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

[Influence of breed and herd size on the intra-herd prevalence of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) in sheep]

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.

[Longitudinal study on the time of infection of sheep lambs with Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7)]

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.

Wild Duck (Anas platyrhynchos) as a Source of Antibiotic-Resistant Salmonella enterica subsp. diarizonae O58—The First Report in Poland

The “One Health” approach increasingly demonstrates the global spread of pathogenic microorganisms and their antimicrobial resistance in the environment, both in animals and humans. Salmonella enterica subsp. diarizonae is nowadays very often isolated from cold-blooded reptiles to a lesser extent from sheep, but unfortunately more and more often from humans. However, there are a few studies describing the isolation of Salmonella enterica subsp. diarizonae from migratory wild birds. The mallard duck (Anas platyrhynchos), a wild animal that traverses the continent of Eurasia, can be an excellent indicator of the spread of intestinal microbes as well as their resistance to antibiotics. This is the first report of the Salmonella enterica subsp. diarizonae detection in Poland in a migrating mallard duck. This research presented the identification difficulties associated with the isolation of Salmonella enterica subsp. diarizonae using three different biochemical tests and advanced serology tests. At the same time, we detected very high antimicrobial resistance in the isolated strain. By using the minimum inhibitory concentration (MIC) method, it was found that the isolated strain of S. enterica subsp. diarizonae has high antibiotic resistance against 14 of the 33 tested antimicrobials agents. The resistance genes that have been identified in S. enterica subsp. diarizonae include aadA, strA/strB, and bla_TEM.

Comparative genomics of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) reveals lineage-specific host adaptation of ST432

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.

Genetic features of Salmonella enterica subspecies diarizonae serovar 61:k:1,5 isolated from abortion cases in sheep, United States, 2020

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.

Complete Genome Sequence of Salmonella enterica subsp. diarizonae Serovar 61:k:1,5,(7) Strain 14-SA00836-0, Isolated from Human Urine

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.

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

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.

First complete genome sequence and comparative analysis of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) indicates host adaptation traits to sheep

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.

An ADAMTS3 missense variant is associated with Norwich Terrier upper airway syndrome

In flat-faced dog breeds, air resistance caused by skull conformation is believed to be a major determinant of Brachycephalic Obstructive Airway Syndrome (BOAS). The clinical presentation of BOAS is heterogeneous, suggesting determinants independent of skull conformation contribute to airway disease. Norwich Terriers, a mesocephalic breed, are predisposed to Upper Airway Syndrome (UAS), a disease whose pathological features overlap with BOAS. Our health screening clinic examined and scored the airways of 401 Norwich terriers by laryngoscopy. Genome-wide association analyses of UAS-related pathologies revealed a genetic association on canine chromosome 13 (rs9043975, p = 7.79x10^-16). Whole genome resequencing was used to identify causal variant(s) within a 414 kb critical interval. This approach highlighted an error in the CanFam3.1 dog assembly, which when resolved, led to the discovery of a c.2786G>A missense variant in exon 20 of the positional candidate gene, ADAM metallopeptidase with thrombospondin type 1 motif 3 (ADAMTS3). In addition to segregating with UAS amongst Norwich Terriers, the ADAMTS3 c.2786G>A risk allele frequency was enriched among the BOAS-susceptible French and (English) Bulldogs. Previous studies indicate that ADAMTS3 loss of function results in lymphoedema. Our results suggest a new paradigm in the understanding of canine upper airway disease aetiology: airway oedema caused by disruption of ADAMTS3 predisposes dogs to respiratory obstruction. These findings will enhance breeding practices and could refine the prognostics of surgical interventions that are often used to treat airway obstruction.

Respiratory diseases are prevalent across dog breeds, particularly in brachycephalic breeds such as the Bulldog and French bulldog. The flat facial conformation of these breeds has long been assumed to be the major predisposing factor, however, the underlying genetics of their respiratory condition has never been elucidated. We became interested in the Norwich Terrier, a breed presenting with many of the same respiratory disease symptoms as the Bulldog. A distinction, however, is that the Norwich terrier is not considered to be a brachycephalic breed and so presented an opportunity to dissociate respiratory disease from head conformation. We performed a genome-wide association analysis for respiratory disease severity in the Norwich Terrier and resolved an association on chromosome 13 to a missense mutation in ADAMTS3. Variants in this gene were previously shown to cause an oedematous phenotype–a disease characteristic in the airways of affected Norwich Terriers and brachycephalic dogs alike. We screened over 100 breeds for the ