Molecular detection of multidrug and methicillin resistance in Staphylococcus aureus isolated from wild pigeons (Columba livia) in South Africa.

Staphylococcus aureus is an important human and veterinary pathogen. The present study aimed to determine the prevalence of antibiotic resistance among S. aureus isolated from samples obtained from free-flying wild pigeons and houseflies from different locations surrounding a local hospital in the Greater Durban area in KwaZulu-Natal Province, South Africa. Environmental fecal samples were obtained from wild pigeons that inhabits the grounds of a local public hospital located on the South Beach area, Durban, South Africa. Housefly samples were collected from three different locations (Kenneth Stainbank Nature Reserve, Montclair/Clairwood, and Glenwood/Berea) in the greater Durban area, all within a close proximity to the hospital. Following enrichment, identification, and antimicrobial resistance profiling, S. aureus isolates were subjected to DNA extraction using the boiling method. It was found that 57 out of 252 samples (22.62%) were positive for S. aureus. The Kirby-Bauer disk diffusion method of antibiotic susceptibility testing was performed and revealed that antibiotic resistance rates to penicillin and rifampicin were the most common, with both returning 48 (84.2%) out of the 57 S. aureus isolates being resistant to penicillin and rifampicin. Antibiotic resistance rates to clindamycin, linezolid, erythromycin, tetracycline, cefoxitin, and ciprofloxacin were 82.5%, 78.9%, 73.7%, 63.2%, 33.3%, and 15.8% respectively. Antibiotic resistance genes were detected using primer-specific PCR and it was found that the prevalence rates of tetM, aac(6')-aph(2″), mecA, tetK, ermc, and blaZ genes were 66.7%, 40.4%, 40.4%, 38.6%, 24.6%, and 3.51% respectively. Statistical analysis revealed significant (p < 0.05) relationships between the tetM, aac(6')-aph(2″), and ermC genes and all parameters tested. A significant correlation between the aac(6')-aph(2″) gene and the tetM (0.506) and ermC (-0.386) genes was identified. It was found that 23 (40.3%) S. aureus isolates were mecA positive, of which 10 (52.6%) out of 19 cefoxitin-resistant isolates were mecA positive and 13 (35.1%) out of 37 cefoxitin-sensitive isolates were mecA positive. The results of the present study demonstrated the detection of methicillin and multidrug resistant S. aureus isolated from samples obtained from wild pigeons and houseflies in the surroundings of a local public hospital in the Greater Durban area in South Africa. The findings of the study may account for the emergence of multidrug-resistant staphylococcal infections. The findings highlight the significant role of wild pigeons and houseflies in the spread of drug-resistant pathogenic S. aureus including MRSA. The conclusions of the present study highlight the improtant role of wildlife and the environment as interconnected contributors of One Health.

Draft genome sequences of Bacillus licheniformis strains MEZBL63 and MEZBL64 harboring the lichenysin toxin operon isolated from livestock in South Africa.

Here, we report the draft genome sequences of two Bacillus licheniformis strains harboring the lichenysin operon that were isolated from healthy goat and horse in South Africa. The genomes were sequenced using Illumina MiSeq and had a length of 4,152,826 and 4,110,075 bp, respectively, with a G + C content of 46%.

Molecular detection of virulence genes in Staphylococcus aureus isolated from wild pigeons (Columba domestica livia) in KwaZulu-Natal in South Africa.

The current study aimed to determine virulence determinants among S. aureus isolated from wild pigeons and houseflies around hospital areas in the Greater Durban area, South Africa. Following enrichment and bacterial growth, DNA extraction using the boiling method was performed. Overall, 57 out of 252 samples (22.6%) were positive for S. aureus. Six known virulence genes were tested, where five known virulence determinants were positive and none of the S. aureus isolates were positive to coagulase (coa) gene. The highest prevalence rates were found in the genes encoding haemolysins, with the hla and hld genes having 8 (14%) and 9 (15.8%) positive isolates respectively. The sea, LukS/F-PV, and spa genes had 5 (8.8%), 4 (7%), and 2 (3.5%) positive isolates respectively. These results demonstrated the detection of pathogenic S. aureus from hospital environment in Durban, South Africa which may account for the emergence staphylococcal infections. The findings of the present study highlights the significant role of wild pigeons and houseflies as potenital infectious disease vectors in a One Health context.

Comparative genomics analysis and characterization of Shiga toxin-producing Escherichia coli O157:H7 strains reveal virulence genes, resistance genes, prophages and plasmids.

Escherichia coli O157:H7 is a foodborne pathogen that has been linked to global disease outbreaks. These diseases include hemorrhagic colitis and hemolytic uremic syndrome. It is vital to know the features that make this strain pathogenic to understand the development of disease outbreaks. In the current study, a comparative genomic analysis was carried out to determine the presence of structural and functional features of O157:H7 strains obtained from 115 National Center for Biotechnology Information database. These strains of interest were analysed in the following programs: BLAST Ring Image Generator, PlasmidFinder, ResFinder, VirulenceFinder, IslandViewer 4 and PHASTER. Five strains (ECP19-198, ECP19-798, F7508, F8952, H2495) demonstrated a great homology with Sakai because of a few regions missing. Five resistant genes were identified, however, Macrolide-associated resistance gene mdf(A) was commonly found in all genomes. Majority of the strains (97%) were positive for 15 of the virulent genes (espA, espB, espF, espJ, gad, chuA, eae, iss, nleA, nleB, nleC, ompT, tccP, terC and tir). The plasmid analysis demonstrated that the IncF group was the most prevalent in the strains analysed. The prophage and genomic island analysis showed a distribution of bacteriophages and genomic islands respectively. The results indicated that structural and functional features of the many O157:H7 strains differ and may be a result of obtaining mobile genetic elements via horizontal gene transfer. Understanding the evolution of O157:H7 strains pathogenicity in terms of their structural and functional features will enable the development of detection and control of transmission strategies.

Antimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock.

The emergence of antimicrobial-resistant, livestock-associated Enterococcus faecalis represents a public health concern. Here, we report the isolation, molecular detection of virulence and antimicrobial resistance determinants, in addition to the phylogenetic analyses of 20 Enterococcus species using whole genome sequencing analysis of 15 Enterococcus faecalis strains including six strains of three novel sequence types, three Enterococcus faecium and two Enterococcus durans. All strains were isolated from food chain animals in South Africa. Enterococcus strains were isolated on bile aesculin azide agar, followed by identification using MALDI-TOF MS analysis. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method. The genomic DNA of the isolates was extracted and sequencing was performed using the Illumina MiSeq platform. Sequence reads were trimmed and de novo assembled. The assembled contigs were analyzed for antimicrobial resistance genes and chromosomal mutations, extra-chromosomal plasmids, and multi-locus sequence type (MLST). Multidrug antimicrobial resistance genes conferring resistance to aminoglycosides (ant(6)-Ia, aph(3')-IIIa, sat4, and spw), lincosamides (lnu(B), lsa(A), and lsa(E)), macrolides (erm(B)), trimethoprim (dfrG) and tetracyclines (tet(L) and tet(M)) were identified. Plasmid replicons were detected in seven E. faecalis and three E. faecium isolates. The sequence type (ST) of each isolate was determined using the Enterococcus PubMLST database. Ten STs were identified in the collection, three of which (ST1240, ST1241, and ST1242) have not been previously reported and are described in the present study for the first time. To compare the sequenced strains to other previously sequenced E. faecalis strains, assembled sequences of E. faecalis from livestock were downloaded from the PubMLST database. Core genome-based phylogenetic analysis was performed using ParSNP. The detection of multiple drug-resistance in Enterococcus including E. faecalis and E. faecium highlights the significance of genomic surveillance to monitor the spread of antimicrobial resistance in food chain animals. In addition, the genome sequences of Enterococcus strains reported in the present study will serve as a reference point for future molecular epidemiological studies of livestock-associated and antibiotic-resistant E. faecalis in Africa. In addition, this study enables the in-depth analysis of E. faecalis genomic structure, as well as provides valuable information on the phenotypic and genotypic antimicrobial resistance, and the pathogenesis of livestock-associated E. faecalis and E. faecium.

Genetic parameter estimates for daily predicted gross feed efficiency and its association with energy-corrected milk in South African Holstein cattle.

