Introduction of NGS in environmental surveillance for Healthcare-associated infections control.

Introduction: Healthcare-associated infections (HAIs) and antibiotic resistance are the most frequent and serious cause of complications related to health care. The monitoring of hospital environmental surfaces takes place with cultural isolation with some performance limitations. Hence the urgency of implementing environmental surveillance systems using new generation methods. In this pilot study next generation sequencing (NGS) technologies were evaluated for hospital environmental surfaces microbiome characterization, compared with traditional and molecular PCR methods. Materials and Methods: Three randomized rooms were selected for two consecutive environmental sampling including floor, footboard and sink for a total of 36 critical points. NGS and comparison culture isolation and a custom molecular qPCR panel kit, were performed. Resistome, using a panel of 84 resistance genes, was additionally evaluated. Results: Pseudomonas, Acinetobacter, Streptococcus, Staphylococcus, Corynebacterium and Propionibacterium represented the most frequently bacterial area profile. Of them only Acinetobacter, Staphylococcus and Pseudomonas were isolated with cultural methods, Acinetobacter: 33/36 NGS vs 4/36; Staphylococcus:36/36 NGS vs 36/36, Pseudomonas: 34/36 NGS vs 1/36. Comparison with custom PCR analysis showed a rate of identification of Acinetobacter:10/36, Staphylococcus:36/36, and Pseudomonas: 29/36. Other microorganisms were detected from 1 to 29% for a total of 8 phyla and 58 different genera, showing the sink as the most representative site. To note, Streptococcus, detected by NGS in many samples was not sought with traditional methods. Basically resistome identified mainly genes conferring resistance to macrolides, aminoglycosides, fluoroquinolones and beta-lactams. Discussion and Conclusions: Data from this study proved as NGS can be an effective method in monitoring hospital indoor microbial communities. NGS data together with resistome, provide a deeper understanding of the development of HAIs leading to create new sanitation protocols.