1
|
Ali MZ, Srinivasan S, Akter S. CTX-M-127 with I176F mutations found in bacteria isolates from Bangladeshi circulating banknotes. Sci Rep 2024; 14:5866. [PMID: 38467683 PMCID: PMC10928162 DOI: 10.1038/s41598-024-56207-x] [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: 10/16/2023] [Accepted: 03/04/2024] [Indexed: 03/13/2024] Open
Abstract
Extended-spectrum beta-lactamase (ESBL)-producing organisms are widely recognized as clinically relevant causes of difficult-to-treat infections. CTX-M has formed a rapidly growing family distributed worldwide among a wide range of clinical bacteria, particularly members of Enterobacteriaceae. Circulating banknotes, exchanged daily among people, pose a potential vehicle for transmitting multidrug resistance. We screened for ESBL-carrying bacteria in the present study and reported CTX-M mutations in Bangladesh's banknotes. We sequenced the genes and performed homology modeling using the Swiss model with CTX-M-15 (4HBT) as a template. Then, we performed molecular docking of mecillinam with the template and the generated model using Autodock 4.2 (Release 4.2.6). After docking, we visually inspected the complexes built using Autodock tools for polar contacts and pi-pi interactions in PyMOL 2.5.4. Our partially sequenced blaCTX-M was related to blaCTX-M-10 and blaCTX-M-15. We observed multiple single-nucleotide substitution mutations, i.e., G613T (silent mutation), A626T (I176F), and A503G (N135D). Homology modeling showed high similarity when the model was superimposed over the template. The orientation of Asn (135) in the template and Asp (135) in the model does not show a significant difference. Likewise, Ile (176) in the template and Phe (176) in the model offer the same orientation. Our generated model could bind to Lys237, Ser240, and Asp135 residues with the lowest binding energy on docking. Our predicted binding of the mecillinam to the mutated D-135 residue in the model indicates contributions and supports previous reports proposing CTX-M-15 to CTX-M-127 mutational conversion on the mecillinum resistance phenotype.
Collapse
Affiliation(s)
- Md Zannat Ali
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Selina Akter
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.
| |
Collapse
|
2
|
Meister TL, Kirchhoff L, Brüggemann Y, Todt D, Steinmann J, Steinmann E. Stability of pathogens on banknotes and coins: A narrative review. J Med Virol 2023; 95:e29312. [PMID: 38100621 DOI: 10.1002/jmv.29312] [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: 06/06/2023] [Revised: 08/28/2023] [Accepted: 11/25/2023] [Indexed: 12/17/2023]
Abstract
For the prevention of infectious diseases, knowledge about potential transmission routes is essential. Pathogens can be transmitted directly (i.e. respiratory droplets, hand-to-hand contact) or indirectly via contaminated surfaces (fomites). In particular, frequently touched objects/surfaces may serve as transmission vehicles for different clinically relevant bacterial, fungal, and viral pathogens. Banknotes and coins offer ample surface area and are frequently exchanged between individuals. Consequently, many concerns have been raised in the recent past, that banknotes and coins could serve as vectors for the transmission of disease-causing microorganisms. This review summarizes the latest research on the potential of paper currency and coins to serve as sources of pathogenic viral, bacterial, and fungal agents. In contrast to the current perception of banknotes and coins as important transmission vehicles, current evidence suggests, that banknotes and coins do not pose a particular risk of pathogen infection for the public.
