1
|
Jia M, Li P, Zhang J, Chen Z, Gao L, Sun Y, Zhang X, Yan Y, Zhu G. Characteristics of Two mcr-1-Harboring IncHI2 Plasmids from Clinical Salmonella Isolates in Jiaxing City. Foodborne Pathog Dis 2023; 20:467-476. [PMID: 37699240 DOI: 10.1089/fpd.2023.0051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
Salmonella is a primary cause of foodborne diseases, and the increasing prevalence of mcr-1-carrying plasmids, which confer colistin resistance to Salmonella, poses significant global health concerns. As the frequency of occurrence of the mcr-1 gene is increasing globally, we studied the prevalence of mcr-1 in clinical Salmonella isolates by analyzing 195 clinical strains isolated in 2020. Of the 195 Salmonella isolates, 41 isolates were resistant to colistin. We found mcr-1 in two strains (Salmonella Typhimurium ZJJX20006 and Salmonella Kentucky ZJJX20014), which we analyzed in detail via whole-genome sequencing and antibiotic susceptibility testing. Two strains displayed resistance to ampicillin, ampicillin-sulbactam, tetracycline, chloramphenicol, and cotrimoxazole, while ZJJX20006 displayed resistance to colistin and ZJJX20014 was sensitive. Genomic analysis revealed that these strains had plasmid-encoded mcr-1 in IncHI2 plasmids, which were not similar to the mcr-1-IncX4 identified in 2016. These two strains also harbored other drug resistance genes, including blaOXA-1 and blaCTX-M-14. Our findings may help clarify the molecular mechanisms of mcr-1 dissemination among Salmonella strains in Jiaxing City and offer insights into the evolution of mcr-1 in Salmonella.
Collapse
Affiliation(s)
- Miaomiao Jia
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Ping Li
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Junyan Zhang
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Zhongwen Chen
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Lei Gao
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Yangming Sun
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Xiaofei Zhang
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Yong Yan
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| | - Guoying Zhu
- Jiaxing Key Laboratory of Pathogenic Microbiology, Jiaxing Center for Disease Control and Prevention, Jiaxing, China
| |
Collapse
|
2
|
Evaluation of Genomic Typing Methods in the Salmonella Reference Laboratory in Public Health, England, 2012-2020. Pathogens 2023; 12:pathogens12020223. [PMID: 36839496 PMCID: PMC9966477 DOI: 10.3390/pathogens12020223] [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: 12/08/2022] [Revised: 01/12/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
We aim to provide an evidence-based evaluation of whole genome sequence (WGS) methods, employed at the Salmonella reference laboratory in England, in terms of its impact on public health and whether these methods remain a fit for purpose test under UKAS ISO 15189. The evaluation of the genomic methods were mapped against the value of detecting microbiological clusters to support the investigation of food-borne outbreaks of Salmonella in England between 2012-2020. The analysis of WGS with both SNP- and allelic-based methods provided an unprecedented level of strain discrimination and detection of additional clusters when comparing to all of the previous typing methods. The robustness of the routine genomic sequencing at the reference laboratory ensured confidence in the microbiological identifications, even in large outbreaks with complex international food distribution networks. There was evidence that the phylogeny derived from the WGS data can be used to inform the provenance of strains and support discrimination between domestic and non-domestic transmission events. Further insight on the evolutionary context of the emerging pathogenic strains was enabled with a deep dive of the phylogenetic data, including the detection of nested clusters. The public availability of the WGS data linked to the clinical, epidemiological and environmental context of the sequenced strains has improved the trace-back investigations during outbreaks. The global expansion in the use of WGS-based typing in reference laboratories has shown that the WGS methods are a fit for purpose test in public health as it has ensured the rapid implementation of interventions to protect public health, informed risk assessment and has facilitated the management of national and international food-borne outbreaks of Salmonella.
Collapse
|
3
|
Gómez-Baltazar A, Vázquez-Marrufo G, Astiazaran-Garcia H, Ochoa-Zarzosa A, Canett-Romero R, García-Galaz A, Torres-Vega C, Vázquez-Garcidueñas MS. Comparative virulence of the worldwide ST19 and emergent ST213 genotypes of Salmonella enterica serotype Typhimurium strains isolated from food. Microbes Infect 2023; 25:105019. [PMID: 35781097 DOI: 10.1016/j.micinf.2022.105019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 06/22/2022] [Accepted: 06/25/2022] [Indexed: 02/04/2023]
Abstract
Salmonella enterica Typhimurium represents one of the most frequent causal agents of food contamination associated to gastroenteritis. The sequence type ST19 is the founder and worldwide prevalent genotype within this serotype, but its replacement by emerging genotypes has been recently reported. Particularly, the ST213 genotype has replaced it as the most prevalent in clinical and contaminated food samples in Mexico and has been recently reported in several countries. In this study, the in vitro and in vivo virulence of ST213 and ST19 strains isolated from food samples in Mexico was evaluated. Three out of the five analyzed ST213 strains, showed a greater internalization capacity and increased secretion of interleukins IL-8 and IL-6 of Caco-2 cells than the ST19 strains. Microbiological counts in feces and tissues showed the ability of all strains tested to establish infection in the rat model. The ST213 strains also caused histopathological damage, characteristic of gastroenteritis in Wistar rats. In contrast to the in vitro result, one of the ST19 strains showed marked damage in the test animals. The ST213 genotype strains showed in vitro and in vivo virulence variability, but significantly higher than the observed in the ST19 genotype strains, thus such emergent genotype represents a public health concern.
