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Sudhakari PA, Ramisetty BCM. Resistome Diversity in Escherichia coli Isolates of Global Wastewaters. Microb Drug Resist 2024; 30:37-49. [PMID: 38150178 DOI: 10.1089/mdr.2022.0296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global health threat requiring urgent attention and effective strategies for containment. AMR is fueled by wastewater mismanagement and global mobility, disseminating multidrug-resistant (MDR) strains worldwide. While global estimates of AMR burden have been informative, community-level understanding has received little attention despite reports of high AMR prevalence in healthy communities. We assessed the "invasion" of antibiotic resistance genes (ARGs) into the normal human flora by characterizing AMR Escherichia coli in local wastewaters contributed by a healthy youth population. This study estimated 26% (out of 300 isolates) resistant and 59% plasmid-bearing E. coli in local wastewater. Of the 78 AMR isolates, the frequency of mono-resistance was higher against tetracycline (32%), followed by kanamycin (17%) and chloramphenicol (9%). Five isolates were potentially MDR. We further sequenced four MDRs and four sensitive strains to comprehend the genome and resistome diversity in comparison to the global wastewater E. coli (genomes from the PATRIC database). The whole-genome analysis revealed extensive genome similarity among global isolates, suggesting global dissemination and colonization of E. coli. Global wastewater resistome majorly comprised ARGs against aminoglycosides (26%), beta-lactam (17%), sulfonamide (11%), and trimethoprim (8%). Resistance to colistin, a last-resort antibiotic, was prevalent in MDRs of European and South Asian isolates. A systems approach is required to address the AMR crisis on a global scale, reduce antibiotic usage, and increase the efficiency of wastewater management and disinfection.
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Affiliation(s)
- Pavithra Anantharaman Sudhakari
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Bhaskar Chandra Mohan Ramisetty
- Laboratory of Molecular Biology and Evolution, 312@ASK1, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
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Wang Y, Xu X, Zhu B, Lyu N, Liu Y, Ma S, Jia S, Wan B, Du Y, Zhang G, Gao GF. Genomic analysis of almost 8,000 Salmonella genomes reveals drivers and landscape of antimicrobial resistance in China. Microbiol Spectr 2023; 11:e0208023. [PMID: 37787535 PMCID: PMC10714754 DOI: 10.1128/spectrum.02080-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/14/2023] [Indexed: 10/04/2023] Open
Abstract
IMPORTANCE We established the largest Salmonella genome database from China and presented the landscape and spatiotemporal dynamics of antimicrobial resistance genes. We also found that economic, climatic, and social factors can drive the rise of antimicrobial resistance. The Chinese local Salmonella genome database version 2 was released as an open-access database (https://nmdc.cn/clsgdbv2) and thus can assist surveillance studies across the globe. This database will help inform interventions for AMR, food safety, and public health.
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Affiliation(s)
- Yanan Wang
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
| | - Xuebin Xu
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Baoli Zhu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- Beijing Key Laboratory of Antimicrobial Resistance and Pathogen Genomics, Beijing, China
- Department of Pathogenic Biology, School of Basic Medical Sciences, Southwest Medical University, Luzhou, Sichuan, China
| | - Na Lyu
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yue Liu
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Sufang Ma
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Shulei Jia
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Bo Wan
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
| | - Yongkun Du
- International Joint Research Center of National Animal Immunology, College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
| | - Gaiping Zhang
- Longhu Laboratory of Advanced Immunology, Zhengzhou, Henan, China
| | - George F. Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
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Yang C, Das Q, Rehman MA, Yin X, Shay J, Gauthier M, Lau CHF, Ross K, Diarra MS. Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces. Microorganisms 2023; 11:1184. [PMID: 37317158 DOI: 10.3390/microorganisms11051184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/20/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
American cranberry (Vaccinium macrocarpon) and lowbush/wild blueberry (V. angustifolium) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of Lactobacillus and a higher abundance of Escherichia coli than non-vaccinated birds (p < 0.05). The highest and lowest abundance of L. crispatus and E. coli, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (p < 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (p < 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (p < 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (p < 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (p < 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, β-lactams, lincosamides, and trimethoprim resistance genes (p < 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens.
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Affiliation(s)
- Chongwu Yang
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada
| | - Quail Das
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada
| | - Muhammad A Rehman
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada
| | - Xianhua Yin
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada
| | - Julie Shay
- Ottawa Laboratory (Carling) Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1Y 4K7, Canada
| | - Martin Gauthier
- Biological Informatics Centre of Excellence, AAFC, Saint-Hyacinthe, QC J2S 8E3, Canada
| | - Calvin Ho-Fung Lau
- Ottawa Laboratory (Carling) Research and Development, Canadian Food Inspection Agency, Ottawa, ON K1Y 4K7, Canada
| | - Kelly Ross
- Summerland Research and Development Center, AAFC, Summerland, BC V0H 1Z0, Canada
| | - Moussa S Diarra
- Guelph Research and Development Center, Agriculture and Agri-Food Canada (AAFC), Guelph, ON N1G 5C9, Canada
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Francis IM, Bergin D, Deflandre B, Gupta S, Salazar JJC, Villagrana R, Stulanovic N, Ribeiro Monteiro S, Kerff F, Loria R, Rigali S. Role of Alternative Elicitor Transporters in the Onset of Plant Host Colonization by Streptomyces scabiei 87-22. Biology (Basel) 2023; 12. [PMID: 36829511 DOI: 10.3390/biology12020234] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
Plant colonization by Streptomyces scabiei, the main cause of common scab disease on root and tuber crops, is triggered by cello-oligosaccharides, cellotriose being the most efficient elicitor. The import of cello-oligosaccharides via the ATP-binding cassette (ABC) transporter CebEFG-MsiK induces the production of thaxtomin phytotoxins, the central virulence determinants of this species, as well as many other metabolites that compose the 'virulome' of S. scabiei. Homology searches revealed paralogues of the CebEFG proteins, encoded by the cebEFG2 cluster, while another ABC-type transporter, PitEFG, is encoded on the pathogenicity island (PAI). We investigated the gene expression of these candidate alternative elicitor importers in S. scabiei 87-22 upon cello-oligosaccharide supply by transcriptomic analysis, which revealed that cebEFG2 expression is highly activated by both cellobiose and cellotriose, while pitEFG expression was barely induced. Accordingly, deletion of pitE had no impact on virulence and thaxtomin production under the conditions tested, while the deletion of cebEFG2 reduced virulence and thaxtomin production, though not as strong as the mutants of the main cello-oligosaccharide transporter cebEFG1. Our results thus suggest that both ceb clusters participate, at different levels, in importing the virulence elicitors, while PitEFG plays no role in this process under the conditions tested. Interestingly, under more complex culture conditions, the addition of cellobiose restored thaxtomin production when both ceb clusters were disabled, suggesting the existence of an additional mechanism that is involved in sensing or importing the elicitor of the onset of the pathogenic lifestyle of S. scabiei.
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Bongiorno D, Bivona DA, Cicino C, Trecarichi EM, Russo A, Marascio N, Mezzatesta ML, Musso N, Privitera GF, Quirino A, Scarlata GGM, Matera G, Torti C, Stefani S. Omic insights into various ceftazidime-avibactam-resistant Klebsiella pneumoniae isolates from two southern Italian regions. Front Cell Infect Microbiol 2023; 12:1010979. [PMID: 36683697 PMCID: PMC9851273 DOI: 10.3389/fcimb.2022.1010979] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/12/2022] [Indexed: 01/06/2023] Open
Abstract
Ceftazidime-avibactam (CZA) is one of the best therapeutic options available for infections caused by Klebsiella pneumoniae carbapenemase (KPC)-producing bacteria. However, sporadic reports of CZA-resistant strains have been rapidly increasing in patients. Herein, we provide detailed case reports of the emergence of ceftazidime-avibactam resistance to identify their resistome and virulome using genomic molecular approaches. Sixteen isolates were collected from 13 patients at three hospitals in Catania and Catanzaro (Italy) between 2020-2021. Antimicrobial susceptibility was determined by broth microdiluition. The samples included in study were analyzed for resistome, virulome and Sequence Type (ST) using Whole Genome Sequencing (WGS). All strains were resistant to ceftazidime/avibactam, ciprofloxacin, extended-spectrum cephalosporins and aztreonam, 13/16 to meropenem, 8/16 to colistin and 7/16 to fosfomycin; 15/16 were susceptible to meropenem/vaborbactam; all strains were susceptible to cefiderocol. Molecular analysis showed circulation of three major clones: ST101, ST307 and ST512. In 10/16 strains, we found a bla KPC-3 gene; in 6/16 strains, four different bla KPC variants (bla KPC28-31-34-50) were detected. A plethora of other beta-lactam genes (bla SHV28-45-55-100-106-187-205-212, bla OXA1-9-48, bla TEM-181 and bla CTX-M-15) was observed; bla OXA-9 was found in ST307 and ST512, instead bla OXA48 in one out four ST101 strains. With regard to membrane permeability, ompK35 and ompK36 harbored frameshift mutations in 15/16 strains; analysis of ompK37 gene revealed that all strains harbored a non-functional protein and carry wild-type PBP3. There is an urgent need to characterize the mechanisms underlying carbapenem resistance and the intrinsic bacterial factors that facilitate the rapid emergence of resistance. Furthermore, it is becoming increasingly important to explore feasible methods for accurate detection of different KPC enzymes.
