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Hyeon JY, Helal ZH, Polkowski R, Vyhnal K, Mishra N, Kim J, Risatti GR, Lee DH. Genomic Features of Salmonella enterica Subspecies houtenae Serotype 45:g,z51:- Isolated from Multiple Abdominal Abscesses of an African Fat-Tailed Gecko, United States, 2020. Antibiotics (Basel) 2021; 10:antibiotics10111322. [PMID: 34827260 PMCID: PMC8614954 DOI: 10.3390/antibiotics10111322] [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: 10/08/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 11/26/2022] Open
Abstract
Salmonella enterica subsp. houtenae (S. houtenae) is a common subspecies in reptiles and has been implicated as a source of serious and life-threatening diseases in humans. Although occurrence and significance of S. houtenae infections have been extensively studied, the genetic features of S. houtenae have remained unknown due to a lack of available high-quality genome sequences. We obtained the complete genome sequence of S. houtenae 45:g,z51:- strain 20-369 isolated from multiple abdominal abscesses of an African fat-tailed gecko (Hemitheconyx caudicinctus) using Nanopore and Illumina sequencing technologies and generated the 4.65Mbp complete genome sequence of the S. houtenae str. 20-369. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity. Overall, this study found several interesting genomic features such as pseudogene formation, virulence gene profile, and novel genomic islands. This study provides basis for an understanding possible genetic mechanism underlying pathogenicity of S. houtenae 45:g,z51:- as well as a high-quality genome reference for future comparison studies.
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Affiliation(s)
- Ji-Yeon Hyeon
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (Z.H.H.); (K.V.); (N.M.); (J.K.); (G.R.R.)
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA;
| | - Zeinab H. Helal
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (Z.H.H.); (K.V.); (N.M.); (J.K.); (G.R.R.)
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA;
| | - Robert Polkowski
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA;
| | - Kristin Vyhnal
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (Z.H.H.); (K.V.); (N.M.); (J.K.); (G.R.R.)
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA;
| | - Neha Mishra
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (Z.H.H.); (K.V.); (N.M.); (J.K.); (G.R.R.)
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA;
| | - Junwon Kim
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (Z.H.H.); (K.V.); (N.M.); (J.K.); (G.R.R.)
| | - Guillermo R. Risatti
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (Z.H.H.); (K.V.); (N.M.); (J.K.); (G.R.R.)
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA;
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT 06269, USA; (J.-Y.H.); (Z.H.H.); (K.V.); (N.M.); (J.K.); (G.R.R.)
- Correspondence: ; Tel.: +1-860-486-1138
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Zhou M, Shi Q, Zhang X, Mei L, Ye Y, Fang C, Shang S. Salmonella enterica subsp. diarizonae Harboring ST233, ST1263, and ST1845 in Children. Front Cell Infect Microbiol 2021; 11:727811. [PMID: 34490148 PMCID: PMC8417408 DOI: 10.3389/fcimb.2021.727811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/02/2021] [Indexed: 01/18/2023] Open
Abstract
Objective This study aims to analyze the molecular epidemiology, resistance, and pathogenicity of Salmonella enterica subsp. diarizonae isolated from children. Methods Whole genome sequencing was carried out, and molecular serotypes, sequence types, resistance genes, and virulence genes of S. enterica subsp. diarizonae isolates were analyzed. Antimicrobial susceptibility test was determined by commercialized microdilution method. Results A total of three isolates of S. enterica subsp. diarizonae were isolated during 2015 to 2020. The molecular serotypes of the three strains were 61:c:z35, 61:l,v:1,5,7:[z57], and 65:k:z, respectively, and the sequence types were ST1845, ST233, and ST1263. All the three isolates were susceptible to ceftriaxone, ceftazidime, cefepime, amoxycillin/clavulanic acid, piperacillin/tazobactam, ertapenem, imipenem, levofloxacin, and trimethoprim/sulfamethoxazole. No other resistant gene was detected except aac(6')-Iaa. There were no resistant plasmids detected in all the three isolates. A total of 76 genes were present in all isolates, containing 49 genes of Type III Secretion System (T3SS) mediated by SPI-1and SPI-2, 13 genes of adherence (type 1 fimbriae, Agf, and MisL-related genes), 11 genes of iron uptake (Yersiniabactin), two genes of magnesium uptake, and one gene of typhoid toxin(cdtB). Conclusion The serotypes and sequence types of S. enterica subsp. diarizonae isolates were rarely reported in children; all the S. enterica subsp. diarizonae isolates were susceptible to detected antibiotics; T3SS, adherence, iron uptake, magnesium uptake, and typhoid toxin were responsible for pathogenicity of the S. enterica subsp. diarizonae isolates in children.
