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Geofrey MA, Sauli E, Kanje LE, Beti M, Shayo MJ, Kuchaka D, van Zwetselaar M, Wadugu B, Mmbaga B, Mkumbaye SI, Kumburu H, Sonda T. Genomic characterization of methicillin-resistant Staphylococcus aureus isolated from patients attending regional referral hospitals in Tanzania. BMC Med Genomics 2024; 17:211. [PMID: 39143496 PMCID: PMC11323609 DOI: 10.1186/s12920-024-01979-4] [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: 03/25/2024] [Accepted: 08/01/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Methicillin-resistant Staphylococcus aureus (MRSA) colonization increases the risk of subsequent infection by MRSA strain complex interlinking between hospital and community-acquired MRSA which increases the chance of drug resistance and severity of the disease. OBJECTIVE Genomic characterization of Staphylococcus aures strains isolated from patients attending regional referral hospitals in Tanzania. METHODOLOGY A laboratory-based cross-sectional study using short read-based sequencing technology, (Nextseq550,Illumina, Inc. San diego, California, USA). The samples used were collected from patients attending selected regional referral hospitals in Tanzania under the SeqAfrica project. Sequences were analyzed using tools available in the center for genomic and epidemiology server, and visualization of the phylogenetic tree was performed in ITOL 6.0. SPSS 28.0 was used for statistical analysis. RESULTS Among 103 sequences of S. aureus, 48.5% (50/103) carry the mecA gene for MRSA. High proportions of MRSA were observed among participants aged between 18 and 34 years (52.4%), in females (54.3%), and among outpatients (60.5%). The majority of observed MRSA carried plasmids rep5a (92.0%), rep16 (90.0%), rep7c (90.0%), rep15 (82.0%), rep19 (80.0%) and rep10 (72.0%). Among all plasmids observed rep5a, rep16, rep20, and repUS70 carried the blaZ gene, rep10 carried the erm(C) gene and rep7a carried the tet(K) gene. MLST and phylogeny analysis reveal high diversity among MRSA. Six different clones were observed circulating at selected regional hospitals and MRSA with ST8 was dominant. CONCLUSION The study reveals a significant presence of MRSA in Staphylococcus aureus strains from Tanzanian regional hospitals, with nearly half carrying the mecA gene. MRSA is notably prevalent among young adults, females, and outpatients, showing high genetic diversity and dominance of ST8. Various plasmids carrying resistance genes indicate a complex resistance profile, highlighting the need for targeted interventions to manage MRSA infections in Tanzania.
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Affiliation(s)
- Mujungu A Geofrey
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania.
- Catholic University of Health and Allied Sciences, Mwanza, Tanzania.
| | - Elingarami Sauli
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Livin E Kanje
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Melkiory Beti
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Mariana J Shayo
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Biological and Pre-Clinical Studies, Muhimbili University, Dar es salaam, Tanzania
| | - Davis Kuchaka
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | | | - Boaz Wadugu
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Blandina Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Department of Clinical Laboratory, Kilimanjaro Christian Medical Centre, Kilimanjaro, Tanzania
| | - Sixbert Isdory Mkumbaye
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Department of Clinical Laboratory, Kilimanjaro Christian Medical Centre, Kilimanjaro, Tanzania
| | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Department of Clinical Laboratory, Kilimanjaro Christian Medical Centre, Kilimanjaro, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Department of Clinical Laboratory, Kilimanjaro Christian Medical Centre, Kilimanjaro, Tanzania
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Khan MAS, Chaity SC, Hosen MA, Rahman SR. Genomic epidemiology of multidrug-resistant clinical Acinetobacter baumannii in Bangladesh. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105656. [PMID: 39116952 DOI: 10.1016/j.meegid.2024.105656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 07/04/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
The rising frequency of multidrug-resistant (MDR) Acinetobacter baumannii infections represents a significant public health challenge in Bangladesh. Genomic analysis of bacterial pathogens enhances surveillance and control efforts by providing insights into genetic diversity, antimicrobial resistance (AMR) profiles, and transmission dynamics. In this study, we conducted a comprehensive bioinformatic analysis of 82 whole-genome sequences (WGS) of A. baumannii from Bangladesh to understand their genomic epidemiological characteristics. WGS of the MDR and biofilm-forming A. baumannii strain S1C revealed the presence of 28 AMR genes, predicting its pathogenicity and classification within sequence type ST2. Multi-locus sequence typing (MLST) genotyping suggested heterogeneity in the distribution of clinical A. baumannii strains in Bangladesh, with a predominance of ST575. The resistome diversity was evident from the detection of 82 different AMR genes, with antibiotic inactivation being the most prevalent resistance mechanism. All strains were predicted to be multidrug-resistant. The observed virulence genes were associated with immune evasion, biofilm formation, adherence, nutrient acquisition, effector delivery, and other mechanisms. Mobile genetic elements carrying AMR genes were predicted in 68.29% (N = 56) of the genomes. The "open" state of the pan-genome and a high proportion of accessory genes highlighted the genome plasticity and diversity of A. baumannii in Bangladesh. Additionally, phylogenomic analysis indicated clustering of A. baumannii strains into three separate clades according to sequence type. In summary, our findings offer detailed insights into the genomic landscape of A. baumannii in Bangladesh, contributing to our understanding of its epidemiology and pathogenicity and informing strategies to combat this pathogen.
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Affiliation(s)
| | | | - Md Arman Hosen
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
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Rolbiecki D, Paukszto Ł, Krawczyk K, Korzeniewska E, Sawicki J, Harnisz M. Genomic and metagenomic analysis reveals shared resistance genes and mobile genetic elements in E. coli and Klebsiella spp. isolated from hospital patients and hospital wastewater at intra- and inter-genus level. Int J Hyg Environ Health 2024; 261:114423. [PMID: 39038407 DOI: 10.1016/j.ijheh.2024.114423] [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: 03/06/2024] [Revised: 06/18/2024] [Accepted: 07/11/2024] [Indexed: 07/24/2024]
Abstract
Antimicrobial resistance (AMR) is a global problem that gives serious cause for concern. Hospital wastewater (HWW) is an important link between the clinical setting and the natural environment, and an escape route for pathogens that cause hospital infections, including urinary tract infections (UTI). Bacteria of the genera Escherichia and Klebsiella are common etiological factors of UTI, especially in children, and they can cause short-term infections, as well as chronic conditions. ESBL-producing Escherichia and Klebsiella have also emerged as potential indicators for estimating the burden of antimicrobial resistance under environmental conditions and the spread of AMR between clinical settings and the natural environment. In this study, whole-genome sequencing and the nanopore technology were used to analyze the complete genomes of ESBL-producing E.coli and Klebsiella spp. and the HWW metagenome, and to characterize the mechanisms of AMR. The similarities and differences in the encoded mechanisms of AMR in clinical isolates (causing UTI) and environmental strains (isolated from HWW and the HWW metagenome) were analyzed. Special attention was paid to the genetic context and the mobility of antibiotic resistance genes (ARGs) to determine the common sources and potential transmission of these genes. The results of this study suggest that the spread of drug resistance from healthcare facilities via HWW is not limited to the direct transmission of resistant clonal lines that are typically found in the clinical setting, but it also involves the indirect transfer of mobile elements carrying ARGs between bacteria colonizing various environments. Hospital wastewater could offer a supportive environment for plasmid evolution through the insertion of new ARGs, including typical chromosomal regions. These results indicate that interlined environments (hospital patients - HWW) should be closely monitored to evaluate the potential transmission routes of drug resistance in bacteria.
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Affiliation(s)
- Damian Rolbiecki
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Katarzyna Krawczyk
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Ewa Korzeniewska
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Monika Harnisz
- Department of Water Protection Engineering and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury in Olsztyn, Poland.
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Keresztény T, Libisch B, Orbe SC, Nagy T, Kerényi Z, Kocsis R, Posta K, Papp PP, Olasz F. Isolation and Characterization of Lactic Acid Bacteria With Probiotic Attributes From Different Parts of the Gastrointestinal Tract of Free-living Wild Boars in Hungary. Probiotics Antimicrob Proteins 2024; 16:1221-1239. [PMID: 37353593 PMCID: PMC11322276 DOI: 10.1007/s12602-023-10113-2] [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] [Accepted: 06/15/2023] [Indexed: 06/25/2023]
Abstract
Lactic acid bacteria (LAB) in the microbiota play an important role in human and animal health and, when used as probiotics, can contribute to an increased growth performance in livestock management. Animals living in their native habitat can serve as natural sources of microorganisms, so isolation of LAB strains from wild boars could provide the opportunity to develop effective probiotics to improve production in swine industry. In this study, the probiotic potential of 56 LAB isolates, originated from the ileum, colon, caecum and faeces of 5 wild boars, were assessed in vitro in details. Their taxonomic identity at species level and their antibacterial activity against four representative strains of potentially pathogenic bacteria were determined. The ability to tolerate low pH and bile salt, antibiotic susceptibility, bile salt hydrolase activity and lack of hemolysis were tested. Draft genome sequences of ten Limosilactobacillus mucosae and three Leuconostoc suionicum strains were determined. Bioinformatic analysis excluded the presence of any known acquired antibiotic resistance genes. Three genes, encoding mesentericin B105 and two different bacteriocin-IIc class proteins, as well as two genes with possible involvement in mesentericin secretion (mesE) and transport (mesD) were identified in two L. suionicum strains. Lam29 protein, a component of an ABC transporter with proved function as mucin- and epithelial cell-adhesion factor, and a bile salt hydrolase gene were found in all ten L. mucosae genomes. Comprehensive reconsideration of all data helps to select candidate strains to assess their probiotic potential further in animal experiments.
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Affiliation(s)
- Tibor Keresztény
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary
| | - Balázs Libisch
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
| | - Stephanya Corral Orbe
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
- Doctoral School of Biological Sciences, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary
| | - Tibor Nagy
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life, Sciences, 2100, Gödöllő, Hungary
| | - Zoltán Kerényi
- Hungarian Dairy Research Institute Ltd, 9200, Mosonmagyaróvár, Hungary
| | - Róbert Kocsis
- Hungarian Dairy Research Institute Ltd, 9200, Mosonmagyaróvár, Hungary
| | - Katalin Posta
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
| | - Péter P Papp
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary
| | - Ferenc Olasz
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences (MATE), 2100, Gödöllő, Hungary.
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Saikat TA, Sayem Khan MA, Islam MS, Tasnim Z, Ahmed S. Characterization and genome mining of Bacillus subtilis BDSA1 isolated from river water in Bangladesh: A promising bacterium with diverse biotechnological applications. Heliyon 2024; 10:e34369. [PMID: 39114027 PMCID: PMC11305188 DOI: 10.1016/j.heliyon.2024.e34369] [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: 02/19/2024] [Revised: 07/08/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024] Open
Abstract
The metabolic versatility of Bacillus subtilis makes it useful for a wide range of applications in biotechnology, from bioremediation to industrially important metabolite production. Understanding the molecular attributes of the biocontrol characteristics of B. subtilis is necessary for its tailored use in the environment and industry. Therefore, the present study aimed to conduct phenotypic characterization and whole genome analysis of the B. subtilis BDSA1 isolated from polluted river water from Dhaka, Bangladesh to explore its biotechnological potential. The chromium reduction capacity at 100 ppm Cr (VI) showed that B. subtilis BDSA1 reduced 40 % of Cr (VI) within 24hrs at 37 °C. Exposure of this bacterium to 200 ppm cadmium resulted in 43 % adsorption following one week of incubation at 37 °C. Molecular detection of chrA and czcC gene confirmed chromium and cadmium resistance characteristics of BDSA1. The size of the genome of the B. subtilis BDSA1 was 4.2 Mb with 43.4 % GC content. Genome annotation detected the presence of numerous genes involved in the degradation of xenobiotics, resistance to abiotic stress, production of lytic enzymes, siderophore formation, and plant growth promotion. The assembled genome also carried chromium, cadmium, copper, and arsenic resistance-related genes, notably cadA, czcD, czrA, arsB etc. Genome mining revealed six biosynthetic gene clusters for bacillaene, bacillibacin, bacilysin, subtilosin, fengycin and surfactin. Importantly, BDSA1 was predicted to be non-pathogenic to humans and had only two acquired antimicrobial resistance genes. The pan-genome analysis showed the openness of the B. subtilis pan-genome. Our findings suggested that B. subtilis BDSA1 might be a promising candidate for diverse biotechnological uses.
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Affiliation(s)
| | - Md Abu Sayem Khan
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Md Saiful Islam
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Zarin Tasnim
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
| | - Sangita Ahmed
- Department of Microbiology, University of Dhaka, Dhaka-1000, Bangladesh
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Hatrongjit R, Wongsurawat T, Jenjaroenpun P, Chopjitt P, Boueroy P, Akeda Y, Okada K, Iida T, Hamada S, Kerdsin A. Genomic analysis of carbapenem- and colistin-resistant Klebsiella pneumoniae complex harbouring mcr-8 and mcr-9 from individuals in Thailand. Sci Rep 2024; 14:16836. [PMID: 39039157 PMCID: PMC11263567 DOI: 10.1038/s41598-024-67838-5] [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: 02/08/2024] [Accepted: 07/15/2024] [Indexed: 07/24/2024] Open
Abstract
The surge in mobile colistin-resistant genes (mcr) has become an increasing public health concern, especially in carbapenem-resistant Enterobacterales (CRE). Prospective surveillance was conducted to explore the genomic characteristics of clinical CRE isolates harbouring mcr in 2015-2020. In this study, we aimed to examine the genomic characteristics and phonotypes of mcr-8 and mcr-9 harbouring carbapenem-resistant K. pneumoniae complex (CRKpnC). Polymerase chain reaction test and genome analysis identified CRKpnC strain AMR20201034 as K. pneumoniae (CRKP) ST147 and strain AMR20200784 as K. quasipneumoniae (CRKQ) ST476, harbouring mcr-8 and mcr-9, respectively. CRKQ exhibited substitutions in chromosomal-mediated colistin resistance genes (pmrB, pmrC, ramA, and lpxM), while CRKP showed two substitutions in crrB, pmrB, pmrC, lpxM and lapB. Both species showed resistance to colistin, with minimal inhibitory concentrations of 8 µg/ml for mcr-8-carrying CRKP isolate and 32 µg/ml for mcr-9-carrying CRKQ isolate. In addition, CRKP harbouring mcr-8 carried blaNDM, while CRKQ harbouring mcr-9 carried blaIMP, conferring carbapenem resistance. Analysis of plasmid replicon types carrying mcr-8 and mcr-9 showed FIA-FII (96,575 bp) and FIB-HI1B (287,118 bp), respectively. In contrast with the plasmid carrying the carbapenemase genes, the CRKQ carried blaIMP-14 on an IncC plasmid, while the CRKP harboured blaNDM-1 on an FIB plasmid. This finding provides a comprehensive insight into another mcr-carrying CRE from patients in Thailand. The other antimicrobial-resistant genes in the CRKP were blaCTX-M-15, blaSHV-11, blaOXA-1, aac(6')-Ib-cr, aph(3')-VI, ARR-3, qnrS1, oqxA, oqxB, sul1, catB3, fosA, and qacE, while those detected in CRKQ were blaOKP-B-15, qnrA1, oqxA, oqxB, sul1, fosA, and qacE. This observation highlights the importance of strengthening official active surveillance efforts to detect, control, and prevent mcr-harbouring CRE and the need for rational drug use in all sectors.
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Affiliation(s)
- Rujirat Hatrongjit
- Department of General Sciences, Faculty of Science and Engineering, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | | | - Kazuhisa Okada
- Japan-Thailand Research Collaboration Centre On Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tetsuya Iida
- Japan-Thailand Research Collaboration Centre On Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shigeyuki Hamada
- Japan-Thailand Research Collaboration Centre On Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Anusak Kerdsin
- Faculty of Public Health, Kasetsart University, Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand.
