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Conco-Biyela T, Malla MA, Olatunji Awolusi O, Allam M, Ismail A, Stenström TA, Bux F, Kumari S. Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents. Int J Hyg Environ Health 2024; 258:114345. [PMID: 38471337 DOI: 10.1016/j.ijheh.2024.114345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024]
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.
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Affiliation(s)
- Thobela Conco-Biyela
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Muneer Ahmad Malla
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Oluyemi Olatunji Awolusi
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Mushal Allam
- NICD Sequencing Core Facility, National Institute for Communicable Diseases, Sandringham, 2192, Pretoria, South Africa; Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates
| | - Arshad Ismail
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa; NICD Sequencing Core Facility, National Institute for Communicable Diseases, Sandringham, 2192, Pretoria, South Africa
| | - Thor A Stenström
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Faizal Bux
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa
| | - Sheena Kumari
- Institute for Water and Wastewater Technology, Durban University of Technology, Durban, 4001, Kwa-Zulu Natal, South Africa.
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Chen CH, Liao CC, Wang YJ, Huang FC, Lin WC. A. castellanii and P. aeruginosa mutually exacerbate damage to corneal cells during coinfection. Microbiol Spectr 2024; 12:e0268323. [PMID: 38095463 PMCID: PMC10783079 DOI: 10.1128/spectrum.02683-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/31/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE At the National Cheng Kung University Hospital, numerous cases of amoebic keratitis had been identified with concurrent bacterial infections. Among these bacterial coinfections, Pseudomonas aeruginosa accounted for 50% of the reported cases. However, the impact of pathogenic bacteria on amoeba-induced corneal damage remains unclear. In our study, we successfully demonstrated that P. aeruginosa accumulated on the Acanthamoeba castellanii surface and caused more severe corneal damage. We also indicated that the exposure of P. aeruginosa to amoeba-soluble antigens enhanced its adhesion ability, promoted biofilm formation, and led to more severe corneal cell damage. These findings significantly contributed to our understanding of the risk associated with P. aeruginosa coinfection in the progression of amoeba keratitis.
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Affiliation(s)
- Chun-Hsien Chen
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chen-Chieh Liao
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Jen Wang
- Department of Parasitology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Fu-Chin Huang
- Department of Ophthalmology, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Chen Lin
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Sarink MJ, Koelewijn R, Stelma F, Kortbeek T, van Lieshout L, Smit PW, Tielens AGM, van Hellemond JJ. An International External Quality Assessment Scheme to Assess the Diagnostic Performance of Polymerase Chain Reaction Detection of Acanthamoeba Keratitis. Cornea 2023; 42:1027-1033. [PMID: 37155347 PMCID: PMC10306335 DOI: 10.1097/ico.0000000000003275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/04/2023] [Accepted: 02/16/2023] [Indexed: 05/10/2023]
Abstract
PURPOSE The purpose of this study was to assess the variation in methods and to determine whether an External Quality Assessment Scheme (EQAS) for polymerase chain reaction (PCR) detection of Acanthamoeba keratitis is valuable for the diagnostic process. METHODS A multicenter EQAS was introduced, covering 16 diagnostic laboratories. Using Acanthamoeba castellanii ATCC strain 30010, 3 sets of samples were prepared, containing different amounts of DNA, cysts, or trophozoites. Samples were masked and sent to the participants with instructions for use and a questionnaire concerning the applied methodologies. Special attention in this questionnaire was given to the used pretreatment methods to assess existing variations in these procedures. RESULTS A large variation in the methodologies and substantial differences in the diagnostic performance were found between participants. In contrast to the DNA samples where all participants had a perfect score, several false negative results were reported for the samples containing cysts or trophozoites. Only 9 participants had an optimal score, whereas one participant reported all samples as negative, one participant reported failures due to inhibition, and the other 5 reported in total 7 false negative results. A clear correlation was noticed between the PCR detection rate and the number of cysts or trophozoites in the sample. CONCLUSIONS The results indicate that a pretreatment procedure can be a risky step in PCR-based detections of Acanthamoeba , but it improves the sensitivity and reliability, especially of samples containing cysts. Therefore, participation in an EQAS is informative for routine diagnostic laboratories and can assist in improving the laboratory procedures used for the diagnosis of Acanthamoeba keratitis.
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Affiliation(s)
- Maarten J. Sarink
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Rob Koelewijn
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Foekje Stelma
- Department of Medical Microbiology, Radboudumc Nijmegen, the Netherlands
| | - Titia Kortbeek
- National Institute of Public Health and the Environment, RIVM, Bilthoven, the Netherlands
| | - Lisette van Lieshout
- Department of Parasitology, Leiden University Medical Centre, Leiden, the Netherlands; and
| | - Pieter W. Smit
- Department of Medical Microbiology, Molecular Diagnostics Unit, Maasstad Hospital, Rotterdam, the Netherlands
| | - Aloysius G. M. Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jaap J. van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, the Netherlands
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Vermamoeba vermiformis resides in water-based heater-cooler units and can enhance Mycobacterium chimaera survival after chlorine exposure. J Hosp Infect 2023; 132:73-77. [PMID: 36572347 DOI: 10.1016/j.jhin.2022.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Mycobacterium chimaera colonizes water-based heater-cooler units (HCUs), from which it can spread to patients during surgery. Vermamoeba vermiformis is a free-living waterborne amoeba, which was consistently present within HCUs. AIM To determine whether these amoebae can be involved in the persistent presence of M. chimaera. METHODS An in-vitro disinfection model. FINDINGS Increased survival of M. chimaera was observed after chlorine exposure in the presence of V. vermiformis. Confocal microscopy demonstrated the intracellular presence of M. chimaera in V. vermiformis. CONCLUSION In this way, V. vermiformis can contribute to the persistent presence of M. chimaera in HCUs. Cleaning and disinfection protocols should take this phenomenon into account.
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Amaro F, Martín-González A. Microbial warfare in the wild-the impact of protists on the evolution and virulence of bacterial pathogens. Int Microbiol 2021; 24:559-571. [PMID: 34365574 DOI: 10.1007/s10123-021-00192-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/03/2021] [Accepted: 06/28/2021] [Indexed: 01/01/2023]
Abstract
During the long history of co-evolution with protists, bacteria have evolved defense strategies to avoid grazing and survive phagocytosis. These mechanisms allow bacteria to exploit phagocytic cells as a protective niche in which to escape from environmental stress and even replicate. Importantly, these anti-grazing mechanisms can function as virulence factors when bacteria infect humans. Here, we discuss how protozoan predation exerts a selective pressure driving bacterial virulence and shaping their genomes, and how bacteria-protist interactions might contribute to the spread of antibiotic resistance as well. We provide examples to demonstrate that besides being voracious bacterial predators, protozoa can serve as melting pots where intracellular organisms exchange genetic information, or even "training grounds" where some pathogens become hypervirulent after passing through. In this special issue, we would like to emphasize the tremendous impact of bacteria-protist interactions on human health and the potential of amoebae as model systems to study biology and evolution of a variety of pathogens. Besides, a better understanding of bacteria-protist relationships will help us expand our current understanding of bacterial virulence and, likely, how pathogens emerge.
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Affiliation(s)
- Francisco Amaro
- Department of Genetics, Physiology and Microbiology, School of Biology, Complutense University of Madrid, 28040, Madrid, Spain.
| | - Ana Martín-González
- Department of Genetics, Physiology and Microbiology, School of Biology, Complutense University of Madrid, 28040, Madrid, Spain
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