Collapse
Affiliation(s)
- Toni Luise Meister
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Lisa Kirchhoff
- Institute of Medical Microbiology, University Hospital of Essen, Essen, Germany
| | - Yannick Brüggemann
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| | - Daniel Todt
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
- European Virus Bioinformatics Center (EVBC), Jena, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University Hospital of Essen, Essen, Germany
- Institute of Clinical Hygiene, Medical Microbiology and Infectiology, General Hospital Nürnberg, Paracelsus Medical University, Nuremberg, Germany
| | - Eike Steinmann
- Department for Molecular and Medical Virology, Ruhr University Bochum, Bochum, Germany
| |
Collapse
|
3
|
Kim HJ, Kim KE, Kim YJ, Kang H, Shin JW, Kim S, Lee SH, Jung SW, Lee TK. Marine Bacterioplankton Community Dynamics and Potentially Pathogenic Bacteria in Seawater around Jeju Island, South Korea, via Metabarcoding. Int J Mol Sci 2023; 24:13561. [PMID: 37686367 PMCID: PMC10487856 DOI: 10.3390/ijms241713561] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
Understanding marine bacterioplankton composition and distribution is necessary for improving predictions of ecosystem responses to environmental change. Here, we used 16S rRNA metabarcoding to investigate marine bacterioplankton diversity and identify potential pathogenic bacteria in seawater samples collected in March, May, September, and December 2013 from two sites near Jeju Island, South Korea. We identified 1343 operational taxonomic units (OTUs) and observed that community diversity varied between months. Alpha- and Gamma-proteobacteria were the most abundant classes, and in all months, the predominant genera were Candidatus Pelagibacter, Leisingera, and Citromicrobium. The highest number of OTUs was observed in September, and Vibrio (7.80%), Pseudoalteromonas (6.53%), and Citromicrobium (6.16%) showed higher relative abundances or were detected only in this month. Water temperature and salinity significantly affected bacterial distribution, and these conditions, characteristic of September, were adverse for Aestuariibacter but favored Citromicrobium. Potentially pathogenic bacteria, among which Vibrio (28 OTUs) and Pseudoalteromonas (six OTUs) were the most abundant in September, were detected in 49 OTUs, and their abundances were significantly correlated with water temperature, increasing rapidly in September, the warmest month. These findings suggest that monthly temperature and salinity variations affect marine bacterioplankton diversity and potential pathogen abundance.
Collapse
Affiliation(s)
- Hyun-Jung Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan 46241, Republic of Korea;
| | - Kang Eun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Yu Jin Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Hangoo Kang
- Vessel Operation & Observation Team, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea;
| | - Ji Woo Shin
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
| | - Soohyun Kim
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
| | - Sang Heon Lee
- Department of Oceanography and Marine Research Institute, Pusan National University, Busan 46241, Republic of Korea;
| | - Seung Won Jung
- Library of Marine Samples, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea; (H.-J.K.); (K.E.K.); (Y.J.K.); (J.W.S.); (S.K.)
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Taek-Kyun Lee
- Department of Ocean Science, University of Science & Technology, Daejeon 34113, Republic of Korea
- Ecological Risk Research Department, Korea Institute of Ocean Science & Technology, Geoje 53201, Republic of Korea
| |
Collapse
|
4
|
Park AM, Khadka S, Sato F, Omura S, Fujita M, Hashiwaki K, Tsunoda I. Bacterial and fungal isolation from face masks under the COVID-19 pandemic. Sci Rep 2022; 12:11361. [PMID: 35851044 PMCID: PMC9293923 DOI: 10.1038/s41598-022-15409-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/23/2022] [Indexed: 02/08/2023] Open
Abstract
The COVID-19 pandemic has led people to wear face masks daily in public. Although the effectiveness of face masks against viral transmission has been extensively studied, there have been few reports on potential hygiene issues due to bacteria and fungi attached to the face masks. We aimed to (1) quantify and identify the bacteria and fungi attaching to the masks, and (2) investigate whether the mask-attached microbes could be associated with the types and usage of the masks and individual lifestyles. We surveyed 109 volunteers on their mask usage and lifestyles, and cultured bacteria and fungi from either the face-side or outer-side of their masks. The bacterial colony numbers were greater on the face-side than the outer-side; the fungal colony numbers were fewer on the face-side than the outer-side. A longer mask usage significantly increased the fungal colony numbers but not the bacterial colony numbers. Although most identified microbes were non-pathogenic in humans; Staphylococcus epidermidis, Staphylococcus aureus, and Cladosporium, we found several pathogenic microbes; Bacillus cereus, Staphylococcus saprophyticus, Aspergillus, and Microsporum. We also found no associations of mask-attached microbes with the transportation methods or gargling. We propose that immunocompromised people should avoid repeated use of masks to prevent microbial infection.