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Seru LV, Forde TL, Roberto-Charron A, Mavrot F, Niu YD, Kutz SJ. Genomic characterization and virulence gene profiling of Erysipelothrix rhusiopathiae isolated from widespread muskox mortalities in the Canadian Arctic Archipelago. BMC Genomics 2024; 25:691. [PMID: 39004696 PMCID: PMC11247837 DOI: 10.1186/s12864-024-10592-9] [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: 03/26/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND Muskoxen are important ecosystem components and provide food, economic opportunities, and cultural well-being for Indigenous communities in the Canadian Arctic. Between 2010 and 2021, Erysipelothrix rhusiopathiae was isolated from carcasses of muskoxen, caribou, a seal, and an Arctic fox during multiple large scale mortality events in the Canadian Arctic Archipelago. A single strain ('Arctic clone') of E. rhusiopathiae was associated with the mortalities on Banks, Victoria and Prince Patrick Islands, Northwest Territories and Nunavut, Canada (2010-2017). The objectives of this study were to (i) characterize the genomes of E. rhusiopathiae isolates obtained from more recent muskox mortalities in the Canadian Arctic in 2019 and 2021; (ii) identify and compare common virulence traits associated with the core genome and mobile genetic elements (i.e. pathogenicity islands and prophages) among Arctic clone versus other E. rhusiopathiae genomes; and iii) use pan-genome wide association studies (GWAS) to determine unique genetic contents of the Arctic clone that may encode virulence traits and that could be used for diagnostic purposes. RESULTS Phylogenetic analyses revealed that the newly sequenced E. rhusiopathiae isolates from Ellesmere Island, Nunavut (2021) also belong to the Arctic clone. Of 17 virulence genes analysed among 28 Arctic clone isolates, four genes - adhesin, rhusiopathiae surface protein-A (rspA), choline binding protein-B (cbpB) and CDP-glycerol glycerophosphotransferase (tagF) - had amino acid sequence variants unique to this clone when compared to 31 other E. rhusiopathiae genomes. These genes encode proteins that facilitate E. rhusiopathiae to attach to the host endothelial cells and form biofilms. GWAS analyses using Scoary found several unique genes to be overrepresented in the Arctic clone. CONCLUSIONS The Arctic clone of E. rhusiopathiae was associated with multiple muskox mortalities spanning over a decade and multiple Arctic islands with distances over 1000 km, highlighting the extent of its spatiotemporal spread. This clone possesses unique gene content, as well as amino acid variants in multiple virulence genes that are distinct from the other closely related E. rhusiopathiae isolates. This study establishes an essential foundation on which to investigate whether these differences are correlated with the apparent virulence of this specific clone through in vitro and in vivo studies.
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Affiliation(s)
| | - Taya L Forde
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK.
| | | | - Fabien Mavrot
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Yan D Niu
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Susan J Kutz
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada.
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Gandham P, Vadla N, Saji A, Srinivas V, Ruperao P, Selvanayagam S, Saxena RK, Rathore A, Gopalakrishnan S, Thakur V. Genome assembly, comparative genomics, and identification of genes/pathways underlying plant growth-promoting traits of an actinobacterial strain, Amycolatopsis sp. (BCA-696). Sci Rep 2024; 14:15934. [PMID: 38987320 PMCID: PMC11237095 DOI: 10.1038/s41598-024-66835-y] [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: 10/16/2023] [Accepted: 07/04/2024] [Indexed: 07/12/2024] Open
Abstract
The draft genome sequence of an agriculturally important actinobacterial species Amycolatopsis sp. BCA-696 was developed and characterized in this study. Amycolatopsis BCA-696 is known for its biocontrol properties against charcoal rot and also for plant growth-promotion (PGP) in several crop species. The next-generation sequencing (NGS)-based draft genome of Amycolatopsis sp. BCA-696 comprised of ~ 9.05 Mb linear chromosome with 68.75% GC content. In total, 8716 protein-coding sequences and 61 RNA-coding sequences were predicted in the genome. This newly developed genome sequence has been also characterized for biosynthetic gene clusters (BGCs) and biosynthetic pathways. Furthermore, we have also reported that the Amycolatopsis sp. BCA-696 produces the glycopeptide antibiotic vancomycin that inhibits the growth of pathogenic gram-positive bacteria. A comparative analysis of the BCA-696 genome with publicly available closely related genomes of 14 strains of Amycolatopsis has also been conducted. The comparative analysis has identified a total of 4733 core and 466 unique orthologous genes present in the BCA-696 genome The unique genes present in BCA-696 was enriched with antibiotic biosynthesis and resistance functions. Genome assembly of the BCA-696 has also provided genes involved in key pathways related to PGP and biocontrol traits such as siderophores, chitinase, and cellulase production.
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Affiliation(s)
- Prasad Gandham
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- School of Plant, Environmental and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, USA
| | - Nandini Vadla
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Angeo Saji
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Vadlamudi Srinivas
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pradeep Ruperao
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Excellence in Breeding, International Maize and Wheat Improvement Center (CIMMYT), Hyderabad, India.
| | - Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania.
| | - Vivek Thakur
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad, India.
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Schlosserová K, Daniel O, Labská K, Jakubů V, Stárková T, Bílý J, Dresler J, Lang C, Fruth A, Flieger A, Žemličková H, Bielaszewska M, Havlíčková M. Enteroaggregative Escherichia coli: Frequent, yet underdiagnosed pathotype among E. coli O111 strains isolated from children with gastrointestinal disorders in the Czech Republic. Int J Med Microbiol 2024; 316:151628. [PMID: 38936338 DOI: 10.1016/j.ijmm.2024.151628] [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: 02/19/2024] [Revised: 05/27/2024] [Accepted: 06/16/2024] [Indexed: 06/29/2024] Open
Abstract
Enteroaggregative Escherichia coli (EAEC) strains including those of serogroup O111 are important causes of diarrhea in children. In the Czech Republic, no information is available on the etiological role of EAEC in pediatric diarrhea due to the lack of their targeted surveillance. To fill this gap, we determined the proportion of EAEC among E. coli O111 isolates from children with gastrointestinal disorders ≤ 2 years of age submitted to the National Reference Laboratory for E. coli and Shigella during 2013-2022. EAEC accounted for 177 of 384 (46.1 %) E. coli O111 isolates, being the second most frequent E. coli O111 pathotype. Most of them (75.7 %) were typical EAEC that carried aggR, usually with aaiC and aatA marker genes; the remaining 24.3 % were atypical EAEC that lacked aggR but carried aaiC and/or aatA. Whole genome sequencing of 11 typical and two atypical EAEC O111 strains demonstrated differences in serotypes, sequence types (ST), virulence gene profiles, and the core genomes between these two groups. Typical EAEC O111:H21/ST40 strains resembled by their virulence profiles including the presence of the aggregative adherence fimbriae V (AAF/V)-encoding cluster to such strains from other countries and clustered with them in the core genome multilocus sequence typing (cgMLST). Atypical EAEC O111:H12/ST10 strains lacked virulence genes of typical EAEC and differed from them in cgMLST. All tested EAEC O111 strains displayed stacked-brick aggregative adherence to human intestinal epithelial cells. The AAF/V-encoding cluster was located on a plasmid of 95,749 bp or 93,286 bp (pAAO111) which also carried aggR, aap, aar, sepA, and aat cluster. EAEC O111 strains were resistant to antibiotics, in particular to aminopenicillins and cephalosporins; 88.3 % produced AmpC β-lactamase, and 4.1 % extended spectrum β-lactamase. We conclude that EAEC are frequent among E. coli O111 strains isolated from children with gastrointestinal disorders in the Czech Republic. To reliably assess the etiological role of EAEC in pediatric diarrhea, a serotype-independent, PCR-based pathotype surveillance system needs to be implemented in the future.
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Affiliation(s)
- Klára Schlosserová
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 2nd Faculty of Medicine, Charles University, Prague, V Úvalu 84, Prague 150 06, Czech Republic
| | - Ondřej Daniel
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 2nd Faculty of Medicine, Charles University, Prague, V Úvalu 84, Prague 150 06, Czech Republic
| | - Klára Labská
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic
| | - Vladislav Jakubů
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 3rd Faculty of Medicine, Charles University, Prague, Ruská 87, Prague 100 00, Czech Republic
| | - Tereza Stárková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic
| | - Jan Bílý
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic
| | - Jiří Dresler
- Central Military Medical Institute, Military University Hospital, U Vojenské nemocnice 1200, Prague 160 01, Czech Republic
| | - Christina Lang
- Division of Enteropathogenic Bacteria and Legionella and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Burgstrasse 37, Wernigerode 38855, Germany
| | - Angelika Fruth
- Division of Enteropathogenic Bacteria and Legionella and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Burgstrasse 37, Wernigerode 38855, Germany
| | - Antje Flieger
- Division of Enteropathogenic Bacteria and Legionella and National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch Institute, Burgstrasse 37, Wernigerode 38855, Germany
| | - Helena Žemličková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 3rd Faculty of Medicine, Charles University, Prague, Ruská 87, Prague 100 00, Czech Republic
| | - Martina Bielaszewska
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic; 2nd Faculty of Medicine, Charles University, Prague, V Úvalu 84, Prague 150 06, Czech Republic.
| | - Monika Havlíčková
- Centre for Epidemiology and Microbiology, National Institute of Public Health, Šrobárova 48, Prague 100 00, Czech Republic
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10
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Erickson VI, Dung TT, Khoi LM, Hounmanou YMG, Phu TM, Dalsgaard A. Genomic Insights into Edwardsiella ictaluri: Molecular Epidemiology and Antimicrobial Resistance in Striped Catfish ( Pangasianodon hypophthalmus) Aquaculture in Vietnam. Microorganisms 2024; 12:1182. [PMID: 38930563 PMCID: PMC11205447 DOI: 10.3390/microorganisms12061182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/21/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Edwardsiella ictaluri is responsible for causing bacillary necrosis (BNP) in striped catfish (Pangasianodon hypophthalmus) in Vietnam. This study offers a comprehensive genomic characterization of E. ictaluri to enhance understanding of the molecular epidemiology, virulence, and antimicrobial resistance. E. ictaluri isolates were collected from diseased striped catfish in the Mekong Delta. The species was confirmed through PCR. Antimicrobial susceptibility testing was conducted using minimum inhibitory concentrations for commonly used antimicrobials. Thirty representative isolates were selected for whole genome sequencing to delineate their genomic profiles and phylogeny. All strains belonged to ST-26 and exhibited genetic relatedness, differing by a maximum of 90 single nucleotide polymorphisms. Most isolates carried multiple antimicrobial resistance genes, with the tet(A) gene present in 63% and floR in 77% of the genomes. The ESBL gene, blaCTX-M-15, was identified in 30% of the genomes. Three plasmid replicon types were identified: IncA, p0111, and IncQ1. The genomes clustered into two clades based on their virulence gene profile, one group with the T3SS genes and one without. The genetic similarity among Vietnamese isolates suggests that disease spread occurs within the Mekong region, underscoring the importance of source tracking, reservoir identification, and implementation of necessary biosecurity measures to mitigate spread of BNP.
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Affiliation(s)
- Vera Irene Erickson
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (V.I.E.); (Y.M.G.H.)
| | - Tu Thanh Dung
- Department of Aquatic Pathology, Can Tho University, Can Tho 94000, Vietnam; (T.T.D.); (L.M.K.)
| | - Le Minh Khoi
- Department of Aquatic Pathology, Can Tho University, Can Tho 94000, Vietnam; (T.T.D.); (L.M.K.)
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (V.I.E.); (Y.M.G.H.)
| | - Tran Minh Phu
- Department of Aquatic Product Processing, Can Tho University, Can Tho 94000, Vietnam;
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1870 Frederiksberg, Denmark; (V.I.E.); (Y.M.G.H.)
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11
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Nyasinga J, Munshi Z, Kigen C, Nyerere A, Musila L, Whitelaw A, Ziebuhr W, Revathi G. Displacement of Hospital-Acquired, Methicillin-Resistant Staphylococcus aureus Clones by Heterogeneous Community Strains in Kenya over a 13-Year Period. Microorganisms 2024; 12:1171. [PMID: 38930553 PMCID: PMC11205442 DOI: 10.3390/microorganisms12061171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 06/28/2024] Open
Abstract
We determined antibiotic susceptibility and employed Oxford Nanopore whole-genome sequencing to explore strain diversity, resistance, and virulence gene carriage among methicillin-resistant Staphylococcus aureus (MRSA) strains from different infection sites and timepoints in a tertiary Kenyan hospital. Ninety-six nonduplicate clinical isolates recovered between 2010 and 2023, identified and tested for antibiotic susceptibility on the VITEK ID/AST platform, were sequenced. Molecular typing, antibiotic resistance, and virulence determinant screening were performed using the relevant bioinformatics tools. The strains, alongside those from previous studies, were stratified into two periods covering 2010-2017 and 2018-2023 and comparisons were made. Mirroring phenotypic profiles, aac(6')-aph(2″) [aminoglycosides]; gyrA (S84L) and grlA (S80Y) [fluoroquinolones]; dfrG [anti-folates]; and tet(K) [tetracycline] resistance determinants dominated the collection. While the proportion of ST239/241-t037-SCCmec III among MRSA reduced from 37.7% to 0% over the investigated period, ST4803-t1476-SCCmec IV and ST152-t355-SCCmec IV were pre-eminent. The prevalence of Panton-Valentine leucocidin (PVL) and arginine catabolic mobile element (ACME) genes was 38% (33/87) and 6.8% (6/87), respectively. We observed the displacement of HA-MRSA ST239/241-t037-SCCmec III with the emergence of ST152-t355-SCCmec IV and a greater clonal heterogeneity. The occurrence of PVL+/ACME+ CA-MRSA in recent years warrants further investigations into their role in the CA-MRSA virulence landscape, in a setting of high PVL prevalence.
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Affiliation(s)
- Justin Nyasinga
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
- Department of Biomedical Sciences and Technology, Technical University of Kenya, Nairobi P.O. Box 52428-00200, Kenya
- Institute of Science, Technology & Innovation, Pan-African University, Nairobi P.O. Box 62000-00200, Kenya;
| | - Zubair Munshi
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
| | - Collins Kigen
- Walter Reed Army Institute of Research—Africa, Kericho P.O. Box 1357-20200, Kenya; (C.K.); (L.M.)
| | - Andrew Nyerere
- Institute of Science, Technology & Innovation, Pan-African University, Nairobi P.O. Box 62000-00200, Kenya;
| | - Lillian Musila
- Walter Reed Army Institute of Research—Africa, Kericho P.O. Box 1357-20200, Kenya; (C.K.); (L.M.)
| | - Andrew Whitelaw
- Division of Medical Microbiology and Immunology, Stellenbosch University, Matieland, Stellenbosch 7602, South Africa;
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, Josef-Schneider Str. 2D/15, D-97080 Wurzburg, Germany;
| | - Gunturu Revathi
- Department of Pathology, Aga Khan University, Nairobi P.O. Box 30270-00100, Kenya; (J.N.); (Z.M.)
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12
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Xiu Y, Dai Y, Yin S, Wei Q. Analysis of the Class 1 Integrons, Carbapenemase Genes and Biofilm Formation Genes Occurrence in Acinetobacter baumannii Clinical Isolates. Pol J Microbiol 2024; 73:189-197. [PMID: 38808771 PMCID: PMC11192457 DOI: 10.33073/pjm-2024-017] [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: 12/09/2023] [Accepted: 03/28/2024] [Indexed: 05/30/2024] Open
Abstract
Acinetobacter baumannii is a non-fermentative Gram-negative bacterium that can cause nosocomial infections in critically ill patients. Carbapenem-resistant A. baumannii (CRAB) has spread rapidly in clinical settings and has become a key concern. The main objective of this study was to identify the distribution of integrons and biofilm-formation-related virulence genes in CRAB isolates. A total of 269 A. baumannii isolates (219 isolates of CRAB and 50 isolates of carbapenem-sensitive A. baumannii (CSAB)) were collected. Carbapenemase genes (bla KPC, bla VIM, bla IMP, bla NDM, and bla OXA-23-like) and biofilm-formation-related virulence genes (abal, bfms, bap, and cusE) were screened with PCR. Class 1 integron was screened with PCR, and common promoters and gene cassette arrays were determined with restriction pattern analysis combined with primer walking sequencing. Whole-genome sequencing was conducted, and data were analyzed for a bla OXA-23-like-negative isolate. All 219 CRAB isolates were negative for bla KPC, bla VIM, bla IMP, and bla NDM, while bla OXA-23-like was detected in 218 isolates. The detection rates for abal, bfms, bap, and cusE in 219 CRAB were 93.15%, 63.93%, 88.13%, and 77.63%, respectively. Class 1 integron was detected in 75 CRAB (34.25%) and in 3 CSAB. The single gene cassette array aacA4-catB8-aadA1 with relatively strong PcH2 promoter was detected in class 1 integrons. The bla OXA-23-like-negative CRAB isolate was revealed to be a new sequence type (Oxford 3272, Pasteur 2520) carrying bla OXA-72, bla OXA-259, and bla ADC-26. In conclusion, bla OXA-23-like was the main reason for CRAB's resistance to carbapenems. A new (Oxford 3272, Pasteur 2520) CRAB sequence type carrying the bla OXA-72, bla OXA-259, and bla ADC-26 was reported.
