Occurrence, identification and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa

Abstract

The increasing occurrence of multidrug-resistant Enterobacteriaceae in clinical and environmental settings has been seen globally as a complex public health challenge, mostly in the developing nations where they significantly impact on freshwater used for a variety of domestic purposes and irrigation. In this paper, we give details as regards the occurrence and antibiogram signatures of Enterobacteriaceae community in Tsomo and Tyhume rivers within the Eastern Cape Province, Republic of South Africa using standard methods. Average distribution of the presumptive Enterobacteriaceae in the rivers ranged from 1 10 2 CFU/100ml to 1.95 10 4 CFU/100ml. We confirmed 56 (70.8%) out of 79 presumptive Enterobacteriaceae isolated being species within the family Enterobacteriaceae through the Matrix-Assisted Laser Desorption Ionization Time of Flight technique. From this, Citrobacter -, Enterobacter -, Klebsiella species and Escherichia coli were selected (n=40) due to their pathogenic potentials for antibiogram profiling. The results of the antibiotic susceptibility testing gave a revelation that all the isolates were phenotypically multidrug-resistant while resistance against ampicillin (95%), tetracycline and doxycycline (88%) and trimethoprim-sulfamethoxazole (85%) antibiotics were most prevalent. The Multiple Antibiotic Resistance indices stretched from 0.22 to 0.94, with the highest index observed in a C. freundii isolate. Molecular characterisation using the PCR technique revealed the dominance of bla TEM (30%; 12/40) among the ten groups of extended-spectrum β-lactamase genes assayed. The prevalence of others was bla CTX-M genes including group 1, 2 and 9 (27.5%), bla SHV (20%), bla KPC (17.6%), bla GES (11.8%), bla IMP (11.8%), bla VIM (11.8%), bla OXA-1-like (10%), bla PER­ (2.5%), bla OXA-48-like (5.9%) and bla VEB (0%). From the six plasmid-mediated AmpC genes investigated bla ACC , bla EBC , bla FOX , bla CIT , bla DHA and bla MOX , only the first four were detected. In this category, the most dominant was bla EBC, with 18.4% (7/38). The prevalence of the non-β-lactamases include tetA (33.3%), tetB (30.5%) , tetC (2.8%), tetD (11.1%), tetK (0%), tetM (13.9%), catI (12%), catII (68%), sulI (14.3%), sulII (22.8%) and aadA (8.3%). Notably, a C. koseri harboured 42.8% (12/28) of the genes assayed for which includes five of the ESBL genes (including the only bla PER detected in this study), two of the pAmpC resistance genes ( bla ACC and bla CIT ) and five of the non-β-lactamase genes. To the best of our knowledge, this study gives the first report on C. koseri exhibiting co-occurrence of ESBL/AmpC β-lactamase genes from the environment. The detection of a bla PER producing Citrobacter spp. in this study is remarkable. These findings provide evidence that freshwater serves as reservoirs of antimicrobial resistance determinants which can then be easily transferred to human beings via the food chain and water.

Extended Spectrum Beta-Lactamase-Resistant Determinants among Carbapenem-Resistant Enterobacteriaceae from Beef Cattle in the North West Province, South Africa: A Critical Assessment of Their Possible Public Health Implications

“…Interestingly, the MAR index value of 129 MDR strains ranged from 0.23 to 0.69, with an average of 0.40. Although these findings were lower than that of the other study [ 29 ], the MAR indices observed in this study were > 0.2. A MAR index of 0.2 or higher indicates high-risk sources of contamination [ 30 , 31 ].…”

The Abundance of Genes Encoding ESBL, pAmpC and Non-β-Lactam Resistance in Multidrug-Resistant Enterobacteriaceae Recovered From Wastewater Effluents

“…Some other researchers have also described the dominance of the bla CTX-M variants in many different surface water (Zarfel et al, 2013;Zurfluh et al, 2013;Ojer-Usoz et al, 2014). Also, the bla CTX-M variants are among the most widespread in South Africa (Njage and Buys, 2015;Fadare et al, 2020). Interestingly, we discovered isolates from various genera such as E. cancerogenus, E. cloacae, C. koseri, C. freundii, K. oxytoca, K. pneumoniae, and E. coli harbouring the various bla CTX-M variants.…”

“…The quality of an effluent discharge is particularly an important criterium in assessing the efficiency of a WWTP. The surface water which receives these municipal WWTP effluents are being abstracted for irrigation, domestic, and religious activities (Fadare et al, 2020), thereby being a public health concern as they are unsuitable for domestic uses.…”

Prevalence, molecular characterization of integrons and its associated gene cassettes in Klebsiella pneumoniae and K. oxytoca recovered from diverse environmental matrices

“…Twenty-nine of the isolates used in this current study were part of our earlier studies. The description of the study sites, sample collection and processing, and isolation were carried out as reported in our previous studies 33 – 35 . The isolates in this study include, 33 Klebsiella pneumoniae recovered from freshwater sources (n = 7), hospital wastewater (HWW) (n = 9), and wastewater treatment plant effluents (WWTP) (n = 7), while the remaining were isolated from animal droppings (FD).…”

“…For subsequent analysis, single pure colonies were transferred to 2 ml BHI broth and incubated overnight at 37 °C. The boiling method 36 was used to extract the genomic DNA with slight modifications, as previously reported elsewhere 35 . The DNA-containing supernatant was then transferred to sterile microcentrifuge tubes (Eppendorf, Germany) and stored at – 20 °C for future assays.…”