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Guzinski J, Tang Y, Chattaway MA, Dallman TJ, Petrovska L. Development and validation of a random forest algorithm for source attribution of animal and human Salmonella Typhimurium and monophasic variants of S. Typhimurium isolates in England and Wales utilising whole genome sequencing data. Front Microbiol 2024; 14:1254860. [PMID: 38533130 PMCID: PMC10963456 DOI: 10.3389/fmicb.2023.1254860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 12/22/2023] [Indexed: 03/28/2024] Open
Abstract
Source attribution has traditionally involved combining epidemiological data with different pathogen characterisation methods, including 7-gene multi locus sequence typing (MLST) or serotyping, however, these approaches have limited resolution. In contrast, whole genome sequencing data provide an overview of the whole genome that can be used by attribution algorithms. Here, we applied a random forest (RF) algorithm to predict the primary sources of human clinical Salmonella Typhimurium (S. Typhimurium) and monophasic variants (monophasic S. Typhimurium) isolates. To this end, we utilised single nucleotide polymorphism diversity in the core genome MLST alleles obtained from 1,061 laboratory-confirmed human and animal S. Typhimurium and monophasic S. Typhimurium isolates as inputs into a RF model. The algorithm was used for supervised learning to classify 399 animal S. Typhimurium and monophasic S. Typhimurium isolates into one of eight distinct primary source classes comprising common livestock and pet animal species: cattle, pigs, sheep, other mammals (pets: mostly dogs and horses), broilers, layers, turkeys, and game birds (pheasants, quail, and pigeons). When applied to the training set animal isolates, model accuracy was 0.929 and kappa 0.905, whereas for the test set animal isolates, for which the primary source class information was withheld from the model, the accuracy was 0.779 and kappa 0.700. Subsequently, the model was applied to assign 662 human clinical cases to the eight primary source classes. In the dataset, 60/399 (15.0%) of the animal and 141/662 (21.3%) of the human isolates were associated with a known outbreak of S. Typhimurium definitive type (DT) 104. All but two of the 141 DT104 outbreak linked human isolates were correctly attributed by the model to the primary source classes identified as the origin of the DT104 outbreak. A model that was run without the clonal DT104 animal isolates produced largely congruent outputs (training set accuracy 0.989 and kappa 0.985; test set accuracy 0.781 and kappa 0.663). Overall, our results show that RF offers considerable promise as a suitable methodology for epidemiological tracking and source attribution for foodborne pathogens.
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Affiliation(s)
- Jaromir Guzinski
- Animal and Plant Health Agency, Bacteriology Department, Addlestone, United Kingdom
| | - Yue Tang
- Animal and Plant Health Agency, Bacteriology Department, Addlestone, United Kingdom
| | - Marie Anne Chattaway
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency, London, United Kingdom
| | - Timothy J. Dallman
- Gastrointestinal Bacteria Reference Unit, UK Health Security Agency, London, United Kingdom
| | - Liljana Petrovska
- Animal and Plant Health Agency, Bacteriology Department, Addlestone, United Kingdom
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Heinemann L, Methner U, Klassen A, Donat K, Moog U. [Influence of breed and herd size on the intra-herd prevalence of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) in sheep]. Tierarztl Prax Ausg G Grosstiere Nutztiere 2023; 51:367-375. [PMID: 37722598 DOI: 10.1055/a-2121-2635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
SUBJECT AND AIM At present, only little information is available on the within-flock prevalence of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) (SASd) in sheep flocks in Germany as well as their possible influencing factors. The aim of the study was to investigate relationships between flock size, breed and within-flock prevalence. MATERIAL AND METHODS A total of 1610 clinically healthy ewes from 14 sheep flocks of 9 different breeds aged 2 to 12 years were microbiologically tested for SASd by nasal swab and fecal samples. Linear multivariable models were used to analyse the associations between within-flock prevalence and farm factors (flock size, breed) or detection frequencies in fecal or nasal swabs. RESULTS SASd was detected in all sheep flocks examined, with 75% of adults having at least one positive nasal or fecal result. In comparison to the 11 flocks in which commercial breeds were kept, the 3 flocks of landraces had a lower apparent within-flock prevalence (p=0.01). No association with herd size was evident. With respect to the age of the ewes, there was a negative relationship (p=0.05) with the frequency of detection of SASd in the nasal swab but not in the fecal swab. The health status and fertility performance of the flocks were in line with a normal range for commercial sheep flocks, with lambing losses of 5% to 10% and lambing scores of 130% to 158%. CONCLUSIONS Despite the high prevalence of SASd infections particularly within commercial breeds, there was no evidence of a relevant risk to sheep health. Compared with commercial breed flocks, a lower spread of SASd within flocks keeping landraces was evident. CLINICAL RELEVANCE Despite a high prevalence, infections with SASd are very unlikely to lead to clinical symptoms or disease. Regulation and monitoring of SASd in sheep are of low priority for animal health authorities.
