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Arjun OK, Sethi M, Parida D, Dash J, Kumar Das S, Prakash T, Senapati S. Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India. Gene 2024; 931:148882. [PMID: 39182659 DOI: 10.1016/j.gene.2024.148882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 08/11/2024] [Accepted: 08/21/2024] [Indexed: 08/27/2024]
Abstract
Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.
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Affiliation(s)
- O K Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India
| | - Manisha Sethi
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Deepti Parida
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Jayalaxmi Dash
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Suraja Kumar Das
- Institute of Life Sciences, Nalco Square, Bhubaneswar, Odisha 751023, India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Himachal Pradesh 175005, India.
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Polemis M, Sideroglou T, Chrysostomou A, Mandilara GD. First Data on WGS-Based Typing and Antimicrobial Resistance of Human Salmonella Enteritidis Isolates in Greece. Antibiotics (Basel) 2024; 13:708. [PMID: 39200008 PMCID: PMC11350896 DOI: 10.3390/antibiotics13080708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/22/2024] [Accepted: 07/24/2024] [Indexed: 09/01/2024] Open
Abstract
Salmonella enterica subsp. enterica serotype Enteritidis (S. Enteritidis) is one of the major causes of foodborne infections and is responsible for many national and multi-country foodborne outbreaks worldwide. In Greece, human salmonellosis is a mandatory notifiable disease, with laboratory surveillance being on a voluntary basis. This study aims to provide the first insights into the genetic characteristics and antimicrobial resistance profiles of 47 S. Enteritidis human isolates using whole-genome sequencing (WGS) technology. The S. Enteritidis population was mainly resistant to fluoroquinolones due to gyrA point mutations, whereas one isolate presented a multi-resistant plasmid-mediated phenotype. ST11 was the most frequent sequence type, and phylogenetic analysis through the cgMLST and SNP methods revealed considerable genetic diversity. Regarding virulence factors, 8 out of the 24 known SPIs and C63PI were detected. Due to the observed variability between countries, it is of utmost importance to record the circulating S. Enteritidis strains' structure and genomic epidemiology at the national level. WGS is a valuable tool that is revolutionizing our approach to Salmonella by providing a deeper understanding of these pathogens and their impact on human health.
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Affiliation(s)
- Michalis Polemis
- Computational Biology Department, Central Public Health Laboratory, National Public Health Organization (EODY), 16672 Vari, Greece;
| | - Theologia Sideroglou
- Directorate of Epidemiological Surveillance and Intervention for Infectious Diseases, National Public Health Organization (EODY), 15123 Maroussi, Greece; (T.S.); (A.C.)
| | - Anthi Chrysostomou
- Directorate of Epidemiological Surveillance and Intervention for Infectious Diseases, National Public Health Organization (EODY), 15123 Maroussi, Greece; (T.S.); (A.C.)
| | - Georgia D. Mandilara
- National Reference Centre for Salmonella, Faculty of Public Health Policies, School of Public Health, University of West Attica, 11521 Athens, Greece
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Chen Z, Grim CJ, Ramachandran P, Meng J. Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing. Microbiol Spectr 2024; 12:e0011724. [PMID: 38687063 PMCID: PMC11237517 DOI: 10.1128/spectrum.00117-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/05/2024] [Indexed: 05/02/2024] Open
Abstract
Oxford Nanopore sequencing is one of the high-throughput sequencing technologies that facilitates the reconstruction of metagenome-assembled genomes (MAGs). This study aimed to assess the potential of long-read assembly algorithms in Oxford Nanopore sequencing to enhance the MAG-based identification of bacterial pathogens using both simulated and mock communities. Simulated communities were generated to mimic those on fresh spinach and in surface water. Long reads were produced using R9.4.1+SQK-LSK109 and R10.4 + SQK-LSK112, with 0.5, 1, and 2 million reads. The simulated bacterial communities included multidrug-resistant Salmonella enterica serotypes Heidelberg, Montevideo, and Typhimurium in the fresh spinach community individually or in combination, as well as multidrug-resistant Pseudomonas aeruginosa in the surface water community. Real data sets of the ZymoBIOMICS HMW DNA Standard were also studied. A bioinformatic pipeline (MAGenie, freely available at https://github.com/jackchen129/MAGenie) that combines metagenome assembly, taxonomic classification, and sequence extraction was developed to reconstruct draft MAGs from metagenome assemblies. Five assemblers were evaluated based on a series of genomic analyses. Overall, Flye outperformed the other assemblers, followed by Shasta, Raven, and Unicycler, while Canu performed least effectively. In some instances, the extracted sequences resulted in draft MAGs and provided the locations and structures of antimicrobial resistance genes and mobile genetic elements. Our study showcases the viability of utilizing the extracted sequences for precise phylogenetic inference, as demonstrated by the consistent alignment of phylogenetic topology between the reference genome and the extracted sequences. R9.4.1+SQK-LSK109 was more effective in most cases than R10.4+SQK-LSK112, and greater sequencing depths generally led to more accurate results.IMPORTANCEBy examining diverse bacterial communities, particularly those housing multiple Salmonella enterica serotypes, this study holds significance in uncovering the potential of long-read assembly algorithms to improve metagenome-assembled genome (MAG)-based pathogen identification through Oxford Nanopore sequencing. Our research demonstrates that long-read assembly stands out as a promising avenue for boosting precision in MAG-based pathogen identification, thus advancing the development of more robust surveillance measures. The findings also support ongoing endeavors to fine-tune a bioinformatic pipeline for accurate pathogen identification within complex metagenomic samples.
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Affiliation(s)
- Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
| | - Christopher J. Grim
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Padmini Ramachandran
- Center for Food Safety and Applied Nutrition, United States Food and Drug Administration, College Park, Maryland, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition, Center for Food Safety and Security Systems, University of Maryland, College Park, Maryland, USA
- Department of Nutrition and Food Science, University of Maryland, College Park, Maryland, USA
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4
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Tan S, Li X, Lu B, Lin Y, Cai Y, He J, Chen S, Gao J, Gao J, Qiang X. Genomic Insights into the First Emergence of blaNDM-5-Carrying Carbapenem-Resistant Salmonella enterica Serovar London Strain in China. Infect Drug Resist 2024; 17:1781-1790. [PMID: 38736433 PMCID: PMC11088413 DOI: 10.2147/idr.s458625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
Carbapenem-resistant Salmonella enterica (S. enterica) pose a significant threat to public health, causing gastroenteritis and invasive infections. We report the first emergence of a carbapenem-resistant S. enterica serovar London strain, A132, carrying the blaNDM-5 gene in China. Whole-genome sequencing and bioinformatics analysis assigned A132 to be ST155, a multidrug-resistant clone frequently reported in China. The strain A132 exhibited resistance to multiple antibiotics, with 20 acquired antibiotic resistance genes (ARGs) identified, predominantly located on the IncFIB plasmid (pA132-1-NDM). Notably, the blaNDM-5 gene was located within an IS26 flanked-class 1 integron-ISCR1 complex, comprising two genetic cassettes. One cassette is the class 1 integron, which may facilitate the transmission of the entire complex, while the other is the blaNDM-5-containing ISCR1-IS26-flanked cassette, carrying multiple other ARGs. Genbank database search based on the blaNDM-5-carrying cassette identified a similar genetic context found in transmissible IncFIA plasmids from Escherichia coli (p91) and Enterobacter hormaechei (p388) with a shared host range, suggesting the potential for cross-species transmission of blaNDM-5. To our knowledge, this is the first reported case of Salmonella serovar London ST155 harboring blaNDM-5 gene. Phylogenetic analysis indicated a close relationship between A132 and eight S. London ST155 strains isolated from the same province. However, A132 differed by carrying the blaNDM-5 gene and four unique ARGs. Given the high transmissibility of the F-type plasmid harboring blaNDM-5 and 18 other ARGs, it is imperative to implement vigilant surveillance and adopt appropriate infection control measures to mitigate the threat to public health.
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Affiliation(s)
- Shaohua Tan
- Department of Clinical Laboratory, The First People’s Hospital of Huzhou, Huzhou, Zhejiang, 313000, People’s Republic of China
| | - Xiangchen Li
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, 310020, People’s Republic of China
| | - Bing Lu
- Department of Clinical Laboratory, The First People’s Hospital of Huzhou, Huzhou, Zhejiang, 313000, People’s Republic of China
- School of Medicine, Huzhou University, Huzhou, Zhejiang, 313000, People’s Republic of China
| | - Yibin Lin
- School of Medicine, Huzhou University, Huzhou, Zhejiang, 313000, People’s Republic of China
| | - Yunxiang Cai
- Department of Clinical Laboratory, The First People’s Hospital of Huzhou, Huzhou, Zhejiang, 313000, People’s Republic of China
| | - Jie He
- Department of Infectious Diseases, The First People’s Hospital of Huzhou, Huzhou, Zhejiang, 313000, People’s Republic of China
| | - Sisi Chen
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, 310020, People’s Republic of China
| | - Junli Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, 310020, People’s Republic of China
| | - Junshun Gao
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang Province, Hangzhou, Zhejiang, 310020, People’s Republic of China
| | - Xinhua Qiang
- Department of Clinical Laboratory, The First People’s Hospital of Huzhou, Huzhou, Zhejiang, 313000, People’s Republic of China
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Barmak SM, Mendenhall IH, Sinyavskiy YA, Berdygaliev AB, Sharmanov TS, Sultankulova GT, Tuigunov DN, Zholdybayeva EV. Whole-genome sequence and annotation of Salmonella enterica subsp. enterica strain QazSL-4. Microbiol Resour Announc 2024; 13:e0087623. [PMID: 38624204 PMCID: PMC11080549 DOI: 10.1128/mra.00876-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 03/09/2024] [Indexed: 04/17/2024] Open
Abstract
Here, we present the whole-genome sequence of Salmonella enterica subsp. enterica strain QazSL-4 isolated from a chicken fillet in 2018, Almaty, Kazakhstan. The genome obtained using Illumina MiSeq technology consists of 49 contigs with a total length of 4,711,816 bp with a GC content of 52.1%.
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Affiliation(s)
- Sabyrkhan M. Barmak
- Department of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore
| | - Yuriy A. Sinyavskiy
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Aidar B. Berdygaliev
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Turegeldy Sh. Sharmanov
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Gulmira T. Sultankulova
- Department of Pediatric Surgery, Asfendiyarov Kazakh National Medical University, Almaty, Kazakhstan
| | - Dilyar N. Tuigunov
- Laboratory of Food Biotechnologies and Specialized foodstuffs, Kazakh Academy of Nutrition LLP, Almaty, Kazakhstan
| | - Elena V. Zholdybayeva
- National scientific shared laboratory of biotechnology, National Center for Biotechnology, Astana, Kazakhstan
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Leite EL, Saraiva MM, Vasconcelos PC, Monte DF, Allard MW, Givisiez PE, Gebreyes WA, Freitas Neto OC, Oliveira CJ. Whole genome sequence datasets of Salmonella enterica serovar Saintpaul ST50 and serovar Worthington ST592 strains isolated from raw milk in Brazil. Data Brief 2024; 53:109965. [PMID: 38425878 PMCID: PMC10904156 DOI: 10.1016/j.dib.2023.109965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 03/02/2024] Open
Abstract
Herein we report the draft genome sequences of Salmonella enterica subsp. enterica serovars Saintpaul ST50 and Worthington ST592 isolated from raw milk samples in Northeastern Brazil. The 4,696,281 bp S. Saintpaul ST50 genome contained 4,628 genes in 33 contigs, while S. Worthington ST592 genome was 4,890,415 bp in length, comprising 4,951 genes in 46 contigs. S. Worthington ST592 carried a conserved Col(pHAD28) plasmid which contains the antimicrobial resistance determinants tet(C), acc(6')-Iaa, and a nonsynonymous point mutation in ParC (p.T57S). The data could support further evolutionary and epidemiologic studies involving Salmonella organisms.
