Antimicrobial resistance profiles of Pseudomonas aeruginosa, Escherichia coli and Klebsiella pneumoniae strains isolated from broiler chickens

Globally, the spread of multidrug-resistant Pseudomonas aeruginosa, Escherichia coli, and Klebsiella pneumoniae from food to humans poses a severe threat to public health. The aim of this study was to assess the co-occurrence of colistin and β-lactamase resistance genes in E. coli, K. pneumoniae, and P. aeruginosa strains isolated from faeces of abattoir broiler chickens. The E. coli, P. aeruginosa and K. pneumoniae isolates were successfully detected from faecal samples by polymerase chain reaction (PCR) at infection rates of 60.7%, 22.5% and 16.7% respectively. The isolates displayed the highest levels of antibiotic resistance (AR) against ampicillin (82.3%) and amoxicillin-clavulanic acid (74.2%) for E. coli, followed by cefoxitin (70.6%) for K. pneumoniae, whilst P. aeruginosa displayed 26.1% antibiotic resistance (AR) against both ampicillin and colistin sulphate. The colistin mcr-1 gene was harboured by 46.8%, 47.1% and 21.7%, E. coli, K. pneumonia and P. aeruginosa isolates respectively. Ten out of 62 (16.1%), 6/17 (35.3%), 4/23 (17.4%) isolates were phenotypically classified as ESBL E. coli, K. pneumoniae, and P. aeruginosa respectively. The ESBL-E. coli isolates respectively possessed blaCTX-M (60%), blaTEM (20%) and blaCTX-M-9 (10%) genes. The ESBL-K. pneumoniae harboured, blaCTX-M (50%), blaOXA (33%), blaCARB (17%), and blaCTX-M-9 (17%) genes respectively, whilst, P. aeruginosa isolates respectively carried blaTEM (75%), blaCTX-M (50%), blaOXA (25%) and blaCARB (25%) genes. Molecular analysis identified the blaCTX-Mβ-lactamase-encoding genes collectively from E. coli, P. aeruginosa, K. pneumoniae isolates. Colistin and β-lactamase genes were present in only 16.7%, 6.9%, and 2.9% of E. coli, K. pneumoniae, and P. aeruginosa isolates, respectively. A total of 17, 7 and 3 isolates for E. coli, K. pneumoniae and P. aeruginosa respectively carried both colistin and β-lactamase antibiotics resistant genes. This is a public health threat that points to a challenge in the treatment of infections caused by these zoonotic bacteria. Data generated from this study will contribute to formulation of new strategies for combating spread of E. coli, K. pneumoniae, and P. aeruginosa isolates as well as prevention of their AR development.

Diversity of selected toll-like receptor genes in cheetahs (Acinonyx jubatus) and African leopards (Panthera pardus pardus)

The anthropogenic impact on wildlife is ever increasing. With shrinking habitats, wild populations are being pushed to co-exist in proximity to humans leading to an increased threat of infectious diseases. Therefore, understanding the immune system of a species is key to assess its resilience in a changing environment. The innate immune system (IIS) is the body's first line of defense against pathogens. High variability in IIS genes, like toll-like receptor (TLR) genes, appears to be associated with resistance to infectious diseases. However, few studies have investigated diversity in TLR genes in vulnerable species for conservation. Large predators are threatened globally including leopards and cheetahs, both listed as 'vulnerable' by IUCN. To examine IIS diversity in these sympatric species, we used next-generation-sequencing to compare selected TLR genes in African leopards and cheetahs. Despite differences, both species show some TLR haplotype similarity. Historic cheetahs from all subspecies exhibit greater genetic diversity than modern Southern African cheetahs. The diversity in investigated TLR genes is lower in modern Southern African cheetahs than in African leopards. Compared to historic cheetah data and other subspecies, a more recent population decline might explain the observed genetic impoverishment of TLR genes in modern Southern African cheetahs. However, this may not yet impact the health of this cheetah subspecies.

Molecular detection of Shiga toxin and extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates from sheep and goats

BACKGROUND

The Shiga toxin (Stx)-producing Escherichia coli (STEC) have become important global public health concerns. This study investigated the prevalence, antimicrobial resistance profile, and extended-spectrum beta-lactamase-producing E. coli in sheep and goat faeces.

METHODS AND RESULTS

A total of 53 E. coli isolates were confirmed by PCR targeting the uidA [β-D glucuronidase] gene. The Shiga toxin genes stx1 and stx2, as well as bfpA, vir, eaeA, lt and aafII virulence genes, were detected in this study. Of the 53 isolates confirmed to be STEC, 100% were positive for stx2 and 47.2% for stx1. Three isolates possessed a combination of stx1 + stx2 + eaeA, while four isolates harboured stx1 + stx2 + vir virulence genes. The isolates displayed phenotypic antimicrobial resistance against erythromycin (66.04%), colistin sulphate (43.4%), chloramphenicol (9.4%) and ciprofloxacin (1.9%). A total of 28.8% of the strains were phenotypically considered ESBL producers and contained the beta-lactamase blaCTX-M-9 and blaCTX-M-25 gene groups. A larger proportion of the E. coli strains (86.8%) contained the antibiotic sulphonamide resistant (sulII) gene, while 62.3%, 62.3%, 52.8%, 43.4%, 41.5%, 20.8%, 18.9%, 11.3%, 11.3%, 9.4%, 9.4% and 5.7% possessed mcr-4, floR, mcr-1, tet(A), sulI, tet(O), tet(W), parC, mcr-2, ampC 5, qnrS and ermB genes, respectively. Thirteen isolates of the ESBL-producing E. coli were considered multi-drug resistant (MDR). One Shiga toxin (stx2) and two beta-lactamase genes (blaCTX-M-9 and blaCTX-M-25 groups) were present in 16 isolates. In conclusion, the E. coli isolates from the small stock in this study contained a large array of high antibiotic resistance and virulence profiles.

CONCLUSIONS

Our findings highlight the importance of sheep and goats as sources of virulence genes and MDR E. coli. From a public health and veterinary medicine perspective, the characterization of ESBL producers originating from small livestock (sheep and goats) is crucial due to their close contact with humans.

The draft genome and pan-genome structure of Paraclostridium bifermentans strain T2 isolated from sheep faeces

Paraclostridium bifermentans is a Gram-positive, rod-shaped bacterium that can inhabit various mesophilic environments such as soil, marine habitats, and polluted waters. Some species of Paraclostridium are reported to cause fatal infections in humans, although mechanisms and capacity for adaptation are still unknown. We hereby present the whole genome sequence data of P. bifermentans T2 strain isolated from sheep faecal matter in Potchefstroom, South Africa. DNA libraries were sequenced on the Oxford Nanopore Mk1B platform. The generated sequence data was assembled and polished using Flye assembler. Genome data analysis yielded a genome size of 2 911,782 bp, comprising of a 27.8 % G + C content. Rapid Annotation using Subsystem Technology (RAST) showed that the draft genome of this strain consists of 6 514 coding sequences (CDS). The pan-genome was defined by a total of 16 288 CDSs, grouping the strain with the genome of P. bifermentans SampleS7P1. The draft genome sequence has been deposited in NCBI GenBank with the accession number of JAUPET000000000.