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Affiliation(s)
- Mingming Zhou
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Qiucheng Shi
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Xiucai Zhang
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Lingling Mei
- Microbiological Laboratory, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yihua Ye
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Chao Fang
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Shiqiang Shang
- Department of Clinical Laboratory, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
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Characterisation of Early Positive mcr-1 Resistance Gene and Plasmidome in Escherichia coli Pathogenic Strains Associated with Variable Phylogroups under Colistin Selection. Antibiotics (Basel) 2021; 10:antibiotics10091041. [PMID: 34572623 PMCID: PMC8466100 DOI: 10.3390/antibiotics10091041] [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: 06/30/2021] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 01/08/2023] Open
Abstract
An antibiotic susceptibility monitoring programme was conducted from 2004 to 2010, resulting in a collection of 143 Escherichia coli cultured from bovine faecal samples (diarrhoea) and milk-aliquots (mastitis). The isolates were subjected to whole-genome sequencing and were distributed in phylogroups A, B1, B2, C, D, E, and G with no correlation for particular genotypes with pathotypes. In fact, the population structure showed that the strains belonging to the different phylogroups matched broadly to ST complexes; however, the isolates are randomly associated with the diseases, highlighting the necessity to investigate the virulence factors more accurately in order to identify the mechanisms by which they cause disease. The antimicrobial resistance was assessed phenotypically, confirming the genomic prediction on three isolates that were resistant to colistin, although one isolate was positive for the presence of the gene mcr-1 but susceptible to colistin. To further characterise the genomic context, the four strains were sequenced by using a single-molecule long read approach. Genetic analyses indicated that these four isolates harboured complex and diverse plasmids encoding not only antibiotic resistant genes (including mcr-1 and bla) but also virulence genes (siderophore, ColV, T4SS). A detailed description of the plasmids of these four E. coli strains, which are linked to bovine mastitis and diarrhoea, is presented for the first time along with the characterisation of the predicted antibiotic resistance genes. The study highlighted the diversity of incompatibility types encoding complex antibiotic resistance elements such as Tn6330, ISEcp1, Tn6029, and IS5075. The mcr-1 resistance determinant was identified in IncHI2 plasmids pCFS3273-1 and pCFS3292-1, thus providing some of the earliest examples of mcr-1 reported in Europe, and these sequences may be a representative of the early mcr-1 plasmidome characterisation in the EU/EEA.
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Uelze L, Borowiak M, Deneke C, Fischer J, Flieger A, Simon S, Szabó I, Tausch SH, Malorny B. Comparative genomics of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) reveals lineage-specific host adaptation of ST432. Microb Genom 2021; 7. [PMID: 34338625 PMCID: PMC8549363 DOI: 10.1099/mgen.0.000604] [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] [Indexed: 11/18/2022] Open
Abstract
Unlike most Salmonella enterica subsp. diarizonae, which are predominantly associated with cold-blooded animals such as reptiles, the serovar IIIb 61:k:1,5,(7) (termed SASd) is regarded as host-adapted to sheep. The bacterium is rarely associated with disease in humans but, nevertheless, SASd isolates are sporadically obtained from human clinical samples. It is unclear whether these transmissions are directly linked to sheep or whether transmissions may, for example, occur through other domestic animals also carrying SASd. For this reason, we utilized whole-genome sequencing to investigate a set of 119 diverse SASd isolates, including sheep-associated and human-associated isolates, as well as isolates obtained from other matrices. We discovered that serovar IIIb 61:k:1,5,(7) is composed of two distinct lineages defined by their sequence types ST432 and ST439. These two lineages are distinguished by a number of genetic features, as well as their prevalence and reservoir. ST432 appears to be the more prevalent sequence type, with the majority of isolates investigated in this study belonging to ST432. In contrast, only a small number of isolates were attributed to ST439. While ST432 isolates were of sheep, human or other origin, all ST439 isolates with source information available, were obtained from human clinical samples. Regarding their genetic features, lineage ST432 shows increased pseudogenization, harbours a virB/D4 plasmid that encodes a type IV secretion system (T4SS) and does not possess the iro gene cluster, which encodes a salmochelin siderophore for iron acquisition. These characteristics likely contribute to the ability of ST432 to persistently colonize the intestines of sheep. Furthermore, we found isolates of the lineage ST432 to be highly clonal, with little variation over the sampling period of almost 20 years. We conclude from the genomic comparisons that SASd underlies a microevolutionary process and that it is specifically lineage ST432 that should be considered as host-adapted to sheep.
