Klebsiella pneumoniae

Kpn-rnfC dendogram fragment
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As with other members of the family Enterobacteriaciae, Klebsiella pneumoniae commonly colonizes the gastrointestinal tract. Its natural habitat extends, however, to the soil, where it can play a beneficial role through nitrogen fixation. Habitats where it is clearly not beneficial are the human lung, bloodstream, or urinary tract where infections can be difficult, or even impossible, to treat.

Typical K. pneumoniae patients have underlying risk factors or chronic health conditions, such as alcoholism, immune suppression, diabetes, malignancy, or lung disease. They are often in the ICU or reliant on respiratory ventilators, intravenous catheters, or long term chemotherapeutics. Not surprisingly, then, this gram negative rod has emerged as a major cause of healthcare-associated (nosocomial) infection (1,2).  To a considerable extent this emergence is due to acquired antibiotic resistance (3,4).

Many bacteria exhibit beta-lactamase-mediated resistance to penicillins and cephalosporins, but remain susceptible to carbapenems (e.g., imipenem) which have an atypical ring structure. Consequently, carbapenems have been considered “antibiotics of last resort” for infections caused by Klebsiella and other Enterobacteriaciae. This status is now threatened by the worldwide, plasmid-mediated dissemination of carbapenem-recognizing beta-lactamases, particularly the K. pneumoniae carbapenemase KPC.  Mortality rates associated with carbapenem-resistant Enterobacteriaciae (CRE) infection approach 50%.

 

In the absence of treatment options, infection containment becomes critical. For example, over a 6 month period in 2011 the NIH Clinical Center experienced an outbreak of carbapenem-resistant K. pneumoniae involving 18 patients (5). Conventional approaches failed to reveal the epidemiology of this outbreak: all isolates had the same multilocus sequence type (MLST) ST258, but since its initial detection in 2001 this lineage has become ubiquitous in U.S. hospitals (6). The outbreak was eventually contained through implementation of rigorous infection control procedures, but not before 11 fatalities.

 

Since MLST alone lacked sufficient resolution, NIH researchers subsequently used next generation whole genome sequencing to identify 41 total single nucleotide variants among the 18 patient isolates (5). Analysis of these SNVs revealed  that most of the K. pneumoniae isolates belonged to one of two clusters derived from the index patient’s strain KPNIH1. Transmission potentially included “silently colonized” patients or healthcare workers, along with the hospital environment and equipment since the outbreak strain was cultured from drains and a ventilator (strain KPNIH7).

 

Unfortunately, whole genome sequencing remains impractical for routine epidemiology due to costs associated with reagents and equipment and the time and technical expertise required for data analysis. Furthermore, SNVs, whether limited to 7 loci (MLST) or expanded to the whole genome, are relatively insensitive markers of strain variation. DNA repeats exhibit higher rates of polymorphism, and hence provide more cost-effective targets for strain identification central to outbreak detection and investigation. DNA repeats are readily identified by bioinformatic analysis of a bacterial genome sequence, and many are present within K. pneumoniae. Traditionally, candidate repeats are tested as typing targets by MLVA (multilocus variable number of tandem repeat analysis) using large sets of related and unrelated isolates.  Currently, a more reliable, efficient, and informative alternative is to test candidate repeats in silico, exploiting the increasing availability of genome sequences in public databases (>300 for K. pneumoniae).

At MicrobiType, two such repeat were identified as ideal targets. As shown in the KpMT1 dendrogram, the genomics-optimized sequence typing service KpMT1 resolved 25 of 28 epidemiologically unrelated K. pneumoniae strains. Notably, it resolved 6 sets of strains which share MLST types (ST258, ST11, ST23, ST48, ST134, and ST14). The 10 NIH Clinical Center patient isolates for which KpMT1 sequences were complete (the next generation sequencing technologies used for to generate these sequences struggle with repeats) form two distinct clusters, analogous to the results obtained by whole genome SNV analysis (5).  To further enhance strain resolution, MicrobiType offers KpMT2 typing, which generated complementary but largely congruent results as KpMT1; e.g., the NIH patient isolates again form two distinct clusters (KpMT2 dendrogram).  KpMT1 and KpMT2 results are reported in dendrogram and sequence alignment formats, with comparison to concurrently or previously submitted isolates from your lab, and to representative database isolates.  To further enhance strain resolution, 

Additionally, MicrobiType offers KpMLST, using established loci but our own genomics-optimized primers to enhance reliability and hence reduce the potentially prohibitive cost of analyzing 7 loci. Results are reported as sequence type according to the public domain MLST database (7).

Last but certainly not least, MicrobiType offers Carb-PCR and Carb-ST services for identification and typing, respectively, of resistance-conferring carbapenemase genes. See the Carbapenemase page for details.

(1)  Bratu S et al. (2005). Arch Intern Med 165:1430.
(2)  Clancy CJ et al. (2013). Am J Transplant 13:2619.
(3)  McKenna M (2013). Nature 499:394.
(4)  Centers for Disease Control and Prevention (2013). www.cdc.gov/drugresistance/threat-report-2013/.
(5)  Snitkin ES et al (2012). Sci Transl Med 4:148ra116.
(6)  Kitchel B et al (2009). Antimicrob Agents Chemother 53:3365.
(7) www.pasteur.fr/recherche/genopole/PF8/mlst/Kpneumoniae.html

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