Genetic parameters for daily predicted gross feed efficiency (pGFE) and energy corrected milk (ECM) in the first three parities of South African Holstein cattle were estimated by repeatability animal models. Data comprised of 11,068 test-day milk production records of 1,575 Holstein cows that calved between 2009 and 2019. Heritability estimates for pGFE were 0.12 ± 0.06, 0.09 ± 0.04 and 0.18 ± 0.05 in early, mid and late lactation, respectively. Estimates were moderate for primiparous (0.21 ± 0.05) and low for multiparous (0.10 ± 0.04) cows. Heritability and repeatability across all lactations were 0.14 ± 0.03 and 0.37 ± 0.03, respectively. Genetic correlations between pGFE in different stages of lactation ranged from 0.87 ± 0.24 (early and mid) to 0.97 ± 0.28 (early and late), while a strong genetic correlation (0.90 ± 0.03) was found between pGFE and ECM, across all lactations. The low to moderate heritability estimates for pGFE suggest potential for genetic improvement of the trait through selection, albeit with a modest accuracy of selection. The high genetic correlation of pGFE with ECM may, however, assist to improve accuracy of selection for feed efficiency by including both traits in multi-trait analyses. These genetic parameters may be used to estimate breeding values for pGFE, which will enable the trait to be incorporated in the breeding objective for South African Holstein cattle.

Prediction of dry matter intake and gross feed efficiency using milk production and live weight in first-parity Holstein cows.

Direct measurement of dry matter intake (DMI) presents a major challenge in estimating gross feed efficiency (GFE) in dairy cattle. This challenge can, however, be resolved through the prediction of DMI and GFE from easy-to-measure traits such as milk production (i.e. milk yield, energy-corrected milk (ECM), butterfat, protein, lactose) and live weight (LW). The main objective of this study was, therefore, to investigate the feasibility of predicting dry matter intake and gross feed efficiency for first-parity Holstein cows using milk production traits and LW. Data comprised of 30 daily measurements of DMI and milk production traits, and 25 daily LW records of a group of 100 first-parity Holstein cows, fed a total mixed ration. Gross feed efficiency was calculated as kg ECM divided by kg DMI. The initial step was to estimate correlations of milk production traits and LW with DMI and GFE, to identify the best potential predictors of DMI and GFE. Subsequently, a forward stepwise regression analysis was used to develop models to predict DMI and GFE from LW and milk production traits, followed by within-herd validations. Means for DMI, butterfat yield (BFY) and LW were 21.91 ± 2.77 kg/day, 0.95 ± 0.14 kg/day and 572 ± 15.58 kg/day, respectively. Mean GFE was 1.32 ± 0.22. Dry matter intake had positive correlations with milk yield (MY) (r = 0.32, p < 0.001) and LW (r = 0.76, p < 0.0001) and an antagonistic association with butterfat percent (BFP) (r = - 0.55, p < 0.001). On the other hand, GFE was positively associated with MY (r = 0.36, p < 0.001), BFP (r = 0.53, p < 0.001) and BFY (r = 0.83, p < 0.0001), and negatively correlated with LW (r = - 0.23, p > 0.05). Dry matter intake was predicted reliably by a model comprising of only LW and MY (R2 = 0.79; root mean squared error (RMSE) = 1.05 kg/day). A model that included BFY, MY and LW had the highest ability to predict GFE (R2 = 0.98; RMSE = 0.05). Live weight and BFY were the main predictor traits for DMI and GFE, respectively. The best models for predicting DMI and GFE were as follows: DMI (kg/day) = - 54.21 - 0.192 × MY (kg/day) + 0.146 × LW (kg/day) and GFE (kg/day) = 4.120 + 0.024 × MY (kg/day) + 1.000 × BFY (kg/day) - 0.008 × LW (kg/day). Thus, daily DMI (kg/day) and GFE can be reliably predicted from LW and milk production traits using these developed models in first-parity Holstein cows. This presents a big promise to generate large quantities of data of individual cow DMI and GFE, which can be used to implement genetic improvement of feed efficiency.

Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective.

Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans and may cause serious morbidity and large outbreaks worldwide. People with bloody diarrhea have an increased risk of developing serious complications such as acute renal failure and neurological damage. The hemolytic-uremic syndrome (HUS) is a serious condition, and up to 50% of HUS patients can develop long-term renal dysfunction or blood pressure-related complications. Children aged two to six years have an increased risk of developing HUS. Clinical enteropathogenic Escherichia coli (EPEC) infections show fever, vomiting, and diarrhea. The EPEC reservoir is unknown but is suggested to be an asymptomatic or symptomatic child or an asymptomatic adult carrier. Spreading is often through the fecal-oral route. The prevalence of EPEC in infants is low, and EPEC is highly contagious in children. EPEC disease in children tends to be clinically more severe than other diarrheal infections. Some children experience persistent diarrhea that lasts for more than 14 days. Enterotoxigenic Escherichia coli (ETEC) strains are a compelling cause of the problem of diarrheal disease. ETEC strains are a global concern as the bacteria are the leading cause of acute watery diarrhea in children and the leading cause of traveler's diarrhea. It is contagious to children and can cause chronic diarrhea that can affect the development and well-being of children. Infections with diarrheagenic E. coli are more common in African countries. Antimicrobial agents should be avoided in the acute phase of the disease since studies showed that antimicrobial agents may increase the risk of HUS in children. The South African National Veterinary Surveillance and Monitoring Programme for Resistance to Antimicrobial Drugs has reported increased antimicrobial resistance in E. coli. Pathogenic bacterial strains have developed resistance to a variety of antimicrobial agents due to antimicrobial misuse. The induced heavy metal tolerance may also enhance antimicrobial resistance. The prevalence of antimicrobial resistance depends on the type of the antimicrobial agent, bacterial strain, dose, time, and mode of administration. Developing countries are severely affected by increased resistance to antimicrobial agents due to poverty, lack of proper hygiene, and clean water, which can lead to bacterial infections with limited treatment options due to resistance.

Ticks of domestic animals in Lesotho: Morphological and molecular characterization.

A total of 3311 tick specimens were randomly collected from domestic animals including cattle, sheep, goats, horses, donkeys, and dogs from Lesotho districts namely, Berea, Butha-Buthe, Leribe, Mafeteng, Maseru, Mohale's Hoek, Mokhotlong, Qacha's Nek, Quthing and Thaba Tseka. Tick species were identified morphologically and verified by amplification and sequencing of the CO1 and 18S rRNA genes. Nine species were identified under different genera namely, Haemaphysalis elliptica 0.1% (n = 2), Hyalomma rufipes 2.6% (n = 87), Hy. truncatum 1.2% (n = 41), Otobius megnini 13.6% (n = 451), Rhipicephalus appendiculatus 0.1% (n = 3), Rhipicephalus decoloratus 9.3% (n = 308), Rhipicephalus evertsi evertsi 65.1% (n = 2156), Rhipicephalus glabroscutatum 1.3% (n = 43) and Rhipicephalus microplus 6.6% (n = 220). There was a significant difference at p = 6.2E-06 (ꭓ2 = 1.923, df = 7) in the distribution of tick species and their abundance p = 0.04 (ꭓ2 = 1.923, df = 7) from each population. The CO1 and 18S rRNA sequences matched the morphological determinations on the NCBI database and clustered with relevant species on the phylogenetic tree. Genetic analysis of CO1 and 18S rRNA provided very strong support for monophyly of the Rhipicephalinae and Ornithodorinae complexes. Both CO1 and 18S rRNA are useful genetic markers for the specific and generic characterization of tick species in Lesotho and elsewhere. This is the first scientific publication of tick species occurring in Lesotho.

Draft Genome Sequence of Listeria innocua Strain MEZLIS29, Isolated from a Cow in South Africa.

Here, we report the draft genome sequence of Listeria innocua strain MEZLIS29, which was isolated from a healthy cow in Flagstaff, Eastern Cape Province, South Africa. The genome was sequenced using the Illumina MiSeq platform and had a length of 2,805,865 bp, with a G+C content of 37.5% and 2,783 coding DNA sequences, 58 tRNAs, 4 noncoding RNAs, and 8 rRNA genes.

Molecular Surveillance and Dissemination of Klebsiella pneumoniae on Frequently Encountered Surfaces in South African Public Hospitals.

Bacteria that cause life-threatening illnesses in humans are also capable of contaminating hospital surfaces, thus pose as a potential source of infection. This study aimed to investigate the prevalence, genetic diversity, virulence, and antibiotic resistance profile of Klebsiella pneumoniae in South Africa. In a nonoutbreak setting involving four public hospitals, 777 samples were collected in three different wards from 11 different sites. Phenotypic and genotypic methods were used for isolation and identification. The Kirby-Bauer disk-diffusion method was used to examine antibiotic resistance followed by the combination disk method to characterize extended-spectrum ß-lactamases (ESBLs). Antibiotic resistance and virulence genes were screened using PCR and clonality was investigated using enterobacterial repetitive intergenic consensus (ERIC)-PCR. Seventy-five (10%) K. pneumoniae isolates were recovered. These isolates were obtained from all four hospitals and all three wards involved. However, only six frequently touched surfaces were contaminated. Thirty (40%) isolates were characterized as ESBLs showing high resistance to antibiotics and mostly harboring the blaCTX-M group one gene. Virulence genes were highly prevalent among all the isolates. ERIC-PCR showed that the isolates recovered from different sites within the same hospital were genetically similar. The study highlighted that K. pneumoniae can contaminate various surfaces and this persistence allows for the dissemination of bacteria within the hospital environment. The information from this study can assist hospitals to evaluate and improve current infection prevention and control interventions in place.

