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Article ; Online: Characterization of the Tissue and Strain-Specific Microbiota of

Chen, Chia-Yu / Chan, Wai-Yin / Ismail, Arshad / Oliver, Shüné V

Tropical medicine and infectious disease

2024 Volume 9, Issue 4

Abstract: The mosquito microbiota is a critical determinant of mosquito life history. It is therefore a target for novel vector control strategies like paratransgenesis. However, the microbiota ... ...

Abstract	The mosquito microbiota is a critical determinant of mosquito life history. It is therefore a target for novel vector control strategies like paratransgenesis. However, the microbiota in
Language	English
Publishing date	2024-04-13
Publishing country	Switzerland
Document type	Journal Article
ISSN	2414-6366
ISSN (online)	2414-6366
DOI	10.3390/tropicalmed9040084
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Article ; Online: A rabies-related lyssavirus from a

Viljoen, Natalie / Ismail, Arshad / Weyer, Jacqueline / Markotter, Wanda

Microbiology resource announcements

2023 Volume 12, Issue 11, Page(s) e0062123

Abstract: We report the coding-complete sequence of a lyssavirus, provisionally designated Phala bat lyssavirus (PBLV), characterized using a metagenomics approach. PBLV was identified in ... ...

Abstract	We report the coding-complete sequence of a lyssavirus, provisionally designated Phala bat lyssavirus (PBLV), characterized using a metagenomics approach. PBLV was identified in a
Language	English
Publishing date	2023-10-06
Publishing country	United States
Document type	Journal Article
ISSN	2576-098X
ISSN (online)	2576-098X
DOI	10.1128/MRA.00621-23
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Article ; Online: Molecular epidemiology and antimicrobial resistance of vaginal Candida glabrata isolates in Namibia.

Dunaiski, Cara M / Kock, Marleen M / Chan, Wai Yin / Ismail, Arshad / Peters, Remco P H

Medical mycology

2024 Volume 62, Issue 2

Abstract: Candida glabrata is the most common non-albicans Candida species that causes vulvovaginal candidiasis (VVC). Given the intrinsically low susceptibility of C. glabrata to azole drugs, investigations into C. glabrata prevalence, fungal susceptibility ... ...

Abstract	Candida glabrata is the most common non-albicans Candida species that causes vulvovaginal candidiasis (VVC). Given the intrinsically low susceptibility of C. glabrata to azole drugs, investigations into C. glabrata prevalence, fungal susceptibility profile, and molecular epidemiology are necessary to optimise the treatment of VVC. This molecular epidemiological study was conducted to determine antifungal drug profile, single nucleotide polymorphisms (SNPs) associated with phenotypic antifungal resistance and epidemic diversity of C. glabrata isolates from women with VVC in Namibia. Candida glabrata isolates were identified using phenotypic and molecular methods. Antifungal susceptibility of strains was determined for fluconazole, itraconazole, amphotericin B, and anidulafungin. Whole genome sequencing was used to determine SNPs in antifungal resistance genes and sequence type (ST) allocation. Among C. glabrata isolates, all (20/20; 100%) exhibited phenotypic resistance to the azole class antifungal drug, (fluconazole), and phenotypic susceptibility to the polyene class (amphotericin B), and the echinocandins (anidulafungin). Non-synonymous SNPs were identified in antifungal resistance genes of all fluconazole-resistant C. glabrata isolates including ERG6 (15%), ERG7 (15%), CgCDR1 (25%), CgPDR1 (60%), SNQ2 (10%), FKS1 (5.0%), FKS2 (5.0%), CgFPS1 (5.0%), and MSH2 (15%). ST15 (n = 8/20, 40%) was predominant. This study provides important insight into phenotypic and genotypic antifungal resistance across C. glabrata isolates from women with VVC in Namibia. In this study, azole resistance is determined by an extensive range of SNPs, while the observed polyene and echinocandin resistance-associated SNPs despite phenotypic susceptibility require further investigation.
MeSH term(s)	Female ; Humans ; Antifungal Agents/pharmacology ; Candida glabrata ; Candidiasis, Vulvovaginal/microbiology ; Candidiasis, Vulvovaginal/veterinary ; Fluconazole ; Amphotericin B ; Anti-Bacterial Agents ; Anidulafungin ; Molecular Epidemiology ; Namibia/epidemiology ; Microbial Sensitivity Tests/veterinary ; Drug Resistance, Bacterial ; Echinocandins ; Azoles ; Polyenes ; Drug Resistance, Fungal/genetics
Chemical Substances	Antifungal Agents ; Fluconazole (8VZV102JFY) ; Amphotericin B (7XU7A7DROE) ; Anti-Bacterial Agents ; Anidulafungin (9HLM53094I) ; Echinocandins ; Azoles ; Polyenes
Language	English
Publishing date	2024-02-02
Publishing country	England
Document type	Journal Article
ZDB-ID	1421796-x
ISSN	1460-2709 ; 1369-3786
ISSN (online)	1460-2709
ISSN	1369-3786
DOI	10.1093/mmy/myae009
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Article ; Online: A Genomic Snapshot of Antibiotic-Resistant