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Affiliation(s)
- Lisa Heinemann
- Thüringer Landesamt für Verbraucherschutz (TLV), Bad Langensalza
| | - Ulrich Methner
- Friedrich-Loeffler Institut - Bundesforschungsinstitut für Tiergesundheit (FLI), Institut für bakterielle Infektionen und Zoonosen, Jena
| | - Anne Klassen
- Thüringer Tierseuchenkasse AdöR, Tiergesundheitsdienst, Jena
| | - Karsten Donat
- Thüringer Tierseuchenkasse AdöR, Tiergesundheitsdienst, Jena
- Klinik für Geburtshilfe, Gynäkologie und Andrologie der Groß- und Kleintiere mit Tierärztlicher Ambulanz, Justus-Liebig-Universität, Gießen
| | - Udo Moog
- Thüringer Tierseuchenkasse AdöR, Tiergesundheitsdienst, Jena
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Heinemann L, Methner U, Donat K, Moog U. [Longitudinal study on the time of infection of sheep lambs with Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7)]. Tierarztl Prax Ausg G Grosstiere Nutztiere 2023; 51:135-143. [PMID: 37567192 DOI: 10.1055/a-2097-7085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
OBJECTIVE Infections with Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) (SASd) are widespread in sheep. SASd is considered as host associated with low virulence. The aim of the study was to determine the time of infection of lambs after birth with consideration of the Salmonella status of the mother. MATERIAL AND METHODS Fecal and nasal swabs from 88 ewes of a flock with known SASd status but unknown intraherd prevalence were examined for SASd in the period of 6 weeks before the beginning of the lambing period. Fecal and nasal swabs from one female lamb from each of these ewes were also examined for SASd at 4-6 time points between the 4th and 50th day of life and at 7, 30 and 40 months of age. RESULTS In the first two weeks after birth, significantly more lambs were positive in the nasal swab than in the fecal swab. SASd positive nasal swabs were mainly found in lambs originating from ewes also positive in nasal swabs. 43 lambs remained SASd-negative until day 50 of age. There was no correlation between the SASd status of ewes and their off-spring. At 7 months of age, the number of animals with a positive detection of SASd increased significantly. 32% of the nasal swabs and 62% of the fecal samples were positive for SASd. CONCLUSIONS There is no rapid and intensive transmission of SASd from ewes to their offspring. Most likely, the infection begins by colonising the nasal mucosa of the lambs and does not cause any clinical symptoms. CLINICAL RELEVANCE Even with a high intraherd prevalence, infections with SASd are very unlikely to cause clinical symptoms.
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Affiliation(s)
- Lisa Heinemann
- Thüringer Landesamt für Verbraucherschutz, Bad Langensalza
| | - Ulrich Methner
- Friedrich-Loeffler Institut - Bundesforschungsinstitut für Tiergesundheit (FLI), Institut für bakterielle Infektionen und Zoonosen, Jena
| | - Karsten Donat
- Thüringer Tierseuchenkasse AdöR, Tiergesundheitsdienst, Jena
- Klinik für Geburtshilfe, Gynäkologie und Andrologie der Groß- und Kleintiere mit Tierärztlicher Ambulanz, Justus-Liebig-Universität Gießen
| | - Udo Moog
- Thüringer Tierseuchenkasse AdöR, Tiergesundheitsdienst, Jena
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Weber M, Zanolari P, Ardüser F, Stucki D, Akarsu H, Overesch G. Prevalence and antimicrobial resistance of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) in Swiss sheep flocks. Prev Vet Med 2022; 206:105697. [DOI: 10.1016/j.prevetmed.2022.105697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 11/28/2022]
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Casalino G, Bellati A, Pugliese N, Camarda A, Faleo S, Lombardi R, Occhiochiuso G, D'Onghia F, Circella E. Salmonella Infection in Turtles: A Risk for Staff Involved in Wildlife Management? Animals (Basel) 2021; 11:1529. [PMID: 34073932 DOI: 10.3390/ani11061529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [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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Chatzopoulos DC, Vasileiou NGC, Ioannidi KS, Katsafadou AI, Mavrogianni VS, Michael CK, Katsarou EI, Karavanis E, Papadopoulos N, Sbiraki A, Athanasiou LV, Billinis C, Fthenakis GC. Experimental Study of the Potential Role of Salmonella enterica subsp. diarizonae in the Diarrhoeic Syndrome of Lambs. Pathogens 2021; 10:pathogens10020113. [PMID: 33498660 PMCID: PMC7912070 DOI: 10.3390/pathogens10020113] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/20/2021] [Indexed: 11/16/2022] Open
