17 research outputs found
Molecular epidemiology of antimicrobial resistance (AMR) and Shiga toxin producing E. coli (STEC) in dairy herds of central Zambia
Antimicrobial resistance (AMR) is a worldwide public health concern. While it is
evident that the use of antibiotics creates selection pressure for the evolution of
antibiotic resistance genes, there are still considerable knowledge gaps relating to the
status quo of antibiotic use, emergence of resistant pathogens in different livestock
production systems and spread within human and animal communities.
This thesis includes a survey of antibiotic use in the dairy sector within a specific area
of Zambia and analysis of AMR and virulence factors in E. coli isolated from dairy
cattle and diarrhoea human patients with the following objectives.
1. To investigate the usage of antibiotics in the dairy sector and the drivers for
use.
2. To determine the prevalence and patterns of antimicrobial resistance in E. coli
isolated from faecal samples of dairy cattle.
3. To use whole genome sequencing (WGS) to investigate the molecular
epidemiology of resistance determinants in E. coli strains isolated from both
dairy cattle and humans.
4. To assess the zoonotic potential of isolated E. coli focusing on Shiga toxin-producing
E. coli (STEC) and relationship to STEC associated with clinical
disease in the UK.
In view of these objectives, the first part of the work was carried out in Zambia and
involved a questionnaire, a field survey, isolation of E. coli from dairy cattle faecal
samples and phenotypic testing for AMR. In addition, E. coli isolates were obtained
from another study that was focused on human patients presenting with diarrhoea at
the University Teaching Hospital in Lusaka. The second part involved whole genome
sequencing and molecular analyses of E. coli for resistance and virulence genotypes at
the Roslin Institute (UK). For the field study, a stratified random sample of 104 farms
was studied, representing approximately 20% of all dairy farms in the region. On each
farm, faecal samples were collected from a random sample of animals and a
standardised questionnaire on the usage of antibiotics was completed. An E. coli
isolate was obtained from 98.67% (371/376) of the sampled animals and tested for
resistance against the six types of antibiotics (tetracycline, ampicillin,
sulfamethoxazole/trimethoprim, cefpodoxime, gentamicin and ciprofloxacin). These
E. coli were then analysed together with those from humans for genotypes in the
laboratory and from Illumina short read whole genome sequences using bioinformatics
tools.
Tetracylines and penicillin were the commonly used antibiotics in dairy herds. This
finding was in line with the resistance phenotypes detected in E. coli isolated from the
dairy cattle. The most prevalent AMR was to tetracycline (10.61; 95%CI: 7.40-13.82),
followed by ampicillin (6.02; 95%CI: 3.31-8.73), sulfamethoxazole/ trimethoprim
(4.49; 95%CI: 2.42-6.56), cefpodoxime (1.91; 95%CI: 0.46-3.36), gentamicin (0.89;
95%CI: 0.06-1.84) and ciprofloxacin (0%). The risk analysis indicated that AMR was
associated with livestock diseases (lumpy skin disease and foot rot), exotic breeds
(Jersey and Friesian), location, farm size and certain management practices.
Analysis of whole genome sequences showed that isolates from humans had both
higher levels and a greater diversity of resistance alleles than the cattle isolates.
Common genotypes in both populations were: tetA (16%), tetB (10%), tetC (2%) for
cattle isolates with tetA (32%), tetB (22%) and tetD (1%) in human isolates. Other
common genotypes were blaTEM (56%), sul1 (29%), sul2 (66%), strA4 (57%) and
strB1 (64%) in isolates of human origin while blaTEM (15%), sul1 (3%), sul2 (17%),
strA4 (13%) and strB1 (19%) were in the cattle isolates.
Whilst the E. coli isolates from cattle encoded resistance to common antibiotics of
limited significance to human clinical medicine, isolates from humans had additional
extended spectrum beta-lactamases (blaOXA, blaCMY, blaNDM, and blaDHA, blaOKP and
blaCTX-M) that encode for resistance to essential antibiotics such as third generation
cephalosporins and carbapenems. This was an evidence that AMR is an ongoing public
health subject in Zambia but the exclusivity of certain resistances in the human
population points to limited or no exchange of genotypes between E. coli of human
origin and those from cattle. AMR in humans was probably independently selected by
the use of antibiotics of clinical importance such as cephalosporin and
fluoroquinolones.