Shobo, Christiana O / Amoako, Daniel G / Allam, Mushal / Ismail, Arshad / Essack, Sabiha Y / Bester, Linda A

Global health, epidemiology and genomics

2023 Volume 2023, Page(s) 6639983

Abstract: Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship ... ...

Abstract	Enterococci are among the most common opportunistic hospital pathogens. This study used whole-genome sequencing (WGS) and bioinformatics to determine the antibiotic resistome, mobile genetic elements, clone and phylogenetic relationship of
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; South Africa/epidemiology ; Phylogeny ; Microbial Sensitivity Tests ; Genomics ; Hospitals, Public
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-06-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2054-4200
ISSN (online)	2054-4200
DOI	10.1155/2023/6639983
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Article ; Online: Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents.

Conco-Biyela, Thobela / Malla, Muneer Ahmad / Olatunji Awolusi, Oluyemi / Allam, Mushal / Ismail, Arshad / Stenström, Thor A / Bux, Faizal / Kumari, Sheena

International journal of hygiene and environmental health

2024 Volume 258, Page(s) 114345

Abstract: Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with ... ...

Abstract	Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with previous studies relying mostly on conventional approaches. In this study we comprehensively analyzed the microbiome, antibiotic resistome and virulence factors (VFs) within FLA isolated from final treated effluents of two wastewater treatment plants (WWTPs) using shotgun metagenomics. Acanthamoeba has been identified as the most common FLA, followed by Entamoeba. The bacterial diversity showed no significant difference (p > 0.05) in FLA microbiomes obtained from the two WWTPs. At phylum level, the most dominant taxa were Proteobacteria, followed by Firmicutes and Actinobacteria. The most abundant genera identified were Enterobacter followed by Citrobacter, Paenibacillus, and Cupriavidus. The latter three genera are reported here for the first time in Acanthamoeba. In total, we identified 43 types of ARG conferring resistance to cephalosporins, phenicol, streptomycin, trimethoprim, quinolones, cephalosporins, tigecycline, rifamycin, and kanamycin. Similarly, a variety of VFs in FLA metagenomes were detected which included flagellar proteins, Type IV pili twitching motility proteins (pilH and rpoN), alginate biosynthesis genes AlgI, AlgG, AlgD and AlgW and Type VI secretion system proteins and general secretion pathway proteins (tssM, tssA, tssL, tssK, tssJ, fha, tssG, tssF, tssC and tssB, gspC, gspE, gspD, gspF, gspG, gspH, gspI, gspJ, gspK, and gspM). To the best of our knowledge, this is the first study of its kind to examine both the microbiomes and resistome in FLA, as well as their potential pathogenicity in treated effluents. Additionally, this study showed that FLA can host a variety of potentially pathogenic bacteria including Paenibacillus, and Cupriavidus that had not previously been reported, indicating that their relationship may play a role in the spread and persistence of antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) as well as the evolution of novel pathogens.
MeSH term(s)	Wastewater ; Anti-Bacterial Agents/pharmacology ; Amoeba/microbiology ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Microbiota/genetics ; Bacteria ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Cephalosporins
Chemical Substances	Wastewater ; Anti-Bacterial Agents ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Cephalosporins
Language	English
Publishing date	2024-03-11
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2009176-X
ISSN	1618-131X ; 1438-4639
ISSN (online)	1618-131X
ISSN	1438-4639
DOI	10.1016/j.ijheh.2024.114345
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Article ; Online: Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing.