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Affiliation(s)
- Dafne Bongiorno
- Microbiology Section, Dept of Biomedical and Biotechnological Science, University of Catania, Catania, Italy,*Correspondence: Dafne Bongiorno,
| | - Dalida A. Bivona
- Microbiology Section, Dept of Biomedical and Biotechnological Science, University of Catania, Catania, Italy
| | - Claudia Cicino
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Enrico M. Trecarichi
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Alessandro Russo
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Nadia Marascio
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Maria Lina Mezzatesta
- Microbiology Section, Dept of Biomedical and Biotechnological Science, University of Catania, Catania, Italy
| | - Nicolò Musso
- Microbiology Section, Dept of Biomedical and Biotechnological Science, University of Catania, Catania, Italy,Unità Operativa Complessa (UOC) Laboratory Analysis, University Hospital Policlinico-San Marco, Catania, Italy
| | - Grete F. Privitera
- Microbiology Section, Dept of Biomedical and Biotechnological Science, University of Catania, Catania, Italy
| | - Angela Quirino
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Giuseppe G. M. Scarlata
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Giovanni Matera
- Unit of Clinical Microbiology, Department of Health Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Carlo Torti
- Unit of Infectious and Tropical Diseases, Department of Medical and Surgical Sciences, “Magna Graecia” University, Catanzaro, Italy
| | - Stefania Stefani
- Microbiology Section, Dept of Biomedical and Biotechnological Science, University of Catania, Catania, Italy,Unità Operativa Complessa (UOC) Laboratory Analysis, University Hospital Policlinico-San Marco, Catania, Italy
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El-Adawy H, Hotzel H, García-Soto S, Tomaso H, Hafez HM, Schwarz S, Neubauer H, Linde J. Genomic insight into Campylobacter jejuni isolated from commercial turkey flocks in Germany using whole-genome sequencing analysis. Front Vet Sci 2023; 10:1092179. [PMID: 36875995 PMCID: PMC9978446 DOI: 10.3389/fvets.2023.1092179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 01/23/2023] [Indexed: 02/18/2023] Open
Abstract
Campylobacter (C.) jejuni is a zoonotic bacterium of public health significance. The present investigation was designed to assess the epidemiology and genetic heterogeneity of C. jejuni recovered from commercial turkey farms in Germany using whole-genome sequencing. The Illumina MiSeq® technology was used to sequence 66 C. jejuni isolates obtained between 2010 and 2011 from commercial meat turkey flocks located in ten German federal states. Phenotypic antimicrobial resistance was determined. Phylogeny, resistome, plasmidome and virulome profiles were analyzed using whole-genome sequencing data. Genetic resistance markers were identified with bioinformatics tools (AMRFinder, ResFinder, NCBI and ABRicate) and compared with the phenotypic antimicrobial resistance. The isolates were assigned to 28 different sequence types and 11 clonal complexes. The average pairwise single nucleotide-polymorphisms distance of 14,585 SNPs (range: 0-26,540 SNPs) revealed a high genetic distinction between the isolates. Thirteen virulence-associated genes were identified in C. jejuni isolates. Most of the isolates harbored the genes flaA (83.3%) and flaB (78.8%). The wlaN gene associated with the Guillain-Barré syndrome was detected in nine (13.6%) isolates. The genes for resistance to ampicillin (bla OXA), tetracycline [tet(O)], neomycin [aph(3')-IIIa], streptomycin (aadE) and streptothricin (sat4) were detected in isolated C. jejuni using WGS. A gene cluster comprising the genes sat4, aph(3')-IIIa and aadE was present in six isolates. The single point mutation T86I in the housekeeping gene gyrA conferring resistance to quinolones was retrieved in 93.6% of phenotypically fluoroquinolone-resistant isolates. Five phenotypically erythromycin-susceptible isolates carried the mutation A103V in the gene for the ribosomal protein L22 inferring macrolide resistance. An assortment of 13 β-lactam resistance genes (bla OXA variants) was detected in 58 C. jejuni isolates. Out of 66 sequenced isolates, 28 (42.4%) carried plasmid-borne contigs. Six isolates harbored a pTet-like plasmid-borne contig which carries the tet(O) gene. This study emphasized the potential of whole-genome sequencing to ameliorate the routine surveillance of C. jejuni. Whole-genome sequencing can predict antimicrobial resistance with a high degree of accuracy. However, resistance gene databases need curation and updates to revoke inaccuracy when using WGS-based analysis pipelines for AMR detection.
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Affiliation(s)
- Hosny El-Adawy
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany.,Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Helmut Hotzel
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Silvia García-Soto
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Herbert Tomaso
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Hafez M Hafez
- Institute of Poultry Diseases, Free University Berlin, Berlin, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.,Veterinary Centre of Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
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Chiu CY, Chang KC, Chang LC, Wang CJ, Chung WH, Hsieh WP, Su SC. Phenotype-specific signatures of systems-level gut microbiome associated with childhood airway allergies. Pediatr Allergy Immunol 2023; 34:e13905. [PMID: 36705037 DOI: 10.1111/pai.13905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 01/14/2023]
Abstract
BACKGROUND Perturbation of gut symbiosis has been linked to childhood allergic diseases. However, the underlying host-microbe interaction connected with specific phenotypes is poorly understood. METHODS To address this, integrative analyses of stool metagenomic and metabolomic profiles associated with IgE reactions in 56 children with mite-sensitized airway allergies (25 with rhinitis and 31 with asthma) and 28 nonallergic healthy controls were conducted. RESULTS We noted a decrease in the number and abundance of gut microbiome-encoded carbohydrate-active enzyme (CAZyme) genes, accompanied with a reduction in species richness, in the asthmatic gut microflora but not in that from allergic rhinitis. Such loss of CAZymes was consistent with the observation that a CAZyme-linked decrease in fecal butyrate was found in asthmatics and negatively correlated with mite-specific IgE responses. Different from the CAZymes, we demonstrated an increase in α diversity at the virulome levels in asthmatic gut microbiota and identified phenotype-specific variations of gut virulome. Moreover, use of fecal metagenomic and metabolomic signatures resulted in distinct effects on differentiating rhinitis and asthma from nonallergic healthy controls. CONCLUSION Overall, our integrative analyses reveal several signatures of systems-level gut microbiome in robust associations with fecal metabolites and disease phenotypes, which may be of etiological and diagnostic implications in childhood airway allergies.
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Affiliation(s)
- Chih-Yung Chiu
- Division of Pediatric Pulmonology, Chang Gung Memorial Hospital at Linkou, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Ko-Chun Chang
- Institute of Statistics, National Tsing-Hua University, Hsinchu, Taiwan
| | - Lun-Ching Chang
- Department of Mathematical Sciences, Florida Atlantic University, Boca Raton, USA
| | - Chia-Jung Wang
- Division of Pediatric Pulmonology, Chang Gung Memorial Hospital at Linkou, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Clinical Metabolomics Core Laboratory, Chang Gung Memorial Hospital at Linkou, Taoyuan, Taiwan
| | - Wen-Hung Chung
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Wen-Ping Hsieh
- Institute of Statistics, National Tsing-Hua University, Hsinchu, Taiwan
| | - Shih-Chi Su
- Whole-Genome Research Core Laboratory of Human Diseases, Chang Gung Memorial Hospital, Keelung, Taiwan
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Salgueiro V, Manageiro V, Bandarra NM, Ferreira E, Clemente L, Caniça M. First comparative genomic characterization of the MSSA ST398 lineage detected in aquaculture and other reservoirs. Front Microbiol 2023; 14:1035547. [PMID: 36970692 PMCID: PMC10030524 DOI: 10.3389/fmicb.2023.1035547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Staphylococcus aureus ST398 can cause diseases in several different animals. In this study we analyzed ten S. aureus ST398 previously collected in three different reservoirs in Portugal (humans, gilthead seabream from aquaculture and dolphin from a zoo). Strains tested against sixteen antibiotics, by disk diffusion or minimum inhibitory concentration, showed decreased susceptibility to benzylpenicillin (all strains from gilthead seabream and dolphin) and to erythromycin with an iMLSB phenotype (nine strains), and susceptibility to cefoxitin (methicillin-susceptible S. aureus, MSSA). All strains from aquaculture belonged to the same spa type, t2383, whereas strains from the dolphin and humans belonged to spa type t571. A more detailed analysis using single nucleotide polymorphisms (SNPs)-based tree and a heat map, showed that all strains from aquaculture origin were highly related with each other and the strains from dolphin and humans were more distinct, although they were very similar in ARG, VF and MGE content. Mutations F3I and A100V in glpT gene and D278E and E291D in murA gene were identified in nine fosfomycin susceptible strains. The blaZ gene was also detected in six of the seven animal strains. The study of the genetic environment of erm(T)-type (found in nine S. aureus strains) allowed the identification of MGE (rep13-type plasmids and IS431R-type), presumably involved in the mobilization of this gene. All strains showed genes encoding efflux pumps from major facilitator superfamily (e.g., arlR, lmrS-type and norA/B-type), ATP-binding cassettes (ABC; mgrA) and multidrug and toxic compound extrusion (MATE; mepA/R-type) families, all associated to decreased susceptibility to antibiotics/disinfectants. Moreover, genes related with tolerance to heavy metals (cadD), and several VF (e.g., scn, aur, hlgA/B/C and hlb) were also identified. Insertion sequences, prophages, and plasmids made up the mobilome, some of them associated with ARG, VF and genes related with tolerance to heavy metals. This study highlights that S. aureus ST398 can be a reservoir of several ARG, heavy metals resistance genes and VF, which are essential in the adaption and survival of the bacterium in the different environments and an active agent in its dissemination. It makes an important contribution to understanding the extent of the spread of antimicrobial resistance, as well as the virulome, mobilome and resistome of this dangerous lineage.
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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, Lisbon, 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, 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, Matosinhos, Portugal
| | - Eugénia Ferreira
- 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, Lisbon, Portugal
| | - Lurdes Clemente
- INIAV–Instituto Nacional de Investigação Agrária e Veterinária, Oeiras, 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, Lisbon, Portugal
- CIISA, Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- *Correspondence: Manuela Caniça,
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Deblais L, Jang H, Kauffman M, Gangiredla J, Sawyer M, Basa S, Poelstra JW, Babu US, Harrison LM, Hiett KL, Balan KV, Rajashekara G. Whole genome characterization of thermophilic Campylobacter species isolated from dairy manure in small specialty crop farms of Northeast Ohio. Front Microbiol 2023; 14:1074548. [PMID: 37025625 PMCID: PMC10071015 DOI: 10.3389/fmicb.2023.1074548] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/30/2023] [Indexed: 04/08/2023] Open
Abstract
Introduction With more public interest in consuming locally grown produce, small specialty crop farms (SSCF) are a viable and growing segment of the food production chain in the United States. Methods The goal of this study was to investigate the genomic diversity of Campylobacter isolated from dairy manure (n = 69) collected from 10 SSCF in Northeast Ohio between 2018 and 2020. Results A total of 56 C. jejuni and 13 C. coli isolates were sequenced. Multi-locus sequence typing (MLST) identified 22 sequence types (STs), with ST-922 (18%) and ST-61 (13%) predominant in C. jejuni and ST-829 (62%) and ST-1068 (38%) predominant in C. coli. Interestingly, isolates with similar genomic and gene contents were detected within and between SSCF over time, suggesting that Campylobacter could be transmitted between farms and may persist in a given SSCF over time. Virulence-associated genes (n = 35) involved in the uptake and utilization of potassium and organic compounds (succinate, gluconate, oxoglutarate, and malate) were detected only in the C. jejuni isolates, while 45 genes associated with increased resistance to environmental stresses (capsule production, cell envelope integrity, and iron uptake) were detected only in the C. coli isolates. Campylobacter coli isolates were also sub-divided into two distinct clusters based on the presence of unique prophages (n = 21) or IncQ conjugative plasmid/type-IV secretion system genes (n = 15). Campylobacter coli isolates harbored genes associated with resistance to streptomycin (aadE-Cc; 54%) and quinolone (gyrA-T86I; 77%), while C. jejuni had resistance genes for kanamycin (aph3'-IIIa; 20%). Both species harbored resistance genes associated with β-lactam (especially, blaOXA-193; up to 100%) and tetracycline (tetO; up to 59%). Discussion/Conclusion Our study demonstrated that Campylobacter genome plasticity associated with conjugative transfer might provide resistance to certain antimicrobials and viral infections via the acquisition of protein-encoding genes involved in mechanisms such as ribosomal protection and capsule modification.