Collapse
Affiliation(s)
- Adrián Gómez-Baltazar
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58020, Mexico; Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58893, Mexico
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58893, Mexico
| | - Humberto Astiazaran-Garcia
- Departamento de Nutrición y Metabolismo, Centro de Investigación en Alimentación y Desarrollo, Carretera al Ejido "La Victoria" Km 0.6, 83304, Mexico
| | - Alejandra Ochoa-Zarzosa
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58893, Mexico
| | - Rafael Canett-Romero
- Departamento de Investigación y Posgrado en Alimentos, Universidad de Sonora, Hermosillo, Sonora, Mexico
| | - Alfonso García-Galaz
- Ciencias de los Alimentos, Centro de Investigación en Alimentación y Desarrollo AC, Carretera al Ejido La Victoria Km 0.6 CP 83304, Mexico
| | - Carlos Torres-Vega
- Laboratorio de Histología, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58020, Mexico
| | - Ma Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo. Morelia, Michoacán, 58020, Mexico.
| |
Collapse
|
4
|
Jacob JJ, Solaimalai D, Rachel T, Pragasam AK, Sugumar S, Jeslin P, Anandan S, Veeraraghavan B. A secular trend in invasive non-typhoidal Salmonella in South India, 2000-2020: Identification challenges and antibiogram. Indian J Med Microbiol 2022; 40:536-540. [PMID: 35987666 DOI: 10.1016/j.ijmmb.2022.07.015] [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: 11/08/2021] [Revised: 06/28/2022] [Accepted: 07/22/2022] [Indexed: 11/29/2022]
Abstract
PURPOSE Invasive non-typhoidal Salmonella (iNTS) disease is an important cause of morbidity and mortality in African countries. However, the incidence in Indian subcontinent remains poorly documented. This study has assessed the incidence of iNTS in India with a perspective on its AMR profiles and serovar distribution for a period of 21 years from 2000 to 2020 from a tertiary care centre in South India. METHODS A total of 461 iNTS isolates were subjected to serotyping and antimicrobial susceptibility testing (AST). A subset of isolates was genotyped by multi locus sequence typing (MLST) and results were compared to serotyping to predict the accuracy. RESULTS Overall, 461 iNTS isolates were characterised mostly comprising of S. Typhimurium (49.2%) and S. Enteritidis (28.8%). Proportion of isolates resistant to first line antibiotics such as ampicillin, chloramphenicol and trimethoprim/sulphamethoxazole were 6.7%, 1.7% and 3.6% respectively. Isolates resistant to third generation cephalosporin are at a gradual rise while decreased susceptibility to quinolones was most common. The incidence of iNTS infection was maximum in the age group of >15 years. MLST analysis showed discrepancies in assigning the serovars by serotyping as three S. Saintpaul were identified as S. Typhimurium. CONCLUSION The clinical epidemiology, serovar distribution and antimicrobial susceptibility patterns of invasive Salmonella isolates from India suggest that there is only a small burden of iNTS disease. However the gradual emergence of AMR in iNTS isolates indicates serious risk for public health warranting the importance enhanced molecular surveillance.
Collapse
Affiliation(s)
- Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Dhanalakshmi Solaimalai
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Tanya Rachel
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Agila Kumari Pragasam
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Saranya Sugumar
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Praveena Jeslin
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore 632004, Tamil Nadu, India.
| |
Collapse
|
5
|
Parra-Flores J, Holý O, Acuña S, Lepuschitz S, Pietzka A, Contreras-Fernández A, Chavarría-Sepulveda P, Cruz-Córdova A, Xicohtencatl-Cortes J, Mancilla-Rojano J, Castillo A, Ruppitsch W, Forsythe S. Genomic Characterization of Cronobacter spp. and Salmonella spp. Strains Isolated From Powdered Infant Formula in Chile. Front Microbiol 2022; 13:884721. [PMID: 35722296 PMCID: PMC9201451 DOI: 10.3389/fmicb.2022.884721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 05/04/2022] [Indexed: 11/14/2022] Open
Abstract
This study characterized five Cronobacter spp. and six Salmonella spp. strains that had been isolated from 155 samples of powdered infant formula (PIF) sold in Chile and manufactured in Chile and Mexico in 2018–2020. Two strains of Cronobacter sakazakii sequence type (ST) ST1 and ST31 (serotypes O:1 and O:2) and one strain of Cronobacter malonaticus ST60 (O:1) were identified. All Salmonella strains were identified as Salmonella Typhimurium ST19 (serotype O:4) by average nucleotide identity, ribosomal multilocus sequence typing (rMLST), and core genome MLST (cgMLST). The C. sakazakii and C. malonaticus isolates were resistant to cephalothin, whereas the Salmonella isolates were resistant to oxacillin and ampicillin. Nineteen antibiotic resistance genes were detected in the C. sakazakii and C. malonaticus isolates; the most prevalent were mcr-9.1, blaCSA, and blaCMA. In Salmonella, 30 genes encoding for aminoglycoside and cephalosporin resistance were identified, including aac(6′)-Iaa, β-lactamases ampH, ampC1, and marA. In the Cronobacter isolates, 32 virulence-associated genes were detected by WGS and clustered as flagellar proteins, outer membrane proteins, chemotaxis, hemolysins, invasion, plasminogen activator, colonization, transcriptional regulator, survival in macrophages, use of sialic acid, and toxin-antitoxin genes. In the Salmonella strains, 120 virulence associated genes were detected, adherence, magnesium uptake, resistance to antimicrobial peptides, secretion system, stress protein, toxin, resistance to complement killing, and eight pathogenicity islands. The C. sakazakii and C. malonaticus strains harbored I-E and I-F CRISPR-Cas systems and carried Col(pHHAD28) and IncFIB(pCTU1) plasmids, respectively. The Salmonella strains harbored type I-E CRISPR-Cas systems and carried IncFII(S) plasmids. The presence of C. sakazakii and Salmonella in PIF is a health risk for infants aged less than 6 months. For this reason, sanitary practices should be reinforced for its production and retail surveillance.