Collapse
Affiliation(s)
- Ah-Mee Park
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
| | - Sundar Khadka
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Fumitaka Sato
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Seiichi Omura
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Mitsugu Fujita
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Kazuki Hashiwaki
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Ikuo Tsunoda
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| |
Collapse
|
5
|
Bischofberger AM, Hall AR. Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment. Mol Ecol 2022; 32:2619-2632. [PMID: 35377495 DOI: 10.1111/mec.16456] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/24/2022] [Accepted: 03/28/2022] [Indexed: 11/30/2022]
Abstract
Humans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear. Here, we used a combination of sampling, sequencing (16S rRNA) and culturing to show that the composition of banknote-associated bacterial communities varies depending on the local collection environment. Using banknotes collected from various locations and types of shops across Switzerland, we found taxonomic diversity dominated by families such as Pseudomonadaceae and Staphylococcaceae, but with banknote samples from particular types of shops (especially butcher shops) having distinct community structure. By contrast, we found no evidence of geographic structure: similarity of community composition did not decrease with increasing distance among sampled locations. These results show that microbial communities associated with banknotes, one of the most commonly encountered and exchanged human-associated surfaces, can reflect the local environmental conditions (in this case, the type of shop), and the signal for this type of variation was stronger than that for geographic structure among the locations sampled here.
Collapse
Affiliation(s)
| | - Alex R Hall
- Institute of Integrative Biology, ETH Zurich, Switzerland
| |
Collapse
|
6
|
Akter S, Roy PC, Ferdaus A, Ibnat H, Alam ASMRU, Nigar S, Jahid IK, Hossain MA. Prevalence and stability of SARS-CoV-2 RNA on Bangladeshi banknotes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 779:146133. [PMID: 33740558 PMCID: PMC9752560 DOI: 10.1016/j.scitotenv.2021.146133] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 05/06/2023]
Abstract
Originating in December 2019 in China, SARS-CoV-2 has emerged as the deadliest pandemic in humankind's history. Along with direct contact and droplet contaminations, the possibility of infections through contaminated surfaces and fomites is investigating. This study aims to assess SARS-CoV-2 viral RNA's prevalence by real-time one-step reverse transcriptase PCR on banknotes circulating in Bangladesh. We also evaluated the persistence of the virus on banknotes spiked with SARS-CoV-2 positive diluted human nasopharyngeal samples. Among the 425 banknote samples collected from different entities, 7.29% (n = 31) were tested positive for targeted genes. Twenty-four positive representative samples were assessed for n gene fragments by conventional PCR and sequenced. All the samples that carry viral RNA belonged to the GR clade, the predominantly circulating clade in Bangladesh. In the stability test, the n gene was detected for up to 72 h on banknotes spiked with nasopharyngeal samples, and CT values increase significantly with time (p < 0.05). orf1b gene was observed to be less stable, especially on old banknotes, and usually went beyond detectable limit within 8 to 10 h. The stability of virus RNA well fitted by the Weibull model and concave curve for new banknotes and convex curve for old banknotes revealed. Handling banknotes is unavoidable; hence, these findings imply that proper hygiene practice is needed to limit SARS-CoV-2 transmission through banknotes.