Abstract
The objectives of this experimental work were the evaluation of the potential role of Salmonella enterica subsp. diarizonae in diarrhoeic syndrome in lambs and the investigation of facets of the pathogenesis of the infection. In total, 12 lambs were challenged orally on the first day of life, with a S. enterica subsp. diarizonae isolate from a clinical case of diarrhoeic syndrome. Sequential blood, faecal and buccal samples were collected from lambs and faecal and milk samples were taken from their dams. Lambs were euthanised 1, 2, 4, 7, 10, 14 and 21 days after challenge. Samples were processed for recovery of the challenge organism; they were also subjected to examination by PCR for detection of the invA gene. Tissue samples from lambs were also examined as above and histopathologically. S. enterica subsp. diarizonae was recovered from faecal samples of all lambs, in total, from 45/77 samples (median duration: 2.4 days post-inoculation). It was also recovered from buccal samples (10/77) from seven lambs (median duration: 0.8 days), and from tissue samples (small intestine, abomasum, liver, gallbladder) of nine lambs. It was recovered from two consecutive milk samples from the same ewe, but not from any faecal sample from ewes. The invA gene was detected in samples from all lambs (median duration: 5.5 days in faecal and 1.3 days in buccal samples), as well as in milk samples from three ewes. Histopathological findings included abomasitis with subepithelial presence of eosinophils, lymphocytes and plasma cells, consistently observed in all lambs. In the small intestine, salient lesions initially included distension and oedema of intestinal villi, leucocytic infiltration and hyperplasia of lymphoid nodules with apparent germinal centres; this was followed at later stages by atrophy and/or degeneration of the lymphoid tissue of the intestine with marked subepithelial infiltration of lymphocytes, plasma cells and eosinophils.
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Affiliation(s)
- Dimitris C. Chatzopoulos
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (K.S.I.); (A.I.K.); (V.S.M.); (C.K.M.); (E.I.K.); (L.V.A.); (C.B.)
| | | | - Katerina S. Ioannidi
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (K.S.I.); (A.I.K.); (V.S.M.); (C.K.M.); (E.I.K.); (L.V.A.); (C.B.)
| | - Angeliki I. Katsafadou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (K.S.I.); (A.I.K.); (V.S.M.); (C.K.M.); (E.I.K.); (L.V.A.); (C.B.)
| | - Vasia S. Mavrogianni
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (K.S.I.); (A.I.K.); (V.S.M.); (C.K.M.); (E.I.K.); (L.V.A.); (C.B.)
| | - Charalambia K. Michael
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (K.S.I.); (A.I.K.); (V.S.M.); (C.K.M.); (E.I.K.); (L.V.A.); (C.B.)
| | - Eleni I. Katsarou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (K.S.I.); (A.I.K.); (V.S.M.); (C.K.M.); (E.I.K.); (L.V.A.); (C.B.)
| | - Emmanouil Karavanis
- Histopathology Laboratory, 3rd Veterinary Hospital of Greek Army, 57000 Thessaloniki, Greece; (E.K.); (N.P.)
| | - Nikolaos Papadopoulos
- Histopathology Laboratory, 3rd Veterinary Hospital of Greek Army, 57000 Thessaloniki, Greece; (E.K.); (N.P.)
| | - Afroditi Sbiraki
- Veterinary Laboratory of Halkida, Hellenic State Veterinary Service, 34150 Halkida, Greece;
| | - Labrini V. Athanasiou
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (K.S.I.); (A.I.K.); (V.S.M.); (C.K.M.); (E.I.K.); (L.V.A.); (C.B.)
| | - Charalambos Billinis
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (K.S.I.); (A.I.K.); (V.S.M.); (C.K.M.); (E.I.K.); (L.V.A.); (C.B.)
| | - George C. Fthenakis
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece; (D.C.C.); (K.S.I.); (A.I.K.); (V.S.M.); (C.K.M.); (E.I.K.); (L.V.A.); (C.B.)
