Genomic analysis of antibiotic-resistant Enterococcus spp. reveals novel enterococci strains and the spread of plasmid-borne Tet(M), Tet(L) and Erm(B) genes from chicken litter to agricultural soil in South Africa

2022 ◽  
Vol 302 ◽  
pp. 114101
Author(s):  
Dorcas Oladayo Fatoba ◽  
Daniel Gyamfi Amoako ◽  
Abia Luther King Akebe ◽  
Arshad Ismail ◽  
Sabiha Y. Essack
Keyword(s):  
South Africa ◽  
Agricultural Soil ◽  
Genomic Analysis ◽  
Antibiotic Resistant ◽  
Enterococcus Spp ◽  
Chicken Litter

scholarly journals Rethinking Manure Application: Increase in Multidrug-Resistant Enterococcus spp. in Agricultural Soil Following Chicken Litter Application

2021 ◽  
Vol 9 (5) ◽  
pp. 885
Author(s):  
Dorcas Oladayo Fatoba ◽  
Akebe Luther King Abia ◽  
Daniel G. Amoako ◽  
Sabiha Y. Essack
Keyword(s):  
Antimicrobial Resistance ◽  
Agricultural Soil ◽  
Multidrug Resistant ◽  
Diffusion Method ◽  
Resistant Bacteria ◽  
Manure Application ◽  
Unamended Soil ◽  
Enterococcus Spp ◽  
Chicken Litter ◽  
Amended Soil

The current study investigated the impact of chicken litter application on the abundance of multidrug-resistant Enterococcus spp. in agricultural soil. Soil samples were collected from five different strategic places on a sugarcane farm before and after manure application for four months. Chicken litter samples were also collected. Enterococci were enumerated using the Enterolert®/Quanti-Tray 2000® system and confirm and differentiated into species using real-time PCR. The antibiotic susceptibility profile of the isolates was determined using the disk diffusion method following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The overall mean bacterial count was significantly higher (p < 0.05) in manure-amended soil (3.87 × 107 MPN/g) than unamended soil (2.89 × 107 MPN/g). Eight hundred and thirty-five enterococci (680 from soil and 155 from litter) were isolated, with E. casseliflavus being the most prevalent species (469; 56.2%) and E. gallinarum being the least (16; 1.2%). Approximately 56% of all the isolates were resistant to at least one antibiotic tested, with the highest resistance observed against tetracycline (33%) and the lowest against chloramphenicol (0.1%); 17% of E. faecium were resistant to quinupristin-dalfopristin. Additionally, 27.9% (130/466) of the isolates were multidrug-resistant, with litter-amended soil harbouring more multidrug-resistant (MDR) isolates (67.7%; 88/130) than unamended soil (10.0%; 13/130). All isolates were susceptible to tigecycline, linezolid and gentamicin. About 7% of the isolates had a multiple antimicrobial resistance index > 0.2, indicative of high antibiotic exposure. Although organic fertilizers are regarded as eco-friendly compared to chemical fertilizers for improving soil fertility, the application of untreated animal manure could promote the accumulation of antibiotics and their residues and antibiotic-resistant bacteria in the soil, creating an environmental reservoir of antimicrobial resistance, with potential human and environmental health risks.

scholarly journals From the Farms to the Dining Table: The Distribution and Molecular Characteristics of Antibiotic-Resistant Enterococcus spp. in Intensive Pig Farming in South Africa

2021 ◽  
Vol 9 (5) ◽  
pp. 882
Author(s):  
Sasha Badul ◽  
Akebe L. K. Abia ◽  
Daniel G. Amoako ◽  
Keith Perrett ◽  
Linda A. Bester ◽  
...  
Keyword(s):  
South Africa ◽  
Antibiotic Resistance ◽  
Real Time ◽  
Real Time Pcr ◽  
Diffusion Method ◽  
Antibiotic Resistant ◽  
Pig Farming ◽  
Enterococcus Spp ◽  
Food Animals ◽  
The Continuum

