Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae

Abstract

Klebsiella pneumoniae is a serious human pathogen associated with resistance to multiple antibiotics and high mortality. K. variicola and K. quasipneumoniae are closely related organisms that are generally considered to be less-virulent opportunistic pathogens. We used a large, comprehensive, population-based strain collection and whole-genome sequencing to investigate infections caused by these organisms in our hospital system. We discovered that K. variicola and K. quasipneumoniae isolates are often misidentified as K. pneumoniae by routine clinical microbiology diagnostics and frequently cause severe life-threatening infections similar to K. pneumoniae. The presence of KPC in K. variicola and K. quasipneumoniae strains as well as NDM-1 metallo-beta-lactamase in one K. variicola strain is particularly concerning because these genes confer resistance to many different beta-lactam antibiotics. The sharing of plasmids, as well as evidence of homologous recombination, between these three species of Klebsiella is cause for additional concern.

Whole-Genome Sequencing of a Human Clinical Isolate of the Novel Species Klebsiella quasivariicola sp. nov

“…In a recent study of 1,777 K. pneumoniae isolates producing extended-spectrum β-lactamase (ESBL), which were recovered from patients in our health care system, we identified strain KPN1705 as a distinct outlier in the phylogenetic analysis (3, 4). It shared a common branch with K. variicola , yet was as distant from the K. pneumoniae , K. quasipneumoniae , and K. variicola reference genomes as they were from each other.…”

Significant temporal shifts on clonal and plasmid backgrounds of Enterobacteriaceae producing acquired AmpC in Portuguese clinical settings

“…Two MDR K. pneumoniae clones were frequently identified: (i) ST1380 (37%; clone KpB), associated with a small outbreak in 2004, producing DHA-1 and diverse SHV-ESBLs; (ii) ST11 (34%; clone KpF), harbouring wzi 75 and the capsular type KL105, detected in different hospitals between 2006 and 2008, producing DHA-1 and OXA-1 (Table 2). Remarkably, three DHA-1 producing isolates reported in 2007 in different wards (paediatrics, medicine) from the same hospital were re-identified as K variicola (Table 2), a species increasingly recognized as a frequent cause of human clinical infections that can be misidentified by automated methods, including MALDI-TOF MS [23] . More recently (2010-2013), the population of K. pneumoniae producing DHA was dominated by the MDR K. pneumoniae ST11-KL105 (KpF clone) (n=11; 85%), that persisted till the end of the period analysed at least in Hospital A (Table 1).…”

Isolation and characterization of heterotrophic nitrifying and aerobic denitrifying Klebsiella pneumoniae and Klebsiella variicola strains from various environments

“…The isolation of K. variicola from other natural environments is necessary to better understand its environmental role. Furthermore, there is evidence to suggest the previous misclassification of K. variicola, i.e., there are numerous cases K. variicola misclassified as K. pneumoniae (Chen et al 2016;Long et al 2017). Therefore, the isolation of new K. variicola strains will help to clarify its taxonomy.…”