Genotypic and Phenotypic Characterizations of Methicillin-Resistant Staphylococcus aureus (MRSA) on Frequently Touched Sites from Public Hospitals in South Africa.

The hospital environment acts as a reservoir in the transmission of pathogens, such as MRSA, which may cause hospital-acquired infections. This study aimed to ascertain the prevalence, genetic relatedness, antibiotic resistance, and virulence profile of MRSA on some frequently touched hospital sites in South Africa. A total of 777 swabs were randomly collected from 11 frequently touched sites in the hospital environment of three wards of four public hospitals in the KwaZulu-Natal province of South Africa. Isolation of S. aureus and confirmation were done using genotypic and phenotypic methods. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk-diffusion method. MRSA isolates were determined by the presence of the mecA gene. Virulence and resistance genes were detected using a standard monoplex PCR assay. ERIC-PCR was conducted to evaluate the genetic relatedness. An overall prevalence of 12.7% for S. aureus isolates was obtained. Out of these, 89.9% (89/99) were confirmed to be MRSA. The sites with the highest prevalence were the occupied beds (16.2% (16/99)), unoccupied beds (16.2% (16/99)), patient files (14.1% (14/99)), ward phones (13.1% (13/99)), and nurses' tables (14.1% (14/99)). The virulence genes with the highest observed frequency were hld (87 (87.9%)) and LukS/F-PV (53 (53.5%)). The resistance genes with the highest frequency were the tetM and tetK genes detected in 60 (60.6%) and 57 (57.6%) isolates, respectively. The ERIC-PCR results obtained indicated a high level of genetic diversity; however, intraclonal (within a hospital) and interclonal (between hospitals) clusters of MRSA were observed. The study showed that MRSA can contaminate various surfaces, and this persistence allows for the dissemination of bacteria within the hospital environment. This highlights the need for improved infection prevention and control (IPC) strategies in public hospitals in the country to curb their potential transmission risks.

Occurrence, Antibiotic Resistance, Virulence Factors, and Genetic Diversity of Bacillus spp. from Public Hospital Environments in South Africa.

This study aimed to assess the molecular dissemination of Bacillus species in public hospitals in South Africa. The study conducted over 3 months during 2017 involved representative samples obtained from three wards (general ward, intensive care unit, and pediatric unit) from four public hospitals denoted as A (Central), B (Tertiary), C (Regional), and D (District). Swabs collected from 11 distinct hospital surfaces were screened using selective media, biochemical testing, and molecular methods. Overall, 17% (135/777) isolates were identified with a prevalence of 24% (32/135) for central, 33% (45/135) for tertiary, 27% (36/135) for regional, and 16% (22/135) for district hospital. Bacillus species were further confirmed to belong to Bacillus cereus (129/135; 96%) and Bacillus subtilis (6/135; 4%). Prevalence was similar across the wards, averaging 33.3% (45/135). The highest prevalence of Bacillus isolates was found on the drip stands (11.8%), sink (11.8%), ward phone (11.5%), and nurses' tables (10.3%). Minimum inhibitory concentration analyses revealed high resistance to ß-lactams, fluoroquinolones, and tetracyclines. The most common resistance genes detected were ermB (56%) and tetM (5%). Enterotoxin virulence genes hblA (77%) and hblD (88%) associated with the diarrheal syndrome were most detected; however, no ces genes (cereulide toxin) for emetic syndrome was found. The enterobacterial repetitive intergenic consensus PCR revealed considerable diversity at the different levels of health care, although the clonal spread of strains between the sites/wards within each specific hospital was revealed. The study highlighted the dissemination of drug-resistant Bacillus spp. in public hospital environments and calls for the design of optimal strategies to curb their spread.

Molecular Detection of Coxiella burnetii, Rickettsia africae and Anaplasma Species in Ticks from Domestic Animals in Lesotho.

