Environmental Presence and Genetic Characteristics of Carbapenemase-Producing <i>Enterobacteriaceae</i> from Hospital Sewage and River Water in the Philippines

Abstract

This study aimed to evaluate the prevalence and genetic characteristics of carbapenemase-producing <i>Enterobacteriaceae</i> (CPE) in hospital sewage and river water in the Philippines, which has a typical tropical maritime climate. We collected 83 water samples from 7 hospital sewage and 10 river water sites. CPE were identified using CHROMagar mSuperCARBA, and Gram-negative strains were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA gene sequencing. Resistance genes in <i>Enterobacteriaceae</i> strains were identified using PCR and DNA sequencing, and transferability of carbapenemase genes from the CPE was investigated with conjugation experiments. Genotyping was performed using multilocus sequence typing (MLST) for <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> Out of 124 <i>Enterobacteriaceae</i> isolates, we identified 51 strains as CPE and divided these into 7 species, 11 <i>E. coli</i>, 14 <i>Klebsiella</i> spp., 15 <i>Enterobacter</i> spp., and 11 others, including 4 additional species. Conjugation experiments via broth mating and using <i>E. coli</i> J53 revealed that 24 isolates can transfer carbapenemase-encoding plasmids. MLST analysis showed that 6 of 11 <i>E. coli</i> isolates belonged to clonal complex 10 (CC10). Of 11 <i>K. pneumoniae</i> strains, 9 unique sequence types (STs) were identified, including ST147. Five types of carbapenemase genes were identified, with the most prevalent being NDM (<i>n </i>= 39), which is epidemic in clinical settings in the Philippines. <i>E. coli</i> CC10 and <i>K. pneumoniae</i> ST147, which are often detected in clinical settings, were the dominant strains. In summary, our results indicate that hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups.<b>IMPORTANCE</b> Carbapenemase-producing <i>Enterobacteriaceae</i> (CPE) cause severe health care-associated infections, and their increasing prevalence is a serious concern. Recently, natural ecosystems have been recognized as important reservoirs of antibiotic resistance genes. We investigated the prevalence and genetic characteristics of CPE isolated from the environment (hospital sewage and river water) in the Philippines and found several CPE, including <i>Escherichia coli</i> and other species, with different carbapenemases. The most prevalent carbapenemase gene type was NDM, which is endemic in clinical settings. This study revealed that isolates belonging to carbapenemase-producing <i>E. coli</i> CC10 and <i>K. pneumoniae</i> sequence type 147 (ST147), which are often detected in clinical settings, were dominant in the natural environment. Our work here provides a report on the presence and characteristics of CPE in the environment in the Philippines and demonstrates that both hospital sewage and river water are contaminated by CPE strains belonging to clinically important clonal groups.