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Affiliation(s)
- Elma L. Leite
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
| | - Mauro M.S. Saraiva
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Priscylla C. Vasconcelos
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
| | - Daniel F.M. Monte
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP, 14884-900, Brazil
| | - Marc W. Allard
- Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U. S. Food and Drug Administration, College Park, MD, USA
| | - Patrícia E.N. Givisiez
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
| | - Wondwossen A. Gebreyes
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Ohio State University, Columbus, OH, USA
- Global One Health Initiative (GOHi), Ohio State University, Columbus, OH, USA
| | - Oliveiro C. Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Celso J.B. Oliveira
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB, Brazil
- Global One Health Initiative (GOHi), Ohio State University, Columbus, OH, USA
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Rheman S, Hossain S, Sarker MS, Akter F, Khor L, Gan HM, Powell A, Card RM, Hounmanou YMG, Dalsgaard A, Mohan CV, Bupasha ZB, Samad MA, Verner-Jeffreys DW, Delamare-Deboutteville J. Nanopore sequencing for identification and characterization of antimicrobial-resistant Escherichia coli and Salmonella spp. from tilapia and shrimp sold at wet markets in Dhaka, Bangladesh. Front Microbiol 2024; 15:1329620. [PMID: 38516018 PMCID: PMC10956512 DOI: 10.3389/fmicb.2024.1329620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 02/09/2024] [Indexed: 03/23/2024] Open
Abstract
Wet markets in low-and middle-income countries are often reported to have inadequate sanitation resulting in fecal contamination of sold produce. Consumption of contaminated wet market-sourced foods has been linked to individual illness and disease outbreaks. This pilot study, conducted in two major wet markets in Dhaka city, Bangladesh during a 4-month period in 2021 aimed to assess the occurrence and characteristics of Escherichia coli and non-typhoidal Salmonella spp. (NTS) from tilapia (Oreochromis niloticus) and shrimp (Penaeus monodon). Fifty-four individuals of each species were collected. The identity of the bacterial isolates was confirmed by PCR and their susceptibility toward 15 antimicrobials was tested by disk diffusion. The whole genome of 15 E. coli and nine Salmonella spp. were sequenced using Oxford Nanopore Technology. E. coli was present in 60-74% of tilapia muscle tissue and 41-44% of shrimp muscle tissue. Salmonella spp. was found in skin (29%) and gills (26%) of tilapia, and occasionally in muscle and intestinal samples of shrimp. The E. coli had several Multilocus sequence typing and serotypes and limited antimicrobial resistance (AMR) determinants, such as point mutations on glpT and pmrB. One E. coli (BD17) from tilapia carried resistance genes for beta-lactams, quinolones, and tetracycline. All the E. coli belonged to commensal phylogroups B1 and A and showed no Shiga-toxin and other virulence genes, confirming their commensal non-pathogenic status. Among the Salmonella isolates, five belonged to Kentucky serovar and had similar AMR genes and phenotypic resistance patterns. Three strains of this serovar were ST198, often associated with human disease, carried the same resistance genes, and were genetically related to strains from the region. The two undetermined sequence types of S. Kentucky were distantly related and positioned in a separate phylogenetic clade. Two Brunei serovar isolates, one Augustenborg isolate, and one Hartford isolate showed different resistance profiles. This study revealed high fecal contamination levels in tilapia and shrimp sold at two main wet markets in Dhaka. Together with the occurrence of Salmonella spp., including S. Kentucky ST198, a well-known human pathogen, these results stress the need to improve hygienic practices and sanitation standards at markets to improve food safety and protect consumer health.
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Affiliation(s)
- Shafiq Rheman
- Laboratory Department of Sustainable Aquaculture, WorldFish, Dhaka, Bangladesh
| | - Sabrina Hossain
- Laboratory Department of Sustainable Aquaculture, WorldFish, Dhaka, Bangladesh
| | - Md Samun Sarker
- Antimicrobial Resistance Action Center (ARAC), Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Bangladesh
| | - Farhana Akter
- Laboratory Department of Sustainable Aquaculture, WorldFish, Dhaka, Bangladesh
| | - Laura Khor
- Department of Sustainable Aquaculture, WorldFish, Penang, Malaysia
| | - Han Ming Gan
- Patriot Biotech Sdn Bhd, Bandar Sunway, Malaysia
| | - Andy Powell
- Weymouth Laboratory, Cefas: Centre for Environment Fisheries and Aquaculture Science, Weymouth, United Kingdom
- Veterinary Medicines Directorate FAO Reference Centre for Antimicrobial Resistance, Weybridge, United Kingdom
| | - Roderick M. Card
- Bacteriology Department, Animal Plant Health Agency, Weybridge, United Kingdom
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Anders Dalsgaard
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Zamila Bueaza Bupasha
- Antimicrobial Resistance Action Center (ARAC), Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Bangladesh
| | - Mohammed A. Samad
- Antimicrobial Resistance Action Center (ARAC), Animal Health Research Division, Bangladesh Livestock Research Institute, Savar, Bangladesh
| | - David W. Verner-Jeffreys
- Weymouth Laboratory, Cefas: Centre for Environment Fisheries and Aquaculture Science, Weymouth, United Kingdom
- Veterinary Medicines Directorate FAO Reference Centre for Antimicrobial Resistance, Weybridge, United Kingdom
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Novak A, Dzelalija M, Goic-Barisic I, Kovacic A, Pirija M, Maravic A, Radic M, Marinovic J, Rubic Z, Carev M, Tonkic M. Phenotypic and Molecular Characterization of a Hospital Outbreak Clonal Lineage of Salmonella enterica Subspecies enterica serovar Mikawasima Containing blaTEM-1B and blaSHV-2 That Emerged on a Neonatal Ward, During the COVID-19 Pandemic. Microb Drug Resist 2024; 30:118-126. [PMID: 38330414 DOI: 10.1089/mdr.2023.0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024] Open
Abstract
Nontyphoid salmonella can cause severe infections in newborns and is therefore declared a pathogen of major health significance at this age. The aim of the study was molecular and antimicrobial characterization of β-lactamase-producing Salmonella Mikawasima outbreak clone on a Neonatal ward, University Hospital of Split (UHS), Croatia during the COVID-19 pandemic. From April 2020, until April 2023, 75 nonrepetitive strains of Salmonella Mikawasima were isolated from stool specimens and tested for antimicrobial resistance. All 75 isolates were resistant to ampicillin and gentamicin, while 98% of isolates were resistant to amoxicillin/clavulanic acid. A high level of resistance was observed to third-generation cephalosporins (36% to ceftriaxone and 47% to ceftazidime). Extended-spectrum β-lactamase production was phenotypically detected by double-disk synergy test in 40% of isolates. Moderate resistance to quinolones was detected; 7% of isolates were resistant to pefloxacin and ciprofloxacin. All isolates were susceptible to carbapenems, chloramphenicol, and co-trimoxazole. Fourteen representative isolates, from 2020, 2021, 2022, and 2023, were analyzed with PFGE and all of them belong to the same clone. Whole-genome sequencing (WGS) analysis of three outbreak-related strains (SM1 and SM2 from 2020 and SM3 from 2023) confirmed that these strains share the same serotype (Mikawasima), multilocus sequence typing profile (ST2030), resistance genes [blaTEM-1B, aac(6')-Iaa, aac(6')-Im, and aph(2'')-Ib)] and carry incompatibility group C (IncC) plasmid. Furthermore, the gene blaSHV-2 was detected in SM1 and SM2. In summary, WGS analysis of three representative strains clearly demonstrates the persistence of β-lactamase-producing Salmonella Mikawasima in UHS during the 4-year period.
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Affiliation(s)
- Anita Novak
- Department of Clinical Microbiology, University Hospital of Split, Croatia, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
- ESCMID Food and Waterborne Infections Study Group - EFWISG, Basel, Switzerland
| | - Mia Dzelalija
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Ivana Goic-Barisic
- Department of Clinical Microbiology, University Hospital of Split, Croatia, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Ana Kovacic
- Teaching Public Health Institute of Split and Dalmatia County, Split, Croatia
| | - Mario Pirija
- Department of Clinical Microbiology, University Hospital of Split, Croatia, Split, Croatia
| | - Ana Maravic
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Marina Radic
- Department of Clinical Microbiology, University Hospital of Split, Croatia, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Jelena Marinovic
- Department of Clinical Microbiology, University Hospital of Split, Croatia, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Zana Rubic
- Department of Clinical Microbiology, University Hospital of Split, Croatia, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
| | - Merica Carev
- School of Medicine, University of Split, Split, Croatia
- ESCMID Food and Waterborne Infections Study Group - EFWISG, Basel, Switzerland
- Teaching Public Health Institute of Split and Dalmatia County, Split, Croatia
- Department of Health Studies, University of Split, Split, Croatia
| | - Marija Tonkic
- Department of Clinical Microbiology, University Hospital of Split, Croatia, Split, Croatia
- School of Medicine, University of Split, Split, Croatia
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9
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Watler S, Toka FN, Lardé H, Johnson A, Butaye P. Epidemiology of Salmonella enterica subspecies enterica serotypes, isolated from imported, farmed and feral poultry in the Cayman Islands. Front Vet Sci 2024; 11:1331916. [PMID: 38406633 PMCID: PMC10884249 DOI: 10.3389/fvets.2024.1331916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 01/18/2024] [Indexed: 02/27/2024] Open
Abstract
Non-typhoidal Salmonellae (NTS) are common foodborne pathogens throughout the world causing acute gastroenteritis. Compared to North America and Europe, there is little information on NTS in the Caribbean. Here we investigated the prevalence and characteristics of NTS present in the local poultry of the Cayman Islands to determine the public health risk. In total, we collected 156 samples. These were made up of boot swabs of 31 broiler farms and 31 layer farms (62 samples), paper bedding from 45 imported chick boxes, and 49 pooled cecum samples from feral chickens, each sample representing 10 individual chickens. Salmonella was isolated using the ISO 6579 protocol and isolates were characterized using Whole Genome Sequencing (WGS) analysis. Eighteen Salmonella isolates were obtained and comprised six S. enterica subspecies enterica serotypes and one subspecies houtenae serotype. Serotypes were: S. Kentucky (n = 9), S. Saintpaul (n = 5), S. Javiana (n = 1), S. Senftenberg (n = 1), S. Poona (n = 1) and S. Agona (n = 1). S. Kentucky strains were all ST152 and clonally related to poultry strains from the United states. S. Saintpaul ST50 strains showed clonality to North American strains. Over half of the strains (n = 11) contained resistance genes to at least two antibiotic groups and five strains were MDR, mainly those from imported day-old chicks. The blaCMY-2 gene was found in S. Kentucky from day-old chicks. Strains from feral poultry had no acquired AMR genes. While serotypes from feral poultry have been identified in human infections, they pose minimal risk due to their low virulence.
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Affiliation(s)
- Simon Watler
- Department of Environmental Health, Ministry of Health and Wellness, Grand Cayman, Cayman Islands
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Felix N. Toka
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Hélène Lardé
- Department of Clinical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Antoinette Johnson
- Department of Environmental Health, Ministry of Health and Wellness, Grand Cayman, Cayman Islands
| | - Patrick Butaye
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
- Faculty of Veterinary Medicine, Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Merelbeke, Belgium
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
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10
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Leão C, Silveira L, Usié A, Gião J, Clemente L, Themudo P, Amaro A, Pista A. Genetic Diversity of Salmonella enterica subsp. enterica Serovar Enteritidis from Human and Non-Human Sources in Portugal. Pathogens 2024; 13:112. [PMID: 38392849 PMCID: PMC10892295 DOI: 10.3390/pathogens13020112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) is one of the leading causes of foodborne infections associated with broilers and laying hens. Portugal has had the lowest notification rates of salmonellosis in recent years, due to the vaccinations of layer and breeder flocks and strict compliance with biosecurity measures. However, data about the genetic diversity of S. Enteritidis in Portugal are scarce. In this study, 102 S. Enteritidis isolates selected from human (n = 63) and non-human sources (n = 39) were characterized by serotyping, antimicrobial susceptibility, and whole genome sequencing. The S. Enteritidis population was mainly resistant to fluoroquinolones, and a sole isolate showed resistance to extended-spectrum cephalosporins. ST11 was the most frequent sequence type, and three novel STs from human isolates (ST9236, ST4457, and ST9995) were assigned. Several Salmonella pathogenic islands (SPI) and Putative SPI were present in the genomes, namely SPI-1, 2, 3, 4, 5, 9, 10, 12, 13, and 14, C63PI, CS54_island, and 170 virulence genes were identified. The phylogenetic analysis revealed that strains from Portugal are genetically heterogeneous regarding sample type, collection date, and genetic content. This study increases the available data, essential to a better characterization of strains in a global context.
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Affiliation(s)
- Célia Leão
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
- MED—Mediterranean Institute for Agriculture, Environment and Development, 7006-554 Évora, Portugal
| | - Leonor Silveira
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal;
| | - Ana Usié
- Department of Animal Genomics and Bioinformatics, Centro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL), Instituto Politécnico de Beja (IPBeja), 7801-908 Beja, Portugal;
- MED—Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento & CHANGE–Global Change and Sustainability Institute, CEBAL, 7801-908 Beja, Portugal
| | - Joana Gião
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
| | - Lurdes Clemente
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Science, 1300-477 Lisbon, Portugal
| | - Patricia Themudo
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
| | - Ana Amaro
- Laboratory of Bacteriology and Mycology, Department of Antimicrobial Resistance, National Institute of Agrarian and Veterinary Research (INIAV, IP), 2780-157 Oeiras, Portugal; (C.L.); (J.G.); (L.C.); (P.T.); (A.A.)
| | - Angela Pista
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, 1649-016 Lisbon, Portugal;
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11
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Kgoale DM, Duvenage S, Du Plessis EM, Gokul JK, Korsten L. Serotype Distribution, Antimicrobial Resistance, Virulence Genes, and Genetic Diversity of Salmonella spp. Isolated from small-scale Leafy Green Vegetable Supply Chains in South Africa. J Food Prot 2024; 87:100195. [PMID: 37977503 DOI: 10.1016/j.jfp.2023.100195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 09/27/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Salmonella have been implicated in foodborne disease outbreaks globally and is a pressing concern in the South African small-scale sector due to inadequate hygiene standards and limited regulatory oversight, leading to a higher risk of foodborne diseases. By investigating irrigation water and leafy green vegetables produced by small-scale growers and sold through unregulated supply chains, this study was able to determine the presence, serotype distribution, virulence gene profiles, antibiotic resistance, and genetic diversity of Salmonella isolated from these sources. From 426 samples, 21 Salmonella-positive samples were identified, providing 53 Salmonella isolates. Of these, six different Salmonella serotypes and sequence types (STs) were identified, including Salmonella II 42:r: ST1208 (33.96%; n = 18), Salmonella Enteritidis: ST11 (22.64%; n = 12), Salmonella II 42:z29: ST4395 (16.98%; n = 9), Salmonella Havana: ST1524 (15.09%; n = 8), Salmonella Typhimurium: ST19 (9.43%; n = 5), and Salmonella IIIb 47:i:z: ST7890 (1.89%; n = 1). A total of 92.45% of the isolates were found to be multidrug-resistant, showing high rates of resistance to aztreonam (88.68%; n = 47), ceftazidime (86.79%; n = 46), nalidixic acid (77.36%; n = 41), cefotaxime (75.47%; n = 40), cefepime (71.70%; n = 38), and streptomycin (69.81%; n = 37). All isolates possessed the aac(6')-Iaa antimicrobial resistance gene, with a range of between 9 and 256 virulence genes. Eleven cluster patterns were observed from Enterobacterial Repetitive Intergenic Consensus sequence analyses, demonstrating high diversity among the Salmonella spp., with water and fresh produce isolates clustering, suggesting water as a potential contamination source. Plasmid replicon types were identified in 41.51% (n = 22) of the isolates, including Col(pHAD28) in Salmonella Havana (5.66%; n = 3), Col156 in Salmonella II 42:z29:- (1.89%; n = 1) and both IncFIB(S) and IncFII(S) in Salmonella Enteritidis (22.64; n = 12), Salmonella Typhimurium (9.43%; n = 5), and Salmonella Havana (1.89%; n = 1). This study highlights the presence of multidrug-resistant and multivirulent Salmonella spp. in the small-scale leafy green vegetable supply chains, underscoring the need for the development of a "fit-for-purpose" food safety management system within this system.