- Correspondence:
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Uelze L, Borowiak M, Flieger A, Simon S, Tausch SH, Malorny B. Complete Genome Sequence of Salmonella enterica subsp. diarizonae Serovar 61:k:1,5,(7) Strain 14-SA00836-0, Isolated from Human Urine. Microbiol Resour Announc 2020; 9:e00683-20. [PMID: 32883784 DOI: 10.1128/MRA.00683-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) is commonly associated with sheep. Occasionally, the serovar has been found to also infect humans. Here, we report the complete genome sequence of strain 14-SA00836-0, isolated from human urine. To our knowledge, this is the first reported complete genome sequence of this serovar isolated from a human clinical sample. Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) is commonly associated with sheep. Occasionally, the serovar has been found to also infect humans. Here, we report the complete genome sequence of strain 14-SA00836-0, isolated from human urine. To our knowledge, this is the first reported complete genome sequence of this serovar isolated from a human clinical sample.
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Figueras L, Ferrer LM, González JM, Bueso JP, Ramos JJ, Rubira I, Burian E, Lacasta D. Prevalence of Salmonella enterica subsp. diarizonae serotype 61:k:1:5:(7) in nasal secretions and stool of sheep flocks with and without cases of chronic proliferative rhinitis. Vet Microbiol 2020; 247:108767. [PMID: 32768219 DOI: 10.1016/j.vetmic.2020.108767] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 11/21/2022]
Abstract
Salmonella enterica subsp. diarizonae serotype 61: k: 1,5, (7) (SED) is a microorganism well adapted to sheep; however, it has also been described producing chronic proliferative rhinitis (CPR) in ovine. CPR causes a proliferative inflammation of the ventral nasal turbinates that may totally obstruct the nasal cavity. The main objective of the present study was to investigate the prevalence of SED in nostrils and stool of sheep without CPR clinical signs in commercial sheep farms of Spain with and without previous clinical cases of CPR. Five samplings were performed in 10 commercial sheep farms for one year. Samples from nostrils and faeces were taken from four animals without CPR visible clinical signs that belonged to four different age ranges at each farm visit. The prevalence of positive animals was 45.3 %, and the number of positive samples in nostrils was higher than in faeces (38.5 % vs 22.5 %). Only on one farm was no positive result obtained in the entire study. In almost all positive farms, sheep belonging to the youngest age ranges accounted for more than 50 % of positive isolates. Finally, farms with a previous diagnosis of CPR were 1.784 times more likely to have an animal with positive isolation than farms without a previous diagnosis. This could suggest that the infection pressure in the farm might favour the occurrence of clinical cases of the disease. However, further studies will be necessary to unravel why this saprophytic bacterium is able to cross the epithelial barrier causing severe rhinitis in certain animals.
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Mahmoud MAM, Megahed G, Yousef MS, Ali FAZ, Zaki RS, Abdelhafeez HH. Salmonella Typhimurium Triggered Unilateral Epididymo-Orchitis and Splenomegaly in a Holstein Bull in Assiut, Egypt: A Case Report. Pathogens 2020; 9:E314. [PMID: 32344573 DOI: 10.3390/pathogens9040314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 11/17/2022] Open
Abstract
This report illustrates, for the first time, a case of unilateral orchitis and epididymitis in a Holstein-Friesian bull, associated with Salmonella enterica infection (Salmonella enterica serovar Typhimurium). A one and a half-year-old Holstein-Friesian bull had arrived at the Veterinary Hospital of Assiut University suffering from anorexia accompanied with persistent fever, which did not respond to oxytetracycline and flunixin meglumine injection for 15 days. Gross examination revealed left scrotal enlargement (three times its normal size), heat sensation, and induration of the testis and epididymis, which was painful on external palpation. Microbiological and pathological examinations of the left testicle, epididymis, and spleen samples were performed. S. Typhimurium was recovered from the affected tissues and its critical virulence genes (stn, avrA and sopB) were identified. Pathological examination revealed a unilateral necrotizing intratubular pyogranulomatus orchitis and epididymitis with severe peri-orchitis. In addition, splenomegaly with a firm and large whitish nodular capsular structure associated with different stages of granulomatous reaction around the white and red pulp. To the authors' knowledge, this report is the first isolation of S. Typhimurium from the epididymis and testicles of a Holstein-Friesian bull. These results highlight the importance of including S. Typhimurium among the health disorders associated with stressful situations in bovine with orchitis and or/epididymitis. In Egypt, Salmonella spp. infection as being enzootic with high probability of dissemination should be considered one of genital health problems among cattle farms.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Methner U, Moog U. Occurrence and characterisation of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) in sheep in the federal state of Thuringia, Germany. BMC Vet Res 2018; 14:401. [PMID: 30558604 PMCID: PMC6296128 DOI: 10.1186/s12917-018-1741-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 12/07/2018] [Indexed: 11/28/2022] Open
