6 research outputs found
Microbial Analysis Of Raw Milk Around Small Scale Farmers In Harrismith Freestate, South Africa
DissertationFood manufacturing and agricultural industry have an ancient history of been observed to provide the most favourable conditions for the multiplication and distribution of microorganisms. These microorganisms may be found in the air (airborne), food (milk) and at the surrounding environment. Food handlers have also been found to harbour some of these microorganisms on their hands or skin surfaces. Dairy environment have been receiving quite an extensive attention especially on the composition of microbes in milk. However, studies that have been conducted mostly utilized conventional/traditional microbiological techniques. Hence, there is still lack of research in South Africa that is focusing on molecular techniques to quantify these microorganisms in raw milk.
The overall aim of this dissertation was to assess different microorganisms confined in raw milk from small-scale farmers in the Eastern part of the Free State Province, South Africa. With reference to the main aim of this study, the objectives of the present study were to use molecular techniques to quantify five mostly isolated microorganisms causing subclinical mastitis in bovine .i.e. E. coli, S. aureus, S. agalactiae, S. dysgalactiae and S. uberis. Then lastly, a metagenomic analysis of raw milk was conducted by targeting the 16S rRNA gene using high throughput sequencing.
The findings of this study in relation to microbial composition as per Chapter 2 showed a high microbial contamination of raw milk and has clearly indicated the need for training of all employees and the enforcement of health and hygiene measures within the dairy environment. While investigating the prevalence of subclinical mastitis around these farms, the author came across some interesting findings. The author isolated streptococcal species that are more prevalent/isolated in the hospital environment especially on samples derived from human subjects after/during streptococcal infections such as meningitis. Instead of isolating streptococcal species more prevalent on the dairy environment such as, S. dysgalactiae or S. uberis, the author identified S. mutans, S. Salivarius, S. pneumonia and S. sanguis which may entail that the employees around the farms are/were the carriers of these species.
The isolation of microorganisms associated with food spoilage and foodborne disease outbreaks, which are known as indicator organisms such as Escherichia coli, Staphylococcus and Bacillus from both air and surface samples, signified possible faecal contamination and could be attributed to poor health and hygiene practices at the dairy farm plant. Despite the isolation of microorganisms associated with food spoilage and foodborne disease outbreaks, the isolation of microorganisms not usually associated with the food processing industry (usually associated with hospital environments) was an enormous and serious concern which suggested a need for further investigations at dairy farm plants as the implications of these pathogenic microorganisms in food is not known
Comprehensive whole genome analysis of Staphylococcus aureus isolates from dairy cows with subclinical mastitis
Staphylococcus species are the primary cause of mastitis in dairy cows across the world. Staphylococcus aureus has recently become a pathogen that is zoonotic and multidrug resistant. This study aimed to sequence whole genomes of 38 S. aureus isolates from 55 subclinical mastitis dairy cows of 7 small-scale farmers in the Free State Province, South Africa and document and their antimicrobial and virulence genes. The 38 isolates were grouped by the in silico multi-locus sequencing types (MLST) into seven sequence types (STs), that is (ST 97, 352, 152, 243) and three new STs (ST8495, ST8500, and ST8501). Thirty-three S. aureus isolates were divided into 7 core single-nucleotide polymorphism (SNP) clusters. Among the 9 distinct spa-types that were detected, Spa-types t2883 accounted for the majority of isolates at 12 (31.57%), followed by t416 with 11 (28.94%) and t2844 with 5 (13.15%). The data also revealed the identification of four (4) plasmids, with Rep_N (rep20) accounting for the majority of isolates with 17 (44.73%), followed by Inc18 (repUS5) with 2 (5.26%). These isolates included 11 distinct antimicrobial resistance genes and 23 genes linked to bacterial virulence. Surprisingly, no methicillin resistance associated genes were detected in these isolates. Genome data of the current study will contribute to understanding epidemiology S. aureus genotypes and ultimately aid in developing treatment and control plans to stop the spread of mastitis in the Free State province and South Africa as a whole
Prevalence of subclinical mastitis, its associated bacterial isolates and risk factors among cattle in Africa : a systematic review and meta-analysis
DATA AVAILABILITY : The datasets on which the findings and conclusions of this article are based can be availed upon request from the corresponding author.BACKGROUND : Subclinical mastitis (SCM) is one of the most economically important diseases affecting the dairy
industry. The SCM does not cause visible changes in the udder or physical changes of the milk as compared to clinical
mastitis, and a clear overview of the prevalence and risk factors in the different regions of Africa is still lacking. The
objective of this study was to investigate the prevalence of SCM and assess the associated risk factors and dominant
bacterial pathogens among cattle in Africa.