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Affiliation(s)
- Yu Xiu
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, Shanghai, China
| | - Yueru Dai
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, Shanghai, China
| | - Shasha Yin
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, Shanghai, China
| | - Quhao Wei
- Department of Laboratory Medicine, Anhui University of Science and Technology Affiliated Fengxian Hospital, Shanghai, China
- Department of Laboratory Medicine, Southern Medical University Affiliated Fengxian Hospital, Shanghai, China
- Department of Laboratory Medicine, Shanghai University of Medicine and Health Sciences Affiliated Sixth People’s Hospital South Campus, Shanghai, China
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13
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Corich L, Losasso C, Meneghel A, Blarasin FI, Basaglia G, Corich MA. The first case of urosepsis caused by Corynebacterium aurimucosum in an immunocompetent patient. Future Microbiol 2024; 19:963-970. [PMID: 39109653 PMCID: PMC11318739 DOI: 10.1080/17460913.2024.2344953] [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: 01/11/2024] [Accepted: 04/16/2024] [Indexed: 08/15/2024] Open
Abstract
Non-diphtheroid Corynebacterium sepsis is rare and has affected only immunocompromised or particularly predisposed patients so far. We present the first case of urosepsis caused by Corynebacterium aurimucosum in a 67-year-old woman, without any known immunodeficiencies and in absence of any immunosuppressive therapy, admitted to the hospital for fever and acute dyspnea. This work suggests a new approach in evaluating the isolation of Corynebacteria, especially if isolated from blood. In particular, it highlights the potential infectious role of C. aurimucosum (often considered a contaminant and only rarely identified as an etiological agent of infections) and its clinical consequences, detailing also interesting aspects about its microbiological diagnosis and relative therapy and clarifying contrasting data of literature.
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Affiliation(s)
- Lucia Corich
- Laboratory of Microbiology & Virology, Azienda Sanitaria Friuli Occidentale Santa Maria degli Angeli, Pordenone, Italy
| | - Carmen Losasso
- Laboratory of Microbial Ecology & Genomics, Istituto Zooprofilattico Sperimentale delle Venezie, Legnaro, Italy
| | - Alessia Meneghel
- Laboratory of Microbiology & Virology, Azienda Sanitaria Friuli Occidentale Santa Maria degli Angeli, Pordenone, Italy
| | | | - Giancarlo Basaglia
- Laboratory of Microbiology & Virology, Azienda Sanitaria Friuli Occidentale Santa Maria degli Angeli, Pordenone, Italy
| | - Maria Ada Corich
- Rehabilitation Medicine Unit, Azienda Sanitaria Universitaria Giuliano Isontina, Trieste, Italy
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14
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Toyting J, Nuanmuang N, Utrarachkij F, Supha N, Thongpanich Y, Leekitcharoenphon P, Aarestrup FM, Sato T, Thapa J, Nakajima C, Suzuki Y. Genomic analysis of Salmonella isolated from canal water in Bangkok, Thailand. Microbiol Spectr 2024; 12:e0421623. [PMID: 38563788 PMCID: PMC11064549 DOI: 10.1128/spectrum.04216-23] [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: 12/20/2023] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
Antimicrobial resistance (AMR) poses an escalating global public health threat. Canals are essential in Thailand, including the capital city, Bangkok, as agricultural and daily water sources. However, the characteristic and antimicrobial-resistance properties of the bacteria in the urban canals have never been elucidated. This study employed whole genome sequencing to characterize 30 genomes of a causal pathogenic bacteria, Salmonella enterica, isolated from Bangkok canal water between 2016 and 2020. The dominant serotype was Salmonella Agona. In total, 35 AMR genes and 30 chromosomal-mediated gene mutations were identified, in which 21 strains carried both acquired genes and mutations associated with fluoroquinolone resistance. Virulence factors associated with invasion, adhesion, and survival during infection were detected in all study strains. 75.9% of the study stains were multidrug-resistant and all the strains harbored the necessary virulence factors associated with salmonellosis. One strain carried 20 resistance genes, including mcr-3.1, mutations in GyrA, ParC, and ParE, and typhoid toxin-associated genes. Fifteen plasmid replicon types were detected, with Col(pHAD28) being the most common type. Comparative analysis of nine S. Agona from Bangkok and 167 from public databases revealed that specific clonal lineages of S. Agona might have been circulating between canal water and food sources in Thailand and globally. These findings provide insight into potential pathogens in the aquatic ecosystem and support the inclusion of environmental samples into comprehensive AMR surveillance initiatives as part of a One Health approach. This approach aids in comprehending the rise and dissemination of AMR and devising sustainable intervention strategies.IMPORTANCEBangkok is the capital city of Thailand and home to a large canal network that serves the city in various ways. The presence of pathogenic and antimicrobial-resistant Salmonella is alarming and poses a significant public health risk. The present study is the first characterization of the genomic of Salmonella strains from Bangkok canal water. Twenty-two of 29 strains (75.9%) were multidrug-resistant Salmonella and all the strains carried essential virulence factors for pathogenesis. Various plasmid types were identified in these strains, potentially facilitating the horizontal transfer of AMR genes. Additional investigations indicated a potential circulation of S. Agona between canal water and food sources in Thailand. The current study underscores the role of environmental water in an urban city as a reservoir of pathogens and these data obtained can serve as a basis for public health risk assessment and help shape intervention strategies to combat AMR challenges in Thailand.
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Affiliation(s)
- Jirachaya Toyting
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Narong Nuanmuang
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Fuangfa Utrarachkij
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Neunghatai Supha
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Yuwanda Thongpanich
- Department of Microbiology, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Toyotaka Sato
- Laboratory of Veterinary Hygiene, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
- Graduate School of Infectious Diseases, Hokkaido University, Sapporo, Japan
- One Health Research Center, Hokkaido University, Sapporo, Japan
| | - Jeewan Thapa
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Sapporo, Japan
- Division of Research Support, Hokkaido University Institute for Vaccine Research & Development, Sapporo, Japan
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15
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Kanje LE, Kumburu H, Kuchaka D, Shayo M, Juma MA, Kimu P, Beti M, van Zwetselaar M, Wadugu B, Mmbaga BT, Mkumbaye SI, Sonda T. Short reads-based characterization of pathotype diversity and drug resistance among Escherichia coli isolated from patients attending regional referral hospitals in Tanzania. BMC Med Genomics 2024; 17:110. [PMID: 38671498 PMCID: PMC11055328 DOI: 10.1186/s12920-024-01882-y] [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: 01/15/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Escherichia coli is known to cause about 2 million deaths annually of which diarrhea infection is leading and typically occurs in children under 5 years old. Although Africa is the most affected region there is little information on their pathotypes diversity and their antimicrobial resistance. OBJECTIVE To determine the pathotype diversity and antimicrobial resistance among E. coli from patients attending regional referral hospitals in Tanzania. MATERIALS AND METHODS A retrospective cross-section laboratory-based study where a total of 138 archived E. coli isolates collected from 2020 to 2021 from selected regional referral hospitals in Tanzania were sequenced using the Illumina Nextseq550 sequencer platform. Analysis of the sequences was done in the CGE tool for the identification of resistance genes and virulence genes. SPSS version 20 was used to summarize data using frequency and proportion. RESULTS Among all 138 sequenced E. coli isolates, the most prevalent observed pathotype virulence genes were of extraintestinal E. coli UPEC fyuA gene 82.6% (114/138) and NMEC irp gene 81.9% (113/138). Most of the E. coli pathotypes observed exist as a hybrid due to gene overlapping, the most prevalent pathotypes observed were NMEC/UPEC hybrid 29.7% (41/138), NMEC/UPEC/EAEC hybrid 26.1% (36/138), NMEC/UPEC/DAEC hybrid 18.1% (25/138) and EAEC 15.2% (21/138). Overall most E. coli carried resistance gene to ampicillin 90.6% (125/138), trimethoprim 85.5% (118/138), tetracycline 79.9% (110/138), ciprofloxacin 76.1% (105/138) and 72.5% (100/138) Nalidixic acid. Hybrid pathotypes were more resistant than non-hybrid pathotypes. CONCLUSION Whole genome sequencing reveals the presence of hybrid pathotypes with increased drug resistance among E. coli isolated from regional referral hospitals in Tanzania.
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Affiliation(s)
- Livin E Kanje
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania.
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania.
| | - Happiness Kumburu
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Davis Kuchaka
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Mariana Shayo
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Masoud A Juma
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- State University of Zanzibar, Zanzibar, Tanzania
| | - Patrick Kimu
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Melkiory Beti
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | | | - Boaz Wadugu
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
| | - Blandina T Mmbaga
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Sixbert Isdory Mkumbaye
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
| | - Tolbert Sonda
- Department of Microbiology and Immunology, Kilimanjaro Christian Medical University College, Kilimanjaro, Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro, Tanzania
- Clinical Laboratory, Kilimanjaro Christian Medical Center, Kilimanjaro, Tanzania
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16
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Di Renzo L, De Angelis ME, Torresi M, Mariani G, Pizzurro F, Mincarelli LF, Esposito E, Oliviero M, Iaccarino D, Di Nocera F, Paduano G, Lucifora G, Cammà C, Ferri N, Pomilio F. Genomic Characterization of Listeria monocytogenes and Other Listeria Species Isolated from Sea Turtles. Microorganisms 2024; 12:817. [PMID: 38674761 PMCID: PMC11052188 DOI: 10.3390/microorganisms12040817] [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: 02/26/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Listeria monocytogenes is a ubiquitous pathogen found both in the environment and food. It can cause listeriosis in a wide range of animals as well as in humans. Investigations on presence, spread and virulence are still limited to terrestrial and human environments. Embracing the One Health Approach, investigating the presence and spread of L. monocytogenes in marine ecosystems and among wildlife, would provide us with useful information for human health. This study investigated the presence of L. monocytogenes and Listeria spp. in two species of sea turtles common in the Mediterranean Sea (Caretta caretta and Chelonia mydas). A total of one hundred and sixty-four carcasses of sea turtles (C. caretta n = 161 and C. mydas n = 3) stranded along the Abruzzo, Molise, Campania, and Calabria coasts, were collected. Brain and fecal samples were taken, enriched, and cultured for the detection of Listeria spp. From the specimens collected, strains of L. monocytogenes (brain n = 1, brain and feces n = 1, multiorgan n = 1 and feces n = 1), L. innocua (feces n = 1 and brain n = 1), and L. ivanovii (brain n = 1) were isolated. Typical colonies were isolated for Whole Genome Sequencing (WGS). Virulence genes, disinfectants/metal resistance, and antimicrobial resistance were also investigated. L. monocytogenes, L. innocua, and L. ivanovii were detected in C. caretta, whilst only L. monocytogenes and L. innocua in C. mydas. Notable among the results is the lack of significant differences in gene distribution between human and sea turtle strains. Furthermore, potentially pathogenic strains of L. monocytogenes were found in sea turtles.
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Affiliation(s)
- Ludovica Di Renzo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
- Centro Studi Cetacei, 65125 Pescara, Italy
| | - Maria Elisabetta De Angelis
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
- Faculty of Bioscience and Agro-Food and Environmental Technology, University of Teramo, 64100 Teramo, Italy
| | - Marina Torresi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Giulia Mariani
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
- Faculty of Bioscience and Agro-Food and Environmental Technology, University of Teramo, 64100 Teramo, Italy
| | - Federica Pizzurro
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Luana Fiorella Mincarelli
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Emanuele Esposito
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | - Maria Oliviero
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | - Doriana Iaccarino
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | - Fabio Di Nocera
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | | | - Giuseppe Lucifora
- Istituto Zooprofilattico Sperimentale del Mezzogiorno, 80055 Portici, Italy; (E.E.); (D.I.); (F.D.N.); (G.L.)
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Nicola Ferri
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale”, Via Campo Boario, 64100 Teramo, Italy; (L.D.R.); (M.T.); (G.M.); (F.P.); (L.F.M.); (C.C.); (N.F.); (F.P.)
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Pena-Fernández N, Kortabarria N, Hurtado A, Ocejo M, Fort M, Pérez-Cobo I, Collantes-Fernández E, Aduriz G. Biochemical and molecular characterization of Campylobacter fetus isolates from bulls subjected to bovine genital campylobacteriosis diagnosis in Spain. BMC Vet Res 2024; 20:131. [PMID: 38566185 PMCID: PMC10985941 DOI: 10.1186/s12917-024-03970-8] [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: 10/19/2023] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Bovine genital campylobacteriosis (BGC) is caused by Campylobacter fetus subsp. venerealis (Cfv) including its biovar intermedius (Cfvi). This sexually transmitted disease induces early reproductive failure causing considerable economic losses in the cattle industry. Using a collection of well-characterized isolates (n = 13), C. fetus field isolates (n = 64) and saprophytic isolates resembling Campylobacter (n = 75) obtained from smegma samples of breeding bulls, this study evaluated the concordance of the most used phenotypic (H2S production in cysteine medium and 1% glycine tolerance) and molecular (PCR) methods for the diagnosis of BGC and assessed possible cross-reactions in the molecular diagnostic methods. RESULTS Characterization at the subspecies level (fetus vs. venerealis) of C. fetus isolated from bull preputial samples using phenotypic and molecular (PCR targeting nahE and ISCfe1) methods showed moderate concordance (κ = 0.462; CI: 0.256-0.669). No cross-reactions were observed with other saprophytic microaerophilic species or with other Campylobacter species that can be present in preputial samples. Whole genome sequencing (WGS) of discrepant isolates showed 100% agreement with PCR identification. For the differentiation of Cfv biovars, comparison of the H2S test (at 72 h and 5 days of incubation) and a PCR targeting the L-cysteine transporter genes showed higher concordance when H2S production was assessed after 5 days (72 h; κ = 0.553, 0.329-0.778 CI vs. 5 days; κ = 0.881, 0.631-1 CI), evidencing the efficacy of a longer incubation time. CONCLUSIONS This study confirmed the limitations of biochemical tests to correctly identify C. fetus subspecies and biovars. However, in the case of biovars, when extended incubation times for the H2S test (5 days) were used, phenotypic identification results were significantly improved, although PCR-based methods produced more accurate results. Perfect agreement of WGS with the PCR results and absence of cross-reactions with non-C. fetus saprophytic bacteria from the smegma demonstrated the usefulness of these methods. Nevertheless, the identification of new C. fetus subspecies-specific genes would help to improve BGC diagnosis.
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Affiliation(s)
- Nerea Pena-Fernández
- SERIDA, Servicio Regional de Investigación y Desarrollo Agroalimentario, Carretera de Oviedo, S/N, Villaviciosa, 33300, Spain
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, Derio, 48160, Spain
| | - Nekane Kortabarria
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, Derio, 48160, Spain
| | - Ana Hurtado
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, Derio, 48160, Spain
| | - Medelin Ocejo
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, Derio, 48160, Spain
| | - Marcelo Fort
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria S/N, Madrid, 28040, Spain
| | - Iratxe Pérez-Cobo
- Central Veterinary-Animal Health Laboratory (LCV), Ctra. Madrid-Algete Km. 8.00, Algete, 28110, Spain
| | - Esther Collantes-Fernández
- SALUVET, Animal Health Department, Faculty of Veterinary Sciences, Complutense University of Madrid, Ciudad Universitaria S/N, Madrid, 28040, Spain.
- Faculty of Veterinary Sciences, SALUVET-Innova S.L, Complutense University of Madrid, Ciudad Universitaria S/N, Madrid, 28040, Spain.
| | - Gorka Aduriz
- Department of Animal Health, NEIKER-Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Parque Científico y Tecnológico de Bizkaia, P812, Derio, 48160, Spain.
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18
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Nie W, Qiu T, Wei Y, Ding H, Guo Z, Qiu J. Advances in phage-host interaction prediction: in silico method enhances the development of phage therapies. Brief Bioinform 2024; 25:bbae117. [PMID: 38555471 PMCID: PMC10981677 DOI: 10.1093/bib/bbae117] [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: 09/10/2023] [Revised: 01/15/2024] [Accepted: 03/02/2024] [Indexed: 04/02/2024] Open
Abstract
Phages can specifically recognize and kill bacteria, which lead to important application value of bacteriophage in bacterial identification and typing, livestock aquaculture and treatment of human bacterial infection. Considering the variety of human-infected bacteria and the continuous discovery of numerous pathogenic bacteria, screening suitable therapeutic phages that are capable of infecting pathogens from massive phage databases has been a principal step in phage therapy design. Experimental methods to identify phage-host interaction (PHI) are time-consuming and expensive; high-throughput computational method to predict PHI is therefore a potential substitute. Here, we systemically review bioinformatic methods for predicting PHI, introduce reference databases and in silico models applied in these methods and highlight the strengths and challenges of current tools. Finally, we discuss the application scope and future research direction of computational prediction methods, which contribute to the performance improvement of prediction models and the development of personalized phage therapy.