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Affiliation(s)
- Degracious M Kgoale
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, South Africa; Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
| | - Stacey Duvenage
- Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa; Food and Markets Department, Natural Resources Institute, University of Greenwich, Chatham Maritime, United Kingdom
| | - Erika M Du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, South Africa; Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa
| | - Jarishma K Gokul
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Hatfield, Pretoria, South Africa; Department of Science and Innovation-National Research Foundation Centre of Excellence in Food Security, South Africa.
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12
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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] [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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13
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Barrera S, Vázquez-Flores S, Needle D, Rodríguez-Medina N, Iglesias D, Sevigny JL, Gordon LM, Simpson S, Thomas WK, Rodulfo H, De Donato M. Serovars, Virulence and Antimicrobial Resistance Genes of Non-Typhoidal Salmonella Strains from Dairy Systems in Mexico. Antibiotics (Basel) 2023; 12:1662. [PMID: 38136696 PMCID: PMC10740734 DOI: 10.3390/antibiotics12121662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 12/24/2023] Open
Abstract
Salmonella isolated from dairy farms has a significant effect on animal health and productivity. Different serogroups of Salmonella affect both human and bovine cattle causing illness in both reservoirs. Dairy cows and calves can be silent Salmonella shedders, increasing the possibility of dispensing Salmonella within the farm. The aim of this study was to determine the genomic characteristics of Salmonella isolates from dairy farms and to detect the presence of virulence and antimicrobial resistance genes. A total of 377 samples were collected in a cross-sectional study from calves, periparturient cow feces, and maternity beds in 55 dairy farms from the states of Aguascalientes, Baja California, Chihuahua, Coahuila, Durango, Mexico, Guanajuato, Hidalgo, Jalisco, Queretaro, San Luis Potosi, Tlaxcala, and Zacatecas. Twenty Salmonella isolates were selected as representative strains for whole genome sequencing. The serological classification of the strains was able to assign groups to only 12 isolates, but with only 5 of those being consistent with the genomic serotyping. The most prevalent serovar was Salmonella Montevideo followed by Salmonella Meleagridis. All isolates presented the chromosomal aac(6')-Iaa gene that confers resistance to aminoglycosides. The antibiotic resistance genes qnrB19, qnrA1, sul2, aph(6)-Id, aph(3)-ld, dfrA1, tetA, tetC, flor2, sul1_15, mph(A), aadA2, blaCARB, and qacE were identified. Ten pathogenicity islands were identified, and the most prevalent plasmid was Col(pHAD28). The main source of Salmonella enterica is the maternity areas, where periparturient shedders are contaminants and perpetuate the pathogen within the dairy in manure, sand, and concrete surfaces. This study demonstrated the necessity of implementing One Health control actions to diminish the prevalence of antimicrobial resistant and virulent pathogens including Salmonella.
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Affiliation(s)
- Stephany Barrera
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - Sonia Vázquez-Flores
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - David Needle
- Veterinary Diagnostic Lab, University of New Hampshire, Durham, NH 03824, USA;
| | - Nadia Rodríguez-Medina
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Cuernavaca 62100, MR, Mexico;
| | - Dianella Iglesias
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - Joseph L. Sevigny
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - Lawrence M. Gordon
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - Stephen Simpson
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - W. Kelley Thomas
- Department Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (J.L.S.); (L.M.G.); (S.S.); (W.K.T.)
| | - Hectorina Rodulfo
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
| | - Marcos De Donato
- Tecnologico de Monterrey, School of Engineering and Sciences, Querétaro 76130, CP, Mexico; (S.B.); (D.I.); (H.R.)
- The Center for Aquaculture Technologies, San Diego, CA 92121, USA
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14
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Bartsch LJ, Borowiak M, Deneke C, Gruetzke J, Hammerl JA, Malorny B, Szabo I, Alter T, Nguyen KK, Fischer J. Genetic characterization of a multidrug-resistant Salmonella enterica serovar Agona isolated from a dietary supplement in Germany. Front Microbiol 2023; 14:1284929. [PMID: 38033583 PMCID: PMC10686068 DOI: 10.3389/fmicb.2023.1284929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/25/2023] [Indexed: 12/02/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Agona has a history of causing food-borne outbreaks and any emergence of multidrug-resistant (MDR) isolates in novel food products is of concern. Particularly, in food products frequently consumed without sufficient heating prior to consumption. Here, we report about the MDR isolate, 18-SA00377, which had been isolated from a dietary supplement in Germany in 2018 and submitted to the German National Reference Laboratory for Salmonella. WGS-based comparative genetic analyses were conducted to find a potential reservoir of the isolate itself or mobile genetic elements associated with MDR. As a phylogenetic analysis did not yield any closely related S. Agona isolates, either globally or from Germany, a detailed analysis of the largest plasmid (295,499 bp) was performed as it is the main carrier of resistances. A combined approach of long-read and short-read sequencing enabled the assembly of the isolate's chromosome and its four plasmids. Their characterization revealed the presence of 23 different antibiotic resistance genes (ARGs), conferring resistance to 12 different antibiotic drug classes, as well as genes conferring resistance to six different heavy metals. The largest plasmid, pSE18-SA00377-1, belongs to the IncHI2 plasmid family and carries 16 ARGs, that are organized as two distinct clusters, with each ARG associated with putative composite transposons. Through a two-pronged approach, highly similar plasmids to pSE18-SA00377-1 were identified in the NCBI database and a search for Salmonella isolates with a highly similar ARG resistance profile was conducted. Mapping and structural comparisons between pSE18-SA00377-1 and these plasmids and Salmonella isolates showed that both the plasmid backbone and identical or similar ARG clusters can be found not only in Salmonella isolates, originating mostly from a wide variety of livestock, but also in a diverse range of bacterial genera of varying geographical origins and isolation sources. Thus, it can be speculated that the host range of pSE18-SA00377-1 is not restricted to Salmonella and its spread already occurred in different bacterial populations. Overall, this hints at a complex history for pSE18-SA00377-1 and highlights the importance of surveilling multidrug-resistant S. enterica isolates, especially in novel food items that are not yet heavily regulated.
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Affiliation(s)
- Lee Julia Bartsch
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Maria Borowiak
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Carlus Deneke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Josephine Gruetzke
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jens-Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Istvan Szabo
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Thomas Alter
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | | | - Jennie Fischer
- Department Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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15
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Syed Abu Thahir S, Rajendiran S, Shaharudin R, Veloo Y. Multidrug-Resistant Salmonella Species and Their Mobile Genetic Elements from Poultry Farm Environments in Malaysia. Antibiotics (Basel) 2023; 12:1330. [PMID: 37627750 PMCID: PMC10451245 DOI: 10.3390/antibiotics12081330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 08/27/2023] Open
Abstract
The prevalence and persistent outbreaks of multidrug-resistant (MDR) Salmonella in low-income countries have received growing attention among the public and scientific community. Notably, the excessive use of antibiotics in chicken feed for the purpose of treatment or as prophylaxis in the poultry industry have led to a rising rate of antimicrobial resistance. Therefore, this study aimed to determine the presence of antimicrobial-resistant Salmonella species and its mobile genetic elements from soil and effluent samples of 33 randomly selected poultry farms in Selangor, Malaysia. Salmonella species were isolated on selective media (CHROMagar™ Salmonella). VITEK® 2 system was used to identify the isolates and their antimicrobial susceptibility. Subsequently, eight isolates were subjected to the whole genome sequencing (WGS). Based on the results, Salmonella spp. was detected in 38.1% (24/63) of samples, with the highest resistance to ampicillin (62.5%), followed by ampicillin/sulbactam (50.0%) and ciprofloxacin (45.8%). Meanwhile, the identified serovars were Salmonella enterica subspecies enterica serovar Weltevreden (S. Weltevreden), S. Jedburgh, and S. Brancaster. The most prevalent resistance genes detected include qnrS1, blaTEM-176, dfrA14, and tet(A). The IncX1 plasmid, with encoded resistance genes, was also detected in four isolates. Furthermore, mutations in the quinolone resistant-determining regions (QRDR) were discovered, specifically in the gyrA, gyrB, and parC genes. In short, surveillance such as continuous monitoring of antimicrobial resistance and emerging trends in resistance patterns through farm environmental samples could provide information to formulate public health interventions for effective infection prevention and disease control.
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Affiliation(s)
- Syahidiah Syed Abu Thahir
- Environmental Health Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health, Setia Alam, Shah Alam 40107, Malaysia
| | - Sakshaleni Rajendiran
- Environmental Health Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health, Setia Alam, Shah Alam 40107, Malaysia
| | - Rafiza Shaharudin
- Environmental Health Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health, Setia Alam, Shah Alam 40107, Malaysia
| | - Yuvaneswary Veloo
- Environmental Health Research Centre, Institute for Medical Research, National Institute of Health, Ministry of Health, Setia Alam, Shah Alam 40107, Malaysia
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16
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Ivanova O, Blumenkrants D, Krylova E, Soltynskaya I, Goncharova A, Chaikin E, Akhmetzyanova A, Panin A. Founding of the culture collection of antibiotic-resistant strains of zoonotic bacteria in the Russian Federation. Vet World 2023; 16:1451-1460. [PMID: 37621551 PMCID: PMC10446724 DOI: 10.14202/vetworld.2023.1451-1460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 05/29/2023] [Indexed: 08/26/2023] Open
Abstract
Background and Aim The main purpose of a national bioresource center is to standardize, centralize, preserve, and ensure accessibility of microbial bioresources that accumulate there because of state research programs. The establishment of national bioresource centers for antibiotic-resistant microorganisms allows to solve practical problems in the field of veterinary service, as well as to develop effective chemotherapeutic and disinfectant drugs to overcome the mechanisms of resistance. This study aimed to outline the process of forming a national culture collection of antibiotic-resistant strains of zoonotic bacteria in the Russian Federation using two microbial strains. Materials and Methods The object of research was isolates of Salmonella spp., Escherichia coli, Enterococcus spp., Campylobacter spp., Listeria monocytogenes, and Staphylococcus spp., all of which were obtained from biomaterials of farm animals, feed samples, bedding, water from livestock buildings, washouts from environmental objects, and food products. The resistance of bacterial isolates was determined using microbiological and molecular-genetic research methods. Results During monitoring studies, 1489 bacterial isolates were isolated. In total, 408 bacterial isolates were tested for sensitivity to antimicrobial agents, including E. coli (47.6%), Salmonella spp. (30.4%), Enterococcus spp. (11.3%), and Campylobacter spp. (10.8%). For genetic characterization, 95 isolates of Salmonella enterica, E. coli, Campylobacter spp., L. monocytogenes, Staphylococcus spp., Enterococcus spp. were chosen from the research collection, which was formed as part of the monitoring program for antibiotic resistance. Conclusion Deposited isolates that underwent whole-genome analysis can be used as positive control samples both in the development and use of methods or test systems for the detection of various resistance genes in zoonotic bacteria. In addition, such isolates can also be used for microbiological studies related to determining the sensitivity of microorganisms to antibacterial drugs, for phenotypic studies in the diagnosis of various bacterial infections in animals and birds, and retrospective analysis of strains from numerous collections.