Collapse
Affiliation(s)
- Selina Akter
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.
| | - Pravas Chandra Roy
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.
| | - Amina Ferdaus
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Habiba Ibnat
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.
| | - Shireen Nigar
- Department of Nutrition and Food Technology, Jashore University of Science and Technology, Jashore, Bangladesh.
| | - Iqbal Kabir Jahid
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.
| | - M Anwar Hossain
- Jashore University of Science and Technology, Jashore, Bangladesh; Department of Microbiology, University of Dhaka, Dhaka, Bangladesh.
| |
Collapse
|
7
|
Lin J, Jiang W, Chen L, Zhang H, Shi Y, Liu X, Cai W. Metagenomic sequencing revealed the potential of banknotes as a repository of microbial genes. BMC Genomics 2021; 22:173. [PMID: 33706718 PMCID: PMC7953773 DOI: 10.1186/s12864-021-07424-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/04/2021] [Indexed: 11/10/2022] Open
Abstract
Background Genetic resources are important natural assets. Discovery of new enzyme gene sequences has been an ongoing effort in biotechnology industry. In the genomic age, genomes of microorganisms from various environments have been deciphered. Increasingly, it has become more and more difficult to find novel enzyme genes. In this work, we attempted to use the easily accessible banknotes to search for novel microbial gene sequences. Results We used high-throughput genomic sequencing technology to comprehensively characterize the diversity of microorganisms on the US dollars and Chinese Renminbis (RMBs). In addition to finding a vast diversity of microbes, we found a significant number of novel gene sequences, including an unreported superoxide dismutase (SOD) gene, whose catalytic activity was further verified by experiments. Conclusions We demonstrated that banknotes could be a good and convenient genetic resource for finding economically valuable biologicals. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07424-5.
Collapse
Affiliation(s)
- Jun Lin
- Institute of Applied Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China.,School of Basic Medical Sciences, Fujian Medical University, No.1 Xuefubei Road, Fuzhou, 350122, China.,College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China.,Fujian Key Laboratory of Marine Enzyme Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China
| | - Wenqian Jiang
- Institute of Applied Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China.,College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China
| | - Lin Chen
- Institute of Applied Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China.,College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China
| | - Huilian Zhang
- Institute of Applied Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China.,College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China
| | - Yang Shi
- Institute of Applied Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China.,College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China
| | - Xin Liu
- Institute of Applied Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China.,College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China
| | - Weiwen Cai
- Institute of Applied Genomics, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China. .,College of Biological Science and Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou, 350108, China.
| |
Collapse
|
8
|
Lin J, Jiang W, Shi Y, Cai W. Metagenomic Sequencing Revealed the Potential Pathogenic Threats of Banknotes. ACS OMEGA 2021; 6:3499-3507. [PMID: 33585735 PMCID: PMC7876676 DOI: 10.1021/acsomega.0c04546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Banknotes have long been suspected to be biologically "dirty" due to their frequent human contact, which may transmit human microbial pathogens. Still, it is an unsettled issue whether the microbes on banknotes pose a real threat to human health. In several previous studies, metagenomic sequencing was used to reveal the diversities of microbes on banknotes but live microorganism culture and functional verification were lacking. In this study, we collected banknotes of RMB in China as well as dollar bills in the United States and analyzed the microbial biodiversity and drug resistance genes carried by the identified microbes by metagenomic sequencing and in vitro culture methods. We identified eight major genera of drug-resistant bacteria through screening of 30 antibiotics, and the blood agar plate culture uncovered six pathogenic fungal species. Numerous phage and six dangerous viral sequences were also found. These results should substantiate our concern about the potential risk of banknotes to human health.