Khethiwe Mtshali / Zamantungwa Thobeka Happiness Khumalo / Stanford Kwenda / Ismail Arshad / Oriel Matlahane Molifi Thekisoe

PLoS ONE, Vol 17, Iss 8, p e

2022 Volume 0273799

Abstract: Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial ... ...

Abstract	Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, ...
Keywords	Medicine ; R ; Science ; Q
Subject code	630
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Genome Analysis of ESBL-Producing Escherichia coli Isolated from Pigs

Founou, Luria Leslie / Founou, Raspail Carrel / Allam, Mushal / Ismail, Arshad / Essack, Sabiha Yusuf

Pathogens. 2022 July 07, v. 11, no. 7

2022

Abstract: The resistome, virulome and mobilome of extended spectrum ß-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec) isolated from pigs in Cameroon and South Africa were assessed using whole genome sequencing (WGS). Eleven clonally related phenotypic ESBL- ... ...

Abstract	The resistome, virulome and mobilome of extended spectrum ß-lactamase (ESBL)-producing Escherichia coli (ESBL-Ec) isolated from pigs in Cameroon and South Africa were assessed using whole genome sequencing (WGS). Eleven clonally related phenotypic ESBL-Ec isolates were subjected to WGS. The prediction of antibiotic resistance genes, virulence factors (VFs) and plasmids was performed using ResFinder, VirulenceFinder and PlasmidFinder, respectively. Diverse sequence types (STs) were detected with ST2144 and ST88 being predominant and blaCTX₋M₋₁₅ (55%) being the principal ESBL gene. All except two isolates harboured various aminoglycoside resistance genes, including aph(3″)-Ib (6/11, 55%) and aph(6)-1d (6/11, 55%), while the qnrS1 gene was identified in four of the isolates. The ESBL-Ec isolates showed a 93.6% score of being human pathogens. The fim, ehaB, ibeB/C were the leading virulence factors detected. All isolates harboured at least three extraintestinal pathogenic E. coli (ExPEC) VFs, with one isolate harbouring up to 18 ExPEC VFs. Five isolates (45.45%) harboured the plasmid incompatibility group IncF (FII, FIB, FIC, FIA). The study revealed that there is an urgent need to implement effective strategies to contain the dissemination of resistant and virulent ESBL-Ec through the food chain in Cameroon and South Africa.
Keywords	aminoglycosides ; antibiotic resistance ; antibiotic resistance genes ; beta-lactamase bacteria ; extraintestinal pathogenic Escherichia coli ; food chain ; humans ; phenotype ; plasmids ; prediction ; sequence analysis ; virulence ; Cameroon ; South Africa
Language	English
Dates of publication	2022-0707
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11070776
Database	NAL-Catalogue (AGRICOLA)

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Article: Epidemiological and Genomic Characterisation of Middelburg and Sindbis Alphaviruses Identified in Horses with Febrile and Neurological Infections, South Africa (2014–2018)

Fourie, Isabel / Snyman, Jumari / Williams, June / Ismail, Arshad / Jansen van Vuren, Petrus / Venter, Marietjie

Viruses. 2022 Sept. 11, v. 14, no. 9

2022

Abstract: Although Old World alphaviruses, Middelburg- (MIDV) and Sindbis virus (SINV), have previously been detected in horses and wildlife with neurologic disease in South Africa, the pathogenesis and clinical presentation of MIDV and SINV infections in animals ... ...