Collapse
Affiliation(s)
- Julio Parra-Flores
- Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán, Chile
| | - Ondřej Holý
- Science and Research Centre, Faculty of Health Sciences, Palacký University Olomouc, Olomouc, Czechia
| | - Sergio Acuña
- Department of Food Engineering, Universidad del Bío-Bío, Chillán, Chile
| | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | | | | | - Ariadnna Cruz-Córdova
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Jetsi Mancilla-Rojano
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico.,Faculty of Medicine, Biological Sciences Graduate Program, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alejandro Castillo
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX, United States
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | | |
Collapse
|
6
|
Zhao X, Li W, Hou S, Wang Y, Wang S, Gao J, Zhang R, Jiang S, Zhu Y. Epidemiological investigation on drug resistance of Salmonella isolates from duck breeding farms in Shandong Province and surrounding areas, China. Poult Sci 2022; 101:101961. [PMID: 35687959 PMCID: PMC9190056 DOI: 10.1016/j.psj.2022.101961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Xinyuan Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 201718, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 201718, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian 271018, China
| | - Wei Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 201718, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 201718, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian 271018, China
| | - Shaopeng Hou
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 201718, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 201718, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian 271018, China
| | - Yanjun Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 201718, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 201718, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian 271018, China
| | - Shuyang Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 201718, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 201718, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian 271018, China
| | - Jing Gao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 201718, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 201718, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian 271018, China
| | - Ruihua Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 201718, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 201718, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian 271018, China
| | - Shijin Jiang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 201718, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 201718, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian 271018, China
| | - Yanli Zhu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian 201718, China; Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Taian 201718, China; Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Taian 271018, China.
| |
Collapse
|
7
|
Mengarda Buosi DT, de Moraes JO, Cheng Y, Cheng RA, Moraru CI, Carciofi BA. Effective pulsed light treatments for inactivating Salmonella enterica serotypes. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
8
|
Antimicrobial resistance and genetic background of non-typhoidal Salmonella enterica strains isolated from human infections in São Paulo, Brazil (2000-2019). Braz J Microbiol 2022; 53:1249-1262. [PMID: 35446010 PMCID: PMC9433476 DOI: 10.1007/s42770-022-00748-8] [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: 12/11/2021] [Accepted: 03/30/2022] [Indexed: 11/02/2022] Open
Abstract
Salmonella enterica causes Salmonellosis, an important infection in humans and other animals. The number of multidrug-resistant (MDR) phenotypes associated with Salmonella spp. isolates is increasing worldwide, causing public health concern. Here, we aim to characterize the antimicrobial-resistant phenotype of 789 non-typhoidal S. enterica strains isolated from human infections in the state of São Paulo, Brazil, along 20 years (2000-2019). Among the non-susceptible isolates, 31.55, 14.06, and 13.18% were resistant to aminoglycosides, tetracycline, and β-lactams, respectively. Moreover, 68 and 11 isolates were considered MDR and Extended Spectrum β-Lactamase (ESBL) producers, respectively, whereas one isolate was colistin-resistant. We selected four strains to obtain a draft of the Genome Sequence; one S. Infantis (ST32), one S. Enteritidis (ST11), one S. I 4,[5],12:i:- (ST19), and one S. Typhimurium (ST313). Among them, three presented at least one of the following antimicrobial resistance genes (AMR) linked to mobile DNA: blaTEM-1B, dfrA1, tetA, sul1, floR, aac(6')-laa, and qnrE1. This is the first description of the plasmid-mediated quinolone resistance (PMQR) gene qnrE1 in a clinical isolate of S. I 4,[5],12:i:-. The S. Typhimurium is a colistin-resistant isolate, but did not harbor mcr genes, but it presented mutations within the mgrB, pmrB, and pmrC regions that might be linked to the colistin-resistant phenotype. The virulence pattern of the four isolates resembled the virulence pattern of the highly pathogenic S. Typhimurium UK-1 reference strain in assays involving the in vivo Galleria mellonella model. In conclusion, most isolates studied here are susceptible, but a small percentage present an MDR or ESBL-producer and pathogenic phenotype. Sequence analyses revealed plasmid-encoded AMR genes, such as β-lactam and fluoroquinolone resistance genes, indicating that these characteristics can be potentially disseminated among other bacterial strains.
Collapse
|
9
|
Darboe S, Bradbury RS, Phelan J, Kanteh A, Muhammad AK, Worwui A, Yang S, Nwakanma D, Perez-Sepulveda B, Kariuki S, Kwambana-Adams B, Antonio M. Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia. Microb Genom 2022; 8:000785. [PMID: 35302932 PMCID: PMC9176284 DOI: 10.1099/mgen.0.000785] [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: 08/17/2021] [Accepted: 01/24/2022] [Indexed: 11/18/2022] Open
Abstract
Non-typhoidal Salmonella associated with multidrug resistance cause invasive disease in sub-Saharan Africa. Specific lineages of serovars Typhimurium and Enteritidis have been implicated. Here we characterized the genomic diversity of 100 clinical non-typhoidal Salmonella collected from 93 patients in 2001 from the eastern, and in 2006-2018 from the western regions of The Gambia respectively. A total of 93 isolates (64 invasive, 23 gastroenteritis and six other sites) representing a single infection episode were phenotypically tested for antimicrobial susceptibility using the Kirby-Bauer disc diffusion technique. Whole genome sequencing of 100 isolates was performed using Illumina, and the reads were assembled and analysed using SPAdes. The Salmonella in Silico Typing Resource (SISTR) was used for serotyping. SNP differences among the 93 isolates were determined using Roary, and phylogenetic analysis was performed in the context of 495 African strains from the European Nucleotide Archive. Salmonella serovars Typhimurium (26/64; 30.6 %) and Enteritidis (13/64; 20.3 %) were associated with invasive disease, whilst other serovars were mainly responsible for gastroenteritis (17/23; 73.9 %). The presence of three major serovar Enteritidis clades was confirmed, including the invasive West African clade, which made up more than half (11/16; 68.8 %) of the genomes. Multidrug resistance was confined among the serovar Enteritidis West African clade. The presence of this epidemic virulent clade has potential for spread of resistance and thus important implications for systematic patient management. Surveillance and epidemiological investigations to inform control are warranted.