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Affiliation(s)
- Wanchun Nie
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Tianyi Qiu
- Institute of Clinical Science, Zhongshan Hospital; Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, 200032, China
| | - Yiwen Wei
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Hao Ding
- Institute of Clinical Science, Zhongshan Hospital; Intelligent Medicine Institute, Fudan University, Shanghai, 200032, China
| | - Zhixiang Guo
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
| | - Jingxuan Qiu
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, 200093, China
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Li W, Lim CH, Zhao Z, Wang Y, Conway PL, Loo SCJ. In Vitro Profiling of Potential Fish Probiotics, Enterococcus hirae Strains, Isolated from Jade Perch, and Safety Properties Assessed Using Whole Genome Sequencing. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10244-0. [PMID: 38498111 DOI: 10.1007/s12602-024-10244-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/03/2024] [Indexed: 03/20/2024]
Abstract
The demands of intensified aquaculture production and escalating disease prevalence underscore the need for efficacious probiotic strategies to enhance fish health. This study focused on isolating and characterising potential probiotics from the gut microbiota of the emerging aquaculture species jade perch (Scortum barcoo). Eighty-seven lactic acid bacteria and 149 other bacteria were isolated from the digestive tract of five adult jade perch. The screening revealed that 24 Enterococcus hirae isolates inhibited the freshwater pathogens Aeromonas sobria and Streptococcus iniae. Co-incubating E. hirae with the host gut suspensions demonstrated a two- to five-fold increase in the size of growth inhibition zones compared to the results when using gut suspensions from tilapia (a non-host), indicating host-specificity. Genome analysis of the lead isolate, E. hirae R44, predicted the presence of antimicrobial compounds like enterolysin A, class II lanthipeptide, and terpenes, which underlay its antibacterial attributes. Isolate R44 exhibited desirable probiotic characteristics, including survival at pH values within the range of 3 to 12, bile tolerance, antioxidant activity, ampicillin sensitivity, and absence of transferable antimicrobial resistance genes and virulence factors commonly associated with hospital Enterococcus strains (IS16, hylEfm, and esp). This study offers a foundation for sourcing host-adapted probiotics from underexplored aquaculture species. Characterisation of novel probiotics like E. hirae R44 can expedite the development of disease mitigation strategies to support aquaculture intensification.
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Affiliation(s)
- Wenrui Li
- NTU Institute for Health Technologies, Interdisciplinary Graduate Programme, Nanyang Technological University, 61 Nanyang Drive, Singapore, 637335, Singapore
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Chiun Hao Lim
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Zhongtian Zhao
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yulan Wang
- Singapore Phenome Centre, Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore
| | - Patricia Lynne Conway
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Centre for Marine Science Innovation, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Say Chye Joachim Loo
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Drive, Singapore, 636921, Singapore.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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Sarenje KL, van Zwetselaar M, Kumburu H, Sonda T, Mmbaga B, Ngalamika O, Maimbolwa MC, Siame A, Munsaka S, Kwenda G. Antimicrobial resistance and heterogeneity of Neisseria gonorrhoeae isolated from patients attending sexually transmitted infection clinics in Lusaka, Zambia. BMC Genomics 2024; 25:290. [PMID: 38500064 PMCID: PMC10949682 DOI: 10.1186/s12864-024-10155-y] [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: 11/23/2023] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) of Neisseria gonorrhoeae is a threat to public health as strains have developed resistance to antimicrobials available for the treatment of gonorrhea. Whole genome sequencing (WGS) can detect and predict antimicrobial resistance to enhance the control and prevention of gonorrhea. Data on the molecular epidemiology of N. gonorrhoeae is sparse in Zambia. This study aimed to determine the genetic diversity of N. gonorrhoeae isolated from patients attending sexually transmitted infection (STI) clinics in Lusaka, Zambia. METHODS A cross-sectional study that sequenced 38 N. gonorrhoeae isolated from 122 patients with gonorrhea from 2019 to 2020 was conducted. The AMR profiles were determined by the E-test, and the DNA was extracted using the NucliSens easyMaG magnetic device. Whole genome sequencing was performed on the Illumina NextSeq550 platform. The Bacterial analysis pipeline (BAP) that is readily available at: https://cge.cbs.dtu.dk/services/CGEpipeline-1.1 was used for the identification of the species, assembling the genome, multi-locus sequence typing (MLST), detection of plasmids and AMR genes. Phylogeny by single nucleotide polymorphisms (SNPs) was determined with the CCphylo dataset. RESULTS The most frequent STs with 18.4% of isolates each were ST7363, ST1921 and ST1582, followed by ST1583 (13%), novel ST17026 (7.9%), ST1588 (7.9%), ST1596 (5.3%), ST11181 (5.3%), ST11750 (2.6/%) and ST11241 (2.6%) among the 38 genotyped isolates. The blaTeM-1B and tetM (55%) was the most prevalent combination of AMR genes, followed by blaTeM-1B (18.4%), tetM (15.8%), and the combination of blaTeM-1B, ermT, and tetL was 2.6% of the isolates. The AMR phenotypes were predicted in ciprofloxacin, penicillin, tetracycline, azithromycin, and cefixime. The combination of mutations 23.7% was gryA (S91F), parC (E91G), ponA (L421) and rpsJ (V57M), followed by 18.4% in gyrA (S91F), ponA (L421P), rpsJ (V57M), and 18.4% in gyrA (D95G, S91F), ponA (L421P), and rpsJ (V57M). The combinations in gyrA (D95G, S91F) and rpsJ (V57M), and gyrA (D95G, S91F), parC (E91F), ponA (L421P) and rpsJ (V57M) were 13.2% each of the isolates. Plasmid TEM-1 (84.2%), tetM (15.8%), and gonococcal genetic island (GGI) was detected in all isolates. CONCLUSION This study revealed remarkable heterogeneity of N. gonorrhoeae with blaTEM-1, tetM, ponA, gyrA, and parC genes associated with high resistance to penicillin, tetracycline, and ciprofloxacin demanding revision of the standard treatment guidelines and improved antimicrobial stewardship in Zambia.
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Affiliation(s)
- Kelvin Lutambo Sarenje
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia.
- Department of Dermato-venereology, University Teaching Hospital, Lusaka, Zambia.
| | | | - Happiness Kumburu
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Tolbert Sonda
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Blandina Mmbaga
- Kilimanjaro Clinical Research Institute, Moshi, Kilimanjaro, Tanzania
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Owen Ngalamika
- Department of Dermato-venereology, University Teaching Hospital, Lusaka, Zambia
| | - Margaret C Maimbolwa
- Department of Midwifery Child, and Women's Health, School of Nursing Sciences, University of Zambia, Lusaka, Zambia
| | - Amon Siame
- Centre for Infectious Disease Research in Zambia, Lusaka, Zambia
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, P.O. Box 50110, Zambia
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Corrales-Martínez J, Jaramillo K, Tadesse DA, Satán C, Villavicencio FX, Sánchez-Gavilanes L, Rivadeneira-Cueva B, Balcázar JL, Calero-Cáceres W. Genomic characterization of a WHO critical priority isolate Enterobacter kobei ST2070 harboring OXA-10, KPC-2, and CTX-M-12 recovered from a water irrigation channel in Ecuador. Heliyon 2024; 10:e26379. [PMID: 38449644 PMCID: PMC10915343 DOI: 10.1016/j.heliyon.2024.e26379] [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: 12/08/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
The discharge of untreated or partially treated wastewater can have detrimental impacts on the quality of water bodies, posing a significant threat to public health and the environment. In Ecuador, previous research indicates a high prevalence of antimicrobial resistant (AMR) bacteria in surface waters affected by human activities, including irrigation channels. In this study, we analyzed sediment samples collected from an irrigation channel utilized for agricultural purposes in northern Ecuador, using microbiological techniques and whole-genome sequencing (WGS). Our investigation revealed the first documented occurrence of E. kobei in Ecuador and the initial report of environmental E. kobei ST2070. Furthermore, we identified the coexistence of OXA-10-type class D β-lactamase and KPC-2-type class A β-lactamase in the E. kobei isolate (UTA41), representing the first report of such a phenomenon in this species. Additionally, we detected various antibiotic resistance genes in the E. kobei UTA41 isolate, including blaCTX-M-12, fosA, aac(6')-lb, sul2, msr(E), and mph(A), as well as virulence genes such as bacterial efflux pump and siderophore biosynthesis genes. We also identified two intact prophage regions (Entero_186 and Klebsi_phiKO2) in the isolate. Our study presents the first evidence of E. kobei isolate containing two carbapenemase-encoding genes in environmental samples from Latin America. This finding indicates the potential spread of critical-priority bacteria in water samples originating from anthropogenic sources, such as urban wastewater discharges and livestock facilities.
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Affiliation(s)
- Joselyn Corrales-Martínez
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
| | - Katherine Jaramillo
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública “Dr. Leopoldo Izquieta Pérez” INSPI, Quito, Ecuador
- Facultad de Ciencias de la Salud, Universidad Técnica de Ambato, Ambato, Ecuador
| | - Daniel A. Tadesse
- U.S. Food &Drug Administration, Center for Veterinary Medicine, Office of Applied Science Laurel, MD 20708, USA
| | - Carolina Satán
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública “Dr. Leopoldo Izquieta Pérez” INSPI, Quito, Ecuador
| | - Fernando X. Villavicencio
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública “Dr. Leopoldo Izquieta Pérez” INSPI, Quito, Ecuador
- Veterinary Medicine, Eugenio Espejo Faculty of Health Sciences, Universidad UTE, Quito, Ecuador
| | - Lissette Sánchez-Gavilanes
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
| | - Brenda Rivadeneira-Cueva
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain
- University of Girona, 17004 Girona, Spain
| | - William Calero-Cáceres
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
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22
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Chen X, Lu M, Wang Y, Zhang H, Jia X, Jia P, Yang W, Chen J, Song G, Zhang J, Xu Y. Emergence and clonal expansion of Aeromonas hydrophila ST1172 that simultaneously produces MOX-13 and OXA-724. Antimicrob Resist Infect Control 2024; 13:28. [PMID: 38433212 PMCID: PMC10910732 DOI: 10.1186/s13756-023-01339-4] [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: 07/26/2023] [Accepted: 11/16/2023] [Indexed: 03/05/2024] Open
Abstract
BACKGROUND Aeromonas hydrophila infections can cause gastrointestinal symptoms such as diarrhea; however, deep infections are rarely reported. Outbreaks of A. hydrophila are reported more frequently in fish, poultry, and snakes than in humans. This study aimed to track clonal relatedness of deep infections caused by A. hydrophila using whole genome sequencing (WGS). METHODS We collected three isolates of A. hydrophila in July 19 to August 29, 2019, from patients that underwent spine surgery. Accurate species identification was performed using whole-genome average nucleotide identity (ANI). Antimicrobial susceptibility testing was performed using a VITEK 2 automated AST-N334 Gram-negative susceptibility card system. Antimicrobial resistance and virulence genes were identified using the Comprehensive Antibiotic Resistance Database and Virulence Factor Database VFanalyzer. RESULTS All three isolates were identified as A. hydrophila based on ANI and multilocus sequence typing analysis revealed that A. hydrophila belonged to a novel sequence type (ST1172). All three isolates were susceptible to amikacin and levofloxacin; however, they were resistant to piperacillin/tazobactam, ceftriaxone, cefuroxime, cefoxitin, and imipenem. Isolate 19W05620 (patient 3) showed increased ceftazidime resistance (minimum inhibitory concentration ≥ 64 µg/mL). All three isolates possessed the same chromosomally encoded β-lactamases, including blaOXA-724 (β-lactamase), imiH (metallo-β-lactamase), and blaMOX-13 (AmpC) in plasmids. CONCLUSIONS Our study validated the transmission of a novel carbapenem-resistant A. hydrophila sequence type (ST1172) in patients that underwent spine surgery. Control measures should be developed to prevent dissemination of A. hydrophila in the hospital setting.
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Affiliation(s)
- Xinfei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Minya Lu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Yao Wang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Han Zhang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Xinmiao Jia
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing, China
| | - Peiyao Jia
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Wenhang Yang
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
| | - Jiawei Chen
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China
- Graduate School, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Guobin Song
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jianguo Zhang
- Department of orthopaedic, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
| | - Yingchun Xu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China.
- Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases (BZ0447), Beijing, China.
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23
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Findlay J, Raro OHF, Poirel L, Nordmann P. Molecular analysis of metallo-beta-lactamase-producing Pseudomonas aeruginosa in Switzerland 2022-2023. Eur J Clin Microbiol Infect Dis 2024; 43:551-557. [PMID: 38233610 PMCID: PMC10917820 DOI: 10.1007/s10096-024-04752-8] [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: 11/23/2023] [Accepted: 01/07/2024] [Indexed: 01/19/2024]
Abstract
OBJECTIVES The occurrence of metallo-beta-lactamase-producing Pseudomonas aeruginosa (MBL-PA) isolates is increasing globally, including in Switzerland. The aim of this study was to characterise, phenotypically and genotypically, the MBL-PA isolates submitted to the Swiss National Reference Center for Emerging Antibiotic Resistance (NARA) reference laboratory over a 12-month period from July 2022 to July 2023. METHODS Thirty-nine non-duplicate MBL-PA Isolates were submitted to NARA over the study period from across Switzerland. Susceptibility was determined by broth microdilution according to EUCAST methodology. Whole-genome sequencing was performed on 34 isolates. Sequence types (STs) and resistance genes were ascertained using the Centre for Genomic Epidemiology platform. MBL genes, blaNDM-1, blaIMP-1, and blaVIM-2, were cloned into vector pUCP24 and transformed into P. aeruginosa PA14. RESULTS The most prevalent MBL types identified in this study were VIM (21/39; 53.8%) followed by NDM (11/39; 28.2%), IMP (6/39; 15.4%), and a single isolate produced both VIM and NDM enzymes. WGS identified 13 different STs types among the 39 isolates. They all exhibited resistance to cephalosporins, carbapenems, and the beta-lactam-beta-lactamase inhibitor combinations, ceftolozane-tazobactam, ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam, and 8 isolates were cefiderocol (FDC) resistant. Recombinant P. aeruginosa strains producing blaNDM-1, blaIMP-1, and blaVIM-2 exhibited FDC MICs of 16, 8, and 1 mg/L, respectively. CONCLUSIONS This study showed that the MBL-PA in Switzerland could be attributed to the wide dissemination of high-risk clones that accounted for most isolates in this study. Although FDC resistance was only found in 8 isolates, MBL carriage was shown to be a major contributor to this phenotype.
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Affiliation(s)
- Jacqueline Findlay
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland.
| | - Otavio Hallal Ferreira Raro
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA) Network, Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, CH-1700, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA) Network, Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
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24
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Mondol SM, Islam MR, Rakhi NN, Shakil SK, Islam I, Mustary JF, Amiruzzaman, Shahjalal HM, Gomes DJ, Rahaman MM. Unveiling a high-risk epidemic clone (ST 357) of 'Difficult to Treat Extensively Drug-Resistant' (DT-XDR) Pseudomonas aeruginosa from a burn patient in Bangladesh: A resilient beast revealing coexistence of four classes of beta lactamases. J Glob Antimicrob Resist 2024; 36:83-95. [PMID: 38122983 DOI: 10.1016/j.jgar.2023.11.014] [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: 08/22/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
OBJECTIVES Pseudomonas aeruginosa (P. aeruginosa) stands out as a key culprit in the colonization of burn wounds, instigating grave infections of heightened severity. In this study, we have performed comparative whole genome analysis of a difficult to treat extensively drug resistant P. aeruginosa isolated from a burn patient in order to elucidate genomic diversity, molecular patterns, mechanisms and genes responsible for conferring antimicrobial resistance and virulence. METHOD P. aeruginosa SHNIBPS206 was isolated from an infected burn wound of a critically injured burn patient. Whole genome sequencing was carried out and annotated with Prokka. Sequence type, serotype, antimicrobial resistance genes and mechanisms, virulence genes, metal resistance genes and CRISPR/Cas systems were investigated. Later, pangenome analysis was carried out to find out genomic diversity. RESULT P. aeruginosa SHNIBPS206 (MLST 357, Serotype O11) was resistant to 14 antibiotics including carbapenems and harboured all four classes of beta lactamase producing genes: Class A (blaPME-1, blaVEB-9), Class B (blaNDM-1), Class C (blaPDC-11) and Class D (blaOXA-846). Mutational analysis of Porin D gave valuable insights. Several efflux pump, virulence and metal resistance genes were also detected. Pangenome analysis revealed high genomic diversity among different strains of P. aeruginosa. CONCLUSION To our knowledge, this is the first report of an extensively drug resistant ST 357 P. aeruginosa from Bangladesh, which is an epidemic high-risk P. aeruginosa clone. Further research and in-depth comprehensive studies are required to investigate the prevalence of such high-risk clone of P. aeruginosa in Bangladesh.
