Environmental Surveillance and Characterization of Antibiotic Resistant Staphylococcus aureus at Coastal Beaches and Rivers on the Island of Hawai'i

Abstract

Staphylococcus aureus are human facultative pathogenic bacteria and can be found as contaminants in the environment. The aim of our study was to determine whether methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolated from coastal beach and river waters, anchialine pools, sand, and wastewater on the island of Hawai'i, Hawai'i, are a potential health risk. Samples were collected from three regions on Hawai'i Island from July to December 2020 during the COVID-19 pandemic and were characterized using whole-genome sequencing (WGS). From WGS data, multilocus sequence typing (MLST), SCCmec type, antimicrobial resistance genes, virulence factors, and plasmids were identified. Of the 361 samples, 98.1% were positive for Staphylococcus spp. and 7.2% were S. aureus positive (n = 26); nine MRSA and 27 MSSA strains were characterized; multiple isolates were chosen from the same sample in two sand and seven coastal beach water samples. The nine MRSA isolates were multi-drug resistant (6-9 genes) sequence type (ST) 8, clonal complex (CC) 8, SCCmec type IVa (USA300 clone), and were clonally related (0-16 SNP differences), and carried 16-19 virulence factors. The 27 MSSA isolates were grouped into eight CCs and 12 STs. Seventy-eight percent of the MSSA isolates carried 1-5 different antibiotic resistance genes and carried 5-19 virulence factors. We found S. aureus in coastal beach and river waters, anchialine pools, and sand at locations with limited human activity on the island of Hawai'i. This may be a public health hazard.

Keywords: MRSA; MSSA; Staphylococcus aureus; USA300; antimicrobial resistance; beaches; rivers; sequence types; virulence factors; whole-genome sequencing.

Figure 1

Geometric mean (±SE) of staphylococci collected from the districts of Hilo (stations #1–21), S. Kohala, N. Kona (stations #22–30), and Puna (stations #31–36) from July–December 2020 on Hawaiʻi Island, Hawaiʻi. (A) Staphylococcus spp. MPN/100 mL counts from water (beach/river/stream/anchialine pool) stations; (B) Staphylococcus spp. MPN/g DW counts from beach sand stations; (C) Staphylococcus spp. MPN/100 mL counts from wastewater collected from the Hilo Wastewater Treatment Plant. Detection of S. aureus is represented by the *. The number of * is how many different isolates were identified from the same station [ranging from one to four]. The prevalence of S. aureus, reported as number of detections in the total sample pool and percent, is shown at the base of each station, if detected.

Figure 2

Map of MRSA and MSSA sequence types (ST) isolated from coastal beach and river waters, anchialine pools, and sand from July–December 2020 in the districts of (A) Hilo, (B) S. Kohala, N. Kona, and (C) Puna on Hawaiʻi Island, Hawaiʻi.

Figure 3

Core genome single nucleotide polymorphism (SNP)-based phylogenetic tree of 12 STs and eight CCs of 36 [nine MRSA, 27 MSSA] isolates collected from coastal beach and river waters, anchialine pools, and sand on Hawaiʻi Island, Hawaiʻi, from July to December 2020. The scale bar denotes genetic distance in number of base substitutions per site. Branch tree labels indicate ST, isolate #, and CC.

Figure 4

Core genome SNP-based phylogenetic tree and SNP matrix of MRSA (n = 9) isolates obtained from the environment in 2020 from Hawaiʻi Island, Hawaiʻi, and clinical MRSA isolates collected from hospital patients (n = 8) in the State of Hawaiʻi in 2011. Clinical isolate data were obtained from Challagundla et al., 2018 [2] under accession #PRJNA330544. The scale bar denotes genetic distance in number of base substitutions per site.

Figure 5

Map of water sampling stations. Sampling was conducted at 36 water (beach/river/stream/anchialine pool) and sand stations in the districts of (A) Hilo (station #1–21), (B) S. Kohala, N. Kona (station #22–30), and (C) Puna (station #31–36) on (D) Hawaiʻi Island, (E) Hawaiʻi from June to December 2020.