Collapse
Affiliation(s)
- Saffiatou Darboe
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | | | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, UK
| | - Abdoulie Kanteh
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | - Abdul-Khalie Muhammad
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | - Archibald Worwui
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | - Shangxin Yang
- University of California, Los Angeles, California, USA
| | - Davis Nwakanma
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| | | | | | - Brenda Kwambana-Adams
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
- University College London, London, UK
| | - Martin Antonio
- Medical Research Council Unit, The Gambia at London School of Hygiene and Tropical Medicine, The Gambia
| |
Collapse
|
10
|
Portes AB, Rodrigues G, Leitão MP, Ferrari R, Conte Junior CA, Panzenhagen P. Global distribution of plasmid-mediated colistin resistance mcr gene in Salmonella: A systematic review. J Appl Microbiol 2021; 132:872-889. [PMID: 34480840 DOI: 10.1111/jam.15282] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/04/2021] [Accepted: 08/31/2021] [Indexed: 11/28/2022]
Abstract
This systematic review focuses on obtaining the most relevant information from multiple studies that detected a mobilized colistin resistance mcr gene in Salmonella for a better comprehension of its global distribution. A group of strategic and systematic keywords were combined to retrieve research data on the detection frequency of the mcr gene globally from four database platforms (Google Scholar, Science Direct, PubMed and Scielo). Forty-eight studies attended all the eligibility criteria and were selected. China was the country with the highest frequency of Salmonella strains with the mcr gene, and Europe exhibited a wide diversity of countries with positive mcr strains. In addition, animals and humans carried the highest frequency of positive strains for the mcr gene. Salmonella Typhimurium was the most frequent serovar carrying the mcr gene. Apparently, colistin overuse in animal husbandry has increased the selective pressure of antimicrobial resistance, resulting in the emergence of a plasmid-mediated colistin resistance mcr gene in China. The mcr-positive Salmonella strains are recently predominant worldwide, which is probably due to the capacity of this gene to be swiftly horizontally transmissible. The transmission ability of mcr-positive Salmonella strains to humans through the consumption of contaminated animal-based food is a public health concern.
Collapse
Affiliation(s)
- Ana Beatriz Portes
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Grazielle Rodrigues
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Mylenna Palma Leitão
- Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Rafaela Ferrari
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Carlos Adam Conte Junior
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Food Science (PPGCAL), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Graduate Program in Veterinary Hygiene (PPGHV), Faculty of Veterinary Medicine, Fluminense Federal University (UFF), Vital Brazil Filho, Niterói, RJ, Brazil.,Graduate Program in Sanitary Surveillance (PPGVS), National Institute of Health Quality Control (INCQS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, RJ, Brazil.,Graduate Program in Chemistry (PGQu), Institute of Chemistry (IQ), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| | - Pedro Panzenhagen
- Center for Food Analysis (NAL), Technological Development Support Laboratory (LADETEC), Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil.,Laboratory of Advanced Analysis in Biochemistry and Molecular Biology (LAABBM), Department of Biochemistry, Federal University of Rio de Janeiro (UFRJ), Cidade Universitária, Rio de Janeiro, RJ, Brazil
| |
Collapse
|
11
|
Wu B, Ed-Dra A, Pan H, Dong C, Jia C, Yue M. Genomic Investigation of Salmonella Isolates Recovered From a Pig Slaughtering Process in Hangzhou, China. Front Microbiol 2021; 12:704636. [PMID: 34305874 PMCID: PMC8298193 DOI: 10.3389/fmicb.2021.704636] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/11/2021] [Indexed: 01/25/2023] Open
Abstract
The pig industry is the principal source of meat products in China, and the presence of pathogens in pig-borne meat is a crucial threat to public health. Salmonella is the major pathogen associated with pig-borne diseases. However, route surveillance by genomic platforms along the food chain is still limited in China. Here, we conducted a study to evaluate the dynamic prevalence of Salmonella in a pig slaughtering process in Hangzhou, Zhejiang Province, China. Fifty-five of 226 (24.37%) samples were positive for Salmonella; from them, 78 different isolates were selected and subjected to whole genome sequencing followed by bioinformatics analyses to determine serovar distribution, MLST patterns, antimicrobial resistance genes, plasmid replicons, and virulence factors. Moreover, phenotypic antimicrobial resistance was performed using the broth dilution method against 14 antimicrobial agents belonging to 10 antimicrobial classes. Our results showed that samples collected from the dehairing area (66.66%) and the splitting area (57.14%) were the most contaminated. Phenotypic antimicrobial resistance classified 67 of 78 isolates (85.90%) as having multidrug resistance (MDR), while the highest resistance was observed in tetracycline (85.90%; 67/78) followed by ampicillin (84.62%; 66/78), chloramphenicol (71.80%; 56/78), and nalidixic acid (61.54%; 48/78). Additionally, serovar prediction showed the dominance of Salmonella Typhimurium ST19 (51.28%; 40/78) among the 78 studied isolates, while plasmid prediction reported the dominance of IncHI2A_1 (20.51%; 16/78), followed by IncX1_1 (17.95%; 14/78) and IncHI2_1 (11.54%; 9/78). Virulence factor prediction showed the detection of cdtB gene encoding typhoid toxins in two Salmonella Goldcoast ST358 and one Salmonella Typhimurium ST19, while one isolate of Salmonella London ST155 was positive for genes encoding for the siderophore “yersiniabactin” and the gene senB encoding for enterotoxin production. From this study, we conclude that pig slaughterhouses are critical points for the dissemination of virulent and multidrug-resistant Salmonella isolates along the food chain which require the implementation of management systems to control the critical points. Moreover, there is an urgent need for the implementation of the whole genome sequencing platform to monitor the emergence of virulent and multidrug-resistant clones along the food chain.