Foodborne pathogens, including antibiotic-resistant species, constitute a severe menace to food safety globally, especially food animals. Identifying points of concern that need immediate mitigation measures to prevent these bacteria from reaching households requires a broad understanding of these pathogens’ spread along the food production chain. We investigated the distribution, antibiotic susceptibility, molecular characterization and clonality of Enterococcus spp. in an intensive pig production continuum in South Africa, using the farm-to-fork approach. Enterococcus spp. were isolated from 452 samples obtained along the pig farm-to-fork continuum (farm, transport, abattoir, and retail meat) using the IDEXX Enterolert®/Quanti-Tray® 2000 system. Pure colonies were obtained on selective media and confirmed by real-time PCR, targeting genus- and species-specific genes. The susceptibility to antibiotics was determined by the Kirby–Bauer disk diffusion method against 16 antibiotics recommended by the WHO-AGISAR using EUCAST guidelines. Selected antibiotic resistance and virulence genes were detected by real-time PCR. Clonal relatedness between isolates across the continuum was evaluated by REP-PCR. A total of 284 isolates, consisting of 79.2% E. faecalis, 6.7% E. faecium, 2.5% E. casseliflavus, 0.4% E. gallinarum, and 11.2% other Enterococcus spp., were collected along the farm-to-fork continuum. The isolates were most resistant to sulfamethoxazole-trimethoprim (78.8%) and least resistant to levofloxacin (5.6%). No resistance was observed to vancomycin, teicoplanin, tigecycline and linezolid. E. faecium displayed 44.4% resistance to quinupristin-dalfopristin. Also, 78% of the isolates were multidrug-resistant. Phenotypic resistance to tetracycline, aminoglycosides, and macrolides was corroborated by the presence of the tetM, aph(3′)-IIIa, and ermB genes in 99.1%, 96.1%, and 88.3% of the isolates, respectively. The most detected virulence gene was gelE. Clonality revealed that E. faecalis isolates belonged to diverse clones along the continuum with major REP-types, mainly isolates from the same sampling source but different sampling rounds (on the farm). E. faecium isolates revealed a less diverse profile. The results suggest that intensive pig farming could serve as a reservoir of antibiotic-resistant bacteria that could be transmitted to occupationally exposed workers via direct contact with animals or consumers through animal products/food. This highlights the need for more robust guidelines for antibiotic use in intensive farming practices and the necessity of including Enterococcus spp. as an indicator in antibiotic resistance surveillance systems in food animals.

Detection of antibiotic resistant E. coli and Enterococcus spp. in stool of healthy growing children in Portugal

2009 ◽  
Vol 49 (6) ◽  
pp. 503-512 ◽  
Author(s):  
Ângela Barreto ◽  
Bruno Guimarães ◽  
Hajer Radhouani ◽  
Carlos Araújo ◽  
Alexandre Gonçalves ◽  
...  
Keyword(s):  
Antibiotic Resistant ◽  
E Coli ◽  
Enterococcus Spp

scholarly journals Antibiogram Signatures of Some Enterobacteria Recovered from Irrigation Water and Agricultural Soil in two District Municipalities of South Africa

2020 ◽  
Vol 8 (8) ◽  
pp. 1206 ◽  
Author(s):  
Chidozie Declan Iwu ◽  
Erika M du Plessis ◽  
Lise Korsten ◽  
Nolonwabo Nontongana ◽  
Anthony Ifeanyi Okoh
Keyword(s):  
South Africa ◽  
Clavulanic Acid ◽  
Irrigation Water ◽  
Agricultural Soil ◽  
Salmonella Enterica Serovar Typhimurium ◽  
Klebsiella Oxytoca ◽  
Eastern Cape Province ◽  
Eastern Cape ◽  
Serovar Typhimurium ◽  
Amoxicillin Clavulanic Acid

This study was undertaken to evaluate the antibiogram fingerprints of some Enterobacteria recovered from irrigation water and agricultural soil in two District Municipalities of the Eastern Cape Province, South Africa using standard culture-based and molecular methods. The prevalent resistance patterns in the isolates follow the order: Salmonella enterica serovar Typhimurium [tetracycline (92.3%), ampicillin (69.2%)]; Enterobacter cloacae [amoxicillin/clavulanic acid (77.6%), ampicillin (84.5%), cefuroxime (81.0%), nitrofurantoin (81%), and tetracycline (80.3%)]; Klebsiella pneumoniae [amoxicillin/clavulanic acid (80.6%), ampicillin (88.9%), and cefuroxime (61.1%)]; and Klebsiella oxytoca [chloramphenicol (52.4%), amoxicillin/clavulanic acid (61.9%), ampicillin (61.9%), and nitrofurantoin (61.9%)]. Antibiotic resistance genes detected include tetC (86%), sulII (86%), and blaAmpC (29%) in Salmonella enterica serovar Typhimurium., tetA (23%), tetB (23%), tetC (12%), sulI (54%), sulII (54%), catII (71%), blaAmpC (86%), blaTEM (43%), and blaPER (17%) in Enterobacter cloacae., tetA (20%), tetC (20%), tetD (10%), sulI (9%), sulII (18%), FOX (11%) and CIT (11%)-type plasmid-mediated AmpC, blaTEM (11%), and blaSHV (5%) in Klebsiella pneumoniae and blaAmpC (18%) in Klebsiella oxytoca. Our findings document the occurrence of some antibiotic-resistant Enterobacteria in irrigation water and agricultural soil in Amathole and Chris Hani District Municipalities, Eastern Cape Province of South Africa, thus serving as a potential threat to food safety.