Collapse
Affiliation(s)
- Jun Lin
- Institute
of Applied Genomics, Fuzhou University, Fuzhou 350108, China
- School
of Basic Medical Sciences, Fujian Medical
University, Fuzhou 350108, China
- College
of Biological Science and Engineering, Fuzhou
University, Fuzhou 350108, China
- Fujian
Key Laboratory of Marine Enzyme Engineering, Fuzhou University, No.2 Xueyuan Road, Fuzhou 350108, China
| | - Wenqian Jiang
- Institute
of Applied Genomics, Fuzhou University, Fuzhou 350108, China
- College
of Biological Science and Engineering, Fuzhou
University, Fuzhou 350108, China
| | - Yang Shi
- Institute
of Applied Genomics, Fuzhou University, Fuzhou 350108, China
- College
of Biological Science and Engineering, Fuzhou
University, Fuzhou 350108, China
| | - Weiwen Cai
- Institute
of Applied Genomics, Fuzhou University, Fuzhou 350108, China
- College
of Biological Science and Engineering, Fuzhou
University, Fuzhou 350108, China
| |
Collapse
|
9
|
Manenzhe RI, Dube FS, Wright M, Lennard K, Zar HJ, Mounaud S, Nierman WC, Nicol MP, Moodley C. Longitudinal changes in the nasopharyngeal resistome of South African infants using shotgun metagenomic sequencing. PLoS One 2020; 15:e0231887. [PMID: 32320455 PMCID: PMC7176138 DOI: 10.1371/journal.pone.0231887] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 04/02/2020] [Indexed: 11/18/2022] Open
Abstract
Introduction Nasopharyngeal (NP) colonization with antimicrobial-resistant bacteria is a global public health concern. Antimicrobial-resistance (AMR) genes carried by the resident NP microbiota may serve as a reservoir for transfer of resistance elements to opportunistic pathogens. Little is known about the NP antibiotic resistome. This study longitudinally investigated the composition of the NP antibiotic resistome in Streptococcus-enriched samples in a South African birth cohort. Methods As a proof of concept study, 196 longitudinal NP samples were retrieved from a subset of 23 infants enrolled as part of broader birth cohort study. These were selected on the basis of changes in serotype and antibiogram over time. NP samples underwent short-term enrichment for streptococci prior to total nucleic acid extraction and whole metagenome shotgun sequencing (WMGS). Reads were assembled and aligned to pneumococcal reference genomes for the extraction of streptococcal and non-streptococcal bacterial reads. Contigs were aligned to the Antibiotic Resistance Gene-ANNOTation database of acquired AMR genes. Results AMR genes were detected in 64% (125/196) of the samples. A total of 329 AMR genes were detected, including 36 non-redundant genes, ranging from 1 to 14 genes per sample. The predominant AMR genes detected encoded resistance mechanisms to beta-lactam (52%, 172/329), macrolide-lincosamide-streptogramin (17%, 56/329), and tetracycline antibiotics (12%, 38/329). MsrD, ermB, and mefA genes were only detected from streptococcal reads. The predominant genes detected from non- streptococcal reads included blaOXA-60, blaOXA-22, and blaBRO-1. Different patterns of carriage of AMR genes were observed, with only one infant having a stable carriage of mefA, msrD and tetM over a long period. Conclusion This study demonstrates that WMGS can provide a broad snapshot of the NP resistome and has the potential to provide a comprehensive assessment of resistance elements present in this niche.
Collapse
Affiliation(s)
- Rendani I. Manenzhe
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | - Felix S. Dube
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Meredith Wright
- J. Craig Venter Institute, Rockville, MD, United States of America
| | - Katie Lennard
- Division of Computational Biology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J. Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children’s Hospital and MRC unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | | | | | - Mark P. Nicol
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- Division of Infection and Immunity, University of Western Australia, Perth, Australia
| | - Clinton Moodley
- Division of Medical Microbiology, Faculty of Health Science, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| |
Collapse
|
10
|
Al-hajj EM, Mohamed MS, Abd Alfadil NA, Altayb HN, Idris AB, El-zaki S, Hassan MA. Contamination of Currency Notes with Kanamycin Resistant Shigella flexneri.. [DOI: 10.1101/2020.03.07.982017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
AbstractShigella flexneriis the main causative agent of shigellosis commonly distributed in developing countries with high morbidity and mortality rates. This study aimed to examine the presence ofShigellaspecies in Sudanese currency notes using both traditional and molecular techniques. One hundred thirty five currency notes were collected and their contaminants were isolated and identified conventionally and genetically using 16S rRNA gene amplification and sequencing. Eight isolates were identified asShigellaspecies in different notes, and 3 of them were resistant to penicillin, kanamycin and nitrofurantoin. OneS. flexneriisolate has insertion mutation of guanine nucleotide at position 730 of life’s essential gene 16S rRNA which known evolutionarily to be stable gene. Banknotes are highly circulating items and therefore, appropriate measures such as regular replacement of the dirty notes with new papers are necessary to protect peoples from being infected with drug resistant pathogens.
