Doctoral Degrees (Medical Microbiology)

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Enterococcus sp. contamination surveillance in different levels of healthcare in eThekwini District, KwaZulu-Natal (KZN) South Africa.
(2021) Shobo, Christiana Omowunmi.; Bester, Linda Antionette.; Essack, Sabiha Yusuf.
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.
Molecular and genomic analysis of clinical multidrug-resistant coagulase-negative staphylococci from the uMgungundlovu District in the KwaZulu-Natal Province, South Africa.
(2020) Asante, Jonathan.; Essack, Sabiha Yusuf.; Amoako, Daniel Gyamfi.; Abia, Akebe Luther King.
Coagulase-negative staphylococci (CoNS) are among the most commonly recovered bacteria in clinical specimens. They are usually colonisers (commensals) of the skin and nasal passages and considered contaminants of microbial cultures. However, they have been recognised as emerging pathogens, frequently causing opportunistic infections. The frequent use of indwelling medical devices and long-term hospitalisation present an increased risk of exposure to CoNS, resulting in infections usually caused by multidrug-resistant pathogens. Few studies focus on CoNS, including characterisation of their mechanisms of resistance, virulence, and persistence. Therefore, this study describes the molecular and genomic profiles of clinical CoNS from public sector hospitals in the uMgungundlovu District in KwaZulu-Natal, South Africa. Eighty-nine clinical CoNS isolates collected from three hospitals within the uMgungundlovu District between October 2019 and February 2020, constituted the sample. Isolates were speciated using the Vitek 2 system. Antibiotic susceptibility testing was done against a panel of 20 antibiotics according to Clinical and Laboratory Standards Institute (CLSI) guidelines using the Kirby-Bauer disk-diffusion method and minimum inhibitory concentration (MIC) was determined using the broth microdilution method for penicillin G, cefoxitin, ceftaroline, ciprofloxacin, moxifloxacin, azithromycin, erythromycin, gentamicin, amikacin, chloramphenicol, tetracycline, doxycycline, teicoplanin, tigecycline, linezolid, clindamycin, rifampicin, sulphamethoxazole/trimethoprim, nitrofurantoin and vancomycin. PCR was used to detect the presence of the mecA gene to confirm phenotypic methicillin resistance. Based on their resistance profiles, a sub-sample of isolates were subjected to wholegenome sequencing (Illumina MiSeq) to ascertain the resistome, virulome, mobilome, clonality and phylogenomic relationships using bioinformatic tools. The SPAdes software was used for the assembly of the raw reads. ResFinder 4.1 and CARD were used to identify antibiotic resistance genes in the isolates, while the virulence factor database (VFDB), Center for Genomic Epidemiology‘s MLST 2.0 server and MobileElementFinder v1.0.3 were used to identify virulence genes, sequence types and mobile genetic elements, respectively. Mutations in fluoroquinolone and rifampicin resistance genes were identified by manual curation using BLASTn alignment which was also used to determine the genetic environment of the resistance genes.S. epidermidis was the most abundant CoNS species isolated. Phenotypic methicillinresistance was detected in 76.4% (n=68) of isolates, 92.6% (n=63) of which were genotypically confirmed by PCR. Multidrug resistance (MDR) was observed in 76.4% (n=68) of isolates, with 51 antibiograms observed. The resistance genes mecA, blaZ, erm(A), erm(B), erm(C), msr(A), aac(6')-aph(2'') and fosB, among others, were detected and corroborated the observed phenotypes. Molecular mechanisms of resistance to tigecycline, teicoplanin, linezolid and nitrofurantoin were not detected even though some isolates were resistant to them. There was no association between ARG type and hospital/department. The ica operon known to facilitate biofilm formation was detected in 7/16 isolates sequenced. Known and putatively novel mutations in the gyrA, parC, parE and rpoB genes were also detected for fluoroquinolone- and rifampicin-resistant isolates. Prediction of isolates’ pathogenicity towards human hosts yielded a high average probability score (Pscore ≈ 0.936), which, together with the several virulence genes detected (including atl, ebh, clfA, ebp, icaA, icaB,icaC), support their pathogenic potential to humans. Seven MLST types were found, while the community-acquired SCCmec type IV was the most common SCCmec type detected. Mobile genetic elements (MGEs) haboured by isolates included plasmid replicon Rep10 and insertion sequence IS256. Defense systems such as arginine catabolic mobile element (type I and III), CRISPR system (16), and the restriction-modification system (type II) were detected. Genetic analysis showed that resistance genes were frequently bracketed by MGEs such as transposons (such as Tn554) and insertion sequences (such as IS257 and IS1182) that facilitated their mobility. Phylogenetic studies showed that the distribution of genes did not coincide with the phylogenetic clades. Despite the relatedness of isolates (clades A and B), there is still considerable variation within individual strains that can facilitate adaptation to local environments. The isolates exhibited several permutations and combinations of ARGs, virulence genes and MGEs, pointing to a complex milieu of mobilized antibiotic resistance and pathogenic characteristics in clonal and multiclonal strains. The study necessitates surveillance of CoNS as emerging pathogens.
