Environmental surveillance of ESBL and carbapenemase-producing gram-negative bacteria in a Ghanaian Tertiary Hospital

Abstract

Background: The burden of antibiotic resistant infection is mainly felt in low-to-middle income countries, where the rate of antimicrobial resistance is largely under-surveyed and under huge pressure from unregulated, disparate and often self-guided access to antimicrobials. Nosocomial infections from hospital environments have been shown to be a particularly prevalent source of multi-drug resistant strains, yet surveillance of hospital environmental contamination is often not investigated.

Methods: The study was prospective, observational and cross-sectional, sampling 231 high and low touch surfaces from 15th March to 13th April 2021, from five wards in the Cape Coast Teaching Hospital, Ghana. Microbial growth in the presence of vancomycin and either meropenem or cefotaxime was examined and bacterial species were identified by MALDI-TOF. The presence of common extended-spectrum β-lactamases (ESBL) and carbapenemase antimicrobial resistance genes (ARG) were identified through PCR screening, which were confirmed by phenotypic antimicrobial susceptibility determination. Isolates positive for carbapenem resistance genes were sequenced using a multi-platform approach.

Results: We recovered microbial growth from 99% of swabs (n = 229/231) plated on agar in the absence of antimicrobials. Multiple sites were found to be colonised with resistant bacteria throughout the hospital setting. Bacteria with multi-drug resistance and ARG of concern were isolated from high and low touch points with evidence of strain dissemination throughout the environment. A total of 21 differing species of bacteria carrying ARG were isolated. The high prevalence of Acinetobacter baumannii carrying bla_NDM-1 observed was further characterised by whole genome sequencing and phylogenetic analysis to determine the relationship between resistant strains found in different wards.

Conclusion: Evidence of multiple clonal incursions of MDR bacteria of high sepsis risk were found in two separate wards for a regional hospital in Ghana. The prevalence of multiple bla_NDM carrying species in combination with combinations of ESBLs was particularly concerning and unexpected in Africa. We also identify strains carrying tet(X3), bla_VIM-5 or bla_DIM-1 showing a high diversity of carbapenamases present as a reservoir in a hospital setting. Findings of multi-drug resistant bacteria from multiple environmental sites throughout the hospital will inform future IPC practices and aid research prioritisation for AMR in Ghana.

Keywords: AFRICA; AMR; Acinetobacter; CRAB; Carbapenemase; ESBL; Ghana; Hospital environment; Infection prevention and control; NDM.

Fig. 1

A stacked bar graph coloured per ward showing the number of hospital surface swabs PCR positive for each antibiotic resistance gene screened. The total number of swabs processed was 231

Fig. 2

a Sunburst diagram summarising bacterial species identified (outer ring); ACB, Acinetobacter baumannii complex; ACS, Acinetobacter spp.; ECO, E. coli; EBU, Enterobacter bugandensis; ECL, Enterobacter cloacae; EHE, Escherichia hermannii; KPN, Klebsiella pneumoniae; LEA, Leclercia adecarboxylata; MIX, Mixta calida; PAA, Pantoea agglomerans; PSF, Pseudomonas fulva; PSS, Pseudomonas stutzeri; UNI, Unidentified. The carriage of ESBL and/or carbapenemase genes (middle ring); ESBL (bla_CTX-M-15 and/or bla_OXA-1 and/or bla_SHV and/or bla_TEM), All (all ESBL genes identified and bla_NDM and bla_OXA-48-like). The ward the sample was collected from (inner ring); AE, accident and emergency; OG, obstetrics and gynaecology; NICU, Neonatal Intensive Care Unit; PW, paediatric ward

Fig. 3

A mid-point rooted core genome phylogenetic tree of bla_NDM positive Acinetobacter isolates. Leaf labels are isolate codes with the ward abbreviation (PW, paediatric ward; OG, obstetrics and gynaecology; NICU, neonatal intensive care) and swab number. The sequence type (ST) follows the leaf node where applicable. The presence/absence of antibiotic resistance genes is colour coded per class; aminoglycoside (green), β-lactam (purple), trimethroprim (olive), phenicol (lilac), macrolide (pink), sulphonamide (blue), tetracycline (orange)

Fig. 4

a An outline of the obstetrics and gynaecology ward with red dots indicating the locations of the swabs containing the cluster of ST109 A. baumannii. b A SNP heatmap revealing the pairwise SNPs between the isolates with sufficient genome coverage for analysis. c A phenotype to genotype linkage for the antibiotics tested, where β-lactam resistance includes antibiotics meropenem and cefotaxime