MATERIALS AND METHODS : We gathered and systematically reviewed literature concerning SCM, published in English
from January 2010 through December 2020 in two databases (PubMed and Web of Science), and meta-analysis was
conducted using the ‘meta’ and ‘metafor’ packages in the R statistical software.
RESULTS : A total of 258 studies were retrieved and at the end of the screening, 82 full-texts were eligible for inclusion
in the meta-analysis. The prevalence of SCM was reported in 11 countries in five regions of Africa, and the randomeffects
model showed that the weighted pooled prevalence estimate (PPE) was 48.2% (95% CI: 43.6–52.8%).
Heterogeneity was high and statistically significant as I2 (proportion of observed variation) was 98.1% (95% CI:
98.0-98.3%), τ2 (true between-study variance) was 0.0433 (95% CI: 0.0322–0.0611), and the Cochran Q statistic was
4362.8 (p < 0.0001). Subgroup and meta-regression analyses showed that East Africa had significantly (p = 0.0092) the
highest PPE of SCM (67.7%, 95% CI: 55.7–78.7) followed by West Africa (50.5%, 95%CI: 31.4–69.5), and the lowest was
in North Africa (40.3%, 95%: 32.2–48.6). Other significant moderators for SCM were age (p < 0.0001), breed (p = 0.0002),
lactation stage (p = 0.019) and parity (p = 0.0008) of cattle. Staphylococcus species (prevalence 43.7%) were the most
predominant pathogens, followed by Streptococcus (18.2%) and Escherichia species (9.5%).
CONCLUSION : The present study showed a high variation of SCM prevalence in various parts of Africa, although there is
a need for more data in some regions. The reported prevalence is a clear sign of inappropriate management practices among cattle herds and an indicator of the threat that SCM poses to the dairy industry. The information about the
predisposing factors may guide effective management and control strategies to reduce transmission of the disease.The Central university of Technology, through the UCDP M&D Grant, and the National Research Foundation.https://bmcvetres.biomedcentral.comam2024Veterinary Tropical DiseasesSDG-02:Zero Hunge
Prevalence of subclinical mastitis, its associated bacterial isolates and risk factors among cattle in Africa: a systematic review and meta-analysis
Abstract Background Subclinical mastitis (SCM) is one of the most economically important diseases affecting the dairy industry. The SCM does not cause visible changes in the udder or physical changes of the milk as compared to clinical mastitis, and a clear overview of the prevalence and risk factors in the different regions of Africa is still lacking. The objective of this study was to investigate the prevalence of SCM and assess the associated risk factors and dominant bacterial pathogens among cattle in Africa. Materials and methods We gathered and systematically reviewed literature concerning SCM, published in English from January 2010 through December 2020 in two databases (PubMed and Web of Science), and meta-analysis was conducted using the ‘meta’ and ‘metafor’ packages in the R statistical software. Results A total of 258 studies were retrieved and at the end of the screening, 82 full-texts were eligible for inclusion in the meta-analysis. The prevalence of SCM was reported in 11 countries in five regions of Africa, and the random-effects model showed that the weighted pooled prevalence estimate (PPE) was 48.2% (95% CI: 43.6–52.8%). Heterogeneity was high and statistically significant as I 2 (proportion of observed variation) was 98.1% (95% CI: 98.0-98.3%), τ2 (true between-study variance) was 0.0433 (95% CI: 0.0322–0.0611), and the Cochran Q statistic was 4362.8 (p < 0.0001). Subgroup and meta-regression analyses showed that East Africa had significantly (p = 0.0092) the highest PPE of SCM (67.7%, 95% CI: 55.7–78.7) followed by West Africa (50.5%, 95%CI: 31.4–69.5), and the lowest was in North Africa (40.3%, 95%: 32.2–48.6). Other significant moderators for SCM were age (p < 0.0001), breed (p = 0.0002), lactation stage (p = 0.019) and parity (p = 0.0008) of cattle. Staphylococcus species (prevalence 43.7%) were the most predominant pathogens, followed by Streptococcus (18.2%) and Escherichia species (9.5%). Conclusion The present study showed a high variation of SCM prevalence in various parts of Africa, although there is a need for more data in some regions. The reported prevalence is a clear sign of inappropriate management practices among cattle herds and an indicator of the threat that SCM poses to the dairy industry. The information about the predisposing factors may guide effective management and control strategies to reduce transmission of the disease
