BACKGROUND : Current research indicates that Klebsiella pneumoniae is a complex of closely related organisms ( K. pneumoniae sensu stricto, K. quasipneumoniae, K. variicola, K. quasivariicola, and K. africana ). There is a paucity of research into the distribution of K. pneumoniae complex members in clinical specimens and the pathogenic potential of complex members other than K. pneumoniae sensu stricto. METHODS : To assess the rates and characteristics of different K. pneumoniae complex members in our 886 bed tertiary care facility in Rochester, New York, we performed whole genome sequencing using the Illumina MiSeq on all inpatient, sterile-source isolates identified by routine culture work-up as K. pneumoniae from October 2018 - October 2019 (n=35). We additionally sequenced all K. pneumoniae liver isolates available in our collection, spanning 2017-2019 (n=12). Analyses were focused on delineating complex members, detection of antibiotic resistance genes, and gene clusters associated with hypervirulent phenotypes. RESULTS : In the yearlong collection of 35 K. pneumoniae complex isolates, we found that 92.4% were K. pneumoniae sensu stricto (n=32), 5.7% were K. quasipneumoniae (n=2), and 2.9% were K. variicola (n=1). In the liver isolate collection, one additional K. variicola was identified. Both K. quasipneumoniae isolates and one K. variicola isolate were from liver. One K. quasipneumoniae isolate was a phenotypic and genotypic extended spectrum beta-lactamase producer. All other K. quasipneumoniae and K. variicola isolates were resistant only to ampicillin. Five K. pneumoniae sensu stricto isolates were identified which carried genes associated with hypervirulence. No K. quasipneumoniae or K. variicola carried any hypervirulence associated genes. CONCLUSIONS : The rates of K. pneumoniae sensu stricto, K. quasipneumoniae , and K. variicola observed in this study are consistent with those observed internationally and in blood isolates. Interestingly, all of our K. quasipneumoniae isolates were isolated from liver abscesses. Genetic loci associated with hypervirulence appear to be restricted to K. pneumoniae sensu stricto.

Infections caused by extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli are a significant cause of morbidity and health care costs. Globally, the prevailing clonal type is ST131 in association with the blaCTX-M-15 β-lactamase gene. However, other ESBLs, such as blaCTX-M-14 and blaCTX-M-27, can also be prevalent in some regions. We identified ST38 ESBL-producing E. coli from different regions in the United States which carry blaCTX-M-27 embedded on two distinct plasmid types, suggesting the potential emergence of new ESBL lineages.

Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae pose significant treatment and infection prevention challenges. Escherichia coli sequence type (ST) 131 associated with the blaCTX-M-15 gene has been the dominant lineage of ESBL-producing E. coli in the US and worldwide. In this study, our objective was to determine the β-lactamase profile, means of dissemination, prevalence, and the clonal identity of ESBL-producing E. coli in our region of Western New York. Whole-genome SNP-based phylogenomics was used to assess 89 ceftriaxone-resistant (CTR) E. coli. Isolates were collected from both inpatients and outpatients and from urine and sterile-sites over a 2 month period in 2017 or throughout the year, respectively. ST131 was the predominant ST (46.0%), followed by ST38 (15.7%). The blaCTX-M-15 gene was commonly found in 53.7% of ST131 isolates, whereas the blaCTX-M-27 gene was found in 26.8% of ST131, though was significantly associated with ST38, and was found in 71.4% of those strains. When compared to ST131, ST38 E. coli exhibited increased frequency of resistance to nitrofurantoin and decreased frequency of resistance to ciprofloxacin and ampicillin-sulbactam. Using Nanopore long-read sequencing technology, an analysis of the ESBL genetic context showed that the blaCTX-M-15 gene was chromosomal in 68.2% of ST131, whereas the blaCTX-M-27 gene was plasmid-borne in all ST131 and 90% of ST38 isolates. Notably, the blaCTX-M-27 gene in ST38 resided on highly-related (99.0–100.0% identity and 65.0–98.0% query coverage) conjugative IncF plasmids of distinct plasmid multi-locus sequence types (pMLSTs) from those in ST131. Furthermore, ST131 and ST38 were found to harbor different antibiotic resistance gene and virulence factor profiles. These findings raise the possibility of an emerging ESBL-producing E. coli lineage in our region.

Klebsiella pneumoniae is an opportunistic pathogen known for multidrug resistance. Current research indicates that K. pneumoniae is a complex of closely related organisms (K. pneumoniae sensu stricto, K. quasipneumoniae, K. variicola, K. quasivariicola, and K. africana). Additionally, some strains of K. pneumoniae sensu stricto, known as hypervirulent K. pneumoniae (hvKp), cause severe infections in healthy members of the community. There is a paucity of research into rates of hvKp in the United States, the distribution of K. pneumoniae complex members in clinical specimens, and the pathogenic potential of complex members other than K. pneumoniae sensu stricto. We assessed the rates of hvKp and K. pneumoniae complex members in our 886 bed tertiary care facility in Rochester, New York. We performed whole genome sequencing on all inpatient, sterile-source isolates identified by routine culture work-up as K. pneumoniae from October 2018 – October 2019 (n=35). We additionally sequenced all K. pneumoniae liver isolates available in our collection, spanning 2017-2019 (n=18). In the yearlong collection of K. pneumoniae complex isolates, we found that 92.4% were K. pneumoniae sensu stricto (n=32), 5.7% were K. quasipneumoniae (n=2), and 2.9% were K. variicola (n=1). Five hvKp isolates were found, representing 5.7% (n=2) of K. pneumoniae sensu stricto isolates in the yearlong collection and 27.7% (n=5) of the liver isolate collection. All hvKp isolates were from liver; 60% were not associated with prior international residence.

Klebsiella aerogenes is a nosocomial pathogen associated with drug resistance and outbreaks in intensive care units. In a 5-month period in 2017, we experienced an increased incidence of cultures for carbapenem-resistant K. aerogenes (CR-KA) from an adult cardiothoracic intensive care unit (CICU) involving 15 patients. Phylogenomic analysis following whole-genome sequencing (WGS) identified the outbreak CR-KA isolates to group together as a tight monoclonal cluster (with no more than six single nucleotide polymorphisms [SNPs]), suggestive of a protracted intraward transmission event. No clonal relationships were identified between the CICU CR-KA strains and additional hospital CR-KA patient isolates from different wards and/or previous years. Carbapenemase-encoding genes and drug-resistant plasmids were absent in the outbreak strains, and carbapenem resistance was attributed to mutations impacting AmpD activity and membrane permeability. The CICU outbreak strains harbored an integrative conjugative element (ICE) which has been associated with pathogenic Klebsiella pneumoniae lineages (ICEKp10). Comparative genomics with global K. aerogenes genomes showed our outbreak strains to group closely with global sequence type 4 (ST4) strains, which, along with ST93, likely represent dominant K. aerogenes lineages associated with human infections. For poorly characterized pathogens, scaling analyses to include sequenced genomes from public databases offer the opportunity to identify emerging trends and dominant clones associated with specific attributes, syndromes, and geographical locations.

The genome sequence of a Facklamia hominis strain isolated from the urine of a patient with acute cystitis and sepsis is reported. The genome contains ermB and tet (M) genes, consistent with the isolate’s phenotypic resistance to macrolides and tetracycline.