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Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Antje Flieger
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstraße 37, 38855 Wernigerode, Germany
| | - Sandra Simon
- Unit for Enteropathogenic Bacteria and Legionella (FG11)/National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute (RKI), Burgstraße 37, 38855 Wernigerode, Germany
| | - István Szabó
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Straße 8-10, 10589 Berlin, Germany
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Hyeon JY, Helal ZH, Polkowski R, Heishima M, Kim J, Lee DH, Risatti GR. Genetic features of Salmonella enterica subspecies diarizonae serovar 61:k:1,5 isolated from abortion cases in sheep, United States, 2020. Res Vet Sci 2021; 138:125-136. [PMID: 34139624 DOI: 10.1016/j.rvsc.2021.06.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/13/2021] [Accepted: 06/07/2021] [Indexed: 11/18/2022]
Abstract
Salmonella enterica subspecies diarizonae serovar 61:(k):1, 5, (7) (sheep associated S. diarizonae, SASd) is the most common Salmonella serotype identified in sheep flocks. Despite the involvement with animal and human infections, there is limited information regarding virulence profiles of SASds and their antibiotic resistance gene complement, particularly for those circulating in the U.S. In this study, we genetically characterized three SASds, 20-265, 20-269, and 20-312, isolated from sheep placental tissues during an abortion storm affecting a flock in Connecticut during 2020. SASds were the only bacteria isolated from analyzed sheep tissues. The isolates were sensitive to all the antibiotics tested, but all these SASd isolates carry the aminoglycoside resistance gene, aac(6')-Iaa, and a chromosomal substitution in the parC gene. The proportion of pseudogenes (5.3-5.5%) was similar among the isolates, and these SASds carry IncX1 type plasmids. Comparing with the SASds isolates from Enterobase, the three isolates showed an identical genomic virulence profile carrying virulence genes in the conserved set of other SASd isolates except for steC, iagB, iacP, sseI, and slrP genes. In the SNP-based phylogenetic analysis, SASd sequences were grouped into group A-C, and the group C was further subdivided into subgroup C1-C6. The three isolates clustered with other SASd isolates from the U.S. and Canada in subgroup C6. SASd isolates in the identical phylogenetic groups tended to have similar geographical origin. The results of our study did not provide conclusive evidence about which are the genetic traits that trigger SASds to become virulent in sheep, but our data will provide a point for comparative studies of this Salmonella serovar.
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Affiliation(s)
- Ji-Yeon Hyeon
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA; Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Zeinab H Helal
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA; Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Robert Polkowski
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Mizuki Heishima
- Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Junwon Kim
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA
| | - Dong-Hun Lee
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA.
| | - Guillermo R Risatti
- Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA; Connecticut Veterinary Medical Diagnostic Laboratory, Department of Pathobiology and Veterinary Science, College of Agriculture, Health and Natural Resources, University of Connecticut, Storrs, CT, USA.