Antibiotic resistance and virulence profiles of Proteus mirabilis isolated from broiler chickens at abattoir in South Africa
Abstract Background Proteus mirabilis has been identified as an important zoonotic pathogen, causing several illnesses such as diarrhoea, keratitis and urinary tract infections. Objective This study assessed the prevalence of P. mirabilis in broiler chickens, its antibiotic resistance (AR) patterns, ESBL‐producing P. mirabilis and the presence of virulence genes. Methods A total of 26 isolates were confirmed as P. mirabilis from 480 pooled broiler chicken faecal samples by polymerase chain reaction (PCR). The disk diffusion method was used to evaluate the antibacterial susceptibility test, while nine virulence genes and 26 AR genes were also screened by PCR. Results All 26 P. mirabilis isolates harboured the ireA (siderophore receptors), ptA, and zapA (proteases), ucaA, pmfA, atfA, and mrpA (fimbriae), hlyA and hpmA (haemolysins) virulence genes. The P. mirabilis isolates were resistant to ciprofloxacin (62%) and levofloxacin (54%), while 8 (30.7%) of the isolates were classified as multidrug resistant (MDR). PCR analysis identified the blaCTX‐M gene (62%), blaTEM (58%) and blaCTX‐M‐2 (38%). Further screening for AMR genes identified mcr‐1, cat1, cat2, qnrA, qnrD and mecA, 12%, 19%, 12%, 54%, 27% and 8%, respectively for P. mirabilis isolates. The prevalence of the integron integrase intI1 and intI2 genes was 43% and 4%, respectively. Conclusions The rise of ciprofloxacin and levofloxacin resistance, as well as MDR strains, is a public health threat that points to a challenge in the treatment of infections caused by these zoonotic bacteria. Furthermore, because ESBL‐producing P. mirabilis has the potential to spread to humans, the presence of blaCTX‐M‐producing P. mirabilis in broilers should be kept under control. This is the first study undertaken to isolate P. mirabilis from chicken faecal samples and investigate its antibiotic resistance status as well as virulence profiles in South Africa
Application of culture, PCR, and PacBio sequencing for determination of microbial composition of milk from subclinical mastitis dairy cows of smallholder farms
Mastitis is a cow disease usually signalized by
irritation, swelling, and soreness of the udder. It is characterized by physical, chemical, and biological changes
in the udder and milk. The aim of this study was to detect
and characterize pathogens causing subclinical mastitis
(SCM) from the milk of dairy cows of small-scale farmers
through culture and molecular techniques. Milk was collected from 32 cows belonging to 8 small-scale farmers around Harrismith District, South Africa. The results showed
that screening of SCM by California mastitis test and somatic
cell counts (SCC) was 21.87 and 25%, respectively. Culture
methods revealed the presence of Staphylococcus aureus at
93% followed by Streptococci spp. and Escherichia coli at
36.4 and 13.3%, respectively. The PCR could only detect
E. coli, while single-molecule real-time sequencing showed
a total of 2 phyla, 5 families, 7 genera, and 131 species.
Clostridiaceae was the most abundant family, while
Romboutsia was the most abundant genus followed by
Turicibacter spp. The present study has documented the
occurrence of SCM causing pathogens in milk collected
from cows of small-scale farmers in Harrismith, indicating
that SCM may be present at higher levels than expected.Central University of Technology Innovation fund and the National Research Foundation (NRF).https://www.degruyter.com/view/j/biolpm2021Veterinary Tropical Disease