Abstract
Background The occurrence of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) (SASd) and other Salmonella organisms in sheep in the German federal state of Thuringia was examined for the first time. Pooled faecal samples from 90 flocks located in this state were monitored. Results Only SASd was detected in 74 (82.2%) out of the 90 sheep herds, other Salmonella serovars were not identified. A positive correlation was found between the flock size and the detection probability of SASd. Despite the agent’s high prevalence, clinical symptoms of a disease exclusively due to SASd have not been observed. The SASd strains were characterised by macrorestriction analysis, antimicrobial testing and the biochemical profile. All strains were sensitive to 13 out of 14 antimicrobial substances and resistant to only sulfamethoxazole. The high number of macrorestriction groups of SASd strains indicated a low clonality of the serovar. Conclusions Data from sheep derived foods and public health data in Germany strongly suggest that the significance of SASd for public health is considerably lower than that of serovars belonging to Salmonella enterica subspecies enterica. For this reason and because of the low disease-causing potential of SASd in sheep, it is worthwile to consider a reduction in ongoing activities from combating to monitoring serovar 61: k: 1, 5, (7) in the sheep population.
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Affiliation(s)
- Ulrich Methner
- Institute of Bacterial Infections and Zoonoses at the Friedrich-Loeffler-Institute, Federal Research Institute for Animal Health, Naumburger Str. 96a, 07743, Jena, Germany.
| | - Udo Moog
- Thuringian Animal Diseases Fund, Victor-Goerttler-Str. 4, 07745, Jena, Germany
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Lamas A, Miranda JM, Regal P, Vázquez B, Franco CM, Cepeda A. A comprehensive review of non-enterica subspecies of Salmonella enterica. Microbiol Res 2018; 206:60-73. [DOI: 10.1016/j.micres.2017.09.010] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/22/2017] [Accepted: 09/26/2017] [Indexed: 12/11/2022]
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Stokar-regenscheit N, Overesch G, Giezendanner R, Roos S, Gurtner C. Salmonella enterica subsp . diarizonae serotype 61:k:1,5,(7) associated with chronic proliferative rhinitis and high nasal colonization rates in a flock of Texel sheep in Switzerland. Prev Vet Med 2017; 145:78-82. [DOI: 10.1016/j.prevetmed.2017.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 06/19/2017] [Accepted: 07/02/2017] [Indexed: 11/22/2022]
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Lacasta D, Figueras L, Bueso J, De las Heras M, Ramos J, Ferrer L, González J, Ruíz de Arcaute M, Ortín A, Marteles D, Navarro T, Fernández A. Experimental infection with Salmonella enterica subsp. diarizonae serotype 61:k:1,5,(7) in sheep: Study of cell mediated immune response. Small Rumin Res 2017. [DOI: 10.1016/j.smallrumres.2017.01.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Amagliani G, Petruzzelli A, Carloni E, Tonucci F, Foglini M, Micci E, Ricci M, Di Lullo S, Rotundo L, Brandi G. Presence of Escherichia coli O157, Salmonella spp., and Listeria monocytogenes in Raw Ovine Milk Destined for Cheese Production and Evaluation of the Equivalence Between the Analytical Methods Applied. Foodborne Pathog Dis 2016; 13:626-632. [DOI: 10.1089/fpd.2016.2159] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Giulia Amagliani
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Urbino (PU), Italy
| | | | - Elisa Carloni
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Urbino (PU), Italy
| | - Franco Tonucci
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Martina Foglini
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Eleonora Micci
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Mariagrazia Ricci
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Stefania Di Lullo
- Istituto Zooprofilattico Sperimentale dell'Umbria e delle Marche, Pesaro, Italy
| | - Luca Rotundo
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Urbino (PU), Italy
| | - Giorgio Brandi
- Dipartimento di Scienze Biomolecolari, Università degli Studi di Urbino Urbino (PU), Italy