Abstract	Although Old World alphaviruses, Middelburg- (MIDV) and Sindbis virus (SINV), have previously been detected in horses and wildlife with neurologic disease in South Africa, the pathogenesis and clinical presentation of MIDV and SINV infections in animals are not well documented. Clinical samples from horses across South Africa with acute or fatal neurologic and febrile infections submitted between 2014–2018 were investigated. In total, 69/1084 (6.36%) and 11/1084 (1.01%) horses tested positive for MIDV and SINV, respectively, by real-time reverse transcription (RT) PCR. Main signs/outcomes for MIDV (n = 69): 73.91% neurological, 75.36% fever, 28.99% icterus and anorexia, respectively, 8.70% fatalities; SINV (n = 11): 54.54% neurological, 72.73% fever, 36.36% anorexia and 18.18% fatalities. MIDV cases peaked in the late summer/autumn across most South African provinces while SINV cases did not show a clear seasonality and were detected in fewer South African provinces. MIDV could still be detected in blood samples via RT-PCR for up to 71,417 and 21 days after onset of signs in 4 horses respectively, suggesting prolonged replication relative to SINV which could only be detected in the initial sample. Phylogenetic analyses based on partial sequences of the nsP4 (MIDV n = 59 and SINV n = 7) and E1 (MIDV n = 45) genes, as well as full genome sequences (MIDV n = 6), clustered the MIDV and SINV strains from the present study with previously detected strains. MIDV infection appears to be more prevalent in horses than SINV infection based on RT-PCR results, however, prevalence estimates might be different when also considering serological surveillance data.
Keywords	Sindbis virus ; anorexia ; autumn ; blood ; fever ; genome ; genomics ; monitoring ; pathogenesis ; phylogeny ; reverse transcription ; summer ; wildlife ; South Africa
Language	English
Dates of publication	2022-0911
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14092013
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Epidemiological and Genomic Characterisation of Middelburg and Sindbis Alphaviruses Identified in Horses with Febrile and Neurological Infections, South Africa (2014-2018).

Fourie, Isabel / Snyman, Jumari / Williams, June / Ismail, Arshad / Jansen van Vuren, Petrus / Venter, Marietjie

Viruses

2022 Volume 14, Issue 9

Abstract	Although Old World alphaviruses, Middelburg- (MIDV) and Sindbis virus (SINV), have previously been detected in horses and wildlife with neurologic disease in South Africa, the pathogenesis and clinical presentation of MIDV and SINV infections in animals are not well documented. Clinical samples from horses across South Africa with acute or fatal neurologic and febrile infections submitted between 2014-2018 were investigated. In total, 69/1084 (6.36%) and 11/1084 (1.01%) horses tested positive for MIDV and SINV, respectively, by real-time reverse transcription (RT) PCR. Main signs/outcomes for MIDV (
MeSH term(s)	Alphavirus Infections/diagnosis ; Alphavirus Infections/epidemiology ; Alphavirus Infections/veterinary ; Animals ; Anorexia ; Genomics ; Horses ; Phylogeny ; Sindbis Virus/genetics ; South Africa/epidemiology
Language	English
Publishing date	2022-09-11
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14092013
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Article: Genome Analysis of ESBL-Producing

Founou, Luria Leslie / Founou, Raspail Carrel / Allam, Mushal / Ismail, Arshad / Essack, Sabiha Yusuf

Pathogens (Basel, Switzerland)

2022 Volume 11, Issue 7

Abstract: The resistome, virulome and mobilome of extended spectrum ß-lactamase (ESBL)- ... ...

Abstract	The resistome, virulome and mobilome of extended spectrum ß-lactamase (ESBL)-producing
Language	English
Publishing date	2022-07-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11070776
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