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Affiliation(s)
- Loic Deblais
- Department of Animal Sciences, Center for Food Animal Health, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Hyein Jang
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Mike Kauffman
- Department of Animal Sciences, Center for Food Animal Health, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Jayanthi Gangiredla
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Marianne Sawyer
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Saritha Basa
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Jelmer W. Poelstra
- Molecular and Cellular Imaging Center, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
| | - Uma S. Babu
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Lisa M. Harrison
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Kelli L. Hiett
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Kannan V. Balan
- Center for Food Safety and Applied Nutrition (CFSAN), Office of Applied Research and Safety Assessment (OARSA), U.S. Food and Drug Administration, Laurel, MD, United States
| | - Gireesh Rajashekara
- Department of Animal Sciences, Center for Food Animal Health, The Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, United States
- *Correspondence: Gireesh Rajashekara,
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10
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Cerbino GN, Traglia GM, Ayala Nuñez T, Parmeciano Di Noto G, Ramírez MS, Centrón D, Iriarte A, Quiroga C. Comparative genome analysis of the genus Shewanella unravels the association of key genetic traits with known and potential pathogenic lineages. Front Microbiol 2023; 14:1124225. [PMID: 36925471 PMCID: PMC10011109 DOI: 10.3389/fmicb.2023.1124225] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 02/06/2023] [Indexed: 03/06/2023] Open
Abstract
Shewanella spp. are Gram-negative rods widely disseminated in aquatic niches that can also be found in human-associated environments. In recent years, reports of infections caused by these bacteria have increased significantly. Mobilome and resistome analysis of a few species showed that they are versatile; however, comprehensive comparative studies in the genus are lacking. Here, we analyzed the genetic traits of 144 genomes from Shewanella spp. isolates focusing on the mobilome, resistome, and virulome to establish their evolutionary relationship and detect unique features based on their genome content and habitat. Shewanella spp. showed a great diversity of mobile genetic elements (MGEs), most of them associated with monophyletic lineages of clinical isolates. Furthermore, 79/144 genomes encoded at least one antimicrobial resistant gene with their highest occurrence in clinical-related lineages. CRISPR-Cas systems, which confer immunity against MGEs, were found in 41 genomes being I-E and I-F the more frequent ones. Virulome analysis showed that all Shewanella spp. encoded different virulence genes (motility, quorum sensing, biofilm, adherence, etc.) that may confer adaptive advantages for survival against hosts. Our data revealed that key accessory genes are frequently found in two major clinical-related groups, which encompass the opportunistic pathogens Shewanella algae and Shewanella xiamenensis together with several other species. This work highlights the evolutionary nature of Shewanella spp. genomes, capable of acquiring different key genetic traits that contribute to their adaptation to different niches and facilitate the emergence of more resistant and virulent isolates that impact directly on human and animal health.
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Affiliation(s)
- Gabriela N Cerbino
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - German M Traglia
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Teolincacihuatl Ayala Nuñez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Gisela Parmeciano Di Noto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - María Soledad Ramírez
- Center for Applied Biotechnology Studies, Department of Biological Science, California State University, Fullerton, Fullerton, CA, United States
| | - Daniela Centrón
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
| | - Andrés Iriarte
- Laboratorio de Biología Computacional, Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Cecilia Quiroga
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Tecnológicas, Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPAM), Facultad de Medicina, Buenos Aires, Argentina
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11
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Torres AG. The Challenge to Control Emergence of Antibiotic Resistance in Virulent Escherichia coli Isolates in Latin America. Microbiol Spectr 2022; 10:e0150622. [PMID: 35762783 PMCID: PMC9430625 DOI: 10.1128/spectrum.01506-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Latin American Coalition for Escherichia coli Research (LACER) was created as a network of investigators using One Health approaches trying to understand infections caused by regional E. coli isolates and to sound the alarm due to the evolution of strains that are multiresistant to antibiotics (resistome) that also display different virulence profiles (virulome). After the COVID19 pandemic, a major concern by investigators has been the appearance of more virulent and resistant strains. Recently, a paper published in Microbiology Spectrum by Brazilian investigators (Fuga B., et al. Microbiol Spectr 10:e0125621, 2022, https://doi.org/10.1128/spectrum.01256-21) has used a genomic approach to demonstrate that during a period of 45 years, a wide resistome and virulome has converged, resulting in the appearance and persistence of high-risk clones affecting humans, animals and the environment, and its rapid dissemination is becoming an unattended international threat.
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Affiliation(s)
- Alfredo G. Torres
- University of Texas Medical Branch, Department of Microbiology and Immunology, Galveston, Texas, USA
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12
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Kostenko VV, Mouzykantov AA, Baranova NB, Boulygina EA, Markelova MI, Khusnutdinova DR, Trushin MV, Chernova OA, Chernov VM. Development of Resistance to Clarithromycin and Amoxicillin-Clavulanic Acid in Lactiplantibacillus plantarum In Vitro Is Followed by Genomic Rearrangements and Evolution of Virulence. Microbiol Spectr 2022;:e0236021. [PMID: 35579444 DOI: 10.1128/spectrum.02360-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ensuring the safety of the use of probiotics is a top priority. Obviously, in addition to studying the beneficial properties of lactic acid bacteria, considerable attention should be directed to assessing the virulence of microorganisms as well as investigating the possibility of its evolution under conditions of selective pressure. To assess the virulence of probiotics, it is now recommended to analyze the genomes of bacteria in relation to the profiles of the virulome, resistome, and mobilome as well as the analysis of phenotypic resistance and virulence in vitro. However, the corresponding procedure has not yet been standardized, and virulence analysis of strains in vivo using model organisms has not been performed. Our study is devoted to testing the assumption that the development of antibiotic resistance in probiotic bacteria under conditions of selective pressure of antimicrobial drugs may be accompanied by the evolution of virulence. In this regard, special attention is required for the widespread in nature commensals and probiotic bacteria actively used in pharmacology and the food industry. As a result of step-by-step selection from the Lactiplantibacillus plantarum 8p-a3 strain isolated from the “Lactobacterin” probiotic (Biomed, Russia), the L. plantarum 8p-a3-Clr-Amx strain was obtained, showing increased resistance simultaneously to amoxicillin-clavulanic acid and clarithromycin (antibiotics, the combined use of which is widely used for Helicobacter pylori eradication) compared to the parent strain (MIC8p-a3-Clr-Amx of 20 μg/mL and 10 μg/mL, and MIC8p-a3 of 0.5 μg/mL and 0.05 μg/mL, respectively). The results of a comparative analysis of antibiotic-resistant and parental strains indicate that the development of resistance to the corresponding antimicrobial drugs in L. plantarum in vitro is accompanied by the following: (i) significant changes in the genomic profile (point mutations as well as deletions, insertions, duplications, and displacement of DNA sequences) associated in part with the resistome and mobilome; (ii) changes in phenotypic sensitivity to a number of antimicrobial drugs; and (iii) an increase in the level of virulence against Drosophila melanogaster, a model organism for which L. plantarum is considered to be a symbiont. The data obtained by us indicate that the mechanisms of adaptation to antimicrobial drugs in L. plantarum are not limited to those described earlier and determine the need for comprehensive studies of antibiotic resistance scenarios as well as the trajectories of virulence evolution in probiotic bacteria in vivo and in vitro to develop a standardized system for detecting virulent strains of the corresponding microorganisms. IMPORTANCE Ensuring the safety of the use of probiotics is a top priority. We found that increased resistance to popular antimicrobial drugs in Lactiplantibacillus plantarum is accompanied by significant changes in the genomic profile and phenotypic sensitivity to a number of antimicrobial drugs as well as in the level of virulence of this bacterium against Drosophila. The data obtained in our work indicate that the mechanisms of antibiotic resistance in this bacterium are not limited to those described earlier and determine the need for comprehensive studies of the potential for the evolution of virulence in lactic acid bacteria in vivo and in vitro and to develop a reliable control system to detect virulent strains among probiotics.
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13
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Nath AN, Retnakumar RJ, Francis A, Chhetri P, Thapa N, Chattopadhyay S. Peptic Ulcer and Gastric Cancer: Is It All in the Complex Host-Microbiome Interplay That Is Encoded in the Genomes of "Us" and "Them"? Front Microbiol 2022; 13:835313. [PMID: 35547123 PMCID: PMC9083406 DOI: 10.3389/fmicb.2022.835313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
It is increasingly being recognized that severe gastroduodenal diseases such as peptic ulcer and gastric cancer are not just the outcomes of Helicobacter pylori infection in the stomach. Rather, both diseases develop and progress due to the perfect storms created by a combination of multiple factors such as the expression of different H. pylori virulence proteins, consequent human immune responses, and dysbiosis in gastrointestinal microbiomes. In this mini review, we have discussed how the genomes of H. pylori and other gastrointestinal microbes as well as the genomes of different human populations encode complex and variable virulome–immunome interplay, which influences gastroduodenal health. The heterogeneities that are encrypted in the genomes of different human populations and in the genomes of their respective resident microbes partly explain the inconsistencies in clinical outcomes among the H. pylori-infected people.