Collapse
|
11
|
Eckstrom K, Barlow JW. Resistome metagenomics from plate to farm: The resistome and microbial composition during food waste feeding and composting on a Vermont poultry farm. PLoS One 2019; 14:e0219807. [PMID: 31751342 PMCID: PMC6874062 DOI: 10.1371/journal.pone.0219807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/27/2019] [Indexed: 12/27/2022] Open
Abstract
Food waste diversion and composting, either mandated or voluntary, are growing alternatives to traditional waste disposal. An acceptable source of agricultural feed and composting material, methane-emitting food residuals, including post-consumer food scraps, are diverted from landfills allowing recapture of nutrients that would otherwise be lost. However, risk associated with the transfer of antimicrobial resistant bacteria (ARB), antibiotic resistance genes (ARGs), or pathogens from food waste is not well characterized. Using shotgun metagenomic sequencing, ARGs, microbial content, and associated virulence factors were successfully identified across samples from an integrated poultry farm that feeds post-consumer food waste. A total of 495 distinct bacterial species or sub-species, 50 ARGs, and 54 virulence gene sequences were found. ARG sequences related to aminoglycoside, tetracycline, and macrolide resistance were most prominent, while most virulence gene sequences were related to transposon or integron activity. Microbiome content was distinct between on-farm samples and off-farm food waste collection sites, with a reduction in pathogens throughout the composting process. While most samples contained some level of resistance, only 3 resistance gene sequences occurred in both on- and off-farm samples and no multidrug resistance (MDR) gene sequences persisted once on the farm. The risk of incorporating novel or multi-drug resistance from human sources appears to be minimal and the practice of utilizing post-consumer food scraps as feed for poultry and composting material may not present a significant risk for human or animal health. Pearson correlation and co-inertia analysis identified a significant interaction between resistance and virulence genes (P = 0.05, RV = 0.67), indicating that ability to undergo gene transfer may be a better marker for ARG risk than presence of specific bacterial species. This work expands the knowledge of ARG fate during food scrap animal feeding and composting and provides a methodology for reproducible analysis.
Collapse
Affiliation(s)
- Korin Eckstrom
- Department of Microbiology and Molecular Genetics, The University of Vermont, Burlington, Vermont, United States of America
| | - John W. Barlow
- Department of Animal and Veterinary Sciences, The University of Vermont, Burlington, Vermont, United States of America
| |
Collapse
|
12
|
Rowe WPM, Winn MD. Indexed variation graphs for efficient and accurate resistome profiling. Bioinformatics 2018; 34:3601-3608. [PMID: 29762644 PMCID: PMC6198860 DOI: 10.1093/bioinformatics/bty387] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 01/05/2023] Open
Abstract
Motivation Antimicrobial resistance (AMR) remains a major threat to global health. Profiling the collective AMR genes within a metagenome (the 'resistome') facilitates greater understanding of AMR gene diversity and dynamics. In turn, this can allow for gene surveillance, individualized treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools. Results Our method combines a variation graph representation of gene sets with a locality-sensitive hashing Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, graphing Resistance Out Of meTagenomes (GROOT), and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 min using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows. Availability and implementation GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license). Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Will P M Rowe
- Institute of Integrative Biology, The University of Liverpool, Liverpool, UK
- Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK
| | - Martyn D Winn
- Scientific Computing Department, The Hartree Centre, STFC Daresbury Laboratory, Warrington, UK
| |
Collapse
|
13
|
Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach. Genes (Basel) 2018; 9:genes9040214. [PMID: 29659545 PMCID: PMC5924556 DOI: 10.3390/genes9040214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 03/19/2018] [Accepted: 04/13/2018] [Indexed: 01/08/2023] Open
Abstract
The worldwide commercial cultivation of transgenic crops, including glyphosate-tolerant (GT) soybeans, has increased widely during the past 20 years. However, it is accompanied with a growing concern about potential effects of transgenic crops on the soil microbial communities, especially on rhizosphere bacterial communities. Our previous study found that the GT soybean line NZL06-698 (N698) significantly affected rhizosphere bacteria, including some unidentified taxa, through 16S rRNA gene (16S rDNA) V4 region amplicon deep sequencing via Illumina MiSeq. In this study, we performed 16S rDNA V5–V7 region amplicon deep sequencing via Illumina MiSeq and shotgun metagenomic approaches to identify those major taxa. Results of these processes revealed that the species richness and evenness increased in the rhizosphere bacterial communities of N698, the beta diversity of the rhizosphere bacterial communities of N698 was affected, and that certain dominant bacterial phyla and genera were related to N698 compared with its control cultivar Mengdou12. Consistent with our previous findings, this study showed that N698 affects the rhizosphere bacterial communities. In specific, N698 negatively affects Rahnella, Janthinobacterium, Stenotrophomonas, Sphingomonas and Luteibacter while positively affecting Arthrobacter, Bradyrhizobium, Ramlibacter and Nitrospira.