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Affiliation(s)
- Olga Ivanova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Dmitry Blumenkrants
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Ekaterina Krylova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Irina Soltynskaya
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Anastasia Goncharova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Evgeny Chaikin
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Anna Akhmetzyanova
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
| | - Alexander Panin
- Federal State Budgetary Institution, The Russian State Center for Animal Feed and Drug Standardization and Quality, Moscow, Russia
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17
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Vilela FP, Rodrigues DDP, Allard MW, Falcão JP. The rare Salmonella enterica serovar Isangi: genomic characterization of the antimicrobial resistance, virulence potential and epidemiology of Brazilian strains in comparison to global isolates. J Med Microbiol 2023; 72. [PMID: 37462464 DOI: 10.1099/jmm.0.001736] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/21/2023] Open
Abstract
Introduction. Salmonella enterica serovar Isangi (S. Isangi) is a rare non-typhoidal serovar, related to invasive nosocomial infections in various countries and to increasing antimicrobial resistance rates.Gap statement. Despite existing reports on S. Isangi, there is a lack of information of specific traits regarding this serovar, which could be improved through genomic analyses.Aim. Our goals were to characterize the antimicrobial resistance, virulence potential and genomic relatedness of 11 S. Isangi strains from Brazil in comparison to 185 genomes of global isolates using whole-genome sequencing (WGS) data.Methodology. Phenotypic resistance was determined by disc-diffusion. The search for resistance genes, plasmids, prophages, Salmonella pathogenicity islands (SPIs) and virulence genes, plus multi-locus sequence typing (MLST) and core-genome MLST (cgMLST) were performed using WGS.Results. Brazilian S. Isangi strains showed phenotypic resistance to nalidixic acid, ciprofloxacin and streptomycin, and harboured antimicrobial resistance [qnrB19, aac(6')-Iaa, mdsAB] and heavy metal tolerance (arsD, golST) genes. Col(pHAD28) and IncFII(S) plasmids, virulence genes related to adherence, macrophage induction, magnesium uptake, regulation and type III secretion systems, 12 SPIs and eight prophages were detected. The 185 additional global genomes analysed harboured resistance genes against 11 classes of antimicrobial compounds, 22 types of plasmids, 32 prophages, 14 SPIs, and additional virulence genes related to serum resistance, stress adaptation and toxins. Sequence type (ST)216 was assigned to genomes from Brazil and other countries, while ST335 was the most frequent ST, especially among South African genomes. cgMLST showed that Brazilian genomes were more closely related to genomes from European and African countries, the USA and Taiwan, while the majority of South African genomes were more closely related among each other.Conclusion. The presence of S. Isangi strains from Brazil and different countries showing a close genomic correlation, antimicrobial resistance profiles to drugs used in human therapy and a large number of virulence determinants reinforced the need for stronger initiatives to monitor rare non-typhoidal Salmonella serovars such as S. Isangi in order to prevent its dissemination among human and non-human sources.
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Affiliation(s)
- Felipe Pinheiro Vilela
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Av. do Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
| | | | - Marc William Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA
| | - Juliana Pfrimer Falcão
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto - USP, Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Av. do Café, s/n, 14040-903, Ribeirão Preto, SP, Brazil
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Fatima S, Ishaq Z, Irfan M, AlAsmari AF, Achakzai JK, Zaheer T, Ali A, Akbar A. Whole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan. Front Public Health 2023; 11:1151805. [PMID: 37261234 PMCID: PMC10227597 DOI: 10.3389/fpubh.2023.1151805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction Salmonella enterica serovar Typhi (S. Typhi) is a major cause of morbidity and mortality in developing countries, contributing significantly to the global disease burden. Methods In this study, S. Typhi strains were isolated from 100 patients exhibiting symptoms of typhoid fever at a tertiary care hospital in Pakistan. Antimicrobial testing of all isolates was performed to determine the sensitivity and resistance pattern. Three MDR strains, namely QS194, QS430, and QS468, were subjected to whole genome sequencing for genomic characterization. Results and Discussion MLST analysis showed that QS194, belonged to ST19, which is commonly associated with Salmonella enterica serovar typhimurium. In contrast, QS430 and QS468, belonged to ST1, a sequence type frequently associated with S. Typhi. PlasmidFinder identified the presence of IncFIB(S) and IncFII(S) plasmids in QS194, while IncQ1 was found in QS468. No plasmid was detected in QS430. CARD-based analysis showed that the strains were largely resistant to a variety of antibiotics and disinfecting agents/antiseptics, including fluoroquinolones, cephalosporins, monobactams, cephamycins, penams, phenicols, tetracyclines, rifamycins, aminoglycosides, etc. The S. Typhi strains possessed various virulence factors, such as Vi antigen, Agf/Csg, Bcf, Fim, Pef, etc. The sequencing data indicated that the strains had antibiotic resistance determinants and shared common virulence factors. Pangenome analysis of the selected S. Typhi strains identified 13,237 genes, with 3,611 being core genes, 2,093 shell genes, and 7,533 cloud genes. Genome-based typing and horizontal gene transfer analysis revealed that the strains had different evolutionary origins and may have adapted to distinct environments or host organisms. These findings provide important insights into the genetic characteristics of S. Typhi strains and their potential association with various ecological niches and host organisms.
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Affiliation(s)
- Sareen Fatima
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
| | - Zaara Ishaq
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, (NUST), Islamabad, Pakistan
| | - Muhammad Irfan
- Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Abdullah F. AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Jahangir Khan Achakzai
- Disipline of Biochemistry, Department of Natural and Basic Sciences, University of Turbat Kech, Balochistan, Pakistan
| | - Tahreem Zaheer
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, (NUST), Islamabad, Pakistan
| | - Ali Akbar
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
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Trofimova E, Asgharzadeh Kangachar S, Weynberg KD, Willows RD, Jaschke PR. A bacterial genome assembly and annotation laboratory using a virtual machine. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2023; 51:276-285. [PMID: 36866633 PMCID: PMC10947226 DOI: 10.1002/bmb.21720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 01/25/2023] [Accepted: 02/13/2023] [Indexed: 05/15/2023]
Abstract
With the global increase of infections caused by antibiotic-resistant bacterial strains, there is an urgent need for new methods of tackling the issue. Genomic analysis of bacterial strains can help to understand their virulence and antibiotic resistance profile. Bioinformatic skills are in great demand across the biological sciences. We designed a workshop that allows university students to learn the process of genome assembly using command-line tools within a virtual machine on a Linux operating system. We use Illumina and Nanopore short and long-read raw sequences to reveal the advantages and disadvantages of short, long, and hybrid assembly methods. The workshop teaches how to assess read and assembly quality, perform genome annotation, and analyze pathogenicity, antibiotic and phage resistance. The workshop is intended for a five-week teaching period and is concluded by a student poster presentation assessment.
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Affiliation(s)
- Ellina Trofimova
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
- ARC Centre of Excellence in Synthetic BiologyMacquarie UniversitySydneyAustralia
| | - Shahla Asgharzadeh Kangachar
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Karen D. Weynberg
- Australian Centre for Ecogenomics, School of Chemistry and Molecular BiosciencesUniversity of QueenslandBrisbaneQueenslandAustralia
| | - Robert D. Willows
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
| | - Paul R. Jaschke
- School of Natural SciencesMacquarie UniversitySydneyNew South WalesAustralia
- ARC Centre of Excellence in Synthetic BiologyMacquarie UniversitySydneyAustralia
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20
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Brenner T, Wang S. Heightened variability observed in resistance and virulence genes across salmonella Kentucky isolates from poultry environments in British Columbia, Canada. Food Microbiol 2023; 111:104192. [PMID: 36681391 DOI: 10.1016/j.fm.2022.104192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 11/02/2022] [Accepted: 11/21/2022] [Indexed: 11/23/2022]
Abstract
Many niche-dependent barriers along the poultry production continuum favour the survival of certain Salmonella serovars over others. Historically, the presence of particular serovars has been determined by niche-specific genes which encode resistance to selective pressures such as host defenses and industrial antimicrobial practices. Over the past decade, Canada has witnessed unexplained shifts in the Salmonella landscape in the poultry sector. Several formerly minor Salmonella serovars, including S. Kentucky and S. Reading, have recently increased in prevalence in live chickens and turkeys, respectively, in British Columbia (BC). The purpose of this research was to investigate the genomic features of the top poultry-associated Salmonella spp. in BC, to probe for serovar-specific characteristics that could address the recently shifting balance of serovars along the poultry continuum. By examining the quantity and diversity of antimicrobial resistance (AMR) genes, virulence factors (VFs), Salmonella Pathogenicity Islands (SPIs), and plasmids across 50 poultry-associated S. enterica isolates using whole genome sequencing and antimicrobial resistance profiling, we have identified serovar-specific differences that likely influence niche survival. Specifically, isolates in our collection from predominantly human pathogenic serovars (S. I 4, [5], 12:i: , S. Typhimurium, and S. Enteritidis) were found to share the IncFIB(S) and IncFII(S) plasmids which carry important VFs known to aid in human host infection. Additionally, these strains held the lowest number of AMR genes, and the highest number of unique SPIs which also facilitate virulence. However, other serovars containing a greater diversity and abundance of resistance genes have been increasing across the poultry sector. S. Kentucky was found to carry unique AMR genes, VFs, SPIs, and plasmids that could bolster persistence in farm and processing environments. Overall, S. Kentucky also had comparatively high levels of intra-serovar genetic variability when compared to other prominent serovars from our collection. In addition, one of our two S. Reading isolates had high carriage of both AMR genes and VFs relative to other isolates in our collection. As the poultry-associated Salmonella landscape continues to evolve in Canada, future studies should monitor the genetic composition of prominent serovars across poultry production to maintain up-to-date risk assessments of these foodborne pathogens to consumers.
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Affiliation(s)
- Thomas Brenner
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Siyun Wang
- Food, Nutrition and Health, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada.
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21
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Rose TFA, Kannan P, Ruban SW, Srinivas K, Milton AAP, Ghatak S, Elango A, Rajalakshmi S, Sundaram S. Isolation, susceptibility profiles and genomic analysis of a colistin-resistant Salmonella enterica serovar Kentucky strain COL-R. 3 Biotech 2023; 13:140. [PMID: 37124985 PMCID: PMC10133420 DOI: 10.1007/s13205-023-03559-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
Salmonella enterica serovar Kentucky is a frequent cause for clinical infections in human patients. They are isolated and reported with multidrug resistance from the foods of animal origin from various countries. However, studies inferring the colistin resistance are limited. Hence, the current study reports the genetic factors and genomic analysis of the colistin-resistant Salmonella enterica serovar Kentucky strain COL-R for better understanding of its pathogenic potential and phylogenetic relatedness. The S. Kentucky strain COL-R was successfully isolated from chicken meat during ongoing surveillance of food of animal origin. Antimicrobial susceptibility testing revealed resistance to cefoxitin, erythromycin, gentamicin, tetracycline, and most disturbingly to ciprofloxacin and colistin (broth microdilution method). Whole-genome sequence of the COL-R strain was subjected to various in silico analysis to identify the virulence factors, antimicrobial resistance genes, pathogenicity islands and sequence type. The S. Kentucky COL-R strain belonged to sequence type (ST) 198 with a high probability (0.943) of being a human pathogen. Besides presence of integrated phage in the S. Kentucky COL-R genome, 38 genes conferring resistance to various antimicrobials and disinfectants were also identified. Nucleotide Polymorphism analysis indicated triple mutations in gyrA and parC genes conferring fluoroquinolone resistance. Phylogenomic analysis with 31 other S. Kentucky genomes revealed discernible clusters with S. Kentucky COL-R strain latching onto a cluster of high diversity (geographic location and isolation sources). Taken together, our results document the first occurrence of colistin resistance in a fluoroquinolone resistant S. Kentucky COL-R strain isolated from retail chicken and provide crucial information on the genomic features of the strain. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03559-2.
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Affiliation(s)
- T. F. Amal Rose
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
| | - Porteen Kannan
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
| | - S. Wilfred Ruban
- Department of Livestock Products Technology, Veterinary College, KVAFSU, Hebbal, Bangalore, 560024 India
| | - Kandhan Srinivas
- Division of Veterinary Public Health, ICAR-Indian Veterinary Research Institute, Izatnagar, 243122 India
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, 793103 India
| | | | - Sandeep Ghatak
- Division of Animal and Fisheries Sciences, ICAR Research Complex for NEH Region, Umiam, 793103 India
| | - A. Elango
- Veterinary College and Research Institute, TANUVAS, Salem, 636112 India
| | - S. Rajalakshmi
- Department of Veterinary Microbiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
| | - Sureshkannan Sundaram
- Department of Veterinary Public Health and Epidemiology, Madras Veterinary College, TANUVAS, Chennai, 600007 India
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22
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Shin H, La TM, Lee HJ, Kim T, Song SU, Park GH, Choi IS, Park SY, Lee JB, Lee SW. Characteristics of a Temperature-Sensitive Mutant Strain of Salmonella Enteritidis and Its Potential as a Live Vaccine Candidate. Vet Sci 2023; 10:vetsci10050313. [PMID: 37235396 DOI: 10.3390/vetsci10050313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/19/2023] [Accepted: 04/24/2023] [Indexed: 05/28/2023] Open
Abstract
Salmonella Enteritidis is a common foodborne pathogen transmitted through poultry products, which are its main carriers. Poultry are vaccinated against Salmonella Enteritidis in many countries, despite the absence of clinical symptoms, using commercially available live-attenuated vaccines. We previously constructed a highly attenuated temperature-sensitive (ts) Salmonella Enteritidis mutant, 2S-G10. In the present study, we describe the construction and attenuation-associated characteristics of 2S-G10. We infected 1-day-old chicks with 2S-G10 and the parental strains to evaluate the attenuation. One week after infection, 2S-G10 was not detected in the liver, cecum, or cecal tonsil tissues of the orally inoculated chicks, contrary to the parental strain. This indicates that 2S-G10 was highly attenuated when compared to the parental stain. In vitro experiments revealed the inability of 2S-G10 to grow at the normal body temperature of chickens and invade chicken liver epithelial cells. Moreover, single nucleotide polymorphism (SNP) analysis between the complete genome sequence of 2S-G10 and its parental strain revealed SNPs in bcsE, recG, rfaF, and pepD_1 genes, which are involved in epithelial cell invasion and persistence in host systems, growth, lipopolysaccharide core biosynthesis, and cellular survival under heat stress, respectively. These potential characteristics are consistent with the findings of in vitro experiments. Conclusively, chemical treatment-induced random genetic mutations highly attenuated 2S-G10, implying its potential to be developed as a novel live-attenuated vaccine against Salmonella Enteritidis.