Collapse
Affiliation(s)
- Beibei Wu
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | | | - Hang Pan
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Chenghang Dong
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Chenghao Jia
- Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Min Yue
- Hainan Institute of Zhejiang University, Sanya, China.,Department of Veterinary Medicine, Institute of Preventive Veterinary Sciences, Zhejiang University College of Animal Sciences, Hangzhou, China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China.,Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
| |
Collapse
|
12
|
Class 1 integron-borne cassettes harboring blaCARB-2 gene in multidrug-resistant and virulent Salmonella Typhimurium ST19 strains recovered from clinical human stool samples, United States. PLoS One 2020; 15:e0240978. [PMID: 33125394 PMCID: PMC7598458 DOI: 10.1371/journal.pone.0240978] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
International lineages, such as Salmonella Typhimurium sequence type (ST) 19, are most often associated with foodborne diseases and deaths in humans. In this study, we compared the whole-genome sequences of five S. Typhimurium strains belonging to ST19 recovered from clinical human stool samples in North Carolina, United States. Overall, S. Typhimurium strains displayed multidrug-resistant profile, being resistance to critically and highly important antimicrobials including ampicillin, ticarcillin/clavulanic acid, streptomycin and sulfisoxazole, chloramphenicol, tetracycline, respectively. Interestingly, all S. Typhimurium strains carried class 1 integron (intl1) and we were able to describe two genomic regions surrounding blaCARB-2 gene, size 4,062 bp and 4,422 bp for S. Typhimurium strains (HS5344, HS5437, and HS5478) and (HS5302 and HS5368), respectively. Genomic analysis for antimicrobial resistome confirmed the presence of clinically important genes, including blaCARB-2, aac(6’)-Iaa, aadA2b, sul1, tetG, floR, and biocide resistance genes (qacEΔ1). S. Typhimurium strains harbored IncFIB plasmid containing spvRABCD operon, as well as rck and pef virulence genes, which constitute an important apparatus for spreading the virulence plasmid. In addition, we identified several virulence genes, chromosomally located, while the phylogenetic analysis revealed clonal relatedness among these strains with S. enterica isolated from human and non-human sources obtained in European and Asian countries. Our results provide new insights into this unusual class 1 integron in virulent S. Typhimurium strains that harbors a pool of genes acting as potential hotspots for horizontal gene transfer providing readily adaptation to new surrounds, as well as being crucially required for virulence in vivo. Therefore, continuous genomic surveillance is an important tool for safeguarding human health.
Collapse
|
13
|
Leite EL, Araújo WJ, Vieira TR, Zenato KS, Vasconcelos PC, Cibulski S, Givisiez PEN, Cardoso MRI, Oliveira CJB. First reported genome of an mcr-9-mediated colistin-resistant Salmonella Typhimurium isolate from Brazilian livestock. J Glob Antimicrob Resist 2020; 23:394-397. [PMID: 33039597 DOI: 10.1016/j.jgar.2020.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/13/2020] [Accepted: 09/08/2020] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVES To investigate the genetic context of colistin resistance in anmcr-9-harbouring Salmonella Typhimurium ST19 strain from swine in Brazil. METHODS Minimum inhibitory concentrations (MIC) to colistin were determined by broth microdilution. Whole-genome sequencing was performed on an Illumina MiSeq system, followed by de novo genome assembly using SPAdes 1.13.1. The draft genome sequence was annotated in Prokka using KBase online server. Downstream analyses for resistome and plasmid detection were performed using online tools available at the Center for Genomic Epidemiology. The strain was typed in silico using MLST 2.0. Phylogenetic analysis involving 24 other genomes ofSalmonella Typhimurium ST19 and mcr-9-harbouring Salmonella Typhimurium isolated from humans, livestock and foodstuff in different regions was also performed. RESULTS Assembly of the draft genome resulted in 5245 protein-coding sequences, 14 rRNAs, 83 tRNAs and a GC content of 51.81%. The strain was identified asSalmonella Typhimurium ST19 harbouring a 265.5-kb pN1566-2 plasmid carrying genes encoding resistance to colistin (mcr-9.1), aminoglycosides (aadA1), tetracycline [tet(C)] and sulfonamides (sul1). Our findings indicate that the Salmonella Typhimurium ST19 strain in this study showed low genetic variability compared with Salmonella Typhimurium ST19 isolated from swine and poultry in Brazil, and was less related to those reported in other countries. CONCLUSIONS This is the first reported genome of a phenotypically colistin-resistantSalmonella Typhimurium harbouring the mcr-9 variant in Brazilian livestock. This genome will aid global investigations on epidemiological and evolutionary aspects of plasmid-mediated colistin resistance and the role of colistin-resistant Salmonella Typhimurium ST19 lineage as a zoonotic pathogen.
