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Triangulating the molecular epidemiology of carbapenem-resistant enterobacterales from humans, food Animals, and the environment.

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Introduction Antimicrobial resistance (AMR) is largely a consequence of selection pressure, from indiscriminate antimicrobial use in humans and animals, however release of other resistance-driving chemicals such as metals and biocides also play a role in development of AMR. Disposal of these drivers of AMR into the environment, requires One Health approach towards its understanding and containment. The ongoing dissemination of carbapenem-resistant Enterobacterales (CRE), particularly carbapenemase-producing Enterobacterales (CPE), represents a significant public health issue threatening the lives of millions globally. Carbapenems, in human health, are antibiotics of last resort, and conserving them for the future is of utmost importance. Therefore, it is critical to conduct surveillance of CRE and CPE in a One Health context using molecular techniques to determine a representative picture of the overall problem of CRE, its evolution and dissemination. This point prevalence study ascertained the carriage of CPE in humans, livestock animals (pigs), and environmental sources within the same geographical area of the uMgungundlovu district, KwaZulu-Natal, South Africa and triangulated the molecular epidemiology of CPE in humans, food animals, and the environment. Methodology The point prevalence study involved collecting rectal swabs from pigs and humans along with environmental water samples collected from a wastewater treatment plant that received water from both the hospital and abattoir. All samples were processed at the accredited National Health Laboratory Service (NHLS) Public Health Laboratory in KwaZulu-Natal. Selective chromogenic agar was used to isolate CPE from all samples obtained across the three sectors. Microbiological processing and analysis of samples were undertaken as per standard operating procedures of the NHLS. Bacterial identification and antibiotic susceptibility testing were performed using the VITEK® 2 automated system. Pure isolates were then subjected to whole genome sequencing (WGS), and generated sequence data were analysed using different bioinformatic tools, to determine the resistomes, virulomes, mobilomes, clonality, and phylogenomics of these isolates. Results Of 587 rectal swab samples screened for CPE, 230 (39.1%) were from humans, 345 (58,7%) were from pigs with 12 (2%) water samples. A total of 19/587 (3.2%) isolates i.e., 15 from humans and four from the environment, were CRE. All the environmental isolates (4) and 12/15 human isolates were carbapenemase producers. The three non-carbapenemase producing human isolates were resistant to ertapenem but susceptible to meropenem and imipenem. No CPE were isolated from the pig samples. Sixteen of the nineteen isolates were CPE. The most common CPE was Klebsiella pneumoniae 9/16 (56%), followed by Enterobacter hormaechei 3/16 (19%), Klebsiella quasipneumoniae 2/16 (13%), a novel ST498 Citrobacter freundii 1/16 (6%), and Serratia marcescens 1/16 (6%). Carbapenem xx resistance was attributed to plasmid-mediated carbapenemase encoding genes: blaOXA-181, blaOXA-48, blaOXA-484, blaNDM-1, and blaGES-5. Notably blaOXA-181 and blaNDM-1 were found in both human and environmental isolates. Common MGEs were found in different bacterial species/clones across humans and the environment. The IncFIB(K) plasmid replicon was found in all isolates of K. quasipneumoniae (2) from the environment and the majority of the K. pneumoniae strains (7/9) from humans. The majority of the K. pneumoniae isolates were OXA-181 (5/9) producers. The vast majority of β–lactamase encoding genes were associated with class 1 integrons IntI1, insertion sequences (IS) (IS91, IS5075, IS30, IS3000, IS3, IS19, ISKpn19, IS5075) and transposons (Tn3). The Col440I plasmid replicon the most common and identified in 11 (26.82%) isolates, mostly E. hormaechei (n = 6). The IncL/M(pMU407) and IncL/M(pOXA48) plasmid replicons were found exclusively in Klebsiella pneumoniae, with all but one of these isolates being OXA-181 producers. Virulence determinants were predicted for the eleven Klebsiella spp. as the most common species isolated where a total of 80 virulence genes were delineated. Phylogenomic analysis with other South African carbapenemase-producing K. pneumoniae, E. hormaechei, S. marcescens, and C. freundii from different sources (animals, environmental sources, and humans) revealed that some species from this study clustered with clinical isolates, some clustered according to sequence type and other species belonged to the same clonal node as other clinical isolates. Phylogenetics linked with metadata revealed that some isolates clustered according to the source. Notably, five Aeromonas spp. isolates, part of a novel sequence type – ST657, and habouring the blaCPHA-3 and blaOXA-12 genes were obtained from pigs during the screening process of this One Health point prevalence study. Although these isolates were resistant to imipenem, they were not CPE. Two ARGs were noted, blaCPHA3 and blaOXA-12, conferring the resistance to imipenem and penicillin (ampicillin and amoxicillin). No MGEs were identified in these isolates. Conclusion This One Health Study delineated the resistome, mobilome, virulome, and phylogeny of CPE in human and the environment sectors, highlighting the potential propagation of carbapenemase antibiotic resistance genes via diverse MGEs across the sectors. Such genomic fluidity highlights the need for comprehensive, integrated genomic surveillance in a One Health context to address AMR successfully.


Doctoral Degree. University of KwaZulu-Natal, Durban.