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Affiliation(s)
- Hyunjin Shin
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Tae-Min La
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Hong-Jae Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Taesoo Kim
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Seung-Un Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Gyu-Hyung Park
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - In-Soo Choi
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Seung-Yong Park
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Joong-Bok Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
| | - Sang-Won Lee
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Republic of Korea
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23
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Elhassan MMO, Adam HBA, Fagir SSAO, Mohamed SB, Khaier MAM, Abdulaziz R, Ismail A, Allam M. Whole-genome sequence data of a Salmonella enterica serovar Rissen sequence type 8877 isolated from cracked table egg in Sudan. Data Brief 2023; 47:109005. [PMID: 36915641 PMCID: PMC10006416 DOI: 10.1016/j.dib.2023.109005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 02/25/2023] Open
Abstract
Salmonella enterica serovar Rissen is an emerging and important Salmonella serovar prevalent in live animals and foods from retail markets worldwide. Here, we describe the whole-genome sequence of Salmonella enterica Serovar Rissen Sequence Type 8877 isolated from a cracked table egg in Sudan. The whole-genome sequencing was obtained using Illumina Miseq platform. The quality of the sequenced read, the De novo assembly, and the sequencing typing was conducted by JEKESA pipeline (https://github.com/stanikae/jekesa). The assembled genome was also uploaded to the Center for Genomic Epidemiology web server to determine acquired antibiotic resistance genes, predict the serovar, and the antigenic profile. The genome of Salmonella enterica serovar Rissen 1-M1 was found to harbor 4,689 protein-coding genes, 96 RNA genes, and 115 pseudogenes, as predicted by NCBI Prokaryotic Genome Annotation Pipeline. This whole genome shotgun project has been deposited at DDBJ/ENA/GenBank under accession JAPSFB000000000.
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Affiliation(s)
| | - Habiba B A Adam
- College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
| | | | - Sofia B Mohamed
- National University Biomedical Research Institute National University, Khartoum, Sudan
| | - Mona A M Khaier
- College of Veterinary Medicine, University of Bahri, Khartoum, Sudan
| | - Romisa Abdulaziz
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Arshad Ismail
- National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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24
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Chacón RD, Ramírez M, Rodríguez-Cueva CL, Sánchez C, Quispe-Rojas WU, Astolfi-Ferreira CS, Piantino Ferreira AJ. Genomic Characterization and Genetic Profiles of Salmonella Gallinarum Strains Isolated from Layers with Fowl Typhoid in Colombia. Genes (Basel) 2023; 14:genes14040823. [PMID: 37107581 PMCID: PMC10138188 DOI: 10.3390/genes14040823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/28/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
Salmonella Gallinarum (SG) is the causative agent of fowl typhoid (FT), a disease that is harmful to the poultry industry. Despite sanitation and prophylactic measures, this pathogen is associated with frequent disease outbreaks in developing countries, causing high morbidity and mortality. We characterized the complete genome sequence of Colombian SG strains and then performed a comparative genome analysis with other SG strains found in different regions worldwide. Eight field strains of SG plus a 9R-derived vaccine were subjected to whole-genome sequencing (WGS) and bioinformatics analysis, and the results were used for subsequent molecular typing; virulome, resistome, and mobilome characterization; and a comparative genome study. We identified 26 chromosome-located resistance genes that mostly encode efflux pumps, and point mutations were found in gyrase genes (gyrA and gyrB), with the gyrB mutation S464T frequently found in the Colombian strains. Moreover, we detected 135 virulence genes, mainly in 15 different Salmonella pathogenicity islands (SPIs). We generated an SPI profile for SG, including C63PI, CS54, ssaD, SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-6, SPI-9, SPI-10, SPI-11, SPI-12, SPI-13, and SPI-14. Regarding mobile genetic elements, we found the plasmids Col(pHAD28) and IncFII(S) in most of the strains and 13 different prophage sequences, indicating a frequently obtained profile that included the complete phage Gifsy_2 and incomplete phage sequences resembling Escher_500465_2, Shigel_SfIV, Entero_mEp237, and Salmon_SJ46. This study presents, for the first time, the genomic content of Colombian SG strains and a profile of the genetic elements frequently found in SG, which can be further studied to clarify the pathogenicity and evolutionary characteristics of this serotype.
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Affiliation(s)
- Ruy D Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo 05508-270, Brazil
- Inter-Units Program in Biotechnology, University of São Paulo, São Paulo 05508-900, Brazil
| | - Manuel Ramírez
- Unidad de Bioinformática, Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Bellavista 07006, Peru
| | - Carmen L Rodríguez-Cueva
- Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Christian Sánchez
- Department of Genetics, Physiology and Microbiology, Faculty of Biological Sciences, Complutense University of Madrid (UCM), 28040 Madrid, Spain
| | - Wilma Ursula Quispe-Rojas
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Claudete S Astolfi-Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo 05508-270, Brazil
| | - Antonio J Piantino Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo 05508-270, Brazil
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Comparison of Phenotype and Genotype Virulence and Antimicrobial Factors of Salmonella Typhimurium Isolated from Human Milk. Int J Mol Sci 2023; 24:ijms24065135. [PMID: 36982209 PMCID: PMC10048834 DOI: 10.3390/ijms24065135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
Salmonella is a common foodborne infection. Many serovars belonging to Salmonella enterica subsp. enterica are present in the gut of various animal species. They can cause infection in human infants via breast milk or cross-contamination with powdered milk. In the present study, Salmonella BO was isolated from human milk in accordance with ISO 6579-1:2017 standards and sequenced using whole-genome sequencing (WGS), followed by serosequencing and genotyping. The results also allowed its pathogenicity to be predicted. The WGS results were compared with the bacterial phenotype. The isolated strain was found to be Salmonella enterica subsp. enterica serovar Typhimurium 4:i:1,2_69M (S. Typhimurium 69M); it showed a very close similarity to S. enterica subsp. enterica serovar Typhimurium LT2. Bioinformatics sequence analysis detected eleven SPIs (SPI-1, SPI-2, SPI-3, SPI-4, SPI-5, SPI-9, SPI-12, SPI-13, SPI-14, C63PI, CS54_island). Significant changes in gene sequences were noted, causing frameshift mutations in yeiG, rfbP, fumA, yeaL, ybeU (insertion) and lpfD, avrA, ratB, yacH (deletion). The sequences of several proteins were significantly different from those coded in the reference genome; their three-dimensional structure was predicted and compared with reference proteins. Our findings indicate the presence of a number of antimicrobial resistance genes that do not directly imply an antibiotic resistance phenotype.
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Xu C, Rao J, Xie Y, Lu J, Li Z, Dong C, Wang L, Jiang J, Chen C, Chen S. The DNA Phosphorothioation Restriction-Modification System Influences the Antimicrobial Resistance of Pathogenic Bacteria. Microbiol Spectr 2023; 11:e0350922. [PMID: 36598279 PMCID: PMC9927239 DOI: 10.1128/spectrum.03509-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 11/30/2022] [Indexed: 01/05/2023] Open
Abstract
Bacterial defense barriers, such as DNA methylation-associated restriction-modification (R-M) and the CRISPR-Cas system, play an important role in bacterial antimicrobial resistance (AMR). Recently, a novel R-M system based on DNA phosphorothioate (PT) modification has been shown to be widespread in the kingdom of Bacteria as well as Archaea. However, the potential role of the PT R-M system in bacterial AMR remains unclear. In this study, we explored the role of PT R-Ms in AMR with a series of common clinical pathogenic bacteria. By analyzing the distribution of AMR genes related to mobile genetic elements (MGEs), it was shown that the presence of PT R-M effectively reduced the distribution of horizontal gene transfer (HGT)-derived AMR genes in the genome, even in the bacteria that did not tend to acquire AMR genes by HGT. In addition, unique gene variation analysis based on pangenome analysis and MGE prediction revealed that the presence of PT R-M could suppress HGT frequency. Thus, this is the first report showing that the PT R-M system has the potential to repress HGT-derived AMR gene acquisition by reducing the HGT frequency. IMPORTANCE In this study, we demonstrated the effect of DNA PT modification-based R-M systems on horizontal gene transfer of AMR genes in pathogenic bacteria. We show that there is no apparent association between the genetic background of the strains harboring PT R-Ms and the number of AMR genes or the kinds of gene families. The strains equipped with PT R-M harbor fewer plasmid-derived, prophage-derived, or integrating mobile genetic element (iMGE)-related AMR genes and have a lower HGT frequency, but the degree of inhibition varies among different bacteria. In addition, compared with Salmonella enterica and Escherichia coli, Klebsiella pneumoniae prefers to acquire MGE-derived AMR genes, and there is no coevolution between PT R-M clusters and bacterial core genes.
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Affiliation(s)
- Congrui Xu
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jing Rao
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yuqing Xie
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jiajun Lu
- Information Engineering Institute, Wuchang Institute of Technology, Wuhan, China
| | - Zhiqiang Li
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Changjiang Dong
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Lianrong Wang
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Jinghong Jiang
- Department of Obstetrics & Gynecology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Chao Chen
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Shi Chen
- Brain Center, Department of Neurosurgery, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, Health Science Center, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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27
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Chacón RD, Chacón JL, Ramírez M, Cueva CLR, Quispe-Rojas WU, Reyes-Moreno CB, Astolfi-Ferreira CS, Ferreira AJP. Complete genome sequence data of two Salmonella enterica subsp. enterica serovar Gallinarum: A 9R vaccine strain and a virulent Brazilian field strain. Data Brief 2023; 47:108959. [PMID: 36865996 PMCID: PMC9972493 DOI: 10.1016/j.dib.2023.108959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/26/2023] [Accepted: 02/01/2023] [Indexed: 02/11/2023] Open
Abstract
Salmonella Gallinarum (SG) is a host-restricted enterobacteria and the causative agent of fowl typhoid in poultry. Here, we report the complete genomes of two strains belonging to this serotype. SA68 is a field strain isolated from the livers of dead hen carcasses of a commercial layer farm presenting high mortality located in São Paulo city, Brazil, in 1990. Strain 9R corresponds to a live attenuated SG commercial vaccine. DNA was extracted from pure cultures and subjected to whole genome sequencing (WGS) using the Ion Torrent PGM System. The assemblies reached lengths of 4,657,435 (SA68) and 4,657,471 (9R) base pairs. Complete genomes were deposited in GenBank under the accession numbers CP110192 (SA68) and CP110508 (9R). Both genomes were analyzed and compared in terms of molecular typing, antibiotic resistance genes, virulence genes, Salmonella pathogenic islands (SPIs), insertion sequences and prophages. The data obtained show many similarities in the genetic content, with the exception of the SPI-12 and CS54 pathogenic islands, which are exclusive to the field strain. The information generated will help to understand the virulence differences of field and vaccinal SG strains and can be used to perform evolutionary and epidemiologic studies.
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Affiliation(s)
- Ruy D. Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando M. Paiva, 87, São Paulo 05508-270, Brazil
- Inter-Units Program in Biotechnology, University of São Paulo, Avenida Prof. Lineu Prestes, 2415, São Paulo 05508-900, Brazil
| | - Jorge L. Chacón
- Ceva Animal Health, R. Manoel Joaquim Filho, 303, São Paulo 13148-115, Brazil
| | - Manuel Ramírez
- Área de Análisis Bioinformático, Centro de Investigaciones Tecnológicas, Biomédicas y Medioambientales, Jirón José Santos Chocano, 199, Bellavista 07006, Perú
| | - Carmen L. Rodríguez Cueva
- Laboratory of Biology and Molecular Genetics, Faculty of Veterinary Medicine, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Wilma Ursula Quispe-Rojas
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - César Bryan Reyes-Moreno
- Laboratory of Molecular Microbiology and Biotechnology, Faculty of Biological Sciences, Universidad Nacional Mayor de San Marcos, Lima 15081, Peru
| | - Claudete S. Astolfi-Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando M. Paiva, 87, São Paulo 05508-270, Brazil
| | - Antonio J. Piantino Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando M. Paiva, 87, São Paulo 05508-270, Brazil
- Corresponding author.