Collapse
Affiliation(s)
- Elma L Leite
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil
| | - Wydemberg J Araújo
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil
| | - Tatiana R Vieira
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 91540-000, Brazil
| | - Karoline S Zenato
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 91540-000, Brazil
| | - Priscylla C Vasconcelos
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil
| | - Samuel Cibulski
- Center for Biotechnology (CBiotec), Federal University of Paraiba (CBiotec/UFPB), João Pessoa, PB 5805-900, Brazil
| | - Patricia E N Givisiez
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil
| | - Marisa R I Cardoso
- Department of Preventive Veterinary Medicine, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, RS 91540-000, Brazil
| | - Celso J B Oliveira
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397-000, Brazil; Global One Health Initiative (GOHi), The Ohio State University (OSU), Columbus, OH 43210, USA.
| |
Collapse
|
14
|
Rodrigues GL, Panzenhagen P, Ferrari RG, Dos Santos A, Paschoalin VMF, Conte-Junior CA. Frequency of Antimicrobial Resistance Genes in Salmonella From Brazil by in silico Whole-Genome Sequencing Analysis: An Overview of the Last Four Decades. Front Microbiol 2020; 11:1864. [PMID: 32849452 PMCID: PMC7426471 DOI: 10.3389/fmicb.2020.01864] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/15/2020] [Indexed: 12/20/2022] Open
Abstract
Salmonella is a leading human pathogen and a significant public health concern worldwide. Massive food production and distribution have contributed to this pathogen dissemination, which, combined with antimicrobial resistance (AMR), creates new control challenges in food safety. The development of AMR is a natural phenomenon and can occur in the bacterial evolutionary process. However, the overuse and the misuse of antimicrobial drugs in humans and in animals have increased AMR selective pressure. In Brazil, there is an accuracy lack in AMR frequency in Salmonella because too many isolates are under-investigated for genetic and phenotypic AMR by the Brazilian health authorities and the research community. This underreporting situation makes the comprehension of the real level of Salmonella AMR in the country difficult. The present study aimed to use bioinformatics tools for a rapid in silico screening of the genetic antimicrobial resistance profile of Salmonella through whole-genome sequences (WGS). A total of 930 whole-genome sequences of Salmonella were retrieved from the public database of the National Biotechnology Information Center (NCBI). A total of 65 distinct resistance genes were detected, and the most frequent ones were tet(A), sul2, and fosA7. Nine point mutations were detected in total, and parC at the 57 position (threonine → serine) was the highest frequent substitution (26.7%, 249/930), followed by gyrA at the 83 position (serine → phenylalanine) (20.0%, 186/930) and at the 87 position (aspartic acid → asparagine) (15.7%, 146/930). The in silico prediction of resistance phenotype showed that 58.0% (540/930) of the strains can display a multidrug resistance (MDR) profile. Ciprofloxacin and nalidixic acid were the antimicrobial drugs with the highest frequency rates of the predicted phenotype resistance among the strains. The temporal analysis through the last four decades showed increased frequency rates of antimicrobial resistance genes and predicted resistance phenotypes in the 2000s and the 2010s when compared with the 1980s and 1990s. The results presented herein contributed significantly to the understanding of the strategic use of WGS associated with in silico analysis and the predictions for the determination of AMR in Salmonella from Brazil.
Collapse
Affiliation(s)
- Grazielle Lima Rodrigues
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Pedro Panzenhagen
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafaela Gomes Ferrari
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Anamaria Dos Santos
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vania Margaret Flosi Paschoalin
- Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos Adam Conte-Junior
- Nucleus of Food Analysis (NAL), Laboratory for the Support of Technological Development (LADETEC), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Food Science Graduate Program (PPGCAL), Chemistry Institute, Department of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Health Surveillance Graduate Program (PPGVS), National Institute for Quality Control in Health (INCQS), Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| |
Collapse
|
15
|
Honeycutt JD, Wenner N, Li Y, Brewer SM, Massis LM, Brubaker SW, Chairatana P, Owen SV, Canals R, Hinton JCD, Monack DM. Genetic variation in the MacAB-TolC efflux pump influences pathogenesis of invasive Salmonella isolates from Africa. PLoS Pathog 2020; 16:e1008763. [PMID: 32834002 PMCID: PMC7446830 DOI: 10.1371/journal.ppat.1008763] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 06/30/2020] [Indexed: 01/23/2023] Open
Abstract
The various sub-species of Salmonella enterica cause a range of disease in human hosts. The human-adapted Salmonella enterica serovar Typhi enters the gastrointestinal tract and invades systemic sites to cause enteric (typhoid) fever. In contrast, most non-typhoidal serovars of Salmonella are primarily restricted to gut tissues. Across Africa, invasive non-typhoidal Salmonella (iNTS) have emerged with an ability to spread beyond the gastrointestinal tract and cause systemic bloodstream infections with increased morbidity and mortality. To investigate this evolution in pathogenesis, we compared the genomes of African iNTS isolates with other Salmonella enterica serovar Typhimurium and identified several macA and macB gene variants unique to African iNTS. MacAB forms a tripartite efflux pump with TolC and is implicated in Salmonella pathogenesis. We show that macAB transcription is upregulated during macrophage infection and after antimicrobial peptide exposure, with macAB transcription being supported by the PhoP/Q two-component system. Constitutive expression of macAB improves survival of Salmonella in the presence of the antimicrobial peptide C18G. Furthermore, these macAB variants affect replication in macrophages and influence fitness during colonization of the murine gastrointestinal tract. Importantly, the infection outcome resulting from these macAB variants depends upon both the Salmonella Typhimurium genetic background and the host gene Nramp1, an important determinant of innate resistance to intracellular bacterial infection. The variations we have identified in the MacAB-TolC efflux pump in African iNTS may reflect evolution within human host populations that are compromised in their ability to clear intracellular Salmonella infections.