The virulence analysis focused on STEC, 11% (41/371) of E. coli isolates from cattle
contained Shiga toxin genes (stx) while none (0/73) of the human isolates were
positive. Phylogenetic analysis showed a random distribution of bovine STEC, with
no indication of clonal spread. Although 89% (16/18) of the STEC tested had a
cytotoxic effect on Vero cells, indicative of Shiga toxin production, only three (O45,
O111, O157) belonged to one of the seven serogroups (O26, O157, O111, O103,
O121, O145 and O45) associated with life-threatening enterohaemorrhagic E. coli
(EHEC) infections in humans. In line with this, only the O157 serotype encoded a type
3 secretion system. This shows that, while Stx-encoding strains are common in these
dairy herds of Zambia, they are not strain backgrounds known to pose an immediate
threat to human health as they lack colonisation factors that are found in typical human
EHEC. However, we must remain vigilant as emergence of EHEC strains in these
animals remains an ever-present threat
Quick PCR to detect M. tuberculosis and M. bovis in swine blood samples
The disease control strategies in livestock are the key areas to enhance improvement of livestock production and safety of livestock product consumers. Therefore, reliable techniques for quick detection and specific identification of disease causing agents need to be developed. In this study a nested PCR was developed using primer primier 5.0 software for primer design targeting IS1081 gene conserved regions in both M. tuberculosis and M. bovis. Two sets of primers TB-Q1/TB-Q2 and TB-B1/TB-B2, were designed to detect M. tuberculosis and M. bovis DNA extracted from blood samples. The findings were, the assay is sensitive enough to detect up to 1.35fg of the antigen DNA with 100% specificity
Whole Genome Sequence Analysis Reveals Lower Diversity and Frequency of Acquired Antimicrobial Resistance (AMR) Genes in E. coli From Dairy Herds Compared With Human Isolates From the Same Region of Central Zambia
Antibiotic treatment of sick dairy cattle is critical for the sustainability of this production system which is vital for food security and societal prosperity in many low and middle-income countries. Given the increasingly high levels of antibiotic resistance worldwide and the challenge this presents for the treatment of bacterial infections, the rational use of antibiotics in humans and animals has been emphatically recommended in the spirit of a âOne Healthâ approach. The aim of this study was to characterize antimicrobial resistance (AMR) genes and their frequencies from whole genome sequences of Escherichia coli isolated from both dairy cattle and human patients in central Zambia. Whole genome sequences of E. coli isolates from dairy cattle (n = 224) and from patients at a local hospital (n = 73) were compared for the presence of acquired AMR genes. In addition we analyzed the publicly available genomes of 317 human E. coli isolates from over the wider African continent. Both acquired antibiotic resistance genes and phylogroups were identified from de novo assemblies and SNP based phylogenetic analyses were used to visualize the distribution of resistance genes in E. coli isolates from the two hosts. Greater acquired AMR gene diversity was detected in human compared to bovine E. coli isolates across multiple classes of antibiotics with particular resistance genes for extended-spectrum beta lactamases (ESBL), quinolones, macrolides and fosfomycin only detected in E. coli genomes of human origin. The striking difference was that the Zambian or wider African human isolates were significantly more likely to possess multiple acquired AMR genes compared to the Zambian dairy cattle isolates. The median number of resistance genes in the Zambian cattle cohort was 0 (0â1 interquartile range), while in the Zambian human and wider African cohorts the medians and interquartile ranges were 6 (4â9) and 6 (0â8), respectively. The lower frequency and reduced diversity of acquired AMR genes in the dairy cattle isolates is concordant with relatively limited antibiotic use that we have documented in this region, especially among smallholder farmers. The relatively distinct resistant profiles in the two host populations also indicates limited sharing of strains or genes
Antimicrobial resistance profiles of Escherichia coli isolated from laying hens in Zambia: implications and significance on one health.