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De Sousa Violante M, Michel V, Romero K, Bonifait L, Baugé L, Perrin-Guyomard A, Feurer C, Radomski N, Mallet L, Mistou MY, Cadel-Six S. Tell me if you prefer bovine or poultry sectors and I'll tell you who you are: Characterization of Salmonella enterica subsp. enterica serovar Mbandaka in France. Front Microbiol 2023; 14:1130891. [PMID: 37089562 PMCID: PMC10116068 DOI: 10.3389/fmicb.2023.1130891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/13/2023] [Indexed: 04/25/2023] Open
Abstract
Introduction In north-western France, Salmonella enterica susp. enterica serovar Mbandaka (S. Mbandaka) is most frequently isolated from bovine and dairy samples. While this serovar most often results in asymptomatic carriage, for a number of years it has caused episodes of abortions, which have serious economic consequences for the sector. Interestingly, this serovar is also isolated from Gallus gallus in the same geographic zone. Despite its prevalence in bovines in north-western France, S. Mbandaka has not been broadly studied at the genomic level, and its prevalence and host adaptation are still not fully understood. Methods In this study, we analyzed the genomic diversity of 304 strains of S. Mbandaka isolated from the bovine and poultry sectors in this area over a period of 5 years. A phylogenetic analysis was carried out and two approaches were followed to identify conserved genes and mutations related to host associations. The first approach targeted the genes compiled in the MEGARESv2, Resfinder, VFDB and SPI databases. Plasmid and phage contents were also investigated. The second approach refers to an in-house algorithm developed for this study that computes sensitivity, specificity, and accuracy of accessory genes and core variants according to predefined genomes groups. Results and discussion All the analyzed strains belong to the multi-locus sequence type profile ST413, and the phylogenomic analysis revealed main clustering by host (bovine and poultry), emphasizing the circulation of 12 different major clones, of which seven circulate in poultry and five in the bovine sector in France and a likely food production chain adaptation of these clones. All strains present resistance determinants including heavy metals and biocides that could explain the ability of this serovar to survive and persist in the environment, within herds, and in food processing plants. To explore the wild animal contribution to the spread of this serovar in north-western France, we retrieved S. Mbandaka genomes isolated from wild birds from EnteroBase and included them in the phylogenomic analysis together with our collection. Lastly, screening of accessory genes and major variants allowed us to identify conserved specific mutations characteristic of each major cluster. These mutations could be used to design useful probes for food safety surveillance.
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Affiliation(s)
| | | | - Karol Romero
- Salmonella and Listeria Unit (SEL), ANSES, Laboratory for Food Safety, Maisons-Alfort, France
| | - Laetitia Bonifait
- Hygiene and Quality of Poultry and Pork Products Unit, ANSES, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | - Louise Baugé
- Hygiene and Quality of Poultry and Pork Products Unit, ANSES, Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France
| | - Agnès Perrin-Guyomard
- ANSES, Fougères Laboratory, National Reference Laboratory for Antimicrobial Resistance, Fougères, France
| | | | - Nicolas Radomski
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “Giuseppe Caporale” (IZSAM), National Reference Centre (NRC) for Whole Genome Sequencing of Microbial Pathogens: Data-Base and Bioinformatics Analysis (GENPAT), Teramo, Italy
| | - Ludovic Mallet
- Institut Universitaire du Cancer de Toulouse–Oncopole, Toulouse, France
| | | | - Sabrina Cadel-Six
- Salmonella and Listeria Unit (SEL), ANSES, Laboratory for Food Safety, Maisons-Alfort, France
- *Correspondence: Sabrina Cadel-Six,
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Schiffer CJ, Grätz C, Pfaffl MW, Vogel RF, Ehrmann MA. Characterization of the Staphylococcus xylosus methylome reveals a new variant of type I restriction modification system in staphylococci. Front Microbiol 2023; 14:946189. [PMID: 36970683 PMCID: PMC10030836 DOI: 10.3389/fmicb.2023.946189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restriction modification (RM) systems are known to provide a strong barrier to the exchange of DNA between and within bacterial species. Likewise, DNA methylation is known to have an important function in bacterial epigenetics regulating essential pathways such as DNA replication and the phase variable expression of prokaryotic phenotypes. To date, research on staphylococcal DNA methylation focused mainly on the two species Staphylococcus aureus and S. epidermidis. Less is known about other members of the genus such as S. xylosus, a coagulase-negative commensal of mammalian skin. The species is commonly used as starter organism in food fermentations but is also increasingly considered to have an as yet elusive function in bovine mastitis infections. We analyzed the methylomes of 14 S. xylosus strains using single-molecular, real-time (SMRT) sequencing. Subsequent in silico sequence analysis allowed identification of the RM systems and assignment of the respective enzymes to the discovered modification patterns. Hereby the presence of type I, II, III and IV RM systems in varying numbers and combinations among the different strains was revealed, clearly distinguishing the species from what is known for other members of the genus so far. In addition, the study characterizes a newly discovered type I RM system, encoded by S. xylosus but also by a variety of other staphylococcal species, with a hitherto unknown gene arrangement that involves two specificity units instead of one (hsdRSMS). Expression of different versions of the operon in E. coli showed proper base modification only when genes encoding both hsdS subunits were present. This study provides new insights into the general understanding of the versatility and function of RM systems as well as the distribution and variations in the genus Staphylococcus.
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Affiliation(s)
- Carolin J. Schiffer
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- *Correspondence: Carolin J. Schiffer,
| | - Christian Grätz
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Michael W. Pfaffl
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Rudi F. Vogel
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthias A. Ehrmann
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil. Microorganisms 2022; 11:microorganisms11010111. [PMID: 36677403 PMCID: PMC9861973 DOI: 10.3390/microorganisms11010111] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/19/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023] Open
Abstract
In Brazil, Salmonella enterica serovar Enteritidis is a significant health threat. Salmonella enterica serovar Enteritidis SE3 was isolated from soil at the Subaé River in Santo Amaro, Brazil, a region contaminated with heavy metals and organic waste. Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing were used for de novo hybrid assembly of the Salmonella SE3 genome. This approach yielded 10 contigs with 99.98% identity with S. enterica serovar Enteritidis OLF-SE2-98984-6. Twelve Salmonella pathogenic islands, multiple virulence genes, multiple antimicrobial gene resistance genes, seven phage defense systems, seven prophages and a heavy metal resistance gene were encoded in the genome. Pangenome analysis of the S. enterica clade, including Salmonella SE3, revealed an open pangenome, with a core genome of 2137 genes. Our study showed the effectiveness of a hybrid sequence assembly approach for environmental Salmonella genome analysis using HiSeq and MinION data. This approach enabled the identification of key resistance and virulence genes, and these data are important to inform the control of Salmonella and heavy metal pollution in the Santo Amaro region of Brazil.
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Luo M, She Y, Jiang Y, Xie L, Yang C, Qiu Y, Cai R, Li Y, Xu L, Hu L, Wang L, Wu S, Chen Q, Shi X, Jiang M, Hu Q. Population dynamics and antimicrobial resistance of Salmonella Derby ST40 from Shenzhen, China. Front Microbiol 2022; 13:1065672. [PMID: 36605513 PMCID: PMC9808032 DOI: 10.3389/fmicb.2022.1065672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 01/07/2023] Open
Abstract
Salmonella enterica subsp. enterica serovar Derby (S. Derby) is one of the most common serotypes responsible for salmonellosis in humans and animals. The two main sequence types (ST) observed in China are ST40 and ST71, with ST40 presently being the most common in Shenzhen. Recent years have seen an increasing number of cases of salmonella caused by ST40 S. Derby, but the epidemiology is not clear. We gathered 314 ST40 S. Derby isolates from food and patient samples for 11 years in Shenzhen; 76 globally prevalent representative strains were also collected. Whole-genome sequencing (WGS) combined with drug resistance phenotyping was used to examine population structural changes, inter-host associations, drug resistance characteristics, and the food-transmission risks of ST40 S. Derby in Shenzhen over this period. The S. enterica evolutionary tree is divided into five clades, and the strains isolated in Shenzhen were primarily concentrated in Clades 2, 4, and 5, and thus more closely related to strains from Asian (Thailand and Vietnam) than European countries. Our 11-year surveillance of S. Derby in Shenzhen showed that Clades 2, 4, and 5 are now the dominant epidemic branches, and branches 2 and 5 are heavily multi-drug resistant. The main resistance pattern is ampicillin-tetracycline-ciprofloxacin-chloramphenicol-nalidixic acid-streptomycin-sulfamethoxazole/trimethoprim. This may lead to a trend of increasing resistance to ST40 S. Derby in Shenzhen. Using a segmentation of ≤3 SNP among clone clusters, we discovered that Clades 2 and 4 contained multiple clonal clusters of both human- and food-derived strains. The food-derived strains were mainly isolated from pig liver, suggesting this food has a high risk of causing disease outbreaks in Shenzhen.
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Affiliation(s)
- Miaomiao Luo
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yiying She
- School of Public Health, Shanxi Medical University, Taiyuan, China
| | - Yixiang Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Li Xie
- School of Public Health, University of South China, Hengyang, China
| | - Chao Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Yaqun Qiu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Rui Cai
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yinghui Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Liangcai Xu
- Shenzhen Futian District Center for Disease Control and Prevention, Shenzhen, China
| | - Lulu Hu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lei Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Shuang Wu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Qiongcheng Chen
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaolu Shi
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China,Min Jiang,
| | - Qinghua Hu
- School of Public Health, Shanxi Medical University, Taiyuan, China,Shenzhen Center for Disease Control and Prevention, Shenzhen, China,*Correspondence: Qinghua Hu,
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Critical Assessment of Short-Read Assemblers for the Metagenomic Identification of Foodborne and Waterborne Pathogens Using Simulated Bacterial Communities. Microorganisms 2022; 10:microorganisms10122416. [PMID: 36557669 PMCID: PMC9784204 DOI: 10.3390/microorganisms10122416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/30/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022] Open
Abstract
Metagenomics offers the highest level of strain discrimination of bacterial pathogens from complex food and water microbiota. With the rapid evolvement of assembly algorithms, defining an optimal assembler based on the performance in the metagenomic identification of foodborne and waterborne pathogens is warranted. We aimed to benchmark short-read assemblers for the metagenomic identification of foodborne and waterborne pathogens using simulated bacterial communities. Bacterial communities on fresh spinach and in surface water were simulated by generating paired-end short reads of Illumina HiSeq, MiSeq, and NovaSeq at different sequencing depths. Multidrug-resistant Salmonella Indiana SI43 and Pseudomonas aeruginosa PAO1 were included in the simulated communities on fresh spinach and in surface water, respectively. ABySS, IDBA-UD, MaSuRCA, MEGAHIT, metaSPAdes, and Ray Meta were benchmarked in terms of assembly quality, identifications of plasmids, virulence genes, Salmonella pathogenicity island, antimicrobial resistance genes, chromosomal point mutations, serotyping, multilocus sequence typing, and whole-genome phylogeny. Overall, MEGHIT, metaSPAdes, and Ray Meta were more effective for metagenomic identification. We did not obtain an optimal assembler when using the extracted reads classified as Salmonella or P. aeruginosa for downstream genomic analyses, but the extracted reads showed consistent phylogenetic topology with the reference genome when they were aligned with Salmonella or P. aeruginosa strains. In most cases, HiSeq, MiSeq, and NovaSeq were comparable at the same sequencing depth, while higher sequencing depths generally led to more accurate results. As assembly algorithms advance and mature, the evaluation of assemblers should be a continuous process.
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Srednik ME, Morningstar-Shaw BR, Hicks JA, Mackie TA, Schlater LK. Antimicrobial resistance and genomic characterization of Salmonella enterica serovar Senftenberg isolates in production animals from the United States. Front Microbiol 2022; 13:979790. [PMID: 36406424 PMCID: PMC9668867 DOI: 10.3389/fmicb.2022.979790] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/02/2022] [Indexed: 07/22/2023] Open
Abstract
In the USA, Salmonella enterica subspecies enterica serovar Senftenberg is among the top five serovars isolated from food and the top 11 serovars isolated from clinically ill animals. Human infections are associated with exposure to farm environments or contaminated food. The objective of this study was to characterize S. Senftenberg isolates from production animals by analyzing phenotypic antimicrobial resistance profiles, genomic features and phylogeny. Salmonella Senftenberg isolates (n = 94) from 20 US states were selected from NVSL submissions (2014-2017), tested against 14 antimicrobial drugs, and resistance phenotypes determined. Resistance genotypes were determined using whole genome sequencing analysis with AMRFinder and the NCBI and ResFinder databases with ABRicate. Plasmids were detected using PlasmidFinder. Integrons were detected using IntFinder and manual alignment with reference genes. Multilocus-sequence-typing (MLST) was determined using ABRicate with PubMLST database, and phylogeny was determined using vSNP. Among 94 isolates, 60.6% were resistant to at least one antimicrobial and 39.4% showed multidrug resistance. The most prevalent resistance findings were for streptomycin (44.7%), tetracycline (42.6%), ampicillin (36.2%) and sulfisoxazole (32.9%). The most commonly found antimicrobial resistance genes were aac(6')-Iaa (100%), aph(3″)-Ib and aph(6)-Id (29.8%) for aminoglycosides, followed by bla TEM-1 (26.6%) for penicillins, sul1 (25.5%) and sul2 (23.4%) for sulfonamides and tetA (23.4%) for tetracyclines. Quinolone-resistant isolates presented mutations in gyrA and/or parC genes. Class 1 integrons were found in 37 isolates. Thirty-six plasmid types were identified among 77.7% of the isolates. Phylogenetic analysis identified two distinct lineages of S. Senftenberg that correlated with the MLST results. Isolates were classified into two distinct sequence types (ST): ST14 (97.9%) and ST 185 (2.1%). The diversity of this serotype suggests multiple introductions into animal populations from outside sources. This study provided antimicrobial susceptibility and genomic characteristics of S. Senftenberg clinical isolates from production animals in the USA during 2014 to 2017. This study will serve as a base for future studies focused on the phenotypic and molecular antimicrobial characterization of S. Senftenberg isolates in animals. Monitoring of antimicrobial resistance to detect emergence of multidrug-resistant strains is critical.