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Affiliation(s)
- Angitha N Nath
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - R J Retnakumar
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India.,Manipal Academy of Higher Education, Manipal, India
| | - Ashik Francis
- Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
| | - Prakash Chhetri
- Department of Zoology, Biotech Hub, Nar Bahadur Bhandari Degree College, Tadong, India
| | - Namrata Thapa
- Department of Zoology, Biotech Hub, Nar Bahadur Bhandari Degree College, Tadong, India
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14
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Cookson AL, Marshall JC, Biggs PJ, Rogers LE, Collis RM, Devane M, Stott R, Wilkinson DA, Kamke J, Brightwell G. Whole-Genome Sequencing and Virulome Analysis of Escherichia coli Isolated from New Zealand Environments of Contrasting Observed Land Use. Appl Environ Microbiol 2022;:e0027722. [PMID: 35442082 DOI: 10.1128/aem.00277-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Generic Escherichia coli is commonly used as an indicator of fecal contamination to assess water quality and human health risk. Where measured E. coli exceedances occur, the presence of other pathogenic microorganisms, such as Shiga toxin-producing E. coli (STEC), is assumed, but confirmatory data are lacking. Putative E. coli isolates (n = 709) were isolated from water, sediment, soil, periphyton, and feces samples (n = 189) from five sites representing native forest and agricultural environments. Ten E. coli isolates (1.41%) were stx2 positive, 19 (2.7%) were eae positive, and stx1-positive isolates were absent. At the sample level, stx2-positive E. coli (5 of 189, 2.6%) and eae-positive isolates (16 of 189, 8.5%) were rare. Using real-time PCR, these STEC-associated virulence factors were determined to be more prevalent in sample enrichments (stx1, 23.9%; stx2, 31.4%; eae, 53.7%) and positively correlated with generic E. coli isolate numbers (P < 0.05) determined using culture-based methods. Whole-genome sequencing (WGS) was undertaken on a subset of 238 isolates with assemblies representing seven E. coli phylogroups (A, B1, B2, C, D, E, and F), 22 Escherichia marmotae isolates, and 1 Escherichia ruysiae isolate. Virulence factors, including those from extraintestinal pathogenic E. coli, were extremely diverse in isolates from the different locations and were more common in phylogroup B2. Analysis of the virulome from WGS data permitted the identification of gene repertoires that may be involved in environmental fitness and broadly align with phylogroup. Although recovery of STEC isolates was low, our molecular data indicate that they are likely to be widely present in environmental samples containing diverse E. coli phylogroups. IMPORTANCE This study takes a systematic sampling approach to assess the public health risk of Escherichia coli recovered from freshwater sites within forest and farmland. The New Zealand landscape is dominated by livestock farming, and previous work has demonstrated that "recreational exposure to water" is a risk factor for human infection by Shiga toxin-producing Escherichia coli (STEC). Though STEC isolates were rarely isolated from water samples, STEC-associated virulence factors were identified more commonly from water sample culture enrichments and were associated with increased generic E. coli concentrations. Whole-genome sequencing data from both E. coli and newly described Escherichia spp. demonstrated the presence of virulence factors from E. coli pathotypes, including extraintestinal pathogenic E. coli. This has significance for understanding and interpreting the potential health risk from E. coli where water quality is poor and suggests a role of virulence factors in survival and persistence of E. coli and Escherichia spp.
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15
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Alekseeva AE, Brusnigina NF, Gordinskaya NA, Makhova MA, Kolesnikova EA. Molecular genetic characteristics of resistome and virulome of carbapenem-resistant Klebsiella pneumoniae clinical strains. Klin Lab Diagn 2022; 67:186-192. [PMID: 35320636 DOI: 10.51620/0869-2084-2022-67-3-186-192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The characteristics of resistome and virulome structure of four carbapenem-resistant Klebsiella pneumoniae clinical strains are present in the work. Two strains belonged to the sequence-type ST395, one strain - ST2262, one strain - to the new sequence-type 5816. The genes of fimbriae, enterobactin, beta-lactamase SHV type, resistance to fosfomycin fosA and transport of fluoroquinolones oqxAB in all Klebsiella strains chromosome structure were identified. The determinants of yersineobactin and aerobactin are enriched the virulome of ST395 NNKP315 and NNKP343 strains. The aerobactin genes are located on IncHI1B plasmids (IncHI1B/FIB) which highly homologous to the virulence pLVPK and pK2044 plasmids. IncR, IncL, IncQ plasmids carrying blaOXA-48, blaCTX-M-15, blaOXA-1, blaTEM-1, qnrS1, tetA, sul1, dfrA1, aac(6 ')-Ib-cr, catA1, catB3 etc. were identified in these strains. As a result of in silico analysis, an assumption about the localization of the blaOXA-48 in the structure of the IncHI1B plasmid of NNKP315 strain was made. This plasmid also contains the aminoglycosidases genes inserted into a class 1 integron In822. The mutations were found in the porin proteins OmpK35, OmpK36 and OmpK37 genes, which increases the carbapenem resistance. The virulome of NNKP16 (ST2262) strain additionally includes of the iron utilization system kfuABC chromosomal genes, and the virulome of NNKP15 (ST5816) strain contains of the capsular polysaccharide kvgAS and microcin E492 genes. Additional determinants of resistance were not identified in the resistome structure of K. pneumoniae NNKP16 and only the blaCTX-M-15 gene was found in the NNKP15 strain. The absence of acquired resistance genes seems to be due to the presence of the type I-E CRISPR-Cas system. Multiple drug resistance of the studied strains is associated with mutations identified in the gene structure of porin proteins OmpK36 and OmpK37, as well as the activity of efflux systems. It was showed the stop codon formation in the nucleotide sequence of the regulatory gene ramR to both strains, which can potentially provide overexpression of AcrAB efflux proteins.
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Affiliation(s)
- A E Alekseeva
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
| | - N F Brusnigina
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
| | - N A Gordinskaya
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
| | - M A Makhova
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
| | - E A Kolesnikova
- Nizhny Novgorod scientific and research institute of epidemiology and microbiology name acad. I.N. Blokhina of the Rospotrebnadzor
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16
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Fuga B, Sellera FP, Cerdeira L, Esposito F, Cardoso B, Fontana H, Moura Q, Cardenas-Arias A, Sano E, Ribas RM, Carvalho AC, Tognim MCB, de Morais MMC, Quaresma AJPG, Santana ÂP, Reis JN, Pilonetto M, Vespero EC, Bonelli RR, Cerqueira AMF, Sincero TCM, Lincopan N. WHO Critical Priority Escherichia coli as One Health Challenge for a Post-Pandemic Scenario: Genomic Surveillance and Analysis of Current Trends in Brazil. Microbiol Spectr 2022;:e0125621. [PMID: 35234515 DOI: 10.1128/spectrum.01256-21] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The dissemination of carbapenem-resistant and third generation cephalosporin-resistant pathogens is a critical issue that is no longer restricted to hospital settings. The rapid spread of critical priority pathogens in Brazil is notably worrying, considering its continental dimension, the diversity of international trade, livestock production, and human travel. We conducted a nationwide genomic investigation under a One Health perspective that included Escherichia coli strains isolated from humans and nonhuman sources, over 45 years (1974–2019). One hundred sixty-seven genomes were analyzed extracting clinically relevant information (i.e., resistome, virulome, mobilome, sequence types [STs], and phylogenomic). The endemic status of extended-spectrum β-lactamase (ESBL)-positive strains carrying a wide diversity of blaCTX-M variants, and the growing number of colistin-resistant isolates carrying mcr-type genes was associated with the successful expansion of international ST10, ST38, ST115, ST131, ST354, ST410, ST648, ST517, and ST711 clones; phylogenetically related and shared between human and nonhuman hosts, and polluted aquatic environments. Otherwise, carbapenem-resistant ST48, ST90, ST155, ST167, ST224, ST349, ST457, ST648, ST707, ST744, ST774, and ST2509 clones from human host harbored blaKPC-2 and blaNDM-1 genes. A broad resistome to other clinically relevant antibiotics, hazardous heavy metals, disinfectants, and pesticides was further predicted. Wide virulome associated with invasion/adherence, exotoxin and siderophore production was related to phylogroup B2. The convergence of wide resistome and virulome has contributed to the persistence and rapid spread of international high-risk clones of critical priority E. coli at the human-animal-environmental interface, which must be considered a One Health challenge for a post-pandemic scenario. IMPORTANCE A One Health approach for antimicrobial resistance must integrate whole-genome sequencing surveillance data of critical priority pathogens from human, animal and environmental sources to track hot spots and routes of transmission and developing effective prevention and control strategies. As part of the Grand Challenges Explorations: New Approaches to Characterize the Global Burden of Antimicrobial Resistance Program, we present genomic data of WHO critical priority carbapenemase-resistant, ESBL-producing, and/or colistin-resistant Escherichia coli strains isolated from humans and nonhuman sources in Brazil, a country with continental proportions and high levels of antimicrobial resistance. The present study provided evidence of epidemiological and clinical interest, highlighting that the convergence of wide virulome and resistome has contributed to the persistence and rapid spread of international high-risk clones of E. coli at the human-animal-environmental interface, which must be considered a One Health threat that requires coordinated actions to reduce its incidence in humans and nonhuman hosts.
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17
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Medvedeva ES, Mouzykantov AA, Kostenko VV, Baranova NB, Markelova MI, Sabouni RG, Khusnutdinova DR, Chernova OA, Chernov VM. Adaptation to Antimicrobials and Pathogenicity in Mycoplasmas: Development of Ciprofloxacin-Resistance and Evolution of Virulence in Acholeplasma laidlawii. DOKL BIOCHEM BIOPHYS 2021; 501:444-448. [PMID: 34966969 DOI: 10.1134/s1607672921060028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 11/22/2022]
Abstract
For the first time it was shown that the development of resistance to ciprofloxacin in vitro in Acholeplasma laidlawii, a mycoplasma which is widely spread in nature and which is the main contaminant of cell cultures and vaccines, is associated with diverse pathways of virulence evolution: virulome and virulence differ significantly between ciprofloxacin-resistant strains, including those with the same level of antimicrobial resistance.
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Affiliation(s)
- E S Medvedeva
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| | - A A Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.
| | - V V Kostenko
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
| | - N B Baranova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| | - M I Markelova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
| | - R G Sabouni
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
| | - D R Khusnutdinova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
| | - O A Chernova
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
| | - V M Chernov
- Kazan Institute of Biochemistry and Biophysics, FRC Kazan Science Center, Russian Academy of Sciences, Kazan, Russia
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18
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Esposito F, Cardoso B, Fontana H, Fuga B, Cardenas-Arias A, Moura Q, Fuentes-Castillo D, Lincopan N. Genomic Analysis of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Urban Rivers Confirms Spread of Clone Sequence Type 277 Carrying Broad Resistome and Virulome Beyond the Hospital. Front Microbiol 2021; 12:701921. [PMID: 34539602 PMCID: PMC8446631 DOI: 10.3389/fmicb.2021.701921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
The dissemination of antibiotic-resistant priority pathogens beyond hospital settings is both a public health and an environmental problem. In this regard, high-risk clones exhibiting a multidrug-resistant (MDR) or extensively drug-resistant (XDR) phenotype have shown rapid adaptation at the human-animal-environment interface. In this study, we report genomic data and the virulence potential of the carbapenemase, São Paulo metallo-β-lactamase (SPM-1)-producing Pseudomonas aeruginosa strains (Pa19 and Pa151) isolated from polluted urban rivers, in Brazil. Bioinformatic analysis revealed a wide resistome to clinically relevant antibiotics (carbapenems, aminoglycosides, fosfomycin, sulfonamides, phenicols, and fluoroquinolones), biocides (quaternary ammonium compounds) and heavy metals (copper), whereas the presence of exotoxin A, alginate, quorum sensing, types II, III, and IV secretion systems, colicin, and pyocin encoding virulence genes was associated with a highly virulent behavior in the Galleria mellonella infection model. These results confirm the spread of healthcare-associated critical-priority P. aeruginosa belonging to the MDR sequence type 277 (ST277) clone beyond the hospital, highlighting that the presence of these pathogens in environmental water samples can have clinical implications for humans and other animals.