Tick-borne diseases (TBDs) hamper the growth of the livestock sector and impose major constraints for the health and management of domestic animals in the tropic and subtropical regions globally. Currently, there is no scientific report on the presence of zoonotic pathogens transmitted by tick species in Lesotho. This study aimed to identify zoonotic tick-borne pathogens of economic importance from ticks infesting domestic animals in Lesotho using molecular techniques. A total of 322 tick DNA pools were subjected to PCR screening for the presence of zoonotic pathogens and sequenced. The overall prevalence of Anaplasma spp. was 35% (113/322), with a 100% infection rate in Rhipicephalus microplus, followed by R. evertsi evertsi (92%), Hyalomma rufipes and Otobius megnini sharing 50% and the lowest infection rate was observed in R. decoloratus with 40%. The prevalence of Coxiella burnetii, a gram-negative pleomorphic etiological agent of Query fever (Q fever), was 1% (2/322) for all screened samples, with 20% of R. decoloratus and 1% of R. e. evertsi infected. Rickettsia africae was detected from Hyalomma rufipes with a 70% prevalence. This study provides a baseline knowledge of tick-borne pathogens of medical and veterinary importance in Lesotho and raises awareness of the prevalence of such diseases within the tourism sector as they are mostly affected.

Activity of Mannose-Binding Lectin on Bacterial-Infected Chickens-A Review.

In recent years, diseases caused by pathogenic bacteria have profoundly impacted chicken production by causing economic loss in chicken products and by-product revenues. MBL (mannose-binding lectin) is part of the innate immune system (IIS), which is the host's first line defense against pathogens. The IIS functions centrally by identifying pathogen-specific microorganism-associated molecular patterns (MAMPs) with the help of pattern recognition receptors (PRRs). Studies have classified mannose-binding lectin (MBL) as one of the PRR molecules which belong to the C-type lectin family. The protective role of MBL lies in its ability to activate the complement system via the lectin pathway and there seems to be a direct link between the chicken's health status and the MBL concentration in the serum. Several methods have been used to detect the presence, the level and the structure of MBL in chickens such as Enzyme-linked immunosorbent assay (ELISA), Polymerase Chain Reaction (PCR) among others. The concentration of MBL in the chicken ranges from 0.4 to 35 µg/mL and can be at peak levels at three to nine days at entry of pathogens. The variations observed are known to depend on the bacterial strains, breed and age of the chicken and possibly the feed manipulation strategies. However, when chicken MBL (cMBL) becomes deficient, it can result in malfunctioning of the innate immune system, which can predispose chickens to diseases. This article aimed to discuss the importance and components of mannose-binding lectin (MBL) in chickens, its mode of actions, and the different methods used to detect MBL. Therefore, more studies are recommended to explore the causes for low and high cMBL production in chicken breeds and the possible effect of feed manipulation strategies in enhancing cMBL production.

Genomic Characterization of Antimicrobial Resistance in Food Chain and Livestock-Associated Salmonella Species.

The rising trend of antimicrobial resistance (AMR) by foodborne bacteria is a public health concern as these pathogens are easily transmitted to humans through the food chain. Non-typhoid Salmonella spp. is one of the leading foodborne pathogens which infect humans worldwide and is associated with food and livestock. Due to the lack of discovery of new antibiotics and the pressure exerted by antimicrobial resistance in the pharmaceutical industry, this review aimed to address the issue of antibiotic use in livestock which leads to AMR in Salmonella. Much attention was given to resistance to carbapenems and colistin which are the last-line antibiotics used in cases of multi drug resistant bacterial infections. In the present review, we highlighted data published on antimicrobial resistant Salmonella species and serovars associated with livestock and food chain animals. The importance of genomic characterization of carbapenem and colistin resistant Salmonella in determining the relationship between human clinical isolates and food animal isolates was also discussed in this review. Plasmids, transposons, and insertion sequence elements mediate dissemination of not only AMR genes but also genes for resistance to heavy metals and disinfectants, thus limiting the therapeutic options for treatment and control of Salmonella. Genes for resistance to colistin (mcr-1 to mcr-9) and carbapenem (blaVIM-1, blaDNM-1, and blaNDM-5) have been detected from poultry, pig, and human Salmonella isolates, indicating food animal-associated AMR which is a threat to human public health. Genotyping, plasmid characterization, and phylogenetic analysis is important in understanding the epidemiology of livestock-related Salmonella so that measures of preventing foodborne threats to humans can be improved.

