This study reports two feces metagenomes (D84 and D85) and six metagenome-assembled genomes (MAGs). The assembled MAGs include Pseudomonas sp. strain NID84 and Acinetobacter sp. strain N2D84 from D84 and Enterococcus sp. strain N4D85, Enterococcus sp. strain N5D85, Lactobacillus sp. strain N6D85, and Leuconostoc sp. strain N7D85 from D85. Acinetobacter sp. N2D84 was identified as a human pathogen with a probability of 92%.

The occurrence and genetic relatedness of AmpC beta-lactamase producing Enterobacteriaceae isolated from clinical environments, groundwater, beef, human and cattle faeces were investigated. One hundred seventy-seven (177) samples were collected and cultured on MacConkey agar. A total of 203 non-repetitive isolates were characterised using genus/species-specific PCRs and the identified isolates were subjected to antibiotic susceptibility testing. The production of AmpC beta-lactamases was evaluated using cefoxitin disc, confirmed by the D96C detection test and their encoding genes detected by PCR. The D64C extended-spectrum beta-lactamases (ESBL) test was also performed to appraise ESBLs/AmpC co-production. The genetic fingerprints of AmpC beta-lactamase producers were determined by ERIC-PCR. A total of 116 isolates were identified as E. coli (n = 65), Shigella spp. (n = 36) and Klebsiella pneumoniae (n = 15). Ciprofloxacin resistance (44.4–55.4%) was the most frequent and resistance against the Cephem antibiotics ranged from 15–43.1% for E. coli, 25–36.1% for Shigella spp., and 20–40% for K. pneumoniae. On the other hand, these bacteria strains were most sensitive to Amikacin (0%), Meropenem (2.8%) and Piperacillin-Tazobactam (6.7%) respectively. Nineteen (16.4%) isolates comprising 16 E. coli and 3 Shigella spp. were confirmed as AmpC beta-lactamase producers. However, only E. coli isolates possessed the corresponding resistance determinants: blaACC (73.7%, n = 14), blaCIT (26%, n = 5), blaDHA (11%, n = 2) and blaFOX (16%, n = 3). Thirty-four (27.3%) Enterobacteriaceae strains were confirmed as ESBL producers and a large proportion (79.4%, n = 27) harboured the blaTEM gene, however, only two were ESBLs/AmpC co-producers. Genetic fingerprinting of the AmpC beta-lactamase-producing E. coli isolates revealed low similarity between isolates. In conclusion, the findings indicate the presence of AmpC beta-lactamase-producing Enterobacteriaceae from cattle, beef products and hospital environments that commonly harbour the associated resistance determinants especially the blaACC gene, nonetheless, there is limited possible cross-contamination between these environments.

The de novo metagenome assembly for C1-TPA is 68,577,389 bp long spread over 10,108 contigs, while that of C3-TPA is 55,517,929 bp distributed over 9,415 contigs. A total of 8 metagenome-assembled genomes (MAGs) were extracted from C1-TPA, and 10 were extracted from C3-TPA. Both samples have a Flavobacterium sp. and a Pseudomonas sp. in common among their bacterial communities.

Bacteria belonging to the family Enterobacteriaceae are facultative anaerobic, Gram-negative, non-spore forming rod-shaped bacilli. Members of this heterogeneous group of bacteria do not only form part of the normal flora of humans and animals, but are also widely distributed in various environments such as water, soil and plants. Most members of the Enterobacteriaceae were previously considered to be harmless. However, there is evidence that some strains potentially cause diseases and pathological conditions such as diarrhoea, gastroenteritis, urinary tract infections and inflammatory bowel diseases in animals and humans. The aim of the present study was to isolate and determine the antibiotic resistant profiles of Enterobacteriaceae isolated from dogs that visited the North West University animal hospital. Fifteen (15) faecal samples were collected from the rectum of dogs that visited the Hospital, using sterile swabs and the samples were placed in transport media. The samples were immediately transported on ice to the laboratory for analysis. MacConkey agar with crystal violet was used for selective isolation of bacteria belonging to the family Enterobacteriaceae. Only isolates that satisfied the preliminary identification tests (Gram staining, triple sugar iron agar test, citrate agar test and oxidase test) and confirmatory identification test (API 20E) were retained for further analyses. Antibiotic susceptibility tests were performed on all positively confirmed isolates to determine their antibiotic resistant profiles against tetracycline (30 µg), ampicillin (10 µg), amoxicillin (10 µg), penicillin (10 µg), gentamycin (30 µg) and streptomycin (10 µg). A total of 120 isolates were positively identified as members of the Enterobacteriaceae. All the isolates were Gram negative rods and oxidase negative. A large proportion (92.5%) of these isolates fermented the sugars in the TSI agar with only a small proportion (23.3%) producing hydrogen sulphide gas. However, a relatively larger proportion of these isolates (62.5%) produced gas from the fermentation of sugars. On characterizing these isolates for the ability to hydrolyze citrate, a large proportion (71.7%) were negative for this test. The API 20E test results indicated that bacteria species belonging to four main genera (Escherichia, Salmonella, Shigella and Klebsiella) were indentified. A large proportion (50%) of these isolates were identified as Escherichia coli while 25, 15.8 and 9.2% were Salmonella spp., Klebsiella spp. and Shigella species, respectively. Isolates from all the samples were most often, resistant to penicillin, ampicillin, tetracycline and amoxicillin while very little resistance was observed against gentamycin and streptomycin. The MDR phenotypes PG-AP-A-T, PG-AP-A-T-S, PG-AP-A, PG-A-T and PG-AP-A-T-GM-S were dominant in isolates from samples analyzed. Although a large proportion of the isolates were resistant to three or more antibiotics, a cause for concern was the fact that some isolates were resistant to all antibiotics screened. Th...

Diarrheal infection is the second leading infectious disease that is killing children under the age of 5 years. This study investigates the microbial community within a fecal sample from a diarrhea-affected child through shotgun metagenomic sequencing.