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Affiliation(s)
- Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Adriana Cardenas-Arias
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Federal Institute of Education, Science and Technology of Espírito Santo, Vila Velha, Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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19
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Bai X, Narayanan A, Nowak P, Ray S, Neogi U, Sönnerborg A. Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. Front Microbiol 2021; 12:667718. [PMID: 34248876 PMCID: PMC8267369 DOI: 10.3389/fmicb.2021.667718] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/31/2021] [Indexed: 01/14/2023] Open
Abstract
Gut microbiome plays a significant role in HIV-1 immunopathogenesis and HIV-1-associated complications. Previous studies have mostly been based on 16S rRNA gene sequencing, which is limited in taxonomic resolution at the genus level and inferred functionality. Herein, we performed a deep shotgun metagenomics study with the aim to obtain a more precise landscape of gut microbiome dysbiosis in HIV-1 infection. A reduced tendency of alpha diversity and significantly higher beta diversity were found in HIV-1-infected individuals on antiretroviral therapy (ART) compared to HIV-1-negative controls. Several species, such as Streptococcus anginosus, Actinomyces odontolyticus, and Rothia mucilaginosa, were significantly enriched in the HIV-1-ART group. Correlations were observed between the degree of immunodeficiency and gut microbiome in terms of microbiota composition and metabolic pathways. Furthermore, microbial shift in HIV-1-infected individuals was found to be associated with changes in microbial virulome and resistome. From the perspective of methodological evaluations, our study showed that different DNA extraction protocols significantly affect the genomic DNA quantity and quality. Moreover, whole metagenome sequencing depth affects critically the recovery of microbial genes, including virulome and resistome, while less than 5 million reads per sample is sufficient for taxonomy profiling in human fecal metagenomic samples. These findings advance our understanding of human gut microbiome and their potential associations with HIV-1 infection. The methodological assessment assists in future study design to accurately assess human gut microbiome.
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Affiliation(s)
- Xiangning Bai
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| | - Aswathy Narayanan
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Piotr Nowak
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden.,The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå, Sweden
| | - Shilpa Ray
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden.,The Laboratory for Molecular Infection Medicine Sweden MIMS, Umeå University, Umeå, Sweden
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden.,Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
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20
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Lienard A, Hosny M, Jneid J, Schuldiner S, Cellier N, Sotto A, La Scola B, Lavigne JP, Pantel A. Escherichia coli Isolated from Diabetic Foot Osteomyelitis: Clonal Diversity, Resistance Profile, Virulence Potential, and Genome Adaptation. Microorganisms 2021; 9:microorganisms9020380. [PMID: 33668594 PMCID: PMC7918245 DOI: 10.3390/microorganisms9020380] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 01/22/2023] Open
Abstract
This study assessed the clonal diversity, the resistance profile and the virulence potential of Escherichia coli strains isolated from diabetic foot infection (DFI) and diabetic foot osteomyelitis (DFOM). A retrospective single-centre study was conducted on patients diagnosed with E. coli isolated from deep DFI and DFOM at Clinique du Pied Diabétique Gard-Occitanie (France) over a two-year period. Phylogenetic backgrounds, virulence factors (VFs) and antibiotic resistance profiles were determined. Whole-genome analysis of E. coli strains isolated from same patients at different periods were performed. From the two-years study period, 35 E. coli strains isolated from 33 patients were analysed; 73% were isolated from DFOM. The majority of the strains belonged to the virulent B2 and D phylogenetic groups (82%). These isolates exhibited a significant higher average of VFs number than strains belonging to other groups (p < 0.001). papG2 gene was significantly more detected in strains belonging to B2 phylogroup isolated from DFI compared to DFOM (p = 0.003). The most prevalent antibiotic resistance pattern was observed for ampicillin (82%), cotrimoxazole (45%), and ciprofloxacin (33%). The genome analysis of strains isolated at two periods in DFOM showed a decrease of the genome size, and this decrease was more important for the strain isolated at nine months (vs. four months). A shared mutation on the putative acyl-CoA dehydrogenase-encoding gene aidB was observed on both strains. E. coli isolates from DFOM were highly genetically diverse with different pathogenicity traits. Their adaptation in the bone structure could require genome reduction and some important modifications in the balance virulence/resistance of the bacteria.
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Affiliation(s)
- Alexi Lienard
- VBIC, INSERM U1047, Université de Montpellier, UFR de Médecine, 30908 Nîmes CEDEX 2, France;
| | - Michel Hosny
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France; (M.H.); (J.J.); (B.L.S.)
| | - Joanne Jneid
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France; (M.H.); (J.J.); (B.L.S.)
| | - Sophie Schuldiner
- VBIC, INSERM U1047, Université de Montpellier, Service des Maladies Métaboliques et Endocriniennes, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
| | - Nicolas Cellier
- Service d’Orthopédie, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
| | - Albert Sotto
- VBIC, INSERM U1047, Université de Montpellier, Service des Maladies Infectieuses et Tropicales, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
| | - Bernard La Scola
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, 13005 Marseille, France; (M.H.); (J.J.); (B.L.S.)
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
- Correspondence:
| | - Alix Pantel
- VBIC, INSERM U1047, Université de Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30029 Nîmes CEDEX 09, France;
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21
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Chernov VM, Baranova NB, Mouzykantov AA, Medvedeva ES, Dramchini MA, Chernova OA. Adaptation of Mycoplasmas to Antimicrobial Peptides: Development of Melittin Resistance in Acholeplasma laidlawii Is Associated with Changes in Genomic and Proteomic Profiles and in Virulence. DOKL BIOCHEM BIOPHYS 2020; 495:300-303. [PMID: 33368039 DOI: 10.1134/s1607672920060034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/10/2020] [Accepted: 08/10/2020] [Indexed: 11/23/2022]
Abstract
For the first time it is shown that the development of resistance to melittin in Acholeplasma laidlawii, a mycoplasma that is widely spread in nature and that is the main contaminant of cell cultures and vaccines, is associated with significant changes in the genomic profile, in cellular and vesicular proteomes, as well as in virulence.
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Affiliation(s)
- V M Chernov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Science Center of the Russian Academy of Sciences, Kazan, Russia
| | - N B Baranova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Science Center of the Russian Academy of Sciences, Kazan, Russia. .,Kazan (Volga Region) Federal University, Kazan, Russia.
| | - A A Mouzykantov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Science Center of the Russian Academy of Sciences, Kazan, Russia
| | - E S Medvedeva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Science Center of the Russian Academy of Sciences, Kazan, Russia
| | - M A Dramchini
- Kazan (Volga Region) Federal University, Kazan, Russia
| | - O A Chernova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Science Center of the Russian Academy of Sciences, Kazan, Russia.,Kazan (Volga Region) Federal University, Kazan, Russia
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22
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Adzitey F, Asante J, Kumalo HM, Khan RB, Somboro AM, Amoako DG. Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana. Genes (Basel) 2020; 11:E1504. [PMID: 33327465 DOI: 10.3390/genes11121504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli are among the most common foodborne pathogens associated with infections reported from meat sources. This study investigated the virulome, pathogenicity, stress response factors, clonal lineages, and the phylogenomic relationship of E. coli isolated from different meat sources in Ghana using whole-genome sequencing. Isolates were screened from five meat sources (beef, chevon, guinea fowl, local chicken, and mutton) and five areas (Aboabo, Central market, Nyorni, Victory cinema, and Tishegu) based in the Tamale Metropolis, Ghana. Following microbial identification, the E. coli strains were subjected to whole-genome sequencing. Comparative visualisation analyses showed different DNA synteny of the strains. The isolates consisted of diverse sequence types (STs) with the most common being ST155 (n = 3/14). Based Upon Related Sequence Types (eBURST) analyses of the study sequence types identified four similar clones, five single-locus variants, and two satellite clones (more distantly) with global curated E. coli STs. All the isolates possessed at least one restriction-modification (R-M) and CRISPR defence system. Further analysis revealed conserved stress response mechanisms (detoxification, osmotic, oxidative, and periplasmic stress) in the strains. Estimation of pathogenicity predicted a higher average probability score (Pscore ≈ 0.937), supporting their pathogenic potential to humans. Diverse virulence genes that were clonal-specific were identified. Phylogenomic tree analyses coupled with metadata insights depicted the high genetic diversity of the E. coli isolates with no correlation with their meat sources and areas. The findings of this bioinformatic analyses further our understanding of E. coli in meat sources and are broadly relevant to the design of contamination control strategies in meat retail settings in Ghana.
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23
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Soliman MS, Soliman NS, El-Manakhly AR, ElBanna SA, Aziz RK, El-Kholy AA. Genomic Characterization of Methicillin-Resistant Staphylococcus aureus (MRSA) by High-Throughput Sequencing in a Tertiary Care Hospital. Genes (Basel) 2020; 11:E1219. [PMID: 33080885 DOI: 10.3390/genes11101219] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/13/2020] [Accepted: 10/14/2020] [Indexed: 11/22/2022] Open
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) strains are associated with serious complications and poor clinical outcome. In Egypt, they contribute to more than 70% of S. aureus healthcare-associated infections. This study combined whole-genome sequencing, bioinformatics, and statistical analyses to identify the phylogeny, resistome, virulome and potential genotype–phenotype–clinical correlation among 18 clinical isolates of MRSA in a tertiary hospital in Cairo, Egypt. The ST1535-V MRSA clone was the most frequently isolated (16.6%), followed by ST5-VI, ST1-V and ST239-III (11.1% each). SCCmec V, VI, IV and III types were detected at frequencies of 50%, 16.6%, 11.1% and 11.1%, respectively. None of the tested virulence genes were detected in all isolates, but they ranged in distribution from 1/18 to 17/18. The Panton–Valentine leukocidin (PVL)-encoding genes were detected in only four isolates and were enriched in isolates causing non-severe cases. Phylogenetic analysis revealed relatedness between three ST1535-Vs, two ST5-VIs, two ST239-IIIs and two ST1-Vs; however, only the two genetically related ST1-V isolates were epidemiologically linked. While disease outcome and source of infection had no correlation with a particular genotypic pattern, the sequence type was the most correlated factor with phylogeny and genotypic patterns, and a few genes were associated with non-severe cases.
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24
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Mwangi C, Njoroge S, Tshibangu-Kabamba E, Moloo Z, Rajula A, Devani S, Matsumoto T, Nyerere K, Kariuki S, Revathi G, Yamaoka Y. Whole Genome Sequencing Reveals Virulence Potentials of Helicobacter pylori Strain KE21 Isolated from a Kenyan Patient with Gastric Signet Ring Cell Carcinoma. Toxins (Basel) 2020; 12:E556. [PMID: 32872465 PMCID: PMC7551074 DOI: 10.3390/toxins12090556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori (H.pylori) infection is etiologically associated with severe diseases including gastric cancer; but its pathogenicity is deeply shaped by the exceptional genomic diversification and geographic variation of the species. The clinical relevance of strains colonizing Africa is still debated. This study aimed to explore genomic features and virulence potentials of H. pylori KE21, a typical African strain isolated from a native Kenyan patient diagnosed with a gastric cancer. A high-quality circular genome assembly of 1,648,327 bp (1590 genes) obtained as a hybrid of Illumina Miseq short reads and Oxford Nanopore MinION long reads, clustered within hpAfrica1 population. This genome revealed a virulome and a mobilome encoding more than hundred features potentiating a successful colonization, persistent infection, and enhanced disease pathogenesis. Furthermore, through an experimental infection of gastric epithelial cell lines, strain KE21 showed the ability to promote interleukin-8 production and to induce cellular alterations resulting from the injection of a functional CagA oncogene protein into the cells. This study shows that strain KE21 is potentially virulent and can trigger oncogenic pathways in gastric epithelial cells. Expended genomic and clinical explorations are required to evaluate the epidemiological importance of H. pylori infection and its putative complications in the study population.