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Salmonella Infection in Turtles: A Risk for Staff Involved in Wildlife Management? Animals (Basel) 2021; 11:ani11061529. [PMID: 34073932 PMCID: PMC8225080 DOI: 10.3390/ani11061529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/23/2022] Open
Abstract
Simple Summary The aim of this study was to investigate the occurrence of non-typhoidal Salmonella in the turtles housed in a regional wildlife rescue centre of Apulia, in southern Italy, to assess the presence of Salmonella serovars that may represent a risk for operators involved in wildlife management. Sixty-nine tortoises, of which 36 were males and 33 were females, belonging to different species (Testudo hermanni hermanni, T. h. boettgeri, T. graeca, and T. marginata) were tested. All the turtles were adults (34 between 6 and 10 years of age and 35 more than 10 years of age). Salmonella was statistically detected more frequently in T. hermanni hermanni. No differences of the infection prevalence related to animal gender or age were found. Two different species, S. enterica and S. bongori, three S. enterica subspecies (enterica, diarizonae, salamae), and five different serovars (Hermannswerder, Abony, Ferruch, Richmond, Vancouver) within the group S. enterica subspecies enterica were identified. Two Salmonella types with different combinations were simultaneously found in specimens of T. h. hermanni. Most of the detected Salmonella types may represent a potential risk for operators in wildlife rescue centres. Abstract Monitoring of infections that may be transmitted to humans by animals in wildlife rescue centres is very important in order to protect the staff engaged in rehabilitation practices. Salmonella may be a natural inhabitant of the intestinal tract of turtles, rarely causing disease. This may represent a potential risk for humans, increasing the sanitary risk for operators in wildlife rescue centres. In this paper, the occurrence of non-typhoidal Salmonella among terrestrial turtles housed in a wildlife rescue centre in Southern Italy was investigated, in order to assess the serovars more frequently carried by turtles and identify those that may represent a risk for operators involved in wildlife management. Sixty-nine adult turtles (Testudo hermanni hermanni, T. h. boettgeri, T. graeca, and T. marginata) were tested. Detection and serotyping of Salmonella strains were performed according to ISO 6579-1 and ISO/TR 6579-3:2013, respectively. The distribution of Salmonella spp. was significantly higher in T. hermanni hermanni than in other species, independent of the age and gender of the animals. Two different Salmonella species, S. enterica and S. bongori, three S. enterica subspecies (enterica, diarizonae, salamae), and five different serovars (Hermannswerder, Abony, Ferruch, Richmond, Vancouver) within the group S. enterica subspecies enterica were identified. Different combinations of Salmonella types were simultaneously found in specimens of T. h. hermanni. Most of detected Salmonella types may represent a potential risk for public health. Adopting correct animal husbandry procedures and informing on potential sanitary risks may be useful for minimising the risk of transmission of Salmonella to workers involved in wildlife management.
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Liu WJ, Pan HJ, Song Y, Li Y, Wang YQ, Zou XN, Zhu DN, Gong YH, Xu YC. Investigation of an enteritis outbreak caused by Salmonella enterica serovar Aberdeen in China. Chin Med J (Engl) 2020; 133:1995-1996. [PMID: 32826468 PMCID: PMC7462223 DOI: 10.1097/cm9.0000000000000938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Indexed: 11/25/2022] Open
Affiliation(s)
- Wen-Juan Liu
- Department of Microbiology Laboratory, Yantai Center for Disease Control and Prevention, Yantai, Shandong 264003, China
| | - Hao-Jie Pan
- Department of Microbiology Laboratory, Fushan Center for Disease Control and Prevention, Yantai, Shandong 265500, China
| | - Yan Song
- Department of Microbiology Laboratory, Yantai Center for Disease Control and Prevention, Yantai, Shandong 264003, China
| | - Yan Li
- Department of Microbiology Laboratory, Yantai Center for Disease Control and Prevention, Yantai, Shandong 264003, China
| | - Yan-Qing Wang
- Department of Microbiology Laboratory, Yantai Center for Disease Control and Prevention, Yantai, Shandong 264003, China
| | - Xiao-Nan Zou
- Department of Microbiology Laboratory, Yantai Center for Disease Control and Prevention, Yantai, Shandong 264003, China
| | - Dong-Nan Zhu
- Department of Microbiology Laboratory, Yantai Center for Disease Control and Prevention, Yantai, Shandong 264003, China
| | - Yue-Hua Gong
- Department of Microbiology Laboratory, Yantai Center for Disease Control and Prevention, Yantai, Shandong 264003, China
| | - Ying-Chun Xu
- Department of Microbiology Laboratory, Yantai Center for Disease Control and Prevention, Yantai, Shandong 264003, China
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Uelze L, Borowiak M, Deneke C, Jacobs C, Szabó I, Tausch SH, Malorny B. First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep. Gut Pathog 2019; 11:48. [PMID: 31636715 PMCID: PMC6791114 DOI: 10.1186/s13099-019-0330-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 09/27/2019] [Indexed: 11/10/2022] Open
Abstract
Background The Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) (SASd) has been found to be host-adapted to sheep, with a high prevalence in sheep herds worldwide. Infections are usually sub-clinical, however the serovar has the potential to cause diarrhea, abortions and chronic proliferative rhinitis. Although occurrence and significance of SASd infections in sheep have been extensively studied, the genetic mechanism underlying this unusual host-adaptation have remained unknown, due to a lack of (a) available high-quality genome sequence(s). Results We utilized Nanopore and Illumina sequencing technologies to generate a de novo assembly of the 4.88-Mbp complete genome sequence of the SASd strain 16-SA00356, isolated from the organs of a deceased sheep in 2016. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity and host adaptation to sheep. Overall, we found a number of interesting genomic features such as several prophage regions, a VirB4/D4 plasmid and novel genomic islands. By comparing the genome of 16-SA00356 to other S. enterica serovars we found that SASd features an increased number of pseudogenes as well as a high level of genomic rearrangements, both known indicators of host-adaptation. Conclusions With this sequence, we provide the first complete and closed genome sequence of a SASd strain. With this study, we provide an important basis for an understanding of the genetic mechanism that underlie pathogenicity and host adaptation of SASd to sheep.
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Affiliation(s)
- Laura Uelze
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Maria Borowiak
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Carlus Deneke
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Cécile Jacobs
- Landeslabor Schleswig-Holstein, Max-Eyth-Straße 5, 24537 Neumünster, Germany
| | - István Szabó
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Simon H Tausch
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Burkhard Malorny
- 1Bundesinstitut für Risikobewertung (BfR), Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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Giner-Lamia J, Vinuesa P, Betancor L, Silva C, Bisio J, Soleto L, Chabalgoity JA, Puente JL, García-del Portillo F. Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256. BMC Genomics 2019; 20:99. [PMID: 30704413 PMCID: PMC6357384 DOI: 10.1186/s12864-018-5352-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 12/05/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasive human infections. The factors contributing to this unusual behavior are currently unknown. RESULTS We report here the genome features of two diarizonae strains, SBO13 and SBO27, isolated from endocervical tissue collected post-abortion and from cerebrospinal fluid of a newborn child, respectively, in the city of Santa Cruz, Bolivia. Although isolated six years apart, SBO27 in 2008 and SBO13 in 2014, both strains belong to the same sequence type 1256 (ST1256) and show a high degree of genome conservation sharing more than 99% of their genes, including the conservation of a ~ 10 kb plasmid. A prominent feature of the two genomes is the presence of 24 genomic islands (GIs), in addition to 10 complete Salmonella pathogenicity islands (SPI) and fragments of SPI-7, a pathogenicity island first reported in the human-adapted serovar Typhi. Some of the GIs identified in SBO13 and SBO27 harbor genes putatively encoding auto-transporters involved in adhesion, lipopolysaccharide modifying enzymes, putative toxins, pili-related proteins, efflux pumps, and several putative membrane cation transport related-genes, among others. These two Bolivian isolates also share genes encoding the type-III secretion system effector proteins SseK2, SseK3 and SlrP with other diarizonae sequence types (ST) mainly-associated with infections in humans. The sseK2, sseK3 and slrP genes were either absent or showing frameshift mutations in a significant proportion of genomes from environmental diarizonae isolates. CONCLUSIONS The comparative genomic study of two diarizonae strains isolated in Bolivia from human patients uncovered the presence of many genes putatively related to virulence. The statistically-significant acquisition of a unique combination of these functions by diarizonae strains isolated from humans may have impacted the ability of these isolates to successfully infect the human host.
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Affiliation(s)
- Joaquín Giner-Lamia
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Laura Betancor
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Claudia Silva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Julieta Bisio
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Lorena Soleto
- Ministerio de Salud de Bolivia, Centro Nacional de Enfermedades Tropicales (CENETROP), Santa Cruz, Bolivia
- Universidad Autónoma Gabriel René Moreno, Santa Cruz, Bolivia
| | - José A. Chabalgoity
- Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - José Luis Puente
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Francisco García-del Portillo
- Laboratorio de Patógenos Bacterianos Intracelulares, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
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Schnydrig P, Overesch G, Regli W, Bee A, Rodriguez-Campos S. Salmonella enterica subspecies diarizonae serovar 61:(k):1,5,(7) as cause of caprine abortion. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2018.07.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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