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Affiliation(s)
| | - Md Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | | | - Shahriar Kabir Shakil
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh; Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Jannatul Ferdous Mustary
- Microbiology Department, Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka, Bangladesh
| | - Amiruzzaman
- Department of Medicine, Sir Salimullah Medical College, Dhaka, Bangladesh
| | - Hussain Md Shahjalal
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, Bangladesh
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25
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Grönthal TSC, Lehto AK, Aarnio SS, Eskola EK, Aimo-Koivisto EM, Karlsson T, Koskinen HI, Barkoff AM, He Q, Lienemann T, Rimhanen-Finne R, Mykkänen A. Pastern dermatitis outbreak associated with toxigenic and non-toxigenic Corynebacterium diphtheriae and non-toxigenic Corynebacterium ulcerans at a horse stable in Finland, 2021. Zoonoses Public Health 2024; 71:127-135. [PMID: 37926867 DOI: 10.1111/zph.13090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/13/2023] [Accepted: 10/21/2023] [Indexed: 11/07/2023]
Abstract
AIMS Corynebacterium diphtheriae and Corynebacterium ulcerans, when producing toxin, are the cause of diphtheria, a potentially life-threatening illness in humans. Horses (Equus ferus caballus) are known to be susceptible to infection that may manifest clinically on rare occasions. In late 2021 and early 2022, specimens from five horses suffering from pastern dermatitis were cultured at the Laboratory of Clinical Microbiology at the Faculty of Veterinary Medicine, University of Helsinki, Finland. C. diphtheriae and/or C. ulcerans were recovered from all of these. This study aimed to (1) analyse the bacterial isolates and (2) describe the outbreak and identify possible sources of the infection and infection routes in the stable. METHODS AND RESULTS Susceptibility testing, PCR for the tox gene, and Elek test for toxin production in PCR-positive isolates were performed. Whole genome sequencing was also conducted to achieve high-resolution strain typing. An epidemiological survey was done by means of a semi-structured interview of horses' caretaker, and contact tracing was done among people at the stable. Two tox gene-positive, toxin-producing C. diphtheriae belonged to sequence type (ST) 822. Other C. diphtheriae (n = 2, ST828) and C. ulcerans (n = 2, ST325 and ST838) isolates did not carry the tox gene. The epidemiological investigation explored numerous possible routes of transmission, but the definite source of infection was not identified. All established human contacts tested negative for diphtheriae. All horses recovered after antimicrobial treatment. CONCLUSIONS Our study shows that C. diphtheriae and C. ulcerans may readily spread among horses at the same stable and complicate pastern dermatitis infections. These potentially zoonotic bacteria can cause outbreaks even in a country with a very low prevalence. Caretakers should be encouraged to wear gloves and practice good hand hygiene when treating infected skin lesions in horses.
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Affiliation(s)
- Thomas Sven Christer Grönthal
- Animal Health Diagnostics Unit, Finnish Food Authority, Helsinki, Finland
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Anna Karoliina Lehto
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Sanna Sofia Aarnio
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Eva Katarina Eskola
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Elina Marjaana Aimo-Koivisto
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Teemu Karlsson
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Heli Irmeli Koskinen
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute of Health and Welfare, Helsinki, Finland
| | - Alex-Mikael Barkoff
- Institute of Biomedicine, Research Center for Infections and Immunity, University of Turku, Turku, Finland
| | - Qiushui He
- Institute of Biomedicine, Research Center for Infections and Immunity, University of Turku, Turku, Finland
| | - Taru Lienemann
- Animal Health Diagnostics Unit, Finnish Food Authority, Helsinki, Finland
| | - Ruska Rimhanen-Finne
- Infectious Disease Control and Vaccinations Unit, Department of Health Security, Finnish Institute of Health and Welfare, Helsinki, Finland
| | - Anna Mykkänen
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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26
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Black CA, Benavides R, Bandy SM, Dallas SD, Gawrys G, So W, Moreira AG, Aguilar S, Quidilla K, Smelter DF, Reveles KR, Frei CR, Koeller JM, Lee GC. Diverse Role of blaCTX-M and Porins in Mediating Ertapenem Resistance among Carbapenem-Resistant Enterobacterales. Antibiotics (Basel) 2024; 13:185. [PMID: 38391571 PMCID: PMC10885879 DOI: 10.3390/antibiotics13020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/07/2024] [Accepted: 02/09/2024] [Indexed: 02/24/2024] Open
Abstract
Among carbapenem-resistant Enterobacterales (CRE) are diverse mechanisms, including those that are resistant to meropenem but susceptible to ertapenem, adding further complexity to the clinical landscape. This study investigates the emergence of ertapenem-resistant, meropenem-susceptible (ErMs) Escherichia coli and Klebsiella pneumoniae CRE across five hospitals in San Antonio, Texas, USA, from 2012 to 2018. The majority of the CRE isolates were non-carbapenemase producers (NCP; 54%; 41/76); 56% of all NCP isolates had an ErMs phenotype. Among ErMs strains, E. coli comprised the majority (72%). ErMs strains carrying blaCTX-M had, on average, 9-fold higher copies of blaCTX-M than CP-ErMs strains as well as approximately 4-fold more copies than blaCTX-M-positive but ertapenem- and meropenem-susceptible (EsMs) strains (3.7 vs. 0.9, p < 0.001). Notably, carbapenem hydrolysis was observed to be mediated by strains harboring blaCTX-M with and without a carbapenemase(s). ErMs also carried more mobile genetic elements, particularly IS26 composite transposons, than EsMs (37 vs. 0.2, p < 0.0001). MGE- ISVsa5 was uniquely more abundant in ErMs than either EsMs or ErMr strains, with over 30 more average ISVsa5 counts than both phenotype groups (p < 0.0001). Immunoblot analysis demonstrated the absence of OmpC expression in NCP-ErMs E. coli, with 92% of strains lacking full contig coverage of ompC. Overall, our findings characterize both collaborative and independent efforts between blaCTX-M and OmpC in ErMs strains, indicating the need to reappraise the term "non-carbapenemase (NCP)", particularly for strains highly expressing blaCTX-M. To improve outcomes for CRE-infected patients, future efforts should focus on mechanisms underlying the emerging ErMs subphenotype of CRE strains to develop technologies for its rapid detection and provide targeted therapeutic strategies.
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Affiliation(s)
- Cody A Black
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Raymond Benavides
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Sarah M Bandy
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Steven D Dallas
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Pathology and Laboratory Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- University Health System, San Antonio, TX 78229, USA
| | - Gerard Gawrys
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- University Health System, San Antonio, TX 78229, USA
| | - Wonhee So
- College of Pharmacy, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Alvaro G Moreira
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Veterans Administration Research Center for AIDS and HIV-1 Infection and Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX 78229, USA
| | - Samantha Aguilar
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- University Health System, San Antonio, TX 78229, USA
| | - Kevin Quidilla
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Dan F Smelter
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Kelly R Reveles
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Christopher R Frei
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- University Health System, San Antonio, TX 78229, USA
| | - Jim M Koeller
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Grace C Lee
- College of Pharmacy, The University of Texas at Austin, Austin, TX 78712, USA
- Joe R. and Teresa Lozano Long School of Medicine, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Veterans Administration Research Center for AIDS and HIV-1 Infection and Center for Personalized Medicine, South Texas Veterans Health Care System, San Antonio, TX 78229, USA
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27
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Gmeiner A, Njage PMK, Hansen LT, Aarestrup FM, Leekitcharoenphon P. Predicting Listeria monocytogenes virulence potential using whole genome sequencing and machine learning. Int J Food Microbiol 2024; 410:110491. [PMID: 38000216 DOI: 10.1016/j.ijfoodmicro.2023.110491] [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: 03/31/2023] [Revised: 10/06/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Contamination with food-borne pathogens, such as Listeria monocytogenes, remains a big concern for food safety. Hence, rigorous and continuous microbial surveillance is a standard procedure. At this point, however, the food industry and authorities only focus on detection of Listeria monocytogenes without characterization of individual strains into groups of more or less concern. As whole genome sequencing (WGS) gains increasing interest in the industry, this methodology presents an opportunity to obtain finer resolution of microbial traits such as virulence. Within this study, we therefore aimed to explore the use of WGS in combination with Machine Learning (ML) to predict L. monocytogenes virulence potential on a sub-species level. The WGS datasets used in this study for ML model training consisted of i) national surveillance isolates (n = 169, covering 38 MLST types) and ii) publicly available isolates acquired through the GenomeTrakr network (n = 2880, spanning 80 MLST types). We used the clinical frequency, i.e., ratio of the number of clinical isolates to total amount of isolates, as estimate for virulence potential. The predictive performance of input features from three different genomic levels (i.e., virulence genes, pan-genome genes, and single nucleotide polymorphisms (SNPs)) and six machine learning algorithms (i.e., Support Vector Machine with a linear kernel, Support Vector Machine with a radial kernel, Random Forrest, Neural Networks, LogitBoost, and Majority Voting) were compared. Our machine learning models predicted sub-species virulence potential with nested cross-validation F1-scores up to 0.88 for the majority voting classifier trained on national surveillance data and using pan-genome genes as input features. The validation of the pre-trained ML models based on 101 previously in vivo studied isolates resulted in F1-scores up to 0.76. Furthermore, we found that the more rapid and less computationally intensive raw read alignment yields comparably accurate models as de novo assembly. The results of our study suggest that a majority voting classifier trained on pan-genome genes is the best and most robust choice for the prediction of clinical frequency. Our study contributes to more rapid and precise characterization of L. monocytogenes virulence and its variation on a sub-species level. We further demonstrated a possible application of WGS data in the context of microbial hazard characterization for food safety. In the future, predictive models may assist case-specific microbial risk management in the food industry. The python code, pre-trained models, and prediction pipeline are deposited at (https://github.com/agmei/LmonoVirulenceML).
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Affiliation(s)
- Alexander Gmeiner
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark.
| | - Patrick Murigu Kamau Njage
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark
| | - Lisbeth Truelstrup Hansen
- National Food Institute, Technical University of Denmark, Research Group for Food Microbiology and Hygiene, Kgs. Lyngby, Denmark
| | - Frank M Aarestrup
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- National Food Institute, Technical University of Denmark, Research Group for Genomic Epidemiology, Kgs. Lyngby, Denmark
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28
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Mondol SM, Islam I, Islam MR, Shakil SK, Rakhi NN, Mustary JF, Amiruzzaman, Gomes DJ, Shahjalal HM, Rahaman MM. Genomic landscape of NDM-1 producing multidrug-resistant Providencia stuartii causing burn wound infections in Bangladesh. Sci Rep 2024; 14:2246. [PMID: 38278862 PMCID: PMC10817959 DOI: 10.1038/s41598-024-51819-9] [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: 09/21/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
The increasing antimicrobial resistance in Providencia stuartii (P. stuartii) worldwide, particularly concerning for immunocompromised and burn patients, has raised concern in Bangladesh, where the significance of this infectious opportunistic pathogen had been previously overlooked, prompting a need for investigation. The two strains of P. stuartii (P. stuartii SHNIBPS63 and P. stuartii SHNIBPS71) isolated from wound swab of two critically injured burn patients were found to be multidrug-resistant and P. stuartii SHNIBPS63 showed resistance to all the 22 antibiotics tested as well as revealed the co-existence of blaVEB-6 (Class A), blaNDM-1 (Class B), blaOXA-10 (Class D) beta lactamase genes. Complete resistance to carbapenems through the production of NDM-1, is indicative of an alarming situation as carbapenems are considered to be the last line antibiotic to combat this pathogen. Both isolates displayed strong biofilm-forming abilities and exhibited resistance to copper, zinc, and iron, in addition to carrying multiple genes associated with metal resistance and the formation of biofilms. The study also encompassed a pangenome analysis utilizing a dataset of eighty-six publicly available P. stuartii genomes (n = 86), revealing evidence of an open or expanding pangenome for P. stuartii. Also, an extensive genome-wide analysis of all the P. stuartii genomes revealed a concerning global prevalence of diverse antimicrobial resistance genes, with a particular alarm raised over the abundance of carbapenem resistance gene blaNDM-1. Additionally, this study highlighted the notable genetic diversity within P. stuartii, significant informations about phylogenomic relationships and ancestry, as well as potential for cross-species transmission, raising important implications for public health and microbial adaptation across different environments.
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Affiliation(s)
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Md Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Shahriar Kabir Shakil
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
- Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, 3814, Bangladesh
| | | | - Jannatul Ferdous Mustary
- Microbiology Department, Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka, 1000, Bangladesh
| | - Amiruzzaman
- Department of Medicine, Sir Salimullah Medical College, Dhaka, 1000, Bangladesh
| | - Donald James Gomes
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Hussain Md Shahjalal
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh
| | - Md Mizanur Rahaman
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh.
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29
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Castañeda-Meléndrez AM, Magaña-Lizárraga JA, Martínez-Valenzuela M, Clemente-Soto AF, García-Cervantes PC, Delgado-Vargas F, Bernal-Reynaga R. Genomic characterization of a multidrug-resistant uropathogenic Escherichia coli and evaluation of Echeveria plant extracts as antibacterials. AIMS Microbiol 2024; 10:41-61. [PMID: 38525046 PMCID: PMC10955171 DOI: 10.3934/microbiol.2024003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/26/2024] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common bacterial agent associated with urinary tract infections, threatening public health systems with elevated medical costs and high morbidity rates. The successful establishment of the infection is associated with virulence factors encoded in its genome, in addition to antibacterial resistance genes, which could limit the treatment and resolution of the infection. In this sense, plant extracts from the genus Echeveria have traditionally been used to treat diverse infectious diseases. However, little is known about the effects of these extracts on bacteria and their potential mechanisms of action. This study aims to sequence a multidrug-resistant UPEC isolate (UTI-U7) and assess the multilocus sequence typing (MLST), virulence factors, antimicrobial resistance profile, genes, serotype, and plasmid content. Antimicrobial susceptibility profiling was performed using the Kirby-Bauer disk diffusion. The antibacterial and anti-adherent effects of the methanol extracts (ME) of Echeveria (E. craigiana, E. kimnachii, and E. subrigida) against UTI-U7 were determined. The isolate was characterized as an O25:H4-B2-ST2279-CH40 subclone and had resistant determinants to aminoglycosides, β-lactams, fluoroquinolones/quinolones, amphenicols, and tetracyclines, which matched with the antimicrobial resistance profile. The virulence genes identified encode adherence factors, iron uptake, protectins/serum resistance, and toxins. Identified plasmids belonged to the IncF group (IncFIA, IncFIB, and IncFII), alongside several prophage-like elements. After an extensive genome analysis that confirmed the pathogenic status of UTI-U7 isolate, Echeveria extracts were tested to determine their antibacterial effects; as an extract, E. subrigida (MIC, 5 mg/mL) displayed the best inhibitory effect. However, the adherence between UTI-U7 and HeLa cells was unaffected by the ME of the E. subrigida extract.