Molecular epidemiology of antibiotic resistant ESKAPE pathogens isolated from public sector hospitals in uMgungundlovu District, KwaZulu-Natal, South Africa.
(2017) Zangue, Raspail Carrel Founou.; Essack, Sabiha Yusuf.
Multi-drug resistant Enterococcus faecium, staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp termed ESKAPE pathogens are commonly implicated in difficult-to-treat infectious diseases in developed and developing countries. The prevalence, risk factors, phenotypic and genotypic profiles including but not limited to clonal relatedness, genetic diversity, resistance and virulence associated with ESKAPE bacteria were investigated in carriage and clinical isolates from patients in a rural, district and an urban tertiary hospital in the public health sector in uMgungundlovu District, Kwazulu- Natal, South Africa. The overall carriage of MDR ESKAPE Gram-negative bacteria in both hospitals was 37.21%, 42.31% and 57.14% at admission, after 48 hours and at discharge, respectively. The prevalence of MDR ESKAPE Gram-negative bacteria in faecal carriage (46%) was higher than clinical samples (28%) and colonization was mainly associated with referral from the district to the tertiary hospital with high statistical significance (OR: 14.40, 95% CI 0.98-210.84). blaCTX-M-group-9, blaCTX-M-group-1 and blaSHV were the main resistance genes identified. Similarly, the overall prevalence of faecal VRE carriage was 53% with patients at the district hospital being more likely to be colonized by VRE at admission (44%), after 48 hours (64%) and discharge (100%) than those of the tertiary level. Fifteen (39%) E. faecium and 23 (61%) E. faecalis, were detected and displayed high level of antibiotic resistance. Extensive genetic diversity of E. faecalis and E. faecium and clonal dissemination of various lineages were observed across wards and within hospitals. The high levels of resistance in S. aureus were attributed to the multi-drug resistant efflux pumps mepA, mexE, AcrB, MATE, qac and qacA. Whole genome analysis revealed that the circulating S. aureus isolates belonged to the extremely virulent ST121 clone that harboured a total of 18 virulence genes. The high prevalence, genetic diversity and virulence of antibiotic-resistant ESKAPE bacteria elucidated in this study necessitates routine screening and surveillance in communities and hospitals, stringent infection prevention and control measures and antibiotic stewardship to monitor epidemiological changes, to contain their spread and inform appropriate antibiotic treatment options respectively.
Molecular epidemiology of antibiotic-resistant Escherichia coli and Enterococcus spp. from agricultural soil fertilized with chicken litter in uMgungundlovu district, KwaZulu-Natal Province, South Africa.
(2021) Fatoba, Dorcas Oladayo.; Abia, Akebe Luther King.; Essack, Sabiha Yusuf.; Amoako, Daniel Gyamfi.