scholarly journals Application of Combined Genomic and Transfer Analyses to Identify Factors Mediating Regional Spread of Antibiotic-resistant Bacterial Lineages

2020 ◽  
Vol 71 (10) ◽  
pp. e642-e649
Author(s):  
Joyce Wang ◽  
Betsy Foxman ◽  
Ali Pirani ◽  
Zena Lapp ◽  
Lona Mody ◽  
...  
Keyword(s):  
Methicillin Resistant Staphylococcus Aureus ◽  
Genomic Analysis ◽  
Patient Characteristics ◽  
Fourth Generation ◽  
Nursing Facilities ◽  
Antibiotic Resistant ◽  
Patient Level ◽  
Vancomycin Resistant ◽  
Healthcare Associated ◽  
Genomic Similarity

Abstract Background Patients entering nursing facilities (NFs) are frequently colonized with antibiotic-resistant organisms (AROs). To understand the determinants of ARO colonization on NF admission, we applied whole-genome sequencing to track the spread of 4 ARO species across regional NFs and evaluated patient-level characteristics and transfer acute care hospitals (ACHs) as risk factors for colonization. Methods Patients from 6 NFs (n = 584) were surveyed for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecalis/faecium (VREfc/VREfm), and ciprofloxacin-resistant Escherichia coli (CipREc) colonization. Genomic analysis was performed to quantify ARO spread between NFs and compared to patient-transfer networks. The association between admission colonization and patient-level variables and recent ACH exposures was examined. Results The majority of ARO isolates belonged to major healthcare-associated lineages: MRSA (sequence type [ST] 5); VREfc (ST6); CipREc (ST131), and VREfm (clade A). While the genomic similarity of strains between NF pairs was positively associated with overlap in their feeder ACHs (P &lt; .05 for MRSA, VREfc, and CipREc), limited phylogenetic clustering by either ACH or NF supported regional endemicity. Significant predictors for ARO colonization on NF admission included lower functional status and recent exposure to glycopeptides (adjusted odds ratio [aOR], &gt; 2 for MRSA and VREfc/VREfm) or third-/fourth-generation cephalosporins (aOR, &gt; 2 for MRSA and VREfm). Transfer from specific ACHs was an independent risk factor for only 1 ARO/ACH pair (VREfm/ACH19: aOR, 2.48). Conclusions In this region, healthcare-associated ARO lineages are endemic among connected NFs and ACHs, making patient characteristics more informative of NF admission colonization risk than exposure to specific ACHs.

scholarly journals Metagenomic Analysis of the Enteric RNA Virome of Infants from the Oukasie Clinic, North West Province, South Africa, Reveals Diverse Eukaryotic Viruses

Viruses ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 1260
Author(s):  
Milton T. Mogotsi ◽  
Peter N. Mwangi ◽  
Phillip A. Bester ◽  
M. Jeffrey Mphahlele ◽  
Mapaseka L. Seheri ◽  
...  
Keyword(s):  
South Africa ◽  
Genomic Analysis ◽  
Illumina Miseq ◽  
Viral Population ◽  
Early Developmental Stage ◽  
Health State ◽  
North West ◽  
Viral Shedding ◽  
Healthy Infants ◽  
Miseq Platform

Establishing a diverse gut microbiota after birth is essential for preventing illnesses later in life. However, little knowledge exists about the total viral population (virome) present in the gut of infants during the early developmental stage, with RNA viruses being generally overlooked. Therefore, this small pilot longitudinal study investigated the diversity and changes in the enteric RNA virome in healthy infants from South Africa. Faecal samples (n = 12) were collected from four infants at three time points (on average at 8, 13, and 25 weeks), and then sequenced on an Illumina MiSeq platform. The genomic analysis revealed a diverse population of human enteric viruses from the infants’ stools, and changes in the enteric virome composition were observed over time. The Reoviridae family, more specifically the Rotavirus genus, was the most common and could be linked to viral shedding due to the administration of live-attenuated oral vaccines in South Africa, followed by the Picornaviridae family including parechoviruses, echoviruses, coxsackieviruses, enteroviruses, and polioviruses. Polioviruses were also linked to vaccine-related shedding. Astroviridae (astroviruses) and Caliciviridae (noroviruses) were present at low abundance. It is evident that an infant’s gut is colonized by distinct viral populations irrespective of their health state. Further characterization of the human virome (with a larger participant pool) is imperative to provide more conclusive insights into the viral community structure and diversity that has been shown in the current study, despite the smaller sample size.

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