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

Abstract

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 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 Enterobacteriaceae 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 Escherichia coli and Klebsiella pneumoniae. Out of 124 Enterobacteriaceae isolates, we identified 51 strains as CPE and divided these into 7 species, 11 E. coli, 14 Klebsiella spp., 15 Enterobacter spp., and 11 others, including 4 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 6 of 11 E. coli isolates belonged to clonal complex 10 (CC10). Of 11 K. pneumoniae strains, 9 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 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 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 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.

Multidrug Resistant Klebsiella pneumoniae ST101 Clone Survival Chain From Inpatients to Hospital Effluent After Chlorine Treatment

“…Our data point that the K. pneumoniae clone presented here may have the ability to survive in the urban wastewater after being released in the hospital sewage. The persistence of this clone in the hospital effluent after chlorination indicates its dissemination potential in surface and recreational waters, as previously suggested by other authors ( Lepuschitz et al, 2019 ; Suzuki et al, 2020 ).…”

“…The identification of VIM and KPC-producing Klebsiella spp. in the treated wastewater of a hospital ( Gomi et al, 2018 ), of OXA-48 producing K. pneumoniae from hospital sewage ( Zurfluh et al, 2017 ), or of the presence of the same clone in the hospital sewage and receiving river ( Suzuki et al, 2020 ) raises concerns. Since its first detection in Székely et al (2013) , OXA-48 was the most frequently encountered carbapenemase in Romania ( Lixandru et al, 2015 ; Grundmann et al, 2017 ; Popescu et al, 2017 ; Baicus et al, 2018 ; Surleac et al, 2020 ).…”

Phenotypic Characterization and Whole-Genome Analysis of a Novel Bacteriophage HCF1 Infecting Citrobacter amalonaticus and C. freundii

“…Furthermore, polymerase chain reaction (PCR)-based detection of resistance genes in these bacterial isolates suggested the presence of β-lactamase genes ( Liu et al, 2017 ). More recently, carbapenemase-producing C. amalonaticus strain has been reported from hospital sewage and river water site in the Philippines ( Suzuki et al, 2020 ). Multidrug resistant (MDR) bacteria of public health importance assume greater significance in the wake of reports from various parts of the world indicating that Citrobacter spp.…”

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“…Our data point that the K. pneumoniae clone presented here may have the ability to survive in the urban wastewater after being released in the hospital sewage. The persistence of this clone in the hospital effluent after chlorination indicates its dissemination potential in surface and recreational waters, as previously suggested by other authors (Lepuschitz et al, 2019;Suzuki et al, 2020). Therefore, multi-level studies are needed for increasing knowledge on ecology, population structure and pathogenicity of resistant K. pneumoniae strains and to elucidate the possible transmission of clinical strains into the environment and the subsequent potential risk posed to human and environmental health (Wyres et al, 2020a).…”

“…The identification of VIM and KPCproducing Klebsiella spp. in the treated wastewater of a hospital (Gomi et al, 2018), of OXA-48 producing K. pneumoniae from hospital sewage (Zurfluh et al, 2017), or of the presence of the same clone in the hospital sewage and receiving river (Suzuki et al, 2020) raises concerns. Since its first detection in Székely et al (2013), OXA-48 was the most frequently encountered carbapenemase in Romania (Lixandru et al, 2015;Grundmann et al, 2017;Popescu et al, 2017;Baicus et al, 2018;Surleac et al, 2020).…”