The application of animal manure contaminated with antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) represents a major route by which antibiotic resistance is transmitted into the soil environment. The introduction and persistence of ARB in agricultural soil may pose a risk to public health via the consumption or handling of contaminated farm produce. Understanding the impact of animal manure application on the agricultural soil resistome and the risk it poses on public health is critical. However, such information is limited in South Africa as most antibiotic resistance research focuses on humans and food animals. This study, therefore, describes the prevalence and the genomic profiles of antibiotic-resistant Escherichia coli and Enterococcus spp. isolated from agricultural soil fertilized with chicken litter and the chicken litter. A total of 237 samples were examined and included soil before litter application, the litter-amended soil, and the chicken litter. Isolation and quantification of Escherichia coli and Enterococci were carried out using the Colilert® -18 / Quantiti-Tray® 2000 system and the Enterolert® -18® Quanti-Tray®/2000 system, respectively. The antibiotic susceptibility profiles of the isolates was determined using the Kirby-Bauer disk diffusion method. Whole-genome sequencing (WGS) and bioinformatics tools were used to determine the resistome, virulome, mobilome, clonal lineages, and phylogenies of the isolates circulating between the soil and the chicken litter. The application of chicken litter to the soil statistically significantly increased Enterococci count and the number of antibiotic-resistant enterococci in the litter-amended soil. A total of 835 enterococci (680 from soil and 155 from litter) isolates recovered from the samples was dominated by E. casseliflavus (56%), followed by E. faecalis (22%), E. faecium (8%), E. gallinarum (2%) and other Enterococcus spp 102 (12%). Overall, 55.8% (466/835) of the enterococci isolates were resistant to one or more antibiotics with the highest rate in the litter-amended soil (68.9%, 321/466), followed by chicken litter (19.9%, 93/466) and the least in the soil samples collected before the litter amendment (11.2%; 52/466). The enterococci isolates were mostly resistant to tetracycline (33%), erythromycin (25%), and trimethoprim-sulfamethoxazole (23%), among others, intimating the high usage of these antibiotics in poultry farms in South Africa. Additionally, multidrug resistance (MDR) was recorded in 27.8% (130/466) of the enterococci isolates with MAR indices ranging from 0.13 (resistance to two antibiotics) to 0.44 (resistance to seven antibiotics). A total of 63 different resistance patterns were recorded in the MDR enterococci isolates. Notably, enterococci count and the number of antibiotic-resistant enterococci in the litter-amended soil were reduced to levels comparable to the unamended soil at 50 and 28 days after soil amendment respectively. The whole-genome analysis of the few selected enterococci isolates revealed eight novel sequence types (STs) (ST1700, ST1752, ST1753, ST1754, ST1755, ST1756, ST1004, and ST1006). Several resistance genes that confer resistance to aminoglycosides (aac(6’)-Ii, aac(6’)-Iih, ant(6)-Ia, aph(3’)-III, ant(9)-Ia), macrolide-lincosamide-streptogramin AB (MLSAB) [erm(B), lnu(B), lnu(G), lsaA, lsaE, eat(A), msr(C)], trimethoprim-sulfamethoxazole (dfrE, and dfrG), tetracycline (tet(M), tet(L), and tet(S)), fluoroquinolones (efmA, and emeA), vancomycin (VanC {VanC-2, VanXY, VanXYC-3, VanXYC-4, VanRC}), and chloramphenicol (cat) were detected in the isolates. The bioinformatics analysis further revealed that the chicken litter amendment increased the number and diversity of ARGs in the soil, resulting in increased detection of tetracycline resistance genes (tet(M), tet(L)), and the macrolide resistance gene erm(B) and appearance of some ARGs (ant(6)-Ia, aph(3’)-III, lnu(G), dfrG)) that were not detected in the unamended soil. ARGs were mostly associated with diverse insertion sequences (ISs) (IS982, ISL3, IS6, IS5, IS3, IS256, IS30) and/or transposons (Tn3, Tn916, Tn6009) on plasmids or chromosome. The tet(M) and erm(B) were also co-located on Tn916-like transposons (Tn644, Tn645, and Tn659) in the three sample groups. Some of the isolates also harboured virulence genes that encoded adherence/biofilm formation (ebpA, ebpB, ebpC), anti-phagocytosis (elrA), and bacterial sex pheromones (Ccf10, cOB1, cad, and camE). Phylogenomic analysis showed that few isolates from litter-amended soil clustered with the chicken litter isolates. The isolates from this study also clustered with clinical and animal isolates from South Africa (Pretoria, Pietermaritzburg), Angola, and Tunisia. There was also an increase (albeit statistically insignificant) in E. coli count and the