BACKGROUND: Antimicrobial resistance (AMR) has been deepening in the layer poultry sector in Zambia partly due to the inappropriate use of antimicrobials. Escherichia coli (E. coli), a commensal and zoonotic bacterium, can potentially be a source of AMR. OBJECTIVES: This study assessed the phenotypic AMR profiles of E. coli isolated from the apparent health-laying hens in Lusaka and Copperbelt provinces of Zambia. METHODS: A cross-sectional study was conducted between September 2020 and April 2021 in which 365 cloacal swabs were collected from 77-layer farms based in Lusaka and Copperbelt provinces of Zambia. E. coli isolation and identification were done using cultural and biochemical properties and confirmed using the 16S rRNA gene sequencing. Antimicrobial susceptibility testing (AST) was done using the Kirby-Bauer disc-diffusion method. Data analysis was done using WHONET 2020 and Stata v.16.1. RESULTS: Of the 365 samples, E. coli was isolated from 92.9% (nâ=â339). The AMR was detected in 96.5% (nâ=â327) of the isolates, of which 64.6% (nâ=â219) were multidrug-resistant (MDR). E. coli was highly resistant to tetracycline (54.6%) and ampicillin (54%) but showed low resistance to meropenem (0.9%), ceftazidime (6.2%) and chloramphenicol (8.8%). CONCLUSION: This study found a high prevalence of E. coli resistant to some commonly used antibiotics in poultry, which is a public health concern because of the potential contamination of eggs and layers of chicken meat that enter the food chain. Urgent attention is needed, including strengthening antimicrobial stewardship and surveillance programmes in layer poultry production in Zambia
Prevalence and antimicrobial resistance patterns of Enterococcus species isolated from laying hens in Lusaka and Copperbelt provinces of Zambia: a call for AMR surveillance in the poultry sector
BACKGROUND: The use of antimicrobials in layer poultry production for improved production, growth promotion, prophylaxis and treatment purposes has contributed to the development of antimicrobial resistance (AMR) in poultry. In Zambia, there is a paucity of information on the prevalence and AMR patterns of Enterococcus species isolated from laying hens. OBJECTIVES: This study investigated the prevalence and AMR patterns of enterococci isolated in layer hens in Lusaka and Copperbelt provinces of Zambia. METHODS: A cross-sectional study was conducted from September 2020 to April 2021. Three hundred and sixty-five pooled cloacal swab samples were collected from 77 layer poultry farms. Enterococci identification and confirmation were performed using Analytical Profile Index (API 20 STREP) and 16S rRNA sequencing, respectively. A panel of nine antibiotics was used for antibiotic susceptibility testing and interpreted according to the CLSI 2020 guidelines. Data were analysed using SPSS version 23 and WHONET 2020. RESULTS: A total of 308 (83%) single Enterococcus species isolates were obtained and showed resistance to tetracycline (80.5%), erythromycin (53.6%), quinupristin/dalfopristin (53.2%), ampicillin (36.72%), vancomycin (32.8%), linezolid (30.2%), ciprofloxacin (11.0%), nitrofurantoin (6.5%) and chloramphenicol (3.9%). The prevalence of enterococci resistant to at least one antibiotic was 99.4% (nâ=â306), of which 86% (nâ=â265) were MDR. CONCLUSIONS: This study found a high prevalence of antimicrobial-resistant enterococci. The presence of MDR requires urgent intervention and implementation of AMR surveillance strategies and antimicrobial stewardship programmes in layer poultry production in Zambia
Drivers of antimicrobial resistance in layer poultry farming: Evidence from high prevalence of multidrug-resistant Escherichia coli and enterococci in Zambia
Background and Aim: Inappropriate use of antimicrobials exacerbates antimicrobial resistance (AMR) in the poultry sector. Information on factors driving AMR in the layer poultry sector is scarce in Zambia. This study examined the drivers of AMR in the layer poultry sector in the Lusaka and Copperbelt Provinces of Zambia.
Materials and Methods: This cross-sectional study employed a structured questionnaire in 77 layer poultry farms in the provinces of Lusaka and Copperbelt, Zambia, from September 2020 to April 2021. Data analysis was conducted using Stata version 16.1. Antimicrobial resistance was defined as the presence of multidrug resistance (MDR) isolates. Multivariable regression analysis was used to identify drivers of AMR.
Results: In total, 365 samples were collected, from which 339 (92.9%) Escherichia coli and 308 (84.4%) Enterococcus spp. were isolated. Multidrug resistance was identified in 39% of the E. coli and 86% of the Enterococcus spp. The overall prevalence of AMR in layer poultry farms was 51.7% (95% confidence interval [CI]: 40.3%â63.5%). Large-scale farmers (Adjusted odds ratio [AOR] = 0.20, 95% CI: 0.04%â0.99%) than small-scale and farmers who were aware of AMR than those who were unaware (AOR = 0.26, 95% CI: 0.08%â0.86%) were less likely to experience AMR problems.
Conclusion: This study found a high prevalence of AMR in layer poultry farming linked to the type of farm management practices and lack of AMR awareness. Evidence of high MDR in our study is of public health concern and requires urgent attention. Educational interventions must increase AMR awareness, especially among small- and medium-scale poultry farmers