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

This study aimed to evaluate the prevalence and genetic characteristics of carbapenemase-producing Enterobacteriaceae (CPE) in hospital sewage and river water in the Philippines, which has a typical tropical maritime climate. We collected 83 water samples from seven hospital sewage and ten river water sites. CPE were identified using CHROMagar™ mSuperCARBA, and Gram-negative strains were identified using MALDI-TOF MS or 16S ribosomal RNA gene sequencing. Resistance genes in Enterobacteriaceae strains were identified by PCR and DNA sequencing, and transferability of carbapenemase genes from the CPE was investigated by conjugation experiments. Genotyping was performed by multilocus sequence typing (MLST) for Escherichia coli and Klebsiella pneumoniae. Out of 124 isolated Enterobacteriaceae, we identified 51 strains as CPE and divided these into seven species, 11 E. coli, 14 Klebsiella spp., 15 Enterobacter spp., and 11 others, including four additional species. Conjugation experiments via broth mating and using E. coli J53 revealed that 24 isolates can transfer carbapenemase-encoding plasmids. MLST analysis showed that six of 11 E. coli isolates belonged to clonal complex 10 (CC10). Of 11 K. pneumoniae, nine unique sequence types (STs) were identified, including ST147. Five types of carbapenemase genes were identified with the most prevalent being NDM (n = 39), which is epidemic in clinical settings in the Philippines. E. coli CC10 and K. pneumoniae 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. Importance Carbapenemase-producing Enterobacteriaceae (CPE) cause severe healthcare-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 Escherichia coli 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 E. coli CC10 and K. pneumoniae 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.