Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines

Abstract

Background: Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied.

Methods: A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data.

Results: Prevalent AMR mechanisms detected include blaCTX-M-15 (76.8%) and blaNDM-1 (37.5%). An epidemic IncFII(Yp) plasmid carrying blaNDM-1 was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year.

Conclusion: WGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs.

Keywords: K. pneumoniae; antimicrobial resistance; outbreak detection; whole genome sequencing.

Figure 1.

Phylogenetic tree of 259 Klebsiella isolates showing deep branches separating Kp I (K. pneumoniae) and Kp II (K. quasipneumoniae). Clusters based on linked genotypic (ST, KL, and O locus types) data showed 3 clusters of possible NICU outbreaks in 3 separate hospitals. Most ST348 isolates were collected in CMC, whereas ST397 and ST283 were unique in VSM and JLM, respectively. Maximum-likelihood tree was inferred from mapping genomes to reference K. pneumoniae strain K2044 (GCA_009497695.1). This interactive view is available at: https://microreact.org/project/p8oycZe8jyu3Aghc3EE99c. NICU, neonatal intensive care unit.

Figure 2.

Phylogenetic tree, linked epidemiological and genotypic data of outbreak isolates at 3 sentinel sites. (a) Maximum-likelihood tree of CMC ST348 (n = 15) isolates was inferred from mapping genomes to reference EuSCAPE_IL028. This interactive view is available at: https://microreact.org/project/p5amCjPTePU6ggNWanXSe1/cb996623. (b) Maximum-likelihood tree of 7 VSM ST397 isolates was inferred from mapping genomes to reference EuSCAPE_DK005. This interactive view is available at: https://microreact.org/project/9K27BJqkWxtpsqhovaK3B3/98829bfe. (c) Maximum-likelihood tree of 9 JLM ST283 isolates was inferred from mapping genomes to reference SRR5514218. This interactive view is available at: https://microreact.org/project/7MrkhkdfoWuCQjiUuRscuS/075c339d. Infection origin was described as either hospital-acquired infection (HAI) or community-acquired infection (CAI). Presence or absence of the following AMR genes was also described: bla_NDM, rmtC, bla_CTX-M, sul1, aac(3)-Il, aac(6′)-lb, bla_OXA-1, cat, dfrA, and qnrB1. Presence of plasmid replicons IncFII(Yp) and IncFIA(pBK30683) was also described, along with plasmid match (≥95% coverage) to p13ARS_MMH0112-3.