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Affiliation(s)
- Catherine Mwangi
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (C.M.); (S.N.); (K.N.)
- Department of Medical Microbiology and Parasitology, Kenyatta University, Nairobi P.O. Box 43844-00100, Kenya
| | - Stephen Njoroge
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (C.M.); (S.N.); (K.N.)
- Department of Medical Microbiology, Technical University of Kenya, Nairobi P.O. Box 52428, Kenya
| | - Evariste Tshibangu-Kabamba
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (T.M.)
| | - Zahir Moloo
- Department of Pathology and Laboratory Medicine, Aga Khan Hospital University, Nairobi P.O. Box 37002-00100, Kenya; (Z.M.); (G.R.)
| | - Allan Rajula
- Gastroenterology section, Aga Khan Hospital University, Nairobi P.O. Box 37002-00100, Kenya; (A.R.); (S.D.)
| | - Smita Devani
- Gastroenterology section, Aga Khan Hospital University, Nairobi P.O. Box 37002-00100, Kenya; (A.R.); (S.D.)
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (T.M.)
| | - Kimang’a Nyerere
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (C.M.); (S.N.); (K.N.)
| | - Samuel Kariuki
- Kenya Medical Research Institute, Nairobi P.O. Box 20778-00202, Kenya;
| | - Gunturu Revathi
- Department of Pathology and Laboratory Medicine, Aga Khan Hospital University, Nairobi P.O. Box 37002-00100, Kenya; (Z.M.); (G.R.)
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Faculty of Medicine, Oita University, Oita 879-5593, Japan; (E.T.-K.); (T.M.)
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25
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Cafiso V, Stracquadanio S, Lo Verde F, De Guidi I, Zega A, Pigola G, Stefani S. Genomic and Long-Term Transcriptomic Imprints Related to the Daptomycin Mechanism of Action Occurring in Daptomycin- and Methicillin-Resistant Staphylococcus aureus Under Daptomycin Exposure. Front Microbiol 2020; 11:1893. [PMID: 32922373 PMCID: PMC7456847 DOI: 10.3389/fmicb.2020.01893] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/20/2020] [Indexed: 01/06/2023] Open
Abstract
Daptomycin (DAP) is one of the last-resort treatments for heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) and vancomycin-intermediate S. aureus (VISA) infections. DAP resistance (DAP-R) is multifactorial and mainly related to cell-envelope modifications caused by single-nucleotide polymorphisms and/or modulation mechanisms of transcription emerging as result of a self-defense process in response to DAP exposure. Nevertheless, the role of these adaptations remains unclear. We aim to investigate the comparative genomics and late post-exponential growth-phase transcriptomics of two DAP-resistant/DAP-susceptible (DAPR/S) methicillin-resistant S. aureus (MRSA) clinical strain pairs to focalize the genomic and long-term transcriptomic fingerprinting and adaptations related to the DAP mechanism of action acquired in vivo under DAP pressure using Illumina whole-genome sequencing (WGS), RNA-seq, bioinformatics, and real-time qPCR validation. Comparative genomics revealed that membrane protein and transcriptional regulator coding genes emerged as shared functional coding-gene clusters harboring mutational events related to the DAP-R onset in a strain-dependent manner. Pairwise transcriptomic enrichment analysis highlighted common and strain pair-dependent Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, whereas DAPR/S double-pair cross-filtering returned 53 differentially expressed genes (DEGs). A multifactorial long-term transcriptomic-network characterized DAPR MRSA includes alterations in (i) peptidoglycan biosynthesis, cell division, and cell-membrane (CM) organization genes, as well as a cidB/lytS autolysin genes; (ii) ldh2 involved in fermentative metabolism; (iii) CM-potential perturbation genes; and (iv) oxidative and heat/cold stress response-related genes. Moreover, a D-alanyl–D-alanine decrease in cell-wall muropeptide characterized DAP/glycopeptide cross-reduced susceptibility mechanisms in DAPR MRSA. Our data provide a snapshot of DAPR MRSA genomic and long-term transcriptome signatures related to the DAP mechanism of action (MOA) evidencing that a complex network of genomic changes and transcriptomic adaptations is required to acquire DAP-R.
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Affiliation(s)
- Viviana Cafiso
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Stefano Stracquadanio
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Flavia Lo Verde
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Irene De Guidi
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Alessandra Zega
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Giuseppe Pigola
- Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
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26
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Mohsin M, Azam M, Ur Rahman S, Esposito F, Sellera FP, Monte DF, Cerdeira L, Lincopan N. Genomic background of a colistin-resistant and highly virulent MCR-1-positive Escherichia coli ST6395 from a broiler chicken in Pakistan. Pathog Dis 2020; 77:5647353. [PMID: 31782775 DOI: 10.1093/femspd/ftz064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/28/2019] [Indexed: 11/12/2022] Open
Abstract
The convergence of high virulence and multidrug resistance (MDR) in Gram-negative pathogens circulating at the human-animal interface is a critical public health issue. We hereby report the genomic characteristics and virulent behavior of a colistin-resistant Escherichia coli, serotype ONT:H26, belonging to ST6395, isolated from a healthy broiler in Pakistan. This strain harbored multiple antimicrobial resistance genes, including mcr-1.1 and blaCARB-2, besides cma (colicin M) and astA [heat-stable enterotoxin 1 (EAST1) toxin] virulence genes. In vivo experiments carried out with the Galleria mellonella infection model revealed that MCR-1-positive E. coli ST6395 killed 96.4% of the larvae at 18 hour post-infection. Interplay between resistance and virulence in clinically important pathogens could be a potential threat, representing a serious challenge to global public health.
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Affiliation(s)
- Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Jhang Road, Faisalabad, Zip Code 38000, Pakistan
| | - Mariya Azam
- Institute of Microbiology, University of Agriculture, Jhang Road, Faisalabad, Zip Code 38000, Pakistan
| | - Sajjad Ur Rahman
- Institute of Microbiology, University of Agriculture, Jhang Road, Faisalabad, Zip Code 38000, Pakistan
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, CEP 05508-000, Brazil
| | - Fábio P Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, Av. Prof. Dr. Orlando Marques de Paiva 87, São Paulo, CEP 05508-270, Brazil
| | - Daniel F Monte
- Department of Food and Experimental Nutrition, Food Research Center, Faculty of Pharmaceutical Sciences, Av. Prof. Lineu Prestes 580, University of São Paulo, São Paulo, CEP 05508-000, Brazil
| | - Louise Cerdeira
- Institute of Microbiology, University of Agriculture, Jhang Road, Faisalabad, Zip Code 38000, Pakistan
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, São Paulo, CEP 05508-000, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 1374, São Paulo, CEP 05508-000, Brazil
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Coussement J, Argudín MA, Heinrichs A, Racapé J, de Mendonça R, Nienhaus L, Le Moine A, Roisin S, Dodémont M, Jacobs F, Abramowicz D, Johnston BD, Johnson JR, Denis O. Host and microbial factors in kidney transplant recipients with Escherichia coli acute pyelonephritis or asymptomatic bacteriuria: a prospective study using whole-genome sequencing. Nephrol Dial Transplant 2020; 34:878-885. [PMID: 30304506 DOI: 10.1093/ndt/gfy292] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Urinary tract infection is the most common infection among kidney transplant recipients (KTRs). Many transplant physicians fear that host compromise will allow low-virulence strains to cause pyelonephritis in KTRs, so they often treat asymptomatic bacteriuria with antibiotics. Identification of the host/microbe factors that determine the clinical presentation (i.e. pyelonephritis versus asymptomatic bacteriuria) once an Escherichia coli strain enters a KTRs bladder could inform management decisions. METHODS We prospectively collected all E. coli isolates causing either pyelonephritis or asymptomatic bacteriuria in KTRs at our institution (December 2012-June 2015). Whole-genome sequencing was used to assess bacterial characteristics (carriage of 48 virulence genes and phylogenetic and clonal background). Host parameters were also collected. RESULTS We analysed 72 bacteriuria episodes in 54 KTRs (53 pyelonephritis, 19 asymptomatic bacteriuria). The pyelonephritis and asymptomatic bacteriuria isolates exhibited a similar total virulence gene count per isolate [median 18 (range 5-33) and 18 (5-30), respectively; P = 0.57] and for individual virulence genes differed significantly only for the prevalence of the pap operon (pyelonephritis 39%,versus asymptomatic bacteriuria 0%; P = 0.002). No other significant between-group differences were apparent for 86 other bacterial and host variables. CONCLUSIONS Our findings suggest that bacterial adherence plays a role in the pathogenesis of pyelonephritis in KTRs despite significantly altered host urinary tract anatomy and weakened immunity. Whether KTRs might benefit from targeted therapies (e.g. vaccination or inhibitors of fimbrial adhesion) has yet to be studied.