number of antibiotic-resistant E. coli in the soil following chicken litter amendment. A total of 126 E. coli was recovered from the soil and chicken litter samples. In total, 76% (96/126) of the E. coli isolates displayed resistance to at least one antibiotic, with the highest prevalence in the litter-amended soil (71.9%, 69/96) and the least (1%, 1/96) in soil samples collected before the litter amendment. The E. coli isolates displayed a high percentage resistance to tetracycline (78.1%), chloramphenicol (63.5%), ampicillin (58.3%), trimethoprim-sulfamethoxazole (39.6%), cefotaxime (30.2%), ceftriaxone (26.0%), and cephalexin (20.8%). Lower percentages of XVI resistance to cefepime (11.5%), amoxicillin-clavulanic acid (11.5%), cefoxitin (10.4%), nalidixic acid (9.4%), amikacin (6.3%), ciprofloxacin (4.2%), imipenem (3.1%), tigecycline (3.1%), and gentamicin (3.1%) were also recorded in the isolates. All the isolates were completely susceptible to meropenem and ceftazidime. Approximately 54% (52/96) of the resistant isolates were MDR, and the MAR indices of the isolates ranged between 0.11 (resistance to two antibiotics) and 0.56 (resistance to ten antibiotics). Overall, 38.5% (37/96) of all the resistant isolates had a MARI > 0.2, with the highest rate (51.4%) in the litter-amended soil and the least in the soil before litter amendment (2.7%). Twenty-one multidrug resistance patterns were observed among the isolates. These results show that the soil resistome was augmented by chicken litter application. Agricultural soil and chicken litter are rich reservoirs of multidrug-resistant E. coli and Enterococcus spp. that could threaten public health through contamination of food products and the surrounding water bodies. There is therefore a need for urgent and stringent measures to mitigate the spread of antibiotic resistance in the environment via prudent use of antibiotics in food animal production and treatment of animal manure before its application onto agricultural soil.
Prevalence, phenotypic and genotypic characterization of resistant clinical gram-negative isolates at Kamuzu Central Hospital, Lilongwe Malawi.
(2022) Choonara, Faheema Ebrahim.; Essack, Sabiha Yusuf.; Sundsfjord, Arnfinn Staale.; Lampiao, Fanuel.
nterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens are the leading cause of nosocomial infections worldwide. They are highly virulent, multi-drug resistant (MDR) and therefore difficult to treat posing major public health and clinical challenges globally, particularly in developing countries where resources and microbiology diagnostic services are limited or not available. The aim was to investigate prevalence, phenotypic and genotypic resistant profiles of selected ESKAPE and other important bacterial pathogens isolated from adult patients admitted at Kamuzu Central Hospital (KCH) Escherichia coli and Staphylococcus aureus were the dominant species isolated. Multi-drug resistance and extended spectrum β-Lactamase -production was evident in K. pneumoniae (n=20/29; 69%) and E. coli (49/92; 53%). Pseudomonas aeruginosa was resistant to meropenem but none were carbapenemase producers. MRSA was detected in 10.5% (n=9/86) of S. aureus. These MDR isolates were mostly isolated from pus specimens from the surgical department Genotypically, the CTX-M type (55/60; 92%) and CMY type (16/21) were most prevalent among phenotypically-positive ESBL and pAmpC β-lactamases respectively. Both CTX-M and CMY were most prevalent in E.coli with 71% (15/21) carrying both CTX-M and CMY The most common sequence type in the CTX-M group 1 and CTX-M group 9 positive E.coli was ST410 (n=14/29; 48%) and ST131 (n=5/7; 71%) respectively; all of which contained the blaCTX-M-15 resistance gene. In CMY positive E. coli, ST410 was the most prevalent and all contained blaCMY- 2 resistance gene. All the E.coli isolates carrying both CTX-M and CMY were ST410 and contained both blaCMY- 2 and blaCTX-M-15 resistance genes. All phenotypically confirmed methicillin resistant Staphylococcus aureus (MRSA) contained mecA gene and t064 was most common spa type. Spa type t355 was most common in S. aureus that were negative for mecA gene Findings demonstrate the need for continuous antibiotic resistance surveillance at the hospital to inform antibiotic treatment options. There is also a need for the establishment of antibiotic stewardship programs to sustain the efficacy of antibiotics in Malawi
Triangulating the molecular epidemiology of carbapenem-resistant enterobacterales from humans, food Animals, and the environment.
(2021) Ramsamy, Yogandree.; Mlisana, Koleka Patience.; Essack, Sabiha Yusuf.
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.

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Browsing Doctoral Degrees (Medical Microbiology) by Author "Essack, Sabiha Yusuf."