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Affiliation(s)
| | | | | | | | | | | | - Rodolfo Bernal-Reynaga
- Unidad de Investigaciones en Salud Pública “Dra. Kaethe Willms”, Facultad de Ciencias Químico-Biológicas. Universidad Autónoma de Sinaloa. Ciudad Universitaria, Culiacán, Sinaloa, México
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30
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Tönz A, Freimüller Leischtfeld S, Stevens MJA, Glinski-Häfeli D, Ladner V, Gantenbein-Demarchi C, Miescher Schwenninger S. Growth Control of Listeria monocytogenes in Raw Sausage via Bacteriocin-Producing Leuconostoc carnosum DH25. Foods 2024; 13:298. [PMID: 38254599 PMCID: PMC10815048 DOI: 10.3390/foods13020298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The current study addresses the critical issue of Listeria monocytogenes growth in raw sausage/meat products leading to human infections, most commonly listeriosis, which is known for its high fatality rate. This research focuses on the isolation, identification, and screening of lactic acid bacteria from various meat and fish products in Switzerland. In total, 274 lactic acid bacteria strains were isolated from 30 different products and were screened for their ability to inhibit Listeria monocytogenes growth, with 51 isolates demonstrating anti-Listeria activity at 8 °C, 15 °C, 25 °C, and 37 °C. Further experiments, using a meat model and a raw sausage challenge test, demonstrated that Leuconostoc carnosum DH25 significantly inhibited Listeria monocytogenes growth during the ripening and storage of the tested meat/sausage. This inhibitory effect was found to be attributed to the bacteriocins produced by Leuconostoc carnosum DH25 rather than factors like pH or water activity. The stability of the anti-Listeria substances was examined, revealing their resistance to temperature and pH changes, making Leuconostoc carnosum DH25 a promising protective culture for raw sausages. The genome sequencing of this strain confirms its safety, with no antibiotic resistance genes or virulence factors detected, and reveals the presence of the structural genes for the production of the bacteriocin LeucocinB-Ta11a. This study underscores the potential of LAB strains and their bacteriocins as effective tools for enhancing food safety and preventing Listeria monocytogenes growth in meat products, offering valuable insights into biocontrol strategies in the food industry.
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Affiliation(s)
- Andrea Tönz
- ZHAW Zurich University of Applied Sciences, Institute of Food and Beverage Innovation, Food Biotechnology Research Group, 8820 Wädenswil, Switzerland; (A.T.); (S.F.L.); (D.G.-H.); (V.L.); (C.G.-D.)
| | - Susette Freimüller Leischtfeld
- ZHAW Zurich University of Applied Sciences, Institute of Food and Beverage Innovation, Food Biotechnology Research Group, 8820 Wädenswil, Switzerland; (A.T.); (S.F.L.); (D.G.-H.); (V.L.); (C.G.-D.)
| | - Marc J. A. Stevens
- University of Zurich, Vetsuisse Faculty, Institute for Food Safety and Hygiene, 8057 Zurich, Switzerland;
| | - Deborah Glinski-Häfeli
- ZHAW Zurich University of Applied Sciences, Institute of Food and Beverage Innovation, Food Biotechnology Research Group, 8820 Wädenswil, Switzerland; (A.T.); (S.F.L.); (D.G.-H.); (V.L.); (C.G.-D.)
| | - Valentin Ladner
- ZHAW Zurich University of Applied Sciences, Institute of Food and Beverage Innovation, Food Biotechnology Research Group, 8820 Wädenswil, Switzerland; (A.T.); (S.F.L.); (D.G.-H.); (V.L.); (C.G.-D.)
| | - Corinne Gantenbein-Demarchi
- ZHAW Zurich University of Applied Sciences, Institute of Food and Beverage Innovation, Food Biotechnology Research Group, 8820 Wädenswil, Switzerland; (A.T.); (S.F.L.); (D.G.-H.); (V.L.); (C.G.-D.)
| | - Susanne Miescher Schwenninger
- ZHAW Zurich University of Applied Sciences, Institute of Food and Beverage Innovation, Food Biotechnology Research Group, 8820 Wädenswil, Switzerland; (A.T.); (S.F.L.); (D.G.-H.); (V.L.); (C.G.-D.)
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Garcia-Fernandez A, Janowicz A, Marotta F, Napoleoni M, Arena S, Primavilla S, Pitti M, Romantini R, Tomei F, Garofolo G, Villa L. Antibiotic resistance, plasmids, and virulence-associated markers in human strains of Campylobacter jejuni and Campylobacter coli isolated in Italy. Front Microbiol 2024; 14:1293666. [PMID: 38260875 PMCID: PMC10800408 DOI: 10.3389/fmicb.2023.1293666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/07/2023] [Indexed: 01/24/2024] Open
Abstract
Campylobacteriosis, a prevalent foodborne gastrointestinal infection in Europe, is primarily caused by Campylobacter jejuni and Campylobacter coli, with rising global concerns over antimicrobial resistance in these species. This study comprehensively investigates 133 human-origin Campylobacter spp. strains (102 C. jejuni and 31 C. coli) collected in Italy from 2013 to 2021. The predominant Multilocus Sequence Typing Clonal complexes (CCs) were ST-21 CC and ST-206 CC in C. jejuni and ST-828 CC in C. coli. Ciprofloxacin and tetracycline resistance, mainly attributed to GyrA (T86I) mutation and tet(O) presence, were prevalent, while erythromycin resistance was associated with 23S rRNA gene mutation (A2075G), particularly in C. coli exhibiting multidrug-resistant pattern CipTE. Notable disparities in virulence factors among strains were observed, with C. jejuni exhibiting a higher abundance compared to C. coli. Notably, specific C. jejuni sequence types, including ST-21, ST-5018, and ST-1263, demonstrated significantly elevated counts of virulence genes. This finding underscores the significance of considering both the species and strain-level variations in virulence factor profiles, shedding light on potential differences in the pathogenicity and clinical outcomes associated with distinct C. jejuni lineages. Campylobacter spp. plasmids were classified into three groups comprising pVir-like and pTet-like plasmids families, exhibiting diversity among Campylobacter spp. The study underscores the importance of early detection through Whole Genome Sequencing to identify potential emergent virulence, resistance/virulence plasmids, and new antimicrobial resistance markers. This approach provides actionable public health data, supporting the development of robust surveillance programs in Italy.
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Affiliation(s)
| | - Anna Janowicz
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Francesca Marotta
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Maira Napoleoni
- Centro di Riferimento Regionale Patogeni Enterici, CRRPE, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “T. Rosati”, Perugia, Italy
| | - Sergio Arena
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Sara Primavilla
- Centro di Riferimento Regionale Patogeni Enterici, CRRPE, Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “T. Rosati”, Perugia, Italy
| | - Monica Pitti
- Centro di Riferimento per la Tipizzazione delle Salmonelle, CeRTiS, Istituto Zooprofilattico Sperimentale del Piemonte Liguria e Valle d'Aosta, Turin, Italy
| | - Romina Romantini
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | | | - Giuliano Garofolo
- National Reference Laboratory for Campylobacter, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", Teramo, Italy
| | - Laura Villa
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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Huang J, Lv C, Li M, Rahman T, Chang YF, Guo X, Song Z, Zhao Y, Li Q, Ni P, Zhu Y. Carbapenem-resistant Escherichia coli exhibit diverse spatiotemporal epidemiological characteristics across the globe. Commun Biol 2024; 7:51. [PMID: 38184739 PMCID: PMC10771496 DOI: 10.1038/s42003-023-05745-7] [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: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/08/2024] Open
Abstract
Carbapenem-resistant Escherichia coli (CREC) poses a severe global public health risk. This study reveals the worldwide geographic spreading patterns and spatiotemporal distribution characteristics of resistance genes in 7918 CREC isolates belonging to 497 sequence types (ST) and originating from 75 countries. In the last decade, there has been a transition in the prevailing STs from highly virulent ST131 and ST38 to higher antibiotic-resistant ST410 and ST167. The rise of multi-drug resistant strains of CREC carrying plasmids with extended-spectrum beta-lactamase (ESBL) resistance genes could be attributed to three important instances of host-switching events. The spread of CREC was associated with the changing trends in blaNDM-5, blaKPC-2, and blaOXA-48, as well as the plasmids IncFI, IncFII, and IncI. There were intercontinental geographic transfers of major CREC strains. Various crucial transmission hubs and patterns have been identified for ST131 in the United Kingdom, Italy, the United States, and China, ST167 in India, France, Egypt, and the United States, and ST410 in Thailand, Israel, the United Kingdom, France, and the United States. This work is valuable in managing CREC infections and preventing CREC occurrence and transmission inside healthcare settings and among diverse hosts.
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Affiliation(s)
- Jiewen Huang
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Lv
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Li
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tanvir Rahman
- Department of Microbiology and Hygiene, Faculty of Veterinary Science, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, Cornell University College of Veterinary Medicine, Ithaca, NY, USA
| | - Xiaokui Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhen Song
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanan Zhao
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Peihua Ni
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yongzhang Zhu
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Contente D, Díaz-Formoso L, Feito J, Hernández PE, Muñoz-Atienza E, Borrero J, Poeta P, Cintas LM. Genomic and Functional Evaluation of Two Lacticaseibacillus paracasei and Two Lactiplantibacillus plantarum Strains, Isolated from a Rearing Tank of Rotifers ( Brachionus plicatilis), as Probiotics for Aquaculture. Genes (Basel) 2024; 15:64. [PMID: 38254954 PMCID: PMC10815930 DOI: 10.3390/genes15010064] [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: 11/06/2023] [Revised: 12/21/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024] Open
Abstract
Aquaculture plays a crucial role in meeting the increasing global demand for food and protein sources. However, its expansion is followed by increasing challenges, such as infectious disease outbreaks and antibiotic misuse. The present study focuses on the genetic and functional analyses of two Lacticaseibacillus paracasei (BF3 and RT4) and two Lactiplantibacillus plantarum (BF12 and WT12) strains isolated from a rotifer cultivation tank used for turbot larviculture. Whole-genome sequencing (WGS) and bioinformatics analyses confirmed their probiotic potential, the absence of transferable antibiotic resistance genes, and the absence of virulence and pathogenicity factors. Bacteriocin mining identified a gene cluster encoding six plantaricins, suggesting their role in the antimicrobial activity exerted by these strains. In vitro cell-free protein synthesis (IV-CFPS) analyses was used to evaluate the expression of the plantaricin genes. The in vitro-synthesized class IIb (two-peptide bacteriocins) plantaricin E/F (PlnE/F) exerted antimicrobial activity against three indicator microorganisms, including the well-known ichthyopathogen Lactococcus garvieae. Furthermore, MALDI-TOF MS on colonies detected the presence of a major peptide that matches the dimeric form of plantaricins E (PlnE) and F (PlnF). This study emphasizes the importance of genome sequencing and bioinformatic analysis for evaluating aquaculture probiotic candidates. Moreover, it provides valuable insights into their genetic features and antimicrobial mechanisms, paving the way for their application as probiotics in larviculture, which is a major bottleneck in aquaculture.
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Affiliation(s)
- Diogo Contente
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Lara Díaz-Formoso
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Javier Feito
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Pablo E. Hernández
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Estefanía Muñoz-Atienza
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Juan Borrero
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
| | - Patrícia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Luis M. Cintas
- Grupo de Seguridad y Calidad de los Alimentos por Bacterias Lácticas, Bacteriocinas y Probióticos (SEGABALBP), Sección Departamental de Nutrición y Ciencia de los Alimentos, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain; (D.C.); (L.D.-F.); (P.E.H.); (E.M.-A.); (J.B.); (L.M.C.)
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Sevillano E, Lafuente I, Peña N, Cintas LM, Muñoz-Atienza E, Hernández PE, Borrero J. Evaluation of Safety and Probiotic Traits from a Comprehensive Genome-Based In Silico Analysis of Ligilactobacillus salivarius P1CEA3, Isolated from Pigs and Producer of Nisin S. Foods 2023; 13:107. [PMID: 38201135 PMCID: PMC10778751 DOI: 10.3390/foods13010107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/13/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Ligilactobacillus salivarius is an important member of the porcine gastrointestinal tract (GIT). Some L. salivarius strains are considered to have a beneficial effect on the host by exerting different probiotic properties, including the production of antimicrobial peptides which help maintain a healthy gut microbiota. L. salivarius P1CEA3, a porcine isolated strain, was first selected and identified by its antimicrobial activity against a broad range of pathogenic bacteria due to the production of the novel bacteriocin nisin S. The assembled L. salivarius P1CEA3 genome includes a circular chromosome, a megaplasmid (pMP1CEA3) encoding the nisin S gene cluster, and two small plasmids. A comprehensive genome-based in silico analysis of the L. salivarius P1CEA3 genome reveals the presence of genes related to probiotic features such as bacteriocin synthesis, regulation and production, adhesion and aggregation, the production of lactic acid, amino acids metabolism, vitamin biosynthesis, and tolerance to temperature, acid, bile salts and osmotic and oxidative stress. Furthermore, the strain is absent of risk-related genes for acquired antibiotic resistance traits, virulence factors, toxic metabolites and detrimental metabolic or enzymatic activities. Resistance to common antibiotics and gelatinase and hemolytic activities have been discarded by in vitro experiments. This study identifies several probiotic and safety traits of L. salivarius P1CEA3 and suggests its potential as a promising probiotic in swine production.
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Affiliation(s)
| | | | | | | | | | | | - Juan Borrero
- Departamento de Nutrición y Ciencia de los Alimentos (NUTRYCIAL), Sección Departamental de Nutrición y Ciencia de los Alimentos (SD-NUTRYCIAL), Facultad de Veterinaria, Universidad Complutense de Madrid (UCM), Avenida Puerta de Hierro, s/n, 28040 Madrid, Spain; (E.S.); (I.L.); (N.P.); (L.M.C.); (E.M.-A.); (P.E.H.)
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Salgueiro V, Manageiro V, Rosado T, Bandarra NM, Botelho MJ, Dias E, Caniça M. Snapshot of resistome, virulome and mobilome in aquaculture. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166351. [PMID: 37604365 DOI: 10.1016/j.scitotenv.2023.166351] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 07/28/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023]
Abstract
Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including blaTEM-1B, blaFOX-18, aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.
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Affiliation(s)
- Vanessa Salgueiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal; AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Portugal
| | - Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal; AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Portugal
| | - Tânia Rosado
- Laboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Narcisa M Bandarra
- Division of Aquaculture, Upgrading and Bioprospecting, Portuguese Institute for the Sea and Atmosphere, IPMA, Lisbon, Portugal; CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Matosinhos, Portugal
| | - Maria João Botelho
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Matosinhos, Portugal; Division of Oceanography and Marine Environment, Portuguese Institute for the Sea and Atmosphere, Lisbon, Portugal
| | - Elsa Dias
- Laboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, Lisbon, Portugal; Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, Porto, Portugal; AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, Portugal; CIISA, Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal.
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Tataje-Lavanda L, Villanueva-Pérez D, Montalván-Avalos A, Vallejos-Sánchez K, Zimic-Peralta M, Fernández-Sánchez M, Fernández-Díaz M. Identification of virulence factors and antibiotic resistance in Salmonella enterica subsp. enterica serovar Javiana (FARPER-220) isolated from broiler chickens. Microbiol Resour Announc 2023; 12:e0032723. [PMID: 37943036 PMCID: PMC10720545 DOI: 10.1128/mra.00327-23] [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: 04/17/2023] [Accepted: 10/04/2023] [Indexed: 11/10/2023] Open
Abstract
Genome sequencing of highly virulent Salmonella enterica subsp. enterica serovar Javiana strain FARPER-220 (ST-1674) isolated from broiler chickens in Peru revealed multiple virulence factors, antibiotic resistance genes, and invasion-related subcategories. The results provide insights into the potential importance of this strain in causing infections in various animals.
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Affiliation(s)
- Luis Tataje-Lavanda
- Laboratorios de Investigación y Desarrollo, FARVET, Chincha Alta, Ica, Peru
- Escuela Profesional de Medicina Humana, Universidad Privada San Juan Bautista, Lima, Peru
| | | | | | | | - Mirko Zimic-Peralta
- Laboratorios de Investigación y Desarrollo, FARVET, Chincha Alta, Ica, Peru
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias, Universidad Peruana Cayetano Heredia, Lima, Peru
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Ružić-Sabljić E, Podgoršek D, Strašek Smrdel K, Celar Šturm A, Logar M, Pavlović A, Remec T, Baklan Z, Pal E, Cerar Kišek T. First Report on Leptospira Species Isolated from Patients in Slovenia. Microorganisms 2023; 11:2739. [PMID: 38004750 PMCID: PMC10672770 DOI: 10.3390/microorganisms11112739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Leptospirosis is an important worldwide zoonosis, and it has also been reported in Slovenia. The cultivation of Leptospira from human material is difficult. Despite that, we successfully isolated 12 human Leptospira strains isolated from patients between 2002 and 2020 and used various methods for the phenotypic and genotypic characterization of the strains, including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) using our own MALDI-TOF data library, melting temperature analysis of the amplified lfb1 gene, determination of Leptospira serogroups using rabbit immune sera, NotI-RFLP of the whole Leptospira genome, multilocus sequence typing (MLST) of seven housekeeping genes, and whole-genome sequencing (WGS)-based typing. We confirmed the presence of four pathogenic Leptospira species (L. kirschneri, L. interrogans, L. borgpetersenii, and L. santarosai) and three serogroups: Grippotyphosa, Icterohaemorrhagiae, and Sejroe. MALDI-TOF identified three of seven isolates at the species level and four isolates at the genus level. Serovars of 8 of the 10 strains were determined using NotI-RFLP. MLST showed that the clinical isolates belonged to sequence types ST17, ST110, and ST155. WGS confirmed the analysis of Leptospira strains using conventional methods. In addition, WGS provided better taxonomic resolution for isolate DDA 10944/10.