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Affiliation(s)
- Julien Coussement
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,Division of Infectious Diseases, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Maria Angeles Argudín
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Amélie Heinrichs
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Judith Racapé
- Research Center "Biostatistiques, Epidémiologie et Recherche Clinique", École de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium.,Department of Nephrology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Ricardo de Mendonça
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Louise Nienhaus
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Alain Le Moine
- Department of Nephrology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Sandrine Roisin
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Magali Dodémont
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Frédérique Jacobs
- Division of Infectious Diseases, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium
| | - Daniel Abramowicz
- Department of Nephrology-Hypertension, Universitair Ziekenhuis Antwerpen, Antwerp University, Antwerpen, Belgium
| | | | - James R Johnson
- Minneapolis Veterans Health Care System, Minneapolis, MN, USA
| | - Olivier Denis
- Department of Microbiology, CUB-Hôpital Erasme, Université Libre de Bruxelles, Brussels, Belgium.,École de Santé Publique, Université Libre de Bruxelles, Brussels, Belgium
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Rodríguez-Villodres Á, Bonnin RA, Ortiz de la Rosa JM, Álvarez-Marín R, Naas T, Aznar J, Pachón J, Lepe JA, Smani Y. Phylogeny, Resistome, and Virulome of Escherichia coli Causing Biliary Tract Infections. J Clin Med 2019; 8:E2118. [PMID: 31810308 PMCID: PMC6947626 DOI: 10.3390/jcm8122118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/27/2019] [Accepted: 11/29/2019] [Indexed: 01/05/2023] Open
Abstract
Escherichia coli is the most frequent Gram-negative bacilli involved in intra-abdominal infections. However, despite high mortality rates associated with biliary tract infections due to E. coli, there is no study focusing on this pathogen. In this study, we have characterized a group of 15 E. coli isolates obtained from 12 patients with biliary tract infections. Demographic and clinical data of the patients were recovered. Phylogeny, resistome, and virulome analysis through whole genome sequencing and biofilm formation were investigated. Among the 15 E. coli isolates, no predominant sequence type (ST) was identified, although 3 of them belonged to unknown STs (20%). Resistance to ampicillin, amoxicillin/clavulanic acid, cotrimoxazole, and quinolones was more present in these isolates; whereas, third and fourth generation cephalosporins, carbapenems, amikacin, tigecycline, and colistin were highly active. Moreover, high diversity of virulence factors has been found, with sfa, fimH, and gad the most frequently detected genes. Interestingly, 26.6% of the E. coli isolates were high biofilm-producers. Altogether, our data characterized for the first time E. coli isolates associated with biliary tract infections in terms of genomic relationship, resistome, and virulome.
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Affiliation(s)
- Ángel Rodríguez-Villodres
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
| | - Rémy A. Bonnin
- LabEx Lermit, EA7361, Université Paris-Sud, Université Paris-Saclay, 91190 Saint-Aubin, France; (R.A.B.); (T.N.)
- The Evolution and Ecology of Resistance to Antibiotics” Unit, Institut Pasteur-APHP-Université Paris Sud, 91400 Orsay, France
| | - José Manuel Ortiz de la Rosa
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
| | - Rocío Álvarez-Marín
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
| | - Thierry Naas
- LabEx Lermit, EA7361, Université Paris-Sud, Université Paris-Saclay, 91190 Saint-Aubin, France; (R.A.B.); (T.N.)
- The Evolution and Ecology of Resistance to Antibiotics” Unit, Institut Pasteur-APHP-Université Paris Sud, 91400 Orsay, France
- Bacteriology Hygiene Unit, APHP, Hôpital Bicêtre, Le Kremlin-Bicêtre, 94270 Paris, France
| | - Javier Aznar
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
- Department of Microbiology, University of Seville, 41009 Seville, Spain
| | - Jerónimo Pachón
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
- Department of Medicine, University of Seville, 41009 Seville, Spain
| | - José Antonio Lepe
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
| | - Younes Smani
- Clinical Unit of Infectious Diseases, Microbiology and Preventive Medicine, University Hospital Virgen del Rocío, 41013 Seville, Spain; (A.R.-V.); (J.M.O.d.l.R.); (J.A.); (J.A.L.)
- Institute of Biomedicine of Seville (IBiS), University Hospital Virgen del Rocío, CSIC, University of Seville, 41013 Seville, Spain
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Furlan JPR, de Almeida OGG, De Martinis ECP, Stehling EG. Characterization of an Environmental Multidrug-Resistant Acinetobacter seifertii and Comparative Genomic Analysis Reveals Co-occurrence of Antimicrobial Resistance and Metal Tolerance Determinants. Front Microbiol 2019; 10:2151. [PMID: 31620107 PMCID: PMC6759475 DOI: 10.3389/fmicb.2019.02151] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 09/02/2019] [Indexed: 11/13/2022] Open
Abstract
Acinetobacter calcoaceticus-Acinetobacter baumannii complex is considered one of the main causes of hospital-acquired infections. Acinetobacter seifertii was recently characterized within this complex and it has been described as an emergent pathogen associated with bacteremia. The emergence of multidrug-resistant (MDR) bacteria, including Acinetobacter sp., is considered a global public health threat and an environmental problem because MDR bacteria have been spreading from several sources. Therefore, this study aimed to characterize an environmental MDR A. seifertii isolate (SAb133) using whole genome sequencing and a comparative genomic analysis was performed with A. seifertii strains recovered from various sources. The SAb133 isolate was obtained from soil of a corn crop field and presented high MICs for antimicrobials and metals. The comparative genomic analyses revealed ANI values higher than 95% of relatedness with other A. seifertii strains than A. calcoaceticus-A. baumannii complex. Resistome and virulome analyses were also performed and showed different antimicrobial resistance determinants and metal tolerance genes as well as virulence genes related to A. baumannii known virulence genes. In addition, genomic islands, IS elements, plasmids and prophage-related sequences were detected. Comparative genomic analysis showed that MDR A. seifertii SAb133 had a high amount of determinants related to antimicrobial resistance and tolerance to metals, besides the presence of virulence genes. To the best of our knowledge, this is the first report of a whole genome sequence of a MDR A. seifertii isolated from soil. Therefore, this study contributed to a better understanding of the genetic relationship among the few known A. seifertii strains worldwide distributed.
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Affiliation(s)
- João Pedro Rueda Furlan
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Otávio Guilherme Gonçalves de Almeida
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Elaine Cristina Pereira De Martinis
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Eliana Guedes Stehling
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
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30
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de Carvalho SP, de Almeida JB, de Freitas LM, Guimarães AMS, do Nascimento NC, Dos Santos AP, Campos GB, Messick JB, Timenetsky J, Marques LM. Genomic profile of Brazilian methicillin-resistant Staphylococcus aureus resembles clones dispersed worldwide. J Med Microbiol 2019; 68:693-702. [PMID: 30900970 DOI: 10.1099/jmm.0.000956] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Comparative genomic analysis of strains may help us to better understand the wide diversity of their genetic profiles. The aim of this study was to analyse the genomic features of the resistome and virulome of Brazilian first methicillin-resistant Staphylococcus aureus (MRSA) isolates and their relationship to other Brazilian and international MRSA strains. METHODOLOGY The whole genomes of three MRSA strains previously isolated in Vitória da Conquista were sequenced, assembled, annotated and compared with other MRSA genomes. A phylogenetic tree was constructed and the pan-genome and accessory and core genomes were constructed. The resistomes and virulomes of all strains were identified.Results/Key findings. Phylogenetic analysis of all 49 strains indicated different clones showing high similarity. The pan-genome of the analysed strains consisted of 4484 genes, with 31 % comprising the gene portion of the core genome, 47 % comprising the accessory genome and 22 % being singletons. Most strains showed at least one gene related to virulence factors associated with immune system evasion, followed by enterotoxins. The strains showed multiresistance, with the most recurrent genes conferring resistance to beta-lactams, fluoroquinolones, aminoglycosides and macrolides. CONCLUSIONS Our comparative genomic analysis showed that there is no pattern of virulence gene distribution among the clones analysed in the different regions. The Brazilian strains showed similarity with clones from several continents.
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Affiliation(s)
- Suzi P de Carvalho
- Department of Biological Sciences, Santa Cruz State University, Ilhéus-Itabuna Road, km 16 Salobrinho, Ilhéus 45662-900, Bahia State, Brazil
| | - Jéssica B de Almeida
- Department of Biological Sciences, Santa Cruz State University, Ilhéus-Itabuna Road, km 16 Salobrinho, Ilhéus 45662-900, Bahia State, Brazil.,Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rio de Contas Street, Square 17, Number 58, Candeias, Vitória da Conquista, 45029-094, Bahia State, Brazil
| | - Leandro M de Freitas
- Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rio de Contas Street, Square 17, Number 58, Candeias, Vitória da Conquista, 45029-094, Bahia State, Brazil
| | - Ana Marcia S Guimarães
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, 1374 Professor Lineu Prestes Avenue, Sao Paulo, 05508-900, São Paulo State, Brazil
| | - Naíla C do Nascimento
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47906, USA
| | - Andrea P Dos Santos
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47906, USA
| | - Guilherme B Campos
- Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rio de Contas Street, Square 17, Number 58, Candeias, Vitória da Conquista, 45029-094, Bahia State, Brazil
| | - Joanne B Messick
- Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University, West Lafayette, IN 47906, USA
| | - Jorge Timenetsky
- Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, 1374 Professor Lineu Prestes Avenue, Sao Paulo, 05508-900, São Paulo State, Brazil
| | - Lucas M Marques
- Multidisciplinary Institute of Health, Universidade Federal da Bahia, Rio de Contas Street, Square 17, Number 58, Candeias, Vitória da Conquista, 45029-094, Bahia State, Brazil.,Department of Biological Sciences, Santa Cruz State University, Ilhéus-Itabuna Road, km 16 Salobrinho, Ilhéus 45662-900, Bahia State, Brazil.,Department of Microbiology, Institute of Biomedical Sciences, University of Sao Paulo, 1374 Professor Lineu Prestes Avenue, Sao Paulo, 05508-900, São Paulo State, Brazil
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31
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Pasquali F, Palma F, Trevisani M, Parisi A, Lucchi A, Cesare AD, Manfreda G. Whole genome sequencing based typing and characterisation of Shiga-toxin producing Escherichia coli strains belonging to O157 and O26 serotypes and isolated in dairy farms. Ital J Food Saf 2018; 7:7673. [PMID: 30854339 PMCID: PMC6379698 DOI: 10.4081/ijfs.2018.7673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 10/22/2018] [Indexed: 01/16/2023] Open
Abstract
In the present study, the genetic relationships as well as the virulome and resistome of newly sequenced O26 and O157 Shiga-toxin producing E. coli (STEC) isolates, collected from dairy farms in Italy, were investigated in comparison to publicly available genomes collected worldwide. The whole genome of Italian isolates was sequenced on Illumina MiSeq Platform. Reads quality control, de novo draft genome assembly, species confirmation and the 7- loci Multi-Locus Sequence Type assignment were performed using INNUca pipeline. Reference-based SNPs calling was performed on O157 and O26 genomes, separately, mapping contigs to high-quality finished genomes. Virulence and antimicrobial resistance determinants were detected in silico using the tool ABRicate. Phylogenetic reconstructions revealed that genomes clustered mainly based on their 7-loci MLST type. The virulome of tested genomes included 190 determinants. O157 genomes carried chu genes associated to heme mediated iron uptake, whereas O26 genomes harboured genes ybt associated to siderophore mediated iron uptake. Resistome analysis showed the presence of tet(34) on all but one O157 genomes and on only one O26 genomes. Only 4 genomes carried genes associated to multiresistance. In the present study, the genes chu and ybt were identified as potential biomarker for the differentiation of O157 and O26 serotypes.
