Resistome-based surveillance identifies ESKAPE pathogens as the predominant gram-negative organisms circulating in veterinary hospitals

Abstract

Introduction: Healthcare-associated infections (HCAIs) associated with extended-spectrum cephalosporin-resistant gram-negative (ESC-R GN) bacteria are an emerging concern in veterinary hospitals, especially in companion animal intensive care units (ICUs).

Methods: To understand the molecular epidemiology of ESC-R GN isolates in two veterinary hospitals (equine and small animal), a 6-month pilot study was performed during which fecal and environmental samples were obtained twice from selected patients, upon ICU admission and after 48 h of hospitalization. In total, 295 ESC-R GNs were analyzed using the Acuitas Resistome^® Test (OpGen, Maryland, US), a PCR-based assay screening for 50 antimicrobial resistance gene families encoding for production of extended-spectrum beta-lactamase (ESBLs), TEM/SHV/OXA or AmpC beta-lactamases and carbapenemases. Combining organism identification and antimicrobial susceptibility data to genotyping results, unique "Acuitas profiles" were generated that can be used for fast typing the isolates and tracking transmission events.

Results: ESKAPE GN pathogens were the most prevalent ESC-R GN isolates circulating in both the small animal and equine hospitals, consisting of Enterobacter cloacae complex (21.7%), Pseudomonas aeruginosa (20%), Klebsiella pneumoniae (15.9%), and Acinetobacter baumannii complex (13.6%) followed by Escherichia coli (12.2%), most harboring a combination of genes encoding for beta-lactamases and ESBLs. Some ESKAPE genotypes showed likely intra-hospital transmission, including E. cloacae (two genotypes, one carrying SHV4, SHV5, and TEM7 and the other TEM1, TEM3, and TEM7 enzymes) in the equine and K. pneumoniae (SHV1, SHV5, and DHA1-positive) in the small animal ICUs, respectively. Furthermore, P. aeruginosa (carrying OXA-50), A. baumannii complex (OXA-51), and E. coli (CTX-M-1) genotypes were isolated across both hospitals, suggesting possible transfer mediated via movement of staff and students. Importantly, isolates carrying transmissible resistance to last-resort antimicrobials (i.e. carbapenems) were identified within the hospital environments, consisting of three environmental Acinetobacter spp. harboring bla_{OXA - 23} and one clinical E. coli with bla_{OXA - 48}.

Conclusion: We describe the widespread occurrence of ESKAPE gram-negative organisms in veterinary ICU patients and hospital environments. Findings from this project provide baseline data on the epidemiology of ESKAPE pathogens in veterinary settings, which can inform infection control policies to aid in patient management and prevent transmission of nosocomial infections associated with these pathogens.

Keywords: ESKAPE; companion animals; gram-negative; infection control; intensive care unit (ICU); surveillance; veterinary; veterinary hospitals.

Figure 1

Overall prevalence of the ESC-R GN organisms (n = 295) circulating in the equine and small animal hospitals between March 2016 and June 2018. Error bars represent 95% confidence intervals.

Figure 2

Prevalence of ESKAPE organisms, E. coli, and all other pathogens circulating in the equine and small animal Intensive Care Units (ICUs) between January and June 2018 during the pilot study (n = 170, consisting of PS-F1 and 2 and PS-ENV1 and 2 isolates). Error bars represent 95% confidence intervals.

Figure 3

Number of ESC-R GN isolates obtained per Intensive Care Unit sample type (PS-F1 and 2 and PS-ENV1 and 2) during the pilot study (January–June 2018) in the equine (A) and small animal (B) hospital Intensive Care Units.

Figure 4

Overall extended-spectrum beta-lactamase (ESBLs), TEM/SHV/OXA, and AmpC beta-lactamase or carbapenemase genes per hospital (A). Heatmap of the distribution of extended-spectrum beta-lactamase (ESBLs), TEM/SHV/OXA and AmpC beta-lactamase or carbapenemase encoding genes (B); [n = 295, March 2016–June 2018].

Figure 5

Adapted and with permission from Reuben et al. (2017). Review of the principal shared resistance profiles. Representation of five groups of MDR-GN organisms identified by Acuitas profiles as genetically related and their distribution amongst the two hospitals and sample type from where isolated during the pilot (PS). Patterns I, II, and IV show possible transmission within veterinary facilities and Patterns III, V, and VI show possible inter-facility transmission.