Collapse
|
14
|
Heshiki Y, Dissanayake T, Zheng T, Kang K, Yueqiong N, Xu Z, Sarkar C, Woo PCY, Chow BKC, Baker D, Yan A, Webster CJ, Panagiotou G, Li J. Toward a Metagenomic Understanding on the Bacterial Composition and Resistome in Hong Kong Banknotes. Front Microbiol 2017; 8:632. [PMID: 28450856 PMCID: PMC5389987 DOI: 10.3389/fmicb.2017.00632] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 03/28/2017] [Indexed: 11/23/2022] Open
Abstract
Currency is possibly one of the main media transmitting pathogens and drug resistance due to its wide circulation in daily life. In this study, we made a comprehensive characterization of the bacterial community present on banknotes collected from different geographical regions of Hong Kong (HK) by performing in vitro characterization of the bacterial presence and resistome profile, as well as metagenomic analysis including microbial diversity, the prevalence of potential pathogens, the dissemination potential of antibiotic-resistance genes (ARGs), among others. When comparing the bacterial community of HK banknotes with other HK environmental samples, including water and marine sediment, we revealed that HK banknotes cover nearly 50% of total genera found in all the environmental samples, implying that banknotes harbor diverse bacteria originated from a variety of environments. Furthermore, the banknotes have higher abundance of potential pathogenic species (~5 times more) and ARGs (~5 times more) with higher dissemination potential (~48 times more) compared with other environmental samples. These findings unveiled the capabilities of this common medium of exchange to accommodate various bacteria, and transmit pathogens and antibiotic resistance. Furthermore, the observed independence of microbiome profile from the city's topological indices led us to formulate a hypothesis that due to their high circulation banknotes may harbor a homogenized microbiome.
Collapse
Affiliation(s)
- Yoshitaro Heshiki
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Thrimendra Dissanayake
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Tingting Zheng
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Kang Kang
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Ni Yueqiong
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| | - Zeling Xu
- School of Biological Sciences, Faculty of Science, University of Hong KongHong Kong, China
| | - Chinmoy Sarkar
- Healthy High Density Cities Lab, HKUrbanLab, University of Hong KongHong Kong, China
| | - Patrick C Y Woo
- Department of Microbiology, University of Hong KongHong Kong, Hong Kong.,State Key Laboratory of Emerging Infectious Diseases, University of Hong KongHong Kong, Hong Kong.,Research Centre of Infection and Immunology, University of Hong KongHong Kong, Hong Kong.,The Carol Yu Centre for Infection, University of Hong KongHong Kong.,Guangzhou Center for Disease Control and PreventionGuangzhou, China
| | - Billy K C Chow
- School of Biological Sciences, Faculty of Science, University of Hong KongHong Kong, China
| | - David Baker
- School of Biological Sciences, Faculty of Science, University of Hong KongHong Kong, China
| | - Aixin Yan
- School of Biological Sciences, Faculty of Science, University of Hong KongHong Kong, China
| | - Christopher J Webster
- Healthy High Density Cities Lab, HKUrbanLab, University of Hong KongHong Kong, China
| | - Gianni Panagiotou
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China.,Department of Systems Biology and Bioinformatics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll InstituteJena, Germany
| | - Jun Li
- Systems Biology and Bioinformatics Group, School of Biological Sciences, Faculty of Sciences, University of Hong KongHong Kong, China
| |
Collapse
|
15
|
Lizarazo-Medina PX, Cabarcas Jaramillo F, Alzate JF. Microbiota bacteriana asociada al papel moneda de circulación en Colombia. INFECTIO 2016. [DOI: 10.1016/j.infect.2015.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
|
16
|
King P, Pham LK, Waltz S, Sphar D, Yamamoto RT, Conrad D, Taplitz R, Torriani F, Forsyth RA. Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes. PLoS One 2016; 11:e0160124. [PMID: 27482891 PMCID: PMC4970769 DOI: 10.1371/journal.pone.0160124] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/05/2016] [Indexed: 12/15/2022] Open
Abstract
We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.