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Affiliation(s)
- Eva Ružić-Sabljić
- Institute of Microbiology and Immunology and Catedra for Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (E.R.-S.); (D.P.); (K.S.S.); (A.C.Š.)
| | - Daša Podgoršek
- Institute of Microbiology and Immunology and Catedra for Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (E.R.-S.); (D.P.); (K.S.S.); (A.C.Š.)
- Department of Pathology and Cytology, General Hospital Celje, Oblakova 5, 3000 Celje, Slovenia
| | - Katja Strašek Smrdel
- Institute of Microbiology and Immunology and Catedra for Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (E.R.-S.); (D.P.); (K.S.S.); (A.C.Š.)
| | - Andraž Celar Šturm
- Institute of Microbiology and Immunology and Catedra for Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (E.R.-S.); (D.P.); (K.S.S.); (A.C.Š.)
| | - Mateja Logar
- Department of Infectious Diseases, University Medical Center, Zaloška 2, 1000 Ljubljana, Slovenia;
- Catedra for Infectious Diseases and Epidemiology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Andrea Pavlović
- Department of Infectious Diseases, General Hospital Celje, Oblakova 5, 3000 Celje, Slovenia;
| | - Tatjana Remec
- Department of Infectious Diseases, General Hospital Novo Mesto, Šmihelska Cesta 1, 8000 Novo Mesto, Slovenia;
| | - Zvonko Baklan
- Department of Infectious Diseases, University Medical Center Maribor, Ljubljanska Ulica 5, 2000 Maribor, Slovenia;
| | - Emil Pal
- Department of Infectious Diseases, General Hospital Murska Sobota, Ulica dr. Vrbnjaka 6, 9000 Murska Sobota, Slovenia;
| | - Tjaša Cerar Kišek
- Institute of Microbiology and Immunology and Catedra for Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia; (E.R.-S.); (D.P.); (K.S.S.); (A.C.Š.)
- National Laboratory of Health, Environment and Food, Prvomajska 1, 2000 Maribor, Slovenia
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Gelalcha BD, Mohammed RI, Gelgie AE, Kerro Dego O. Molecular epidemiology and pathogenomics of extended-spectrum beta-lactamase producing- Escherichia coli and - Klebsiella pneumoniae isolates from bulk tank milk in Tennessee, USA. Front Microbiol 2023; 14:1283165. [PMID: 38029210 PMCID: PMC10658008 DOI: 10.3389/fmicb.2023.1283165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction The rise in extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in dairy cattle farms poses a risk to human health as they can spread to humans through the food chain, including raw milk. This study was designed to determine the status, antimicrobial resistance, and pathogenic potential of ESBL-producing -E. coli and -Klebsiella spp. isolates from bulk tank milk (BTM). Methods Thirty-three BTM samples were collected from 17 dairy farms and screened for ESBL-E. coli and -Klebsiella spp. on CHROMagar ESBL plates. All isolates were confirmed by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and subjected to antimicrobial susceptibility testing and whole genome sequencing (WGS). Results Ten presumptive ESBL-producing bacteria, eight E. coli, and two K. pneumoniae were isolated. The prevalence of ESBL-E. coli and -K. pneumoniae in BTM was 21.2% and 6.1%, respectively. ESBL-E. coli were detected in 41.2% of the study farms. Seven of the ESBL-E. coli isolates were multidrug resistant (MDR). The two ESBL-producing K. pneumoniae isolates were resistant to ceftriaxone. Seven ESBL-E. coli strains carry the blaCTX-M gene, and five of them co-harbored blaTEM-1. ESBL-E. coli co-harbored blaCTX-M with other resistance genes, including qnrB19, tet(A), aadA1, aph(3'')-Ib, aph(6)-Id), floR, sul2, and chromosomal mutations (gyrA, gyrB, parC, parE, and pmrB). Most E. coli resistance genes were associated with mobile genetic elements, mainly plasmids. Six sequence types (STs) of E. coli were detected. All ESBL-E. coli were predicted to be pathogenic to humans. Four STs (three ST10 and ST69) were high-risk clones of E. coli. Up to 40 virulence markers were detected in all E. coli isolates. One of the K. pneumoniae was ST867; the other was novel strain. K. pneumoniae isolates carried three types of beta-lactamase genes (blaCTX-M, blaTEM-1 and blaSHV). The novel K. pneumoniae ST also carried a novel IncFII(K) plasmid ST. Conclusion Detection of high-risk clones of MDR ESBL-E. coli and ESBL-K. pneumoniae in BTM indicates that raw milk could be a reservoir of potentially zoonotic ESBL-E. coli and -K. pneumoniae.
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Affiliation(s)
- Benti D. Gelalcha
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
| | - Ruwaa I. Mohammed
- Department of Genome Science and Technology, The University of Tennessee, Knoxville, TN, United States
| | - Aga E. Gelgie
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
| | - Oudessa Kerro Dego
- Department of Animal Science, The University of Tennessee, Knoxville, TN, United States
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Davidovich C, Awwad A, Fleker M, Weisblit L, Cytryn E, Blum SE. Complete genome sequence of multi-drug-resistant Salmonella enterica subsp. enterica serovar Typhimurium strain Bnaya isolated from a dairy calf in Israel. Microbiol Resour Announc 2023; 12:e0035123. [PMID: 37787537 PMCID: PMC10586145 DOI: 10.1128/mra.00351-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/27/2023] [Indexed: 10/04/2023] Open
Abstract
This manuscript reports the complete genome sequence of a Salmonella enterica subsp. enterica serovar Typhimurium strain (designated "Bnaya"), isolated from a dead dairy calf with severe diarrhea in Israel. The isolate exhibited multi-drug resistance, which is highly unusual in bovine Salmonella spp. in Israel, prompting further investigation.
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Affiliation(s)
- Chagai Davidovich
- Water and Environmental Sciences, Institute of Soil, Agricultural Research Organization, Rishon-Lezion, Israel
- Department of Agroecology and Plant Health, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Aya Awwad
- Department of Bacteriology and Mycology, Kimron Veterinary Institute, Bet Dagan, Israel
- Department of Animal Sciences, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Marcelo Fleker
- Department of Bacteriology and Mycology, Kimron Veterinary Institute, Bet Dagan, Israel
| | - Limor Weisblit
- Department of Bacteriology and Mycology, Kimron Veterinary Institute, Bet Dagan, Israel
| | - Eddie Cytryn
- Water and Environmental Sciences, Institute of Soil, Agricultural Research Organization, Rishon-Lezion, Israel
| | - Shlomo E. Blum
- Department of Bacteriology and Mycology, Kimron Veterinary Institute, Bet Dagan, Israel
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Hazarika DJ, Bora SS, Naorem RS, Sharma D, Boro RC, Barooah M. Genomic insights into Bacillus subtilis MBB3B9 mediated aluminium stress mitigation for enhanced rice growth. Sci Rep 2023; 13:16467. [PMID: 37777563 PMCID: PMC10542363 DOI: 10.1038/s41598-023-42804-9] [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: 06/07/2023] [Accepted: 09/14/2023] [Indexed: 10/02/2023] Open
Abstract
Aluminium (Al) toxicity in acid soil ecosystems is a major impediment to crop production as it drastically affects plant root growth, thereby acquisition of nutrients from the soil. Plant growth-promoting bacteria offers an interesting avenue for promoting plant growth under an Al-phytotoxic environment. Here, we report the plant growth-promoting activities of an acid-tolerant isolate of Bacillus subtilis that could ameliorate acid-induced Al-stress in rice (Oryza sativa L.). The whole genome sequence data identified the major genes and genetic pathways in B. subtilis MBB3B9, which contribute to the plant growth promotion in acidic pH. Genetic pathways for organic acid production, denitrification, urea metabolism, indole-3-acetic acid (IAA) production, and cytokinin biosynthesis were identified as major genetic machinery for plant growth promotion and mitigation of Al-stress in plants. The in-vitro analyses revealed the production of siderophores and organic acid production as primary mechanisms for mitigation of Al-toxicity. Other plant growth-promoting properties such as phosphate solubilization, zinc solubilization, and IAA production were also detected in significant levels. Pot experiments involving rice under acidic pH and elevated concentrations of aluminium chloride (AlCl3) suggested that soil treatment with bacterial isolate MBB3B9 could enhance plant growth and productivity compared to untreated plants. A significant increase in plant growth and productivity was recorded in terms of plant height, chlorophyll content, tiller number, panicle number, grain yield, root growth, and root biomass production.
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Affiliation(s)
- Dibya Jyoti Hazarika
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sudipta Sankar Bora
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Romen Singh Naorem
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Darshana Sharma
- DBT - North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India.
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Erickson VI, Khoi LM, Hounmanou YMG, Dung TT, Phu TM, Dalsgaard A. Comparative genomic analysis of Aeromonas dhakensis and Aeromonas hydrophila from diseased striped catfish fingerlings cultured in Vietnam. Front Microbiol 2023; 14:1254781. [PMID: 37808293 PMCID: PMC10556525 DOI: 10.3389/fmicb.2023.1254781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
Introduction Motile Aeromonas septicemia (MAS) is a burden for striped catfish (Pangasius hypophthalmus) farmers in Vietnam. MAS can be caused by several species of Aeromonas but Aeromonas hydrophila is seen as the leading cause of MAS in aquaculture, but recent reports suggest that A. dhakensis is also causing MAS. Methods Here we investigated the bacterial etiology of MAS and compared the genomic features of A. hydrophila and A. dhakensis. We collected 86 isolates from diseased striped catfish fingerlings over 5 years from eight provinces in Vietnam. Species identification was done using PCR, MALDI-TOF and whole genome sequence (WGS). The MICs of commonly used antimicrobials was established. Thirty presumed A. hydrophila isolates were sequenced for species confirmation and genomic comparison. A phylogenetic analysis was conducted using publicly available sequences and sequences from this study. Results A total of 25/30 isolates were A. dhakensis sequence type (ST) 656 and 5/30 isolates were A. hydrophila ST 251. Our isolates and all publicly available A. hydrophila isolates from Vietnam belonged to ST 251 and differed with <200 single nucleotide polymorphisms (SNP). Similarly, all A. dhakensis isolates from Vietnam belonged to ST 656 and differed with <100 SNPs. The tet(A) gene was found in 1/5 A. hydrophila and 19/25 A. dhakensis. All A. hydrophila had an MIC ≤2 mg/L while 19/25 A. dhakensis had MIC ≥8 mg/L for oxytetracycline. The floR gene was only found in A. dhakensis (14/25) which showed a MIC ≥8 mg/L for florfenicol. Key virulence genes, i.e., aerA/act, ahh1 and hlyA were present in all genomes, while ast was only present in A. dhakensis. Discussion This study confirms previous findings where A. dhakensis was the dominating pathogen causing MAS and that the importance of A. hydrophila has likely been overestimated. The differences in antimicrobial susceptibility between the two species could indicate a need for targeted antimicrobial treatment plans. The lipopolysaccharide regions and outer membrane proteins did not significantly differ in their immunogenic potentials, but it remains to be determined with in vivo experiments whether there is a difference in the efficacy of available vaccines against A. hydrophila and A. dhakensis.
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Affiliation(s)
- Vera Irene Erickson
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Le Minh Khoi
- Department of Aquatic Pathology, Can Tho University, Can Tho, Vietnam
| | | | - Tu Thanh Dung
- Department of Aquatic Pathology, Can Tho University, Can Tho, Vietnam
| | - Tran Minh Phu
- Department of Aquatic Product Processing, Can Tho University, Can Tho, Vietnam
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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Vieira ADA, Piccoli BC, Y Castro TR, Casarin BC, Tessele LF, Martins RCR, Schwarzbold AV, Trindade PDA. Pipeline validation for the identification of antimicrobial-resistant genes in carbapenem-resistant Klebsiella pneumoniae. Sci Rep 2023; 13:15189. [PMID: 37709838 PMCID: PMC10502106 DOI: 10.1038/s41598-023-42154-6] [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: 03/21/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023] Open
Abstract
Antimicrobial-resistant Klebsiella pneumoniae is a global threat to healthcare and an important cause of nosocomial infections. Antimicrobial resistance causes prolonged treatment periods, high mortality rates, and economic impacts. Whole Genome Sequencing (WGS) has been used in laboratory diagnosis, but there is limited evidence about pipeline validation to parse generated data. Thus, the present study aimed to validate a bioinformatics pipeline for the identification of antimicrobial resistance genes from carbapenem-resistant K. pneumoniae WGS. Sequences were obtained from a publicly available database, trimmed, de novo assembled, mapped to the K. pneumoniae reference genome, and annotated. Contigs were submitted to different tools for bacterial (Kraken2 and SpeciesFinder) and antimicrobial resistance gene identification (ResFinder and ABRicate). We analyzed 201 K. pneumoniae genomes. In the bacterial identification by Kraken2, all samples were correctly identified, and in SpeciesFinder, 92.54% were correctly identified as K. pneumoniae, 6.96% erroneously as Pseudomonas aeruginosa, and 0.5% erroneously as Citrobacter freundii. ResFinder found a greater number of antimicrobial resistance genes than ABRicate; however, many were identified more than once in the same sample. All tools presented 100% repeatability and reproducibility and > 75% performance in other metrics. Kraken2 was more assertive in recognizing bacterial species, and SpeciesFinder may need improvements.
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Affiliation(s)
- Andressa de Almeida Vieira
- Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Bruna Candia Piccoli
- Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Thaís Regina Y Castro
- Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Bruna Campestrini Casarin
- Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Luiza Funck Tessele
- Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil
| | - Roberta Cristina Ruedas Martins
- Laboratório de Parasitologia Médica (LIM-46), Departamento de Doenças Infecciosas e Parasitárias, Instituto de Medicina Tropical da Universidade de São Paulo, Faculdade de Medicina da Universidade de São Paulo, São Paulo, 01246-903, Brazil
| | | | - Priscila de Arruda Trindade
- Laboratório de Biologia Molecular e Bioinformática Aplicada à Microbiologia Clínica, Programa de Pós-Graduação em Ciências Farmacêuticas, Universidade Federal de Santa Maria, Santa Maria, 97105-900, Brazil.
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Nuanmuang N, Leekitcharoenphon P, Njage PMK, Gmeiner A, Aarestrup FM. An Overview of Antimicrobial Resistance Profiles of Publicly Available Salmonella Genomes with Sufficient Quality and Metadata. Foodborne Pathog Dis 2023; 20:405-413. [PMID: 37540138 PMCID: PMC10510693 DOI: 10.1089/fpd.2022.0080] [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] [Indexed: 08/05/2023] Open
Abstract
Salmonella enterica (S. enterica) is a commensal organism or pathogen causing diseases in animals and humans, as well as widespread in the environment. Antimicrobial resistance (AMR) has increasingly affected both animal and human health and continues to raise public health concerns. A decade ago, it was estimated that the increased use of whole genome sequencing (WGS) combined with sharing of public data would drastically change and improve the surveillance and understanding of Salmonella epidemiology and AMR. This study aimed to evaluate the current usefulness of public WGS data for Salmonella surveillance and to investigate the associations between serovars, antibiotic resistance genes (ARGs), and metadata. Out of 191,306 Salmonella genomes deposited in European Nucleotide Archive and NCBI databases, 47,452 WGS with sufficient minimum metadata (country, year, and source) of S. enterica were retrieved from 116 countries and isolated between 1905 and 2020. For in silico analysis of the WGS data, KmerFinder, SISTR, and ResFinder were used for species, serovars, and AMR identification, respectively. The results showed that the five common isolation sources of S. enterica are human (29.10%), avian (22.50%), environment (11.89%), water (9.33%), and swine (6.62%). The most common ARG profiles for each class of antimicrobials are β-lactam (blaTEM-1B; 6.78%), fluoroquinolone [(parC[T57S], qnrB19); 0.87%], folate pathway antagonist (sul2; 8.35%), macrolide [mph(A); 0.39%], phenicol (floR; 5.94%), polymyxin B (mcr-1.1; 0.09%), and tetracycline [tet(A); 12.95%]. Our study reports the first overview of ARG profiles in publicly available Salmonella genomes from online databases. All data sets from this study can be searched at Microreact.