Genome sequences of two multidrug-resistant Escherichia coli strains MEZEC8 and MEZEC10 isolated from livestock in South Africa.

OBJECTIVES: The emergence of antimicrobial-resistant livestock-associated Escherichia coli represents a great public health concern. Here we report the draft genome sequences of two multidrug-resistant livestock-associated E. coli strains MEZEC8 and MEZEC10 isolated from sheep in South Africa. METHODS: Genomic DNA of E. coli strains MEZEC8 and MEZEC10 was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids, and the sequence type (ST) was determined by multilocus sequence typing (MLST). To compare strains MEZEC8 and MEZEC10 with other previously published sequences of E. coli strains, raw read sequences of E. coli from livestock were downloaded from the NCBI's Sequence Read Archive and all sequence files were treated identically to generate a core genome bootstrapped maximum likelihood phylogenetic tree. RESULTS: Antimicrobial resistance genes were detected in MEZEC8 and MEZEC10 conferring resistance to tetracycline and macrolides. MEZEC10 harboured two extrachromosomal plasmids (pO111 and Incl2), while MEZEC8 did not contain any extrachromosomal plasmids. Strain MEZEC8 belonged to serotype H25:O9 and ST58, whereas strain MEZEC10 belonged to serotype H49:O8 and ST1844. CONCLUSION: The genome sequences of E. coli strains MEZEC8 and MEZEC10 will serve as a reference point for molecular epidemiological studies of antimicrobial-resistant livestock-associated E. coli in Africa. In addition, this study allows in-depth analysis of genomic structure and will provide valuable information enabling us understand the antimicrobial resistance of livestock-associated E. coli.

Study on the prevalence and genetic diversity of Eimeria species from broilers and free-range chickens in KwaZulu-Natal province, South Africa.

This study was conducted from January to October 2018 with the objective to determine the prevalence and genetic diversity of Eimeria species in broiler and free-range chickens in KwaZulu-Natal province, South Africa. A total of 342 faecal samples were collected from 12 randomly selected healthy broiler chicken farms and 40 free-range chickens from 10 different locations. Faecal samples were screened for the presence of Eimeria oocysts using a standard flotation method. The species of Eimeria isolates were confirmed by amplification of the internal transcribed spacer 1 (ITS-1) partial region and sequences analysis. Among broiler and free-ranging chickens, 19 out of 41 pens (46.3%) and 25 out of 42 faecal samples (59.5%) were positive for Eimeria infection. Molecular detection revealed the following species: Eimeria maxima, Eimeria tenella, Eimeria acervulina, Eimeria brunetti and Eimeria mitis in all the samples screened. Similarly, polymerase chain reaction assays specific for three cryptic Eimeria operational taxonomic units were negative for all the samples. Phylogenetic analysis of the ITS-1 sequences supported species identity with the greatest variation detected for E. mitis. This study provides information on the range and identity of Eimeria species, and their genetic relatedness, circulating in commercially reared broilers and free-ranging chickens from different locations in KwaZulu-Natal province.

Genome sequences of two Salmonella enterica strains (MEZSAL74 and MEZSAL81) harbouring multiple antimicrobial resistance genes isolated from livestock in South Africa.

OBJECTIVES: Antimicrobial-resistant livestock-associated Salmonella enterica infections pose a significant public-health threat worldwide. Here we report for the first time the draft genome sequences of two multidrug-resistant livestock-associated S. enterica strains isolated from a chicken and a cow in South Africa. METHODS: Genomic DNA of S. enterica strains MEZSAL74 and MEZSAL81 was sequenced using an Illumina MiSeq platform. The generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids. Multilocus sequence typing (MLST) was also performed. In order to compare isolates MEZSAL74 and MEZSAL81 with other previously sequenced S. enterica isolates, raw read sequences were downloaded and all sequence files were treated identically to generate a bootstrapped maximum likelihood phylogenetic tree. RESULTS: Extrachromosomal plasmids and genetic determinants of antimicrobial resistance were detected in both sequenced bacterial isolates to aminoglycosides and fluoroquinolones. By MLST, strain MEZSAL74 belonged to an unknown sequence type (ST) and strain MEZSAL81 belonged to ST33. CONCLUSION: The genome sequences of strains MEZSAL74 and MEZSAL81 reported here will serve as a reference for molecular epidemiological studies of antimicrobial-resistant livestock-associated S. enterica in Africa.