Collapse
Affiliation(s)
- Jared D. Honeycutt
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Nicolas Wenner
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Yan Li
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Susan M. Brewer
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Liliana M. Massis
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Sky W. Brubaker
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - Phoom Chairatana
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Siân V. Owen
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Rocío Canals
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Jay C. D. Hinton
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Denise M. Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| |
Collapse
|
16
|
Prevalence, antibiotic resistance, PFGE and MLST characterization of Salmonella in swine mesenteric lymph nodes. Prev Vet Med 2020; 179:105024. [PMID: 32417637 DOI: 10.1016/j.prevetmed.2020.105024] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 11/21/2022]
Abstract
This study evaluated 250 animals from 25 different processing lots, processed in four slaughterhouses in São Paulo state, Brazil for the presence of Salmonella in the mesenteric lymph nodes (10 g sample of each animal) and characterized the antibiotics resistance profile, the Pulsed Field Gel Electrophoresis - PFGE and Multi Locus Sequence Typing - MLST profiles of selected strains. The pathogen was present in 36.4% (n = 91, CL 95% 30.4-43.4) of samples and 72% (n = 18, CL 95% 50.6-87.9%) of the analyzed lots. The main serovars were S. Typhimurium (n = 23), Salmonella enterica subsp. enterica 1.4,5,12:i:- (n = 17), followed by S. Infantis (n = 12) and S. Havana (n = 11). Twenty-eight strains (30%) were classified as other serovars. Sixty-eight percent of the strains were resistant to Streptomycin and tetracycline, followed by ampicillin and sulphonamides (62.6%), chloramphenicol (56.0%), trimethoprim-sulfamethoxazole (41.8%) and nalidixic acid (40.7%). The antibiotics with lower resistance rates were cephalothin and aztreonam (both with 3.3% resistant), and ceftriaxone and cefepime (both with 7.7%). Multidrug-resistant strains (MDR) accounted for 70.3% of the isolates. Eight strains were submitted to MLST: four S. Typhimurium and one S.1.4,5,12:i:-, all belonging to the ST 19, two Salmonella Infantis, belonging to the ST 32 and one S. Derby, belonging to ST 40. Twenty-one isolates with different antibiotics resistance profiles from the most prevalent serovars were selected for PFGE analysis. Serovar S. Typhimurium (n = 11) revealed 4 pulsotypes and 1 cluster and S. 1.4,5,12:i:- (n = 10) revealed 5 pulsotypes and 4 clusters. The high prevalence of the pathogen, with its high rates of antibiotics resistance and belonging to genetic groups that are often associated with disease in humans, shows that the production chain of pork is a potential source of infection in salmonellosis cases. Therefore, effective preventive measures for pathogen control are needed to reduce the risk of foodborne diseases.
Collapse
|
17
|
Seribelli AA, Gonzales JC, de Almeida F, Benevides L, Cazentini Medeiros MI, Dos Prazeres Rodrigues D, de C Soares S, Allard MW, Falcão JP. Phylogenetic analysis revealed that Salmonella Typhimurium ST313 isolated from humans and food in Brazil presented a high genomic similarity. Braz J Microbiol 2020; 51:53-64. [PMID: 31728978 PMCID: PMC7058764 DOI: 10.1007/s42770-019-00155-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/07/2019] [Indexed: 12/16/2022] Open
Abstract
Salmonella Typhimurium sequence type 313 (S. Typhimurium ST313) has caused invasive disease mainly in sub-Saharan Africa. In Brazil, ST313 strains have been recently described, and there is a lack of studies that assessed by whole genome sequencing (WGS)-the relationship of these strains. The aims of this work were to study the phylogenetic relationship of 70 S. Typhimurium genomes comparing strains of ST313 (n = 9) isolated from humans and food in Brazil among themselves, with other STs isolated in this country (n = 31) and in other parts of the globe (n = 30) by 16S rRNA sequences, the Gegenees software, whole genome multilocus sequence typing (wgMLST), and average nucleotide identity (ANI) for the genomes of ST313. Additionally, pangenome analysis was performed to verify the heterogeneity of these genomes. The phylogenetic analyses showed that the ST313 genomes were very similar among themselves. However, the ST313 genomes were usually clustered more distantly to other STs of strains isolated in Brazil and in other parts of the world. By pangenome calculation, the core genome was 2,880 CDSs and 4,171 CDSs singletons for all the 70 S. Typhimurium genomes studied. Considering the 10 ST313 genomes analyzed the core genome was 4,112 CDSs and 76 CDSs singletons. In conclusion, the ST313 genomes from Brazil showed a high similarity among them which information might eventually help in the development of vaccines and antibiotics. The pangenome analysis showed that the S. Typhimurium genomes studied presented an open pangenome, but specifically tending to become close for the ST313 strains.
Collapse
Affiliation(s)
- Amanda Ap Seribelli
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Av. do Café, s/n°-Campus Universitário USP, Ribeirão Preto, SP, 14040-903, Brazil.
| | - Júlia C Gonzales
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Av. do Café, s/n°-Campus Universitário USP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Fernanda de Almeida
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Av. do Café, s/n°-Campus Universitário USP, Ribeirão Preto, SP, 14040-903, Brazil
| | - Leandro Benevides
- National Laboratory of Scientific Computation - LNCC, Petrópolis, Brazil
| | | | | | | | - Marc W Allard
- Food and Drug Administration - FDA, College Park, MA, USA
| | - Juliana P Falcão
- Departamento de Análises Clínicas, Toxicológicas e Bromatológicas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo - USP, Av. do Café, s/n°-Campus Universitário USP, Ribeirão Preto, SP, 14040-903, Brazil
| |
Collapse
|
18
|
Occurrence and Characterization of Salmonella Isolated from Table Egg Layer Farming Environments in Western Australia and Insights into Biosecurity and Egg Handling Practices. Pathogens 2020; 9:pathogens9010056. [PMID: 31941158 PMCID: PMC7168610 DOI: 10.3390/pathogens9010056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 01/06/2020] [Accepted: 01/10/2020] [Indexed: 01/04/2023] Open
Abstract
The aim of this study was to investigate the occurrence and distribution of Salmonella in commercial layer farming environments of 26 flocks belonging to seven egg businesses (free-range and barn-laid) in Western Australia (WA). Between November 2017 and June 2018, a total of 265 environmental samples of dust, feed, water, pooled feces, and boot swabs were tested for detection of Salmonella according to standard culture-based methods. Isolates were assayed for serovar and subtyped by multilocus sequence typing (MLST). Salmonella spp. were recovered from 35% (93/265) of all tested samples. Dust (53.8%, 28/52) and pooled fecal (54.5%, 18/33) samples provided the highest Salmonella recovery rates. Nine different Salmonella serovars were characterized across the positive (n = 93) environmental samples, of which S. Typhimurium (60/93, 64.5%) and S. Infantis (21/93, 22.5%) were the most prevalent. MLST revealed that all S. Typhimurium isolates were of sequence type ST-19. Microbiological screening of Salmonella was not routinely practiced in any of the surveyed egg businesses. Some of the egg businesses exhibited variable levels of compliance with basic biosecurity measures as well as high-risk egg handling practices. Egg businesses in WA should be encouraged to adopt a voluntary program of environmental sampling and verification testing for Salmonella. Such voluntary programs will aid in supporting solutions for the management of this pathogen in the human food chain.