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Ferreras MDC, Muñioz M, Pérez V, Benavides J, García-Pariente C, Fuertes M, Adúriz G, García-Marín JF. Unilateral Orchitis and Epididymitis Caused by Salmonella Enterica Subspecies Diarizonae Infection in a Ram. J Vet Diagn Invest 2016; 19:194-7. [PMID: 17402617 DOI: 10.1177/104063870701900211] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
A case of unilateral suppurative epididymo-orchitis associated with Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) infection is described in a 2-year-old ram. Gross lesions were characterized by severe enlargement of the scrotal contents, fibrous adhesions between testicular layers, coexistence of epididymal abscesses and foci of fibrinous exudate, and testicular atrophy. Microscopically, testicular and epididymal microabscesses and diffuse inflammatory infiltrates with abundant macrophages containing short Gram-negative rods were observed. Superimposed on the chronic lesions were fibrin deposits with clusters of neutrophils, as well as walled-off granulation tissue. Bacterial colonies were also identified in thrombosed spermatic cord vessels, scrotal lymph nodes, lung, and liver. S. enterica subsp. diarizonae serovar 61:k:1,5,(7) was isolated from the affected testis. To the authors' knowledge, this is the first report of infection of the testis and epididymis by Salmonella in rams. This organism must be taken into account in the differential diagnosis of ovine genital infections.
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Affiliation(s)
- Ma del Carmen Ferreras
- Dpto. Patologia Animal: Medicina Animal (Anatomia Patológica), Facultad de Veterinaria, Universidad de León, Campus de Vegazana, s/n, 24071 León, Spain.
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Chatzopoulos DC, Sarrou S, Vasileiou NGC, Ioannidi KS, Peteinaki E, Valiakos G, Tsokana CN, Papadopoulos E, Spyrou V, Mavrogianni VS, Giannakopoulos A, Sbiraki A, Lacasta D, Bueso JP, Athanasiou LV, Billinis C, Fthenakis GC. Dissemination of intestinal pathogens between lambs and puppies in sheep farms. Small Rumin Res 2016; 141:5-10. [PMID: 32288209 DOI: 10.1016/j.smallrumres.2016.06.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 02/24/2016] [Accepted: 06/09/2016] [Indexed: 11/22/2022]
Abstract
Rotavirus was detected in samples from lambs with diarrhoea. Salmonella enterica subsp. diarizonae was isolated in samples from lambs with diarrhoea. Antibiotic resistance was detected in >60% of Escherichia coli strains isolated in the study. Escherichia coli with identical antibacterial resistance were detected in lambs and puppies.
Objectives of the present work were (i) to confirm pathogens implicated in cases of diarrhoea in newborn and young lambs in sheep farms in Greece and (ii) to investigate a possible relation in dissemination of pathogens between lambs and dogs present in the farm. Work was carried out in 22 sheep farms, with (i) flock size over 150 animals, (ii) presence of clinical signs of diarrhoea in lambs in the flock and (iii) close and continuous contact and movement of shepherd dogs within the animal shed of each farm. Faecal sample collection from lambs was performed within 48 h of onset of clinical signs and prior to administration of any antimicrobial or antiparasitic medication to lambs. Faecal samples were also collected from puppies in the farm. In total, samples were collected from 126 lambs and 58 puppies. Samples were processed by using established techniques for isolation of bacteria, detection of viruses and observation of protozoan oocycts. Escherichia coli isolates obtained during the study, were tested for antimicrobial resistance against a variety of antimicrobial agents. In total, 236 bacterial isolates were recovered from faecal samples of lambs and 165 isolates from faecal samples of puppies. E. coli was the most frequently isolated microorganism: 104 isolates from lambs and 109 isolates from puppies were recovered. Other bacteria isolated were Enterobacter spp., Proteus spp., Klebsiella spp., (lambs and puppies), Clostridium perfringens, Citrobacter freundi, Salmonella enterica subsp. diarizonae (only lambs) and Streptococcus spp. (only puppies). Group A Rotavirus was detected in samples from lambs (2.5%) and Parvovirus in samples from puppies (5%). Cryptosporidium spp. oocysts were observed in samples from lambs and puppies. This is the first report of isolation of S. enterica subsp. diarizonae and of detection of Rotavirus from lambs in Greece. Rates of E. coli isolates from puppies resistant to antimicrobial agents were, in general, smaller than respective rates in isolates from lambs. Two pairs of isolates from the same farm (one from a lamb and one from a puppy) with identical patterns of resistance to antimicrobial agents were detected, which provides some evidence in support of a hypothesis that members of each pair might possibly have been spread from one animal species to the other.
