Healthcare-Associated Infections-Related Bacteriome and Antimicrobial Resistance Profiling: Assessing Contamination Hotspots in a Developing Country Public Hospital

Aline Fernanda Rodrigues Sereia; Ana Paula Christoff; Giuliano Netto Flores Cruz; Patrícia Amorim da Cunha; Guilherme Cezar Kniphoff da Cruz; Daniela Cristina Tartari; Caetana Paes Zamparette; Taise Costa Ribeiro Klein; Ivete Ioshiko Masukawa; Clarice Iomara Silva; Maria Luiza Vieira E Vieira; Mara Cristina Scheffer; Luiz Felipe Valter de Oliveira; Thaís Cristine Marques Sincero; Edmundo Carlos Grisard

doi:10.3389/fmicb.2021.711471

Healthcare-Associated Infections-Related Bacteriome and Antimicrobial Resistance Profiling: Assessing Contamination Hotspots in a Developing Country Public Hospital

Front Microbiol. 2021 Aug 16:12:711471. doi: 10.3389/fmicb.2021.711471. eCollection 2021.

Authors

Aline Fernanda Rodrigues Sereia^{1

2}, Ana Paula Christoff², Giuliano Netto Flores Cruz², Patrícia Amorim da Cunha¹, Guilherme Cezar Kniphoff da Cruz², Daniela Cristina Tartari³, Caetana Paes Zamparette³, Taise Costa Ribeiro Klein⁴, Ivete Ioshiko Masukawa⁴, Clarice Iomara Silva⁴, Maria Luiza Vieira E Vieira⁴, Mara Cristina Scheffer⁴, Luiz Felipe Valter de Oliveira², Thaís Cristine Marques Sincero³, Edmundo Carlos Grisard¹

Affiliations

¹ Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis, Brazil.
² BiomeHub, Florianópolis, Brazil.
³ Department of Clinical Analysis, Federal University of Santa Catarina, Florianopólis, Brazil.
⁴ Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, Brazil.

Abstract

Hospital-built environment colonization by healthcare-associated infections-related bacteria (HAIrB) and the interaction with their occupants have been studied to support more effective tools for HAI control. To investigate HAIrB dynamics and antimicrobial resistance (AMR) profile we carried out a 6-month surveillance program in a developing country public hospital, targeting patients, hospital environment, and healthcare workers, using culture-dependent and culture-independent 16S rRNA gene sequencing methods. The bacterial abundance in both approaches shows that the HAIrB group has important representativeness, with the taxa Enterobacteriaceae, Pseudomonas, Staphylococcus, E. coli, and A. baumannii widely dispersed and abundant over the time at the five different hospital units included in the survey. We observed a high abundance of HAIrB in the patient rectum, hands, and nasal sites. In the healthcare workers, the HAIrB distribution was similar for the hands, protective clothing, and mobile phones. In the hospital environment, the healthcare workers resting areas, bathrooms, and bed equipment presented a wide distribution of HAIrB and AMR, being classified as contamination hotspots. AMR is highest in patients, followed by the environment and healthcare workers. The most frequently detected beta-lactamases genes were, bla _SHV-like, bla _OXA- ₂₃ _-like, bla _OXA- ₅₁ _-like, bla _KPC-like, bla _CTX-M- ₁, bla _CTX-M- ₈, and bla _CTX-M- ₉ groups. Our results demonstrate that there is a wide spread of antimicrobial resistance due to HAIrB in the hospital environment, circulating among patients and healthcare workers. The contamination hotspots identified proved to be constant over time. In the fight for patient safety, these findings can reorient practices and help to set up new guidelines for HAI control.

Keywords: 16S rRNA gene sequencing; antimicrobial resistance; bacteriome; beta-lactamases; healthcare workers; healthcare-associated infections; hospital environment; microbiome.