Collapse
|
19
|
Genomic analysis of human invasive Salmonella enterica serovar Typhimurium ST313 isolate B3589 from India. INFECTION GENETICS AND EVOLUTION 2019; 73:416-424. [DOI: 10.1016/j.meegid.2019.05.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 04/14/2019] [Accepted: 05/31/2019] [Indexed: 01/08/2023]
|
20
|
Monte DF, Lincopan N, Berman H, Cerdeira L, Keelara S, Thakur S, Fedorka-Cray PJ, Landgraf M. Genomic Features of High-Priority Salmonella enterica Serovars Circulating in the Food Production Chain, Brazil, 2000-2016. Sci Rep 2019; 9:11058. [PMID: 31363103 PMCID: PMC6667439 DOI: 10.1038/s41598-019-45838-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/11/2019] [Indexed: 11/09/2022] Open
Abstract
Multidrug-resistant (MDR) Salmonella enterica has been deemed a high-priority pathogen by the World Health Organization. Two hundred and sixty-four Salmonella enterica isolates recovered over a 16-year period (2000 to 2016) from the poultry and swine production chains, in Brazil, were investigated by whole-genome sequencing (WGS). Most international lineages belonging to 28 serovars, including, S. enterica serovars S. Schwarzengrund ST96, S. Typhimurium ST19, S. Minnesota ST548, S. Infantis ST32, S. Heidelberg ST15, S. Newport ST45, S. Brandenburg ST65 and S. Kentucky ST198 displayed MDR and virulent genetic backgrounds. In this regard, resistome analysis revealed presence of qnrE1 (identified for the first time in S. Typhimurium from food chain), qnrB19, qnrS1, blaCTX-M-8, blaCTX-M-2 and blaCMY-2 genes, as well as gyrA mutations; whereas ColpVC, IncHI2A, IncHI2, IncFIA, Incl1, IncA/C2, IncR, IncX1 and po111 plasmids were detected. In addition, phylogenetic analysis revealed multiple independent lineages such as S. enterica serovars S. Infantis, S. Schwarzengrund, S. Minnesota, S. Kentucky and S. Brandenburg. In brief, ocurrence and persistence of international lineages of S. enterica serovars in food production chain is supported by conserved genomes and wide virulome and resistome.
Collapse
Affiliation(s)
- Daniel F Monte
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil. .,Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA.
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Hanna Berman
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Louise Cerdeira
- Department of Clinical Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | - Shivaramu Keelara
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Siddhartha Thakur
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Paula J Fedorka-Cray
- Department of Population Health and Pathobiology, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, USA
| | - Mariza Landgraf
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, Food Research Center, University of São Paulo, São Paulo, Brazil.
| |
Collapse
|
21
|
Gómez-Baltazar A, Vázquez-Garcidueñas MS, Larsen J, Kuk-Soberanis ME, Vázquez-Marrufo G. Comparative stress response to food preservation conditions of ST19 and ST213 genotypes of Salmonella enterica serotype Typhimurium. Food Microbiol 2019; 82:303-315. [PMID: 31027788 DOI: 10.1016/j.fm.2019.03.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 01/30/2019] [Accepted: 03/07/2019] [Indexed: 11/27/2022]
Abstract
The replacement of the most prevalent Salmonella enterica genotypes has been documented worldwide. Here we tested the hypothesis that the current prevalent sequence type ST213 of serotype Typhimurium in Mexico has a higher resistance to stressful food preservation conditions than the displaced sequence ST19. ST19 showed higher cell viability percentages than ST213 in osmotic (685 mM NaCl) and acidic (pH 3.5) stress conditions and in combination with refrigeration (4 °C) and ambient (≈22 °C) temperatures. Both genotypes showed the same poststress recovery growth. ST213 formed biofilm and filamentous cells (FCs) under stress, whereas ST19 did not. ST213 cells also showed higher motility. The capacity of ST213 to form FCs may explain its lower viability percentages when compared with ST19, i.e., ST213 cells divided less under stress conditions, but FCs had the same recovery capacity of ST19 cells. ST213 presented a higher unsaturated/saturated fatty acids ratio (0.5-0.6) than ST19 (0.2-0.5), which indicates higher membrane fluidity. The transcript levels of the rpoS gene were similar between genotypes under the experimental conditions employed. Biofilm formation, the generation of FCs, cell motility and membrane modification seem to make ST213 more resistant than ST19 to food preservation environments.
Collapse
Affiliation(s)
- Adrián Gómez-Baltazar
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, CP 58893, Mexico.
| | - Ma Soledad Vázquez-Garcidueñas
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, CP 58020, Mexico.
| | - John Larsen
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad (IIES), Universidad Nacional Autónoma de México, Morelia, Michoacá, CP 58190, Mexico.
| | - Mariana Esther Kuk-Soberanis
- División de Estudios de Posgrado, Facultad de Ciencias Médicas y Biológicas "Dr. Ignacio Chávez", Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, CP 58020, Mexico.
| | - Gerardo Vázquez-Marrufo
- Centro Multidisciplinario de Estudios en Biotecnología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, CP 58893, Mexico.
| |
Collapse
|