Enterococcus sp. contamination surveillance in different levels of healthcare in eThekwini District, KwaZulu-Natal (KZN) South Africa.
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Date
2021
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Abstract
Hospital-acquired infections (HAIs) have been identified as long-standing setbacks affecting
hospitals' quality of health care. While one of the major challenges related to HAIs is controlling
cross-transmission, the role and significance of the inanimate hospital environment chain of
transmission are yet to be unequivocally elucidated. Therefore, this study investigated the
functional profile and diverseness of bacteria from various inanimate environmental sources, from
two different wards in public hospitals at various healthcare levels in eThekwini District,
KwaZulu-Natal, South Africa. True to the study focus on investigating the dissemination of
bacteria from equipment within the hospital, the study further used Enterococcus as well-known
HAI as target bacteria and described the molecular and genomic profiles of this specie isolated
from the hospital environments.
Samples were collected for a period of three months (September – November 2017) from the four
levels of healthcare in eThekwini district, KwaZulu-Natal. The intensive care unit and peadiatic
ward were employed in this study. An overall of 620 swabs were collected from areas frequently
touched by healthcare workers (HCWs) and patients. These sites include the occupied bed linen,
unoccupied bed linen, drip stands, patient files, ward phones, ventilators, nurses' tables, blood
pressure apparatus, sinks, linen room door handle and mops. Swabs were placed in Amies transport
medium and transported in a cooler box to the laboratory facility to be processed within four hours.
The collected swabs (n=620) were pooled and incubated in tryptone soya broth containing 6.5%
NaCl at 36.5oC for 24 hrs and subsequently plated on enterococci chromogenic media. The
microbial diversity and functional profiles from the sites were identified using 16S rRNA
metagenomics.
Positive colonies were sub-cultured on bile esculin azide agar, and screened using standard
microbiological methods, including haemolytic, oxidase and catalase, and API. Identifications
were confirmed with polymerase chain reaction (PCR) with the added genus-specific tuf-gene and
species-specific sodA-gene. Antibiotic resistance patterns in the Enterococcus spp. isolates were
determined by the Kirby-Bauer disk diffusion method against 14 antibiotics as recommended by
the Clinical and Laboratory Standard Institute (CLSI) guidelines.
Thirty-seven samples from E. faecalis showed intermediate Resistance to vancomycin and were
further analyzed using molecular tools viz. whole-genome sequencing (WGS) and bioinformatics
analyses. This enabled determining the resistome, mobile genetic elements (MGEs), and clonal
lineages circulating across the sites, wards, and hospitals. Metagenomics identified a total of 288
species, 190 genera, 105 families, 50 orders, 29 classes and 11 phyla from the samples analyzed.
The dominant functional metabolic pathways implicated in causing human infection discovered
were the signal transduction mechanisms, citrate cycle (TCA), transcription-factor bisphenol
degradation, tyrosine metabolism. A total of 295 Enterococcus spp. isolates were recovered from
the hospitals` environmental sites, 83% (n=245) were identified as Enterococcus faecium, 13%
(n=38) as Enterococcus faecalis, 2% (n=6) Enterococcus gallinarum and another 2% (n=6)
Enterococcus casseliflavus. Notably, the pediatric wards had the highest isolation rate compared
to ICU, 64% and 36%, respectively. Overall, the sites with the highest isolation rate were occupied
beds and mops (to clean ward floors) with 14.9% (n=44) each. The tertiary hospital were the most
affected.
The most prominent MDR antibiogram for E. faecium was CIP-RIF-NIT-TET-ERY and for WGS
analysis of the E. faecalis samples confirmed that the tet(M) and erm(C) genes were the prevalent
antibiotic resistance genes found in hospitals. The isolates harboured mobile genetic elements
consisting of plasmids (n =11) and prophages (n=14), predominantly clonally specific. The 37
isolates analyzed consisted of 15 clonal lineages with six major sequence types (ST).
Phylogenomic analysis showed that major lineages were mostly conserved within specific hospital
environments. This study highlighted the inanimate hospital environment as a possible source of
opportunistic nosocomial pathogens using Enterococcus as an illustrative example and
emphasized the urgent necessity to optimize infection prevention and control measures to
intercept/moderate the spread of bacteria in the hospital environments.
Description
Doctoral Degree. University of KwaZulu-Natal, Durban.