Collapse
Affiliation(s)
- Paula King
- FLIR Systems, Inc., La Jolla, California, United States of America
- Singlera Genomics, Inc., La Jolla, California, United States of America
| | - Long K. Pham
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Shannon Waltz
- FLIR Systems, Inc., La Jolla, California, United States of America
| | - Dan Sphar
- FLIR Systems, Inc., La Jolla, California, United States of America
| | | | - Douglas Conrad
- Department of Medicine, Division of Pulmonary Medicine, UC San Diego Health System, San Diego, California, United States of America
| | - Randy Taplitz
- Department of Medicine, Division of Infectious Diseases and Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health System, San Diego, California, United States of America
| | - Francesca Torriani
- Department of Medicine, Division of Infectious Diseases and Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health System, San Diego, California, United States of America
| | - R. Allyn Forsyth
- FLIR Systems, Inc., La Jolla, California, United States of America
- Singlera Genomics, Inc., La Jolla, California, United States of America
- Department of Biology, San Diego State University, San Diego, California, United States of America
- * E-mail:
| |
Collapse
|
17
|
Lim KMK, Li C, Chng KR, Nagarajan N. @MInter: automated text-mining of microbial interactions. Bioinformatics 2016; 32:2981-7. [PMID: 27312413 DOI: 10.1093/bioinformatics/btw357] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 05/31/2016] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Microbial consortia are frequently defined by numerous interactions within the community that are key to understanding their function. While microbial interactions have been extensively studied experimentally, information regarding them is dispersed in the scientific literature. As manual collation is an infeasible option, automated data processing tools are needed to make this information easily accessible. RESULTS We present @MInter, an automated information extraction system based on Support Vector Machines to analyze paper abstracts and infer microbial interactions. @MInter was trained and tested on a manually curated gold standard dataset of 735 species interactions and 3917 annotated abstracts, constructed as part of this study. Cross-validation analysis showed that @MInter was able to detect abstracts pertaining to one or more microbial interactions with high specificity (specificity = 95%, AUC = 0.97). Despite challenges in identifying specific microbial interactions in an abstract (interaction level recall = 95%, precision = 25%), @MInter was shown to reduce annotator workload 13-fold compared to alternate approaches. Applying @MInter to 175 bacterial species abundant on human skin, we identified a network of 357 literature-reported microbial interactions, demonstrating its utility for the study of microbial communities. AVAILABILITY AND IMPLEMENTATION @MInter is freely available at https://github.com/CSB5/atminter CONTACT nagarajann@gis.a-star.edu.sg SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Kun Ming Kenneth Lim
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore Computational Biology Program, Faculty of Science
| | - Chenhao Li
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore Department of Computer Science, National University of Singapore, Singapore, Singapore
| | - Kern Rei Chng
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Niranjan Nagarajan
- Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore Department of Computer Science, National University of Singapore, Singapore, Singapore
| |
Collapse
|