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Liu X, Wang D, Yin Z, Sun L, Pang S, Liu J, Li W, Cui S, Huang W, Du Y, Xie Z. Insights into Evolutionary, Genomic, and Biogeographic Characterizations of Chryseobacterium nepalense Represented by a Polyvinyl Alcohol-Degrading Bacterium, AC3. Microbiol Spectr 2022; 10:e0217922. [PMID: 36000867 PMCID: PMC9602593 DOI: 10.1128/spectrum.02179-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/10/2022] [Indexed: 12/31/2022] Open
Abstract
Chryseobacterium spp. are Gram-negative rods found ubiquitously in the environment, with certain species being reported as having unusual degrading properties. Polyvinyl alcohol (PVA) is used widely in industry but causes serious global environmental pollution. Here, we report the complete genome sequence of a novel bacterium, AC3, that efficiently degrades PVA. As the representative genome of Chryseobacterium nepalense, key genomic characteristics (e.g., mobile genetic elements, horizontal genes, genome-scale metabolic network, secondary metabolite biosynthesis gene clusters, and carbohydrate-active enzymes) were comprehensively investigated to reveal the potential genetic features of this species. Core genome phylogenetic analysis in combination with average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization values provided an accurate taxonomic position of C. nepalense in the genus Chryseobacterium. Comparative genomic analysis of AC3 with closely related species suggested evolutionary dynamics characterized by a species-specific genetic repertoire, dramatic rearrangements, and evolutionary constraints driven by selective pressure, which facilitated the speciation and adaptative evolution of C. nepalense. Biogeographic characterization indicated that this species is ubiquitously distributed not only in soil habitats but also in a variety of other source niches. Bioinformatic analysis revealed the potential genetic basis of PVA degradation in AC3, which included six putative genes associated with the synthesis of PVA dehydrogenase, cytochrome c, oxidized PVA hydrolase, and secondary alcohol dehydrogenase. Our study reports the first complete genome of C. nepalense with PVA-degrading properties, providing comprehensive insights into the genomic characteristics of this species and increasing our understanding of the microbial degradation of PVA. IMPORTANCE Although PVA is a biodegradable polymer, the widespread use of PVA in global industrialization has resulted in serious environmental problems. To date, knowledge of effective and applicable PVA-degrading bacteria is limited, and thus, the discovery of novel PVA biodegraders is pertinent. Here, we isolated a novel bacterial strain, AC3, which efficiently degraded PVA. The complete genome of AC3 was sequenced as the first genome sequence of the species C. nepalense. Comparative genomic analysis was performed to comprehensively investigate the phylogenetic relationships, genome-scale metabolic network, key genomic characteristics associated with genomic evolution, evolutionary dynamics between AC3 and its close relatives, and biogeographic characterization of C. nepalense, particularly regarding the potential genetic basis of PVA degradation. These findings could advance our understanding of the genomic characteristics of C. nepalense and PVA bioremediation.
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Affiliation(s)
- Xinbei Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Dandan Wang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Zhiqiu Yin
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Li Sun
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Shiqi Pang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Jianing Liu
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Wei Li
- College of Plant Protection, Shanxi Agricultural University, Taiyuan, People’s Republic of China
| | - Shiyu Cui
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Weiwei Huang
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
| | - Yuhui Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhihong Xie
- National Engineering Research Center for Efficient Utilization of Soil and Fertilizer Resources, College of Resources and Environment of Shandong Agricultural University, Tai’an, China
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Complete Genome Sequence of a Salmonella enterica subsp.
enterica
Serovar Tennessee Strain from Tahini. Microbiol Resour Announc 2022; 11:e0040722. [PMID: 35894624 PMCID: PMC9387254 DOI: 10.1128/mra.00407-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Salmonella sp. infections are associated with contaminated low-moisture foods (with high fat content) with increasing frequency. Here, we report the complete genome sequence of Salmonella enterica subsp. enterica serovar Tennessee, which was isolated from tahini (a paste made from ground sesame seeds) purchased at a local retailer in Berlin, Germany.
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Molecular Epidemiology and Virulence of Non-Typhoidal Salmonella in Armenia. Int J Mol Sci 2022; 23:ijms23169330. [PMID: 36012591 PMCID: PMC9409446 DOI: 10.3390/ijms23169330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/16/2022] [Accepted: 08/16/2022] [Indexed: 11/24/2022] Open
Abstract
In this work, we analysed human isolates of nontyphoidal Salmonella enterica subsp. enterica (NTS), which were collected from salmonellosis cases in Armenia from 1996 to 2019. This disease became a leading food-borne bacterial infection in the region, with the younger age groups especially affected. The isolates were characterised by serotyping, Enterobacterial Repetitive Intergenic Consensus (ERIC-PCR) typing, and whole genome sequencing (WGS). The main serotypes were S. Typhimurium, S. Enteritidis, and S. Arizonae. ERIC-PCR indicated a high degree of clonality among S. Typhimurium strains, which were also multidrug-resistant and produced extended spectrum beta-lactamases. During the study period, the frequency of S. Typhimurium and S. Arizonae isolations decreased, but with the increase in S. Enteritidis and other NTS. A total of 42 NTS isolates were subjected to WGS and explored for virulence-related traits and the corresponding genetic elements. Some virulence and genetic factors were shared by all NTS serotypes, while the main differences were attributed to the serotype-specific diversity of virulence genes, SPIs, virulence plasmids, and phages. The results indicated the variability and dynamics in the epidemiology of salmonellosis and a high virulence potential of human NTS isolates circulating in the region.
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Chukamnerd A, Pomwised R, Jeenkeawpiam K, Sakunrang C, Chusri S, Surachat K. Genomic insights into bla NDM-carrying carbapenem-resistant Klebsiella pneumoniae clinical isolates from a university hospital in Thailand. Microbiol Res 2022; 263:127136. [PMID: 35870342 DOI: 10.1016/j.micres.2022.127136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/04/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022]
Abstract
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates is a serious threat to global health. Here, we elucidate the genetic features of blaNDM-carrying CRKP clinical isolates from a university hospital in Thailand. The entire genomes of 19 CRKP isolates were extracted and then sequenced using the MGISEQ200 platform. Using various bioinformatics tools, we analyzed the antimicrobial resistance (AMR), virulence factors, gene transfer, bacterial defense mechanisms, and genomic diversity of the CRKP isolates. The sequence type (ST) 16 was found in most of the isolates, along with carriages of the blaNDM-1, blaOXA-232, and blaCTX-M-15 genes. The IncFIB(pQil), Col440II, and ColKP3 plasmids were identified with high frequency. The CRKP isolates harbored genes encoding for virulence factors such as adherence, biofilm formation, immune evasion, and iron uptake. The CRISPR-Cas region in the CRKP9 isolate consisted of 28 distinct spacer sequences. The genomes of the CRKP isolates presented restriction-modification (R-M) sites (M.Kpn34618Dcm and M.Kpn928I) and integrated bacteriophage genomes (Klebsiella phage ST16-OXA48phi5.4 and Enterobacteria phage mEp390). Bottromycin and sactipeptides were also identified. The isolates could be separated into three clades according to STs and pairwise single nucleotide polymorphism (SNP) distance. Pairwise average nucleotide identity (ANI) values revealed intra-species. These findings support the importance of whole-genome sequencing (WGS) to the rapid and accurate genomic analysis of clinical isolates of CRKP.
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Affiliation(s)
- Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Sarunyou Chusri
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
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Eriksen RS, Malhotra N, Seshasayee ASN, Sneppen K, Krishna S. Emergence of networks of shared restriction-modification systems in phage–bacteria ecosystems. J Biosci 2022. [DOI: 10.1007/s12038-022-00274-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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39
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Saraiva MDMS, Benevides VP, da Silva NMV, Varani ADM, de Freitas Neto OC, Berchieri Â, Delgado-Suárez EJ, Rocha ADDL, Eguale T, Munyalo JA, Kariuki S, Gebreyes WA, de Oliveira CJB. Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa. Front Cell Infect Microbiol 2022; 12:772829. [PMID: 35795189 PMCID: PMC9251186 DOI: 10.3389/fcimb.2022.772829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 04/20/2022] [Indexed: 11/14/2022] Open
Abstract
Since its emergence in the beginning of the 90’s, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, blaTEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1–4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.
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Affiliation(s)
- Mauro de Mesquita Sousa Saraiva
- Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, United States
| | - Valdinete Pereira Benevides
- Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
| | | | | | - Oliveiro Caetano de Freitas Neto
- Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Ângelo Berchieri
- Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp), Jaboticabal, Brazil
| | - Enrique Jesús Delgado-Suárez
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Alan Douglas de Lima Rocha
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, Brazil
| | - Tadesse Eguale
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Janet Agnes Munyalo
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Wondwossen Abebe Gebreyes
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, United States
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, United States
| | - Celso José Bruno de Oliveira
- Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, Brazil
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, United States
- *Correspondence: Celso José Bruno de Oliveira,
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40
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Li Y, Li K, Peng K, Wang Z, Song H, Li R. Distribution, antimicrobial resistance and genomic characterization of Salmonella along the pork production chain in Jiangsu, China. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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41
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Detection of Antimicrobial Resistance, Pathogenicity, and Virulence Potentials of Non-Typhoidal Salmonella Isolates at the Yaounde Abattoir Using Whole-Genome Sequencing Technique. Pathogens 2022; 11:pathogens11050502. [PMID: 35631023 PMCID: PMC9148033 DOI: 10.3390/pathogens11050502] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/27/2023] Open
Abstract
One of the crucial public health problems today is the emerging and re-emerging of multidrug-resistant (MDR) bacteria coupled with a decline in the development of new antimicrobials. Non-typhoidal Salmonella (NTS) is classified among the MDR pathogens of international concern. To predict their MDR potentials, 23 assembled genomes of NTS from live cattle (n = 1), beef carcass (n = 19), butchers’ hands (n = 1) and beef processing environments (n = 2) isolated from 830 wet swabs at the Yaounde abattoir between December 2014 and November 2015 were explored using whole-genome sequencing. Phenotypically, while 22% (n = 5) of Salmonella isolates were streptomycin-resistant, 13% (n = 3) were MDR. Genotypically, all the Salmonella isolates possessed high MDR potentials against several classes of antibiotics including critically important drugs (carbapenems, third-generation cephalosporin and fluoroquinolone). Moreover, >31% of NTS exhibited resistance potentials to polymyxin, considered as the last resort drug. Additionally, ≤80% of isolates harbored “silent resistant genes” as a potential reservoir of drug resistance. Our isolates showed a high degree of pathogenicity and possessed key virulence factors to establish infection even in humans. Whole-genome sequencing unveiled both broader antimicrobial resistance (AMR) profiles and inference of pathogen characteristics. This study calls for the prudent use of antibiotics and constant monitoring of AMR of NTS.
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Comparative Genomic Analysis of Vibrio cincinnatiensis Provides Insights into Genetic Diversity, Evolutionary Dynamics, and Pathogenic Traits of the Species. Int J Mol Sci 2022; 23:ijms23094520. [PMID: 35562911 PMCID: PMC9101195 DOI: 10.3390/ijms23094520] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 01/22/2023] Open
Abstract
Vibrio cincinnatiensis is a poorly understood pathogenic Vibrio species, and the underlying mechanisms of its genetic diversity, genomic plasticity, evolutionary dynamics, and pathogenicity have not yet been comprehensively investigated. Here, a comparative genomic analysis of V. cincinnatiensis was constructed. The open pan-genome with a flexible gene repertoire exhibited genetic diversity. The genomic plasticity and stability were characterized by the determinations of diverse mobile genetic elements (MGEs) and barriers to horizontal gene transfer (HGT), respectively. Evolutionary divergences were exhibited by the difference in functional enrichment and selective pressure between the different components of the pan-genome. The evolution on the Chr I and Chr II core genomes was mainly driven by purifying selection. Predicted essential genes in V. cincinnatiensis were mainly found in the core gene families on Chr I and were subject to stronger evolutionary constraints. We identified diverse virulence-related elements, including the gene clusters involved in encoding flagella, secretion systems, several pili, and scattered virulence genes. Our results indicated the pathogenic potential of V. cincinnatiensis and highlighted that HGT events from other Vibrio species promoted pathogenicity. This pan-genome study provides comprehensive insights into this poorly understood species from the genomic perspective.