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Mashooq M, Kumar D, Niranjan AK, Agarwal RK, Rathore R. Development and evaluation of probe based real time loop mediated isothermal amplification for Salmonella: A new tool for DNA quantification. J Microbiol Methods 2016; 126:24-9. [PMID: 27130353 DOI: 10.1016/j.mimet.2016.04.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/23/2016] [Accepted: 04/25/2016] [Indexed: 11/26/2022]
Abstract
A one step, single tube, accelerated probe based real time loop mediated isothermal amplification (RT LAMP) assay was developed for detecting the invasion gene (InvA) of Salmonella. The probe based RT LAMP is a novel method of gene amplification that amplifies nucleic acid with high specificity and rapidity under isothermal conditions with a set of six primers. The whole procedure is very simple and rapid, and amplification can be obtained in 20min. Detection of gene amplification was accomplished by amplification curve, turbidity and addition of DNA binding dye at the end of the reaction results in colour difference and can be visualized under normal day light and in UV. The sensitivity of developed assay was found 10 fold higher than taqman based qPCR. The specificity of the RT LAMP assay was validated by the absence of any cross reaction with other members of enterobacteriaceae family and other gram negative bacteria. These results indicate that the probe based RT LAMP assay is extremely rapid, cost effective, highly specific and sensitivity and has potential usefulness for rapid Salmonella surveillance.
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Affiliation(s)
- Mohmad Mashooq
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar 243122, UP, India
| | - Deepak Kumar
- Division of Veterinary Biotechnology, Indian Veterinary Research Institute, Izatnagar 243122, UP, India
| | - Ankush Kiran Niranjan
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar 243122, UP, India
| | - Rajesh Kumar Agarwal
- Division of Bacteriology & Mycology, Indian Veterinary Research Institute, Izatnagar 243122, UP, India
| | - Rajesh Rathore
- CADRAD, Indian Veterinary Research Institute, Izatnagar 243122, UP, India.
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Vela AI, Casas-Díaz E, Fernández-Garayzábal JF, Serrano E, Agustí S, Porrero MC, Sánchez del Rey V, Marco I, Lavín S, Domínguez L. Estimation of cultivable bacterial diversity in the cloacae and pharynx in Eurasian griffon vultures (Gyps fulvus). Microb Ecol 2015; 69:597-607. [PMID: 25388757 DOI: 10.1007/s00248-014-0513-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 10/08/2014] [Indexed: 06/04/2023]
Abstract
In this work, we describe the biodiversity of cloacal and pharynx culture-based bacteria (commensal and pathogenic), in 75 Eurasian griffon vultures (Gyps fulvus) from two geographic areas. We address the question of whether the cultivable microbiota of vultures is organised into assemblages occurring by chance. In addition, we assess bacterial diversity in both anatomic regions and geographic areas. Bacterial diversity was represented by 26 Gram-negative and 20 Gram-positive genera. The most common genera were Escherichia, Enterococcus, Staphylococcus, Clostridium and Lactococcus. Escherichia coli and Enterococcus faecalis were the most common species in cloacal and pharyngeal samples. Staphylococcus and Erysipelothrix were isolated from the pharynx and Salmonella and Corynebacterium from the cloacae, and no Campylobacter was isolated from the cloacal swabs. Ten cloacal swabs were positive for Salmonella, of which five isolates were Salmonella enterica serotype 4,(5),12:i:-, one isolate was S. enterica serotype Derby, three isolates were S. enterica serotype 61:k:1,5,7 and one isolate was S. enterica serotype Infantis. The null modelling approach revealed that the commensal bacteria of vultures are not structured in assemblages. On the other hand, differences in bacterial genus and species richness between cloacal and pharyngeal samples or between geographic areas were clear, with the pharynx in vultures from both geographic areas being richer. The results of this study indicate also that vultures can serve as a reservoir of certain pathogenic zoonotic bacteria. The dissemination of these zoonotic pathogens in wildlife could be prevented by periodic sanitary surveys.