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Affiliation(s)
- Frederique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna
| | - Federica Palma
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna
| | - Marcello Trevisani
- Department of Veterinary Medical Sciences, Alma Mater Studiorum – University of Bologna
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Bari, Italy
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna
| | - Alessandra De Cesare
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, Alma Mater Studiorum – University of Bologna
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Campos Calero G, Caballero Gómez N, Benomar N, Pérez Montoro B, Knapp CW, Gálvez A, Abriouel H. Deciphering Resistome and Virulome Diversity in a Porcine Slaughterhouse and Pork Products Through Its Production Chain. Front Microbiol 2018; 9:2099. [PMID: 30258416 PMCID: PMC6144875 DOI: 10.3389/fmicb.2018.02099] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/16/2018] [Indexed: 12/11/2022] Open
Abstract
We aimed to better understand resistome and virulome patterns on animal and process-area surfaces through a pig slaughterhouse to track possible contamination within the food production chain. Culture-dependent methods revealed high levels of microbial contamination, corresponding to mesophilic and pathogenic bacteria on both the animal and process-area surfaces mainly in the anesthesia (AA and AS) zone followed by “scorching and whip” (FA and FS) zone and also in the end products. To evaluate the potential risk of antibiotic resistance and virulence determinants, shotgun metagenomic DNA-sequencing of isolates from selected areas/products uncovered a high diversity and richness of antibiotic resistance genes (ARGs): 55–62 genes in the anesthesia area (AA and AS) and 35–40 in “animal-arrival zone” (MA and MS). The “scorching and whip” (FA and FS) area, however, exhibited lowered abundance of ARGs (1–6), indicating that the scalding and depilating process (an intermediate zone between “anesthesia” and “scorching and whip”) significantly decreased bacterial load by 1–3 log10 but also diminished the resistome. The high prevalence of antibiotic-inactivating enzyme genes in the “animal-arrival zone” (60–65%) and “anesthesia” area (56%) were mainly represented by those for aminoglycoside (46–51%) and lincosamide (14–19%) resistance, which did not reflect selective pressures by antibiotics most commonly used in pig therapy—tetracyclines and beta-lactams. Contrary to ARGs, greater number of virulence resistance genes were detected after evisceration in some products such as kidney, which reflected the poor hygienic practices. More than 19 general virulence features—mainly adherence, secretion system, chemotaxis and motility, invasion and motility were detected in some products. However, immune evasion determinants were detected in almost all samples analyzed from the beginning of the process, with highest amounts found from the anesthesia area. We conclude that there are two main sources of contamination in a pig slaughterhouse: the microorganisms carried on the animals’ hide, and those from the evisceration step. As such, focussing control measures, e.g., enhanced disinfection procedures, on these contamination-source areas may reduce risks to food safety and consumer health, since the antibiotic and virulence determinants may spread to end products and the environment; further, ARG and virulence traits can exacerbate pathogen treatments.
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Affiliation(s)
- Guillermo Campos Calero
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Natacha Caballero Gómez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Nabil Benomar
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Beatriz Pérez Montoro
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Charles W Knapp
- Centre for Water, Environment, Sustainability & Public Health, Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, United Kingdom
| | - Antonio Gálvez
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Hikmate Abriouel
- Área de Microbiología, Departamento de Ciencias de la Salud, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
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Hourigan SK, Subramanian P, Hasan NA, Ta A, Klein E, Chettout N, Huddleston K, Deopujari V, Levy S, Baveja R, Clemency NC, Baker RL, Niederhuber JE, Colwell RR. Comparison of Infant Gut and Skin Microbiota, Resistome and Virulome Between Neonatal Intensive Care Unit (NICU) Environments. Front Microbiol 2018; 9:1361. [PMID: 29988506 PMCID: PMC6026636 DOI: 10.3389/fmicb.2018.01361] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 06/05/2018] [Indexed: 01/08/2023] Open
Abstract
Background: There is a growing move to provide care for premature infants in a single family, private room neonatal intensive care unit (NICU) in place of the traditional shared space, open bay NICU. The resultant effect on the developing neonatal microbiota is unknown. Study Design: Stool and groin skin swabs were collected from infants in a shared-space NICU (old NICU) and a single-family room NICU (new NICU) on the same hospital campus. Metagenomic sequencing was performed and data analyzed by CosmosID bioinformatics software package. Results: There were no significant differences between the cohorts in gestational age, length of stay, and delivery mode; infants in the old NICU received significantly more antibiotics (p = 0.03). Differentially abundant antimicrobial resistance genes and virulence associated genes were found between the cohorts in stool and skin, with more differentially abundant antimicrobial resistance genes in the new NICU. The entire bacterial microbiota analyzed to the genus level significantly differed between cohorts in skin (p = 0.0001) but not in stool samples. There was no difference in alpha diversity between the two cohorts. DNA viruses and fungi were detected but did not differ between cohorts. Conclusion: Differences were seen in the resistome and virulome between the two cohorts with more differentially abundant antimicrobial resistance genes in the new NICU. This highlights the influence that different NICU environments can have on the neonatal microbiota. Whether the differences were due to the new NICU being a single-family NICU or located in a newly constructed building warrants exploration. Long term health outcomes from the differences observed must be followed longitudinally.
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Affiliation(s)
- Suchitra K Hourigan
- Department of Pediatrics, Inova Children's Hospital, Falls Church, VA, United States.,Inova Translational Medicine Institute, Falls Church, VA, United States.,Department of Pediatric Gastroenterology, Pediatric Specialists of Virginia, Fairfax, VA, United States
| | | | | | - Allison Ta
- Department of Pediatrics, Inova Children's Hospital, Falls Church, VA, United States
| | - Elisabeth Klein
- Inova Translational Medicine Institute, Falls Church, VA, United States
| | - Nassim Chettout
- Inova Translational Medicine Institute, Falls Church, VA, United States
| | - Kathi Huddleston
- Inova Translational Medicine Institute, Falls Church, VA, United States
| | - Varsha Deopujari
- Inova Translational Medicine Institute, Falls Church, VA, United States
| | - Shira Levy
- Inova Translational Medicine Institute, Falls Church, VA, United States
| | - Rajiv Baveja
- Fairfax Neonatal Associates PC, Falls Church, VA, United States
| | - Nicole C Clemency
- Inova Translational Medicine Institute, Falls Church, VA, United States
| | - Robin L Baker
- Fairfax Neonatal Associates PC, Falls Church, VA, United States
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Lebughe M, Phaku P, Niemann S, Mumba D, Peters G, Muyembe-Tamfum JJ, Mellmann A, Strauß L, Schaumburg F. The Impact of the Staphylococcus aureus Virulome on Infection in a Developing Country: A Cohort Study. Front Microbiol 2017; 8:1662. [PMID: 28900424 PMCID: PMC5581934 DOI: 10.3389/fmicb.2017.01662] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 08/16/2017] [Indexed: 12/31/2022] Open
Abstract
We performed a cohort study to analyze the virulome of Staphylococcus aureus from the Democratic Republic of the Congo using whole genome sequencing and to assess its impact on the course of S. aureus infections. Community-associated S. aureus from nasal colonization (n = 100) and infection (n = 86) were prospectively collected. Phenotypic susceptibility testing and WGS was done for each isolate. WGS data were used to screen for 79 different virulence factors and for genotyping purposes (spa typing, multilocus sequence typing). The majority of the 79 virulence factors were equally distributed among isolates from colonization and infection. Panton-Valentine leukocidin (PVL) and the non-truncated hemolysin β were associated with skin and soft tissue infection (SSTI) and recurrence of disease but did not influence the course of infection (i.e., mortality, surgical intervention). For the first time, we show that not only PVL but also hemolysin β could contribute to the development of SSTI in PVL-endemic areas such as Africa.
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Affiliation(s)
- Marthe Lebughe
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | - Patrick Phaku
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | - Silke Niemann
- Institute of Medical Microbiology, University Hospital MünsterMünster, Germany
| | - Dieudonné Mumba
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | - Georg Peters
- Institute of Medical Microbiology, University Hospital MünsterMünster, Germany
| | - Jean-Jacques Muyembe-Tamfum
- Institut National de Recherche Bio-Médicale, Université de KinshasaKinshasa, Democratic Republic of the Congo
| | | | - Lena Strauß
- Institute of Hygiene, University Hospital MünsterMünster, Germany
| | - Frieder Schaumburg
- Institute of Medical Microbiology, University Hospital MünsterMünster, Germany
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Fernández-Romero N, Romero-Gómez MP, Mora-Rillo M, Rodríguez-Baño J, López-Cerero L, Pascual Á, Mingorance J. Uncoupling between core genome and virulome in extraintestinal pathogenic Escherichia coli. Can J Microbiol 2015; 61:647-52. [PMID: 26063294 DOI: 10.1139/cjm-2014-0835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) are among the most frequently isolated bacterial pathogens in hospitals. They are considered opportunistic pathogens and are found mostly in urinary and bloodstream infections. They are genetically diverse, and many studies have sought associations between genotypes or virulence genes and infection site, severity, or outcome, with varied, often contradictory, results. To understand these difficulties, we have analyzed the diversity patterns in the core genomes and virulomes of more than 500 ExPEC isolates from 5 different collections. The core genome was analyzed using a multilocus sequence type-based single-nucleotide polymorphism (SNP) pyrosequencing approach, while the virulence gene content (the virulome) was studied by polymerase chain reaction detection of 25 representative genes. SNP typing showed a similar population structure in the different collections: half of the isolates belong to a few sequence types (5 to 8), while the other half is composed of a large diversity of sequence types that are found once or twice. Sampling analysis by rarefaction plots of SNP profiles showed saturation curves indicative of a limited diversity. Contrary to this, the virulome shows an extremely high diversity, with almost as many gene profiles as isolates, and linear, nonsaturating, rarefaction plots, even within sequence types. These data show that genetic exchange rates are very heterogeneous along the chromosome, being much higher in the virulome fraction of the genome than in the core genome.
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Affiliation(s)
- Natalia Fernández-Romero
- a Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261 28046 Madrid, Spain
| | - María Pilar Romero-Gómez
- a Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261 28046 Madrid, Spain
| | - Marta Mora-Rillo
- b Unidad de Enfermedades Infecciosas y Microbiología Clínica, Hospital Universitario La Paz, IdiPAZ, Madrid, Spain
| | - Jesús Rodríguez-Baño
- c Unidad Clínica Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Sevilla, Spain.,d Departamento de Medicina, Universidad de Sevilla, Spain.,e Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Lorena López-Cerero
- c Unidad Clínica Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Sevilla, Spain.,e Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain.,f Departamento de Microbiología, Universidad de Sevilla, Spain
| | - Álvaro Pascual
- c Unidad Clínica Intercentros de Enfermedades Infecciosas, Microbiología y Medicina Preventiva, Hospitales Universitarios Virgen Macarena y Virgen del Rocío, Sevilla, Spain.,e Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain.,f Departamento de Microbiología, Universidad de Sevilla, Spain
| | - Jesús Mingorance
- a Servicio de Microbiología, Hospital Universitario La Paz, IdiPAZ, Paseo de La Castellana, 261 28046 Madrid, Spain.,e Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
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