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Affiliation(s)
- Narong Nuanmuang
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Patrick Murigu Kamau Njage
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Alexander Gmeiner
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Frank M. Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kgs. Lyngby, Denmark
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Choi H, Navarathna DH, Harston BL, Hwang M, Corona B, San Juan MR, Jinadatha C. Case of Extensively Drug-Resistant Shigella sonnei Infection, United States. Emerg Infect Dis 2023; 29:1708-1711. [PMID: 37486233 PMCID: PMC10370867 DOI: 10.3201/eid2908.230411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
We report extensively drug-resistant (XDR) Shigella sonnei infection in an immunocompromised patient in Texas, USA. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry failed to identify XDR Shigella, but whole-genome sequencing accurately characterized the strain. First-line antimicrobials are not effective against emerging XDR Shigella. Fosfomycin, carbapenems, and tigecycline are potential alternatives.
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Mazumder R, Hussain A, Rahman MM, Phelan JE, Campino S, Abdullah A, Clark TG, Mondal D. Genomic and functional portrait of multidrug-resistant, hydrogen sulfide (H 2S)-producing variants of Escherichia coli. Front Microbiol 2023; 14:1206757. [PMID: 37577429 PMCID: PMC10414542 DOI: 10.3389/fmicb.2023.1206757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Atypical Escherichia coli forms exhibit unusual characteristics compared to typical strains. The H2S-producing variants of some atypical E. coli strains cause a wide range of illnesses in humans and animals. However, there are sparse reports on such strains worldwide. We performed whole-genome sequencing (WGS) and detailed characterization of four H2S-producing E. coli variants from poultry and human clinical sources in Dhaka, Bangladesh. All four isolates were confirmed as E. coli using biochemical tests and genomic analysis, and were multidrug-resistant (MDR). WGS analysis including an additional Chinese strain, revealed diverse STs among the five H2S-producing E. coli genomes, with clonal complex ST10 being detected in 2 out of 5 genomes. The predominant phylogroup detected was group A (n = 4/5). The blaTEM1B (n = 5/5) was the most predominant extended-spectrum beta-lactamase (ESBL) gene, followed by different alleles of blaCTX-M (blaCTX-M -55,-65,-123; n = 3/5). Multiple plasmid replicons were detected, with IncX being the most common. One E. coli strain was classified as enteropathogenic E. coli. The genomes of all five isolates harbored five primary and four secondary function genes related to H2S production. These findings suggest the potential of these isolates to cause disease and spread antibiotic resistance. Therefore, such atypical E. coli forms should be included in differential diagnosis to understand the pathogenicity, antimicrobial resistance and evolution of H2S-producing E. coli.
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Affiliation(s)
- Razib Mazumder
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Arif Hussain
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | | | - Jody E. Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Ahmed Abdullah
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dinesh Mondal
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
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Hassell JM, Muloi DM, VanderWaal KL, Ward MJ, Bettridge J, Gitahi N, Ouko T, Imboma T, Akoko J, Karani M, Muinde P, Nakamura Y, Alumasa L, Furmaga E, Kaitho T, Amanya F, Ogendo A, Fava F, Wee BA, Phan H, Kiiru J, Kang’ethe E, Kariuki S, Robinson T, Begon M, Woolhouse MEJ, Fèvre EM. Epidemiological connectivity between humans and animals across an urban landscape. Proc Natl Acad Sci U S A 2023; 120:e2218860120. [PMID: 37450494 PMCID: PMC10629570 DOI: 10.1073/pnas.2218860120] [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: 11/04/2022] [Accepted: 05/19/2023] [Indexed: 07/18/2023] Open
Abstract
Urbanization is predicted to be a key driver of disease emergence through human exposure to novel, animal-borne pathogens. However, while we suspect that urban landscapes are primed to expose people to novel animal-borne diseases, evidence for the mechanisms by which this occurs is lacking. To address this, we studied how bacterial genes are shared between wild animals, livestock, and humans (n = 1,428) across Nairobi, Kenya-one of the world's most rapidly developing cities. Applying a multilayer network framework, we show that low biodiversity (of both natural habitat and vertebrate wildlife communities), coupled with livestock management practices and more densely populated urban environments, promotes sharing of Escherichia coli-borne bacterial mobile genetic elements between animals and humans. These results provide empirical support for hypotheses linking resource provision, the biological simplification of urban landscapes, and human and livestock demography to urban dynamics of cross-species pathogen transmission at a landscape scale. Urban areas where high densities of people and livestock live in close association with synanthropes (species such as rodents that are more competent reservoirs for zoonotic pathogens) should be prioritized for disease surveillance and control.
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Affiliation(s)
- James M. Hassell
- Global Health Program, Smithsonian’s National Zoo and Conservation Biology Institute, Washington, DC20008
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, CT06510
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolL69 3BX, United Kingdom
| | - Dishon M. Muloi
- Usher Institute, University of Edinburgh, EdinburghEH16 4SS, United Kingdom
- International Livestock Research Institute, 00100Nairobi, Kenya
- Centre for Immunity, Infection and Evolution, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Kimberly L. VanderWaal
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN55108
| | - Melissa J. Ward
- Usher Institute, University of Edinburgh, EdinburghEH16 4SS, United Kingdom
- Nuffield Department of Clinical Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
- Faculty of Medicine, University of Southampton, SouthamtonSO17 1BJ, United Kingdom
| | - Judy Bettridge
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolL69 3BX, United Kingdom
- International Livestock Research Institute, 00100Nairobi, Kenya
| | | | - Tom Ouko
- Kenya Medical Research Institute, 00200Nairobi, Kenya
| | | | - James Akoko
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Maurice Karani
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Patrick Muinde
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Yukiko Nakamura
- Faculty of Veterinary Medicine, Hokkaido University, Sapporo060-0818, Japan
| | - Lorren Alumasa
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Erin Furmaga
- Department of Epidemiology, Columbia University, New York, NY10032
| | - Titus Kaitho
- Veterinary Services Department, Kenya Wildlife Service, 00100Nairobi, Kenya
| | - Fredrick Amanya
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Allan Ogendo
- International Livestock Research Institute, 00100Nairobi, Kenya
| | - Francesco Fava
- International Livestock Research Institute, 00100Nairobi, Kenya
- Department of Environmental Science and Policy, Università degli Studi di Milano, 20133Milan, Italy
| | - Bryan A. Wee
- Usher Institute, University of Edinburgh, EdinburghEH16 4SS, United Kingdom
| | - Hang Phan
- Nuffield Department of Clinical Medicine, University of Oxford, OxfordOX3 7BN, United Kingdom
| | - John Kiiru
- Kenya Medical Research Institute, 00200Nairobi, Kenya
| | | | - Sam Kariuki
- Kenya Medical Research Institute, 00200Nairobi, Kenya
| | - Timothy Robinson
- Food and Agriculture Organization of the United Nations, 00153Rome, Italy
| | - Michael Begon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolL69 3BX, United Kingdom
| | - Mark E. J. Woolhouse
- Usher Institute, University of Edinburgh, EdinburghEH16 4SS, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Eric M. Fèvre
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, LiverpoolL69 3BX, United Kingdom
- International Livestock Research Institute, 00100Nairobi, Kenya
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Carlsen L, Büttner H, Christner M, Cordts L, Franke G, Hoffmann A, Knobling B, Lütgehetmann M, Nakel J, Werner T, Knobloch JK. Long time persistence and evolution of carbapenemase-producing Enterobacterales in the wastewater of a tertiary care hospital in Germany. J Infect Public Health 2023; 16:1142-1148. [PMID: 37267681 DOI: 10.1016/j.jiph.2023.05.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023] Open
Abstract
BACKGROUND Worldwide observations revealed increased frequencies of multi-resistant Enterobacterales and resistance genes in hospital wastewater compared to any other type of wastewater. Despite the description of clonal lineages possibly adapted to hospital wastewater, little is known about long term persistence as well as evolution of these lineages. METHODS In this study, wastewater isolates of different Enterobacterales species from a tertiary care hospital were investigated with 2.5 years distance. Whole Genome Sequencing (WGS) and resistance gene identification were performed for E. coli, C. freundii, S. marcescens, K. pneumoniae, K. oxytoca, and E. cloacae isolates (n = 59), isolated in 2022 and compared with strains isolated from the same wastewater pipeline in 2019 (n = 240). RESULTS Individual clonal lineages with highly related isolates could be identified in all species identified more than once in 2022 that appear to persist in the wastewater drainage. A common motif of all persistent clonal lineages was the carriage of mobile genetic elements encoding carbapenemase genes with hints for horizontal gene transfer in persistent clones in this environment observed over the 2.5-year period. Multiple plasmid replicons could be detected in both years. In 2022 isolates blaVIM-1 replaced blaOXA-48 as the most common carbapenemase gene compared to 2019. Interestingly, despite a similar abundance of carbapenemase genes (>80% of all isolates) at both time points genes encoding extended spectrum β-lactamases decreased over time. CONCLUSIONS This data indicates that hospital wastewater continuously releases genes encoding carbapenemases to the urban wastewater system. The evolution of the resident clones as well as the reasons for the selection advantage in this specific ecological niche needs to be further investigated in the future.
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Affiliation(s)
- Laura Carlsen
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Henning Büttner
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Martin Christner
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Lukas Cordts
- HAMBURG WASSER, Billhorner Deich 2, 20539 Hamburg, Germany
| | - Gefion Franke
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Armin Hoffmann
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Birte Knobling
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology, and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany
| | - Jacqueline Nakel
- Virus Genomics, Heinrich-Pette-Institute, Leibniz Institute for Experimental Biology, Martinistraße 52, 20251 Hamburg, Germany
| | - Thomas Werner
- HAMBURG WASSER, Billhorner Deich 2, 20539 Hamburg, Germany
| | - Johannes K Knobloch
- Institute of Medical Microbiology, Virology, and Hygiene, Department for Infection Prevention and Control, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246 Hamburg, Germany.
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Cantelmi MC, Merola C, Averaimo D, Chiaverini A, Cito F, Cocco A, Di Teodoro G, De Angelis ME, Di Bernardo D, Auzino D, Petrini A. Identification of the Novel Streptococcus equi subsp. zooepidemicus Sequence Type 525 in Donkeys of Abruzzo Region, Italy. Pathogens 2023; 12:750. [PMID: 37375440 PMCID: PMC10305129 DOI: 10.3390/pathogens12060750] [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: 04/26/2023] [Revised: 05/15/2023] [Accepted: 05/21/2023] [Indexed: 06/29/2023] Open
Abstract
Streptococcus equi sub. zooepidemicus (SEZ) is described as a commensal bacterium of several animal species, including humans. Growing evidence supports the potential role of SEZ in the onset and progression of severe clinical manifestations of diseases in horses and other animals. In the present communication, we describe the diagnostic procedure applied to characterize the streptococcal infections caused by a novel SEZ sequence type (ST525) in donkeys raised on a farm in Abruzzo, Italy. The diagnostic process began with anamnesis and anatomopathological analysis, which revealed a severe bacterial suppurative bronchopneumonia associated with systemic vascular damage and haemorrhages. Then, SEZ infection was confirmed by applying an integrative diagnostic strategy that included standard bacterial isolation techniques, analytical tools for bacteria identification (MALDI-TOF MS), and molecular analysis (qPCR). Furthermore, the application of the whole-genome sequencing approach helped us to identify the bacterial strains and the virulence factors involved in animal diseases. The novel SEZ-ST525 was identified in two cases of the disease. This new sequence type was isolated from the lung, liver, and spleen in Case 1, and from retropharyngeal lymph nodes in Case 2. Moreover, the presence of the virulence gene mf2, a virulence factor carried by prophages in Streptococcus pyogenes, was also found for the first time in an SEZ strain. The results of the present study highlight the need to apply an integrated diagnostic approach for the identification and tracking of pathogenic strains of SEZ, shedding new light on the re-evaluation of these bacteria as a causative agent of disease in animals and humans.
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Affiliation(s)
- Maria Chiara Cantelmi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Carmine Merola
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Daniela Averaimo
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | - Alexandra Chiaverini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | - Francesca Cito
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
- Department of Veterinary Medicine, University of Teramo, 64100 Teramo, Italy
| | - Antonio Cocco
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | - Giovanni Di Teodoro
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | - Maria Elisabetta De Angelis
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
| | | | - Davide Auzino
- Freelance Veterinary Practitioner, 65019 Pescara, Italy; (D.D.B.); (D.A.)
| | - Antonio Petrini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e Molise “G. Caporale”, Campo Boario, 64100 Teramo, Italy; (M.C.C.); (D.A.); (A.C.); (F.C.); (A.C.); (G.D.T.); (M.E.D.A.); (A.P.)
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49
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Bosica S, Chiaverini A, De Angelis ME, Petrini A, Averaimo D, Martino M, Rulli M, Saletti MA, Cantelmi MC, Ruggeri F, Lodi F, Calistri P, Cito F, Cammà C, Di Domenico M, Rinaldi A, Fazii P, Cedrone F, Di Martino G, Accorsi P, Morelli D, De Luca N, Pomilio F, Parruti G, Savini G. Severe Streptococcus equi Subspecies zooepidemicus Outbreak from Unpasteurized Dairy Product Consumption, Italy. Emerg Infect Dis 2023; 29:1020-1024. [PMID: 37081588 PMCID: PMC10124651 DOI: 10.3201/eid2905.221338] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
During November 2021-May 2022, we identified 37 clinical cases of Streptococcus equi subspecies zooepidemicus infections in central Italy. Epidemiologic investigations and whole-genome sequencing showed unpasteurized fresh dairy products were the outbreak source. Early diagnosis by using sequencing technology prevented the spread of life-threatening S. equi subsp. zooepidemicus infections.
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50
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Rose TFA, Kannan P, Ruban SW, Srinivas K, Milton AAP, Ghatak S, Elango A, Rajalakshmi S, Sundaram S. Isolation, susceptibility profiles and genomic analysis of a colistin-resistant Salmonella enterica serovar Kentucky strain COL-R. 3 Biotech 2023; 13:140. [PMID: 37124985 PMCID: PMC10133420 DOI: 10.1007/s13205-023-03559-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Salmonella enterica serovar Kentucky is a frequent cause for clinical infections in human patients. They are isolated and reported with multidrug resistance from the foods of animal origin from various countries. However, studies inferring the colistin resistance are limited. Hence, the current study reports the genetic factors and genomic analysis of the colistin-resistant Salmonella enterica serovar Kentucky strain COL-R for better understanding of its pathogenic potential and phylogenetic relatedness. The S. Kentucky strain COL-R was successfully isolated from chicken meat during ongoing surveillance of food of animal origin. Antimicrobial susceptibility testing revealed resistance to cefoxitin, erythromycin, gentamicin, tetracycline, and most disturbingly to ciprofloxacin and colistin (broth microdilution method). Whole-genome sequence of the COL-R strain was subjected to various in silico analysis to identify the virulence factors, antimicrobial resistance genes, pathogenicity islands and sequence type. The S. Kentucky COL-R strain belonged to sequence type (ST) 198 with a high probability (0.943) of being a human pathogen. Besides presence of integrated phage in the S. Kentucky COL-R genome, 38 genes conferring resistance to various antimicrobials and disinfectants were also identified. Nucleotide Polymorphism analysis indicated triple mutations in gyrA and parC genes conferring fluoroquinolone resistance. Phylogenomic analysis with 31 other S. Kentucky genomes revealed discernible clusters with S. Kentucky COL-R strain latching onto a cluster of high diversity (geographic location and isolation sources). Taken together, our results document the first occurrence of colistin resistance in a fluoroquinolone resistant S. Kentucky COL-R strain isolated from retail chicken and provide crucial information on the genomic features of the strain. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03559-2.
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Affiliation(s)
- T. F. Amal Rose
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
| | - Porteen Kannan
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
| | - S. Wilfred Ruban
- Department of Livestock Products Technology, Veterinary College, KVAFSU, Hebbal, Bangalore, 560024 India
| | - Kandhan Srinivas
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122 India
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, 793103 India
| | | | - Sandeep Ghatak
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, 793103 India
| | - A. Elango
- Veterinary College and Research Institute, TANUVAS, Salem, 636112 India
| | - S. Rajalakshmi
- Department of Veterinary Microbiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
| | - Sureshkannan Sundaram
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
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