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Affiliation(s)
- Ana I Vela
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, 28040, Madrid, Spain
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Sörén K, Lindblad M, Jernberg C, Eriksson E, Melin L, Wahlström H, Lundh M. Changes in the risk management of Salmonella enterica subspecies diarizonae serovar 61:(k):1, 5, (7) in Swedish sheep herds and sheep meat due to the results of a prevalence study 2012. Acta Vet Scand 2015; 57:6. [PMID: 25644506 PMCID: PMC4324828 DOI: 10.1186/s13028-015-0096-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 01/15/2015] [Indexed: 11/16/2022] Open
Abstract
Background The prevalence of Salmonella in food producing animals is very low in Sweden due to rigorous control programmes. However, no active surveillance is in place in sheep. The authorities decided to perform a prevalence study in sheep herds because findings at slaughter indicated that sheep associated S. diarizonae (S. enterica subspecies diarizonae serovar 61:(k):1, 5, (7)) might be common in sheep. Sampling was stratified by herd size in two groups, small herds with ≤ 30 animals and large herds with > 30 animals. In each stratum, 237 herds were selected at random. Faecal samples received from 244 out of the 474 randomly selected herds were analysed. Results A total of 40 of 100 (40%) of large herds and 17 of 144 (12%) of small herds were positive. The overall adjusted prevalence was 17.6% (95% CI, 12.9-22.2). Sheep associated S. diarizonae was detected in all counties (n = 21). Scientific opinions and an evaluation of on-farm control measures performed concluded that the impact of sheep associated S. diarizonae on human health is very low, and that risk management measures applied in response to findings of sheep associated S. diarizonae in sheep or sheep meat can be expected to have very little impact on reducing risks to human health. As a result, Swedish authorities decided to make an exemption for sheep associated Salmonella diarizonae in sheep and sheep meat in the current Salmonella control measures. Conclusions Sheep associated S. diarizonae is endemic in Swedish sheep herds. It is more common in large herds and not limited to certain parts of the country. The responsible authorities concluded that current risk management actions regarding sheep associated S. diarizonae in sheep and sheep meat are not proportional to the risk. This is the first time in the history of the Swedish Salmonella control programme that an exemption from the legislation has been made for a specific serovar. If there is any future indication of an increasing risk, due to e.g. change in the pathogenicity or development of antimicrobial resistance, the risk assessment will be re-evaluated and control measures reinforced if needed.
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Lacasta D, Ferrer LM, Ramos JJ, Bueso JP, Borobia M, Ruiz de Arcaute M, Figueras L, González-Sainz JM, De Las Heras M. Chronic proliferative rhinitis associated with Salmonella enterica subspecies diarizonae serovar 61:k:1, 5, (7) in sheep in Spain. J Comp Pathol 2012; 147:406-9. [PMID: 22572396 DOI: 10.1016/j.jcpa.2012.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 03/05/2012] [Accepted: 03/19/2012] [Indexed: 11/18/2022]
Abstract
A chronic proliferative rhinitis in sheep associated with Salmonella enterica subspecies diarizonae serovar 61:k:1, 5, (7) is described. Ten adult sheep from eight traditionally managed Rasa Aragonesa flocks located in Aragon (Spain) were studied. Clinical signs began with bilateral thick mucus nasal discharge, wheezing and snoring and progressed to partial or complete obstruction of the nostrils. Necropsy examination revealed swollen ventral nasal turbinates with a roughened mucosal surface partially covered by small polyps. Histopathology revealed chronic proliferative rhinitis with a predominant population of neutrophils that infiltrated the mucosal epithelium. Plasma cells and macrophages were present in the lamina propria. Organisms expressing Salmonella antigen immunohistochemically were detected within epithelial cells. Salmonella enterica subspecies diarizonae serovar 61:k:1, 5, (7) was isolated as a sole microorganism from nasal swabs taken from five animals. The implication of finding this bacterium in various diseases in sheep and its role as a potential zoonosis are discussed.
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Affiliation(s)
- D Lacasta
- Departamento de Patología Animal, Universidad de Zaragoza, Zaragoza, Spain
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Bonke R, Wacheck S, Bumann C, Thum C, Stüber E, König M, Stephan R, Fredriksson-ahomaa M. High prevalence of Salmonella enterica subsp. diarizonae in tonsils of sheep at slaughter. Food Res Int 2012; 45:880-4. [DOI: 10.1016/j.foodres.2011.01.050] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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