of cultured organisms. While these susceptibility data are important, accurate tracking requires identification of resistance mechanisms at the genotype level, since the resistance phenotype can be mediated in multiple ways. Genotyping begins with a PCR screen to identify the resistance gene(s), followed by sequence typing to identify the specific allele (see, for example, ref. 2).

MicrobiType offers a comprehensive panel of PCR screens and sequence typing services to assist in the genotyping of beta-lactam resistance mechanisms in Enterobacteriaciae, Pseudomonas, and Acinetobacter species. These services employ genomics-optimized modifications of previously validated methods to maximize both reliability and affordability. Carbapenemase services are listed here; see also the ESBL page.

Carb-PCR:  Screens for the 5 major groups of carbapenemase genes KPC, VIM, IMP, OXA-48, and NDM. Results are reported as positive or negative for each group.

Carb-ST:  Samples submitted for Carb-PCR above that are positive for a given carbapenemase gene are subsequently  characerized by genomics-optimized sequence typing. Results are reported as sequence type (i.e., allele number such as KPC-3) based on comparison to carbapenemase databases (NCBI and Additionally, a sequence alignment and dendrogram (see Carbapenemase dendograms for examples) is provided to illustrate the relationship of the sample allele to concurrently or previously submitted alleles from your lab, and to a representative panel of previously characterized alleles.


Note that for each service substantial discounts are applied for multiple isolates.

(2)  Castanheira M et al. (2013). Antimicrob Agents Chemother 57:3012.