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Kerdsin A, Hatrongjit R, Wongsurawat T, Jenjaroenpun P, Chopjitt P, Boueroy P, Fittipaldi N, Zheng H, Gottschalk M. Genomic Characterization of Streptococcus suis Serotype 24 Clonal Complex 221/234 From Human Patients. Front Microbiol 2022; 12:812436. [PMID: 35003043 PMCID: PMC8733411 DOI: 10.3389/fmicb.2021.812436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/06/2021] [Indexed: 12/26/2022] Open
Abstract
Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Although S. suis serotype 2 is prevalent among patient and swine infections, other serotypes are occasionally detected in humans. Of these, serotype 24 clonal complex (CC) 221/234 are recognized as emerging clones of human infection. Genomic exploration of three S. suis serotype 24 CC221/234 strains revealed antimicrobial resistance genes, pathotyping, virulence-associated gene (VAG) profiles, minimum core genome (MCG) typing, and comparison of the genomes. Based on these analyzes, all three serotype 24 strains were MCG7-3 and should be classified in the intermediate/weakly virulent (I/WV) group. All selected serotype 24 strains were susceptible to several antibiotics including β-lactam, fluoroquinolone, and chloramphenicol. Resistance to tetracycline, macrolide, and clindamycin was observed and attributed to the genes tet(O) and erm(B). Genomic comparison revealed the strains S12X, LSS66, LS0L, LS0E, 92–4,172, and IMT40201 that had phylogenetic affinity with serotype 24 CC221/234. Analysis of 80 virulence-associated genes (VAG) showed that all three serotype 24 strains lacked 24 genes consisting of adhesin P, epf, hyl, ihk, irr, mrp, nadR, neuB, NisK/R, ofs, permease (SSU0835), rgg, revS, salK/R, sao, sly, spyM3_0908, srtBCD, srtF, srtG, SSU05_0473, virA, virB4, and virD4. Eleven specific sequences were identified in the 3 serotype 24 genomes that differed from the genomes of the representative strains of epidemic (E; SC84), highly virulent (HV; P1/7), I/WV (89–1,591), and avirulent (T15 and 05HAS68).
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Affiliation(s)
- Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Rujirat Hatrongjit
- Department of General Sciences, Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Thidathip Wongsurawat
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Department of Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Nahuel Fittipaldi
- Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Quebec, QC, Canada
| | - Han Zheng
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Marcelo Gottschalk
- Research Group on Infectious Diseases in Production Animals (GREMIP), Faculty of Veterinary Medicine, University of Montreal, Quebec, QC, Canada
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Komatsu T, Ohya K, Ota A, Nishiuchi Y, Yano H, Matsuo K, Odoi JO, Suganuma S, Sawai K, Hasebe A, Asai T, Yanai T, Fukushi H, Wada T, Yoshida S, Ito T, Arikawa K, Kawai M, Ato M, Baughn AD, Iwamoto T, Maruyama F. Genomic features of Mycobacterium avium subsp. hominissuis isolated from pigs in Japan. GIGABYTE 2021; 2021:gigabyte33. [PMID: 36824340 PMCID: PMC9650289 DOI: 10.46471/gigabyte.33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 11/05/2021] [Indexed: 11/09/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is one of the most important agents causing non-tuberculosis mycobacterial infection in humans and pigs. There have been advances in genome analysis of MAH from human isolates, but studies of isolates from pigs are limited despite its potential source of infection to human. Here, we obtained 30 draft genome sequences of MAH from pigs reared in Japan. The 30 draft genomes were 4,848,678-5,620,788 bp in length, comprising 4652-5388 coding genes and 46-75 (median: 47) tRNAs. All isolates had restriction modification-associated genes and 185-222 predicted virulence genes. Two isolates had tRNA arrays and one isolate had a clustered regularly interspaced short palindromic repeat (CRISPR) region. Our results will be useful for evaluation of the ecology of MAH by providing a foundation for genome-based epidemiological studies.
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Affiliation(s)
- Tetsuya Komatsu
- Aichi Prefectural Chuo Livestock Hygiene Service Center, Okazaki, Aichi, Japan
| | - Kenji Ohya
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan,United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Atsushi Ota
- Data Science Center, Division of Biological Science, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | - Yukiko Nishiuchi
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan
| | - Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Kayoko Matsuo
- Kumamoto Prefectural Aso Public Health Center, Aso, Kumamoto, Japan
| | - Justice Opare Odoi
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Shota Suganuma
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan
| | - Kotaro Sawai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan,Viral Disease and Epidemiology Research Division, National Institute of Animal Health, National Agriculture Research Organization, Tsukuba, Ibaraki, Japan
| | - Akemi Hasebe
- Toyama Prefectural Meat Inspection Center, Imizu, Toyama, Japan
| | - Tetsuo Asai
- United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Tokuma Yanai
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan,United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan,Hiwa Natural History Museum, Shobara, Hiroshima, Japan
| | - Hideto Fukushi
- Faculty of Applied Biological Sciences, Gifu University, Gifu, Gifu, Japan,United Graduate School of Veterinary Sciences, Gifu University, Gifu, Gifu, Japan
| | - Takayuki Wada
- Graduate School of Human Life Science, Osaka City University, Osaka, Osaka, Japan
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-Chuo Chest Medical Center, Sakai, Osaka, Japan
| | - Toshihiro Ito
- Laboratory of Proteome Research, Proteome Research Center, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Mikihiko Kawai
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Kyoto, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Anthony D Baughn
- Department of Microbiology and Immunology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Fumito Maruyama
- Office of Academic Research and Industry-Government Collaboration, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan,Project Research Center for Holobiome and Built Environment (CHOBE), Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan,Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco, Chile, Corresponding author. E-mail:
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Virulence Comparison of Salmonella enterica Subsp. enterica Isolates from Chicken and Whole Genome Analysis of the High Virulent Strain S. Enteritidis 211. Microorganisms 2021; 9:microorganisms9112239. [PMID: 34835366 PMCID: PMC8619400 DOI: 10.3390/microorganisms9112239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/12/2021] [Accepted: 10/20/2021] [Indexed: 01/28/2023] Open
Abstract
Background: Salmonellaenterica is one of the common pathogens in both humans and animals that causes salmonellosis and threatens public health all over the world. Methods and Results: Here we determined the virulence phenotypes of nine Salmonellaenterica subsp. enterica (S. enterica) isolates in vitro and in vivo, including pathogenicity to chicken, cell infection, biofilm formation and virulence gene expressions. S. Enteritidis 211 (SE211) was highly pathogenic with notable virulence features among the nine isolates. The combination of multiple virulence genes contributed to the conferring of the high virulence in SE211. Importantly, many mobile genetic elements (MGEs) were found in the genome sequence of SE211, including a virulence plasmid, genomic islands, and prophage regions. The MGEs and CRISPR-Cas system might function synergistically for gene transfer and immune defense. In addition, the neighbor joining tree and the minimum spanning tree were constructed in this study. Conclusions: This study provided both the virulence phenotypes and genomic features, which might contribute to the understanding of bacterial virulence mechanisms in Salmonella enterica subsp. enterica. The first completed genomic sequence for the high virulent S. Enteritidis isolate SE211 and the comparative genomics and phylogenetic analyses provided a preliminary understanding of S. enterica genetics and laid the foundation for further study.
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Complete Genome Sequences of Six Salmonella enterica Strains (S. enterica subsp. arizonae, S. enterica subsp. diarizonae, and S. enterica subsp. salamae) Isolated from Poultry Houses. Microbiol Resour Announc 2021; 10:e0076821. [PMID: 34647803 PMCID: PMC8515881 DOI: 10.1128/mra.00768-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Non-enterica subspecies of Salmonella enterica are associated with cold-blood animals. We report the complete genomes of six S. enterica strains (one S. enterica subsp. arizonae strain, four S. enterica subsp. salamae strains, and one S. enterica subsp. diarizonae strain) isolated from Spanish poultry houses. This will increase our knowledge of these non-enterica subspecies.
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Richter L, du Plessis EM, Duvenage S, Allam M, Ismail A, Korsten L. Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa. Front Microbiol 2021; 12:734649. [PMID: 34659162 PMCID: PMC8517129 DOI: 10.3389/fmicb.2021.734649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M. du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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Kerdsin A, Chopjitt P, Hatrongjit R, Boueroy P, Gottschalk M. Zoonotic infection and clonal dissemination of Streptococcus equi subspecies zooepidemicus sequence type 194 isolated from humans in Thailand. Transbound Emerg Dis 2021; 69:e554-e565. [PMID: 34558797 DOI: 10.1111/tbed.14331] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 09/08/2021] [Accepted: 09/20/2021] [Indexed: 12/18/2022]
Abstract
Streptococcus equi subsp. zooepidemicus (SEZ) is a zoonotic pathogen associated with diseases in a wide range of animals as well as in humans. SEZ sequence type (ST) 194 strains have been associated with outbreaks in China, the USA, and Canada and have caused high mortality in pigs. Nevertheless, human infection by this ST has never been reported. This study conducted a retrospective analysis of 18 SEZ strains from human patients in Thailand during 2005-2020. The study revealed clonal dissemination of ST194 with the identical pulsotype in human patients throughout Thailand. Clinical manifestation was mainly septicemia (61.1%), while 72.2% had a history of eating raw pork products. There were six fatal cases (33.3%). Antimicrobial susceptibility testing revealed that all strains were susceptible to penicillin, ampicillin, cefotaxime, erythromycin, levofloxacin, clindamycin, chloramphenicol, tetracycline and vancomycin. Virulence-associated genes, including bifA, szM, szP, sdzD, spaZ, and fszF, were present in all tested strains. Some representative genes in four pathogenicity islands found in the swine outbreak SEZ-ATCC35246 (ST194) strain were detected in these SEZ strains. Whole-genome sequencing analysis of three representative SEZs in this study revealed no acquired antimicrobial-resistant genes and they contained the same virulence factors. The single-nucleotide polymorphism phylogenetic tree demonstrated that the current strains were clustered with swine ST194 strains. The results should be highlighted as a public health concern, especially to those who may directly or indirectly have contact with livestock or companion animals or have consumed raw meat products as risk factors for infections with SEZ.
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Affiliation(s)
- Anusak Kerdsin
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Peechanika Chopjitt
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Rujirat Hatrongjit
- Faculty of Science and Engineering, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
| | - Parichart Boueroy
- Faculty of Public Health, Kasetsart University Chalermphrakiat Sakon Nakhon Province Campus, Sakon Nakhon, Thailand
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Asante J, Hetsa BA, Amoako DG, Abia ALK, Bester LA, Essack SY. Genomic Analysis of Antibiotic-Resistant Staphylococcus epidermidis Isolates From Clinical Sources in the Kwazulu-Natal Province, South Africa. Front Microbiol 2021; 12:656306. [PMID: 34421833 PMCID: PMC8374169 DOI: 10.3389/fmicb.2021.656306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
Staphylococcus epidermidis has become an important nosocomial pathogen. Multidrug resistance makes S. epidermidis infections difficult to treat. The study aims to describe the genomic characteristics of methicillin-resistant S. epidermidis (MRSE) isolated from clinical sources, to comprehend the genetic basis of antibiotic resistance, virulence, and potential pathogenicity. Sixteen MRSE underwent whole-genome sequencing, and bioinformatics analyses were carried out to ascertain their resistome, virulome, mobilome, clonality, and phylogenomic relationships. In all, 75% of isolates displayed multidrug resistance and were associated with the carriage of multiple resistance genes including mecA, blaZ, tet(K), erm(A), erm(B), erm(C), dfrG, aac(6')-aph(2''), and cat(pC221) conferring resistance to β-lactams, tetracyclines, macrolide-lincosamide-streptogramin B, aminoglycosides, and phenicols, which were located on both plasmids and chromosomes. Their virulence profiles were evidenced by the presence of genes involved in adherence/biofilm formation (icaA, icaB, icaC, atl, ebh, and ebp), immune evasion (adsA, capC, and manA), and antiphagocytosis (rmlC, cdsA, and A). The community-acquired SCCmec type IV was the most common SCCmec type. The CoNS belonged to seven multilocus sequence types (MLSTs) and carried a diversity of mobile genetic elements such as phages, insertion sequences, and plasmids. The bacterial anti-phage defense systems clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) immunity phage system and restriction-modification system (R-M system) and the arginine catabolic mobile element (ACME) involved in immune evasion and transport of virulence genes were also found. The insertion sequence, IS256, linked with virulence, was found in 56.3% of isolates. Generally, the isolates clustered according to STs, with some similarity but also considerable variability within isolates. Whole-genome sequencing and bioinformatics analysis provide insights into the likely pathogenicity and antibiotic resistance of S. epidermidis, necessitating surveillance of this emerging pathogen.
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Affiliation(s)
- Jonathan Asante
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Bakoena A Hetsa
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Akebe L K Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Linda A Bester
- Biomedical Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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50
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Vaid RK, Thakur Z, Anand T, Kumar S, Tripathi BN. Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes. PLoS One 2021; 16:e0255612. [PMID: 34411120 PMCID: PMC8375982 DOI: 10.1371/journal.pone.0255612] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/19/2021] [Indexed: 12/27/2022] Open
Abstract
Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S.enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as virulence factors, genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. Core genome identified in the study can give important leads in the direction of design of rapid and reliable diagnostics, and vaccine design for effective infection control as well as eradication. Additionally, the identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, structure based inhibitor development by future experimental investigations on the data generated.
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Affiliation(s)
- Rajesh Kumar Vaid
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Zoozeal Thakur
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Taruna Anand
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Sanjay Kumar
- Bacteriology Laboratory, ICAR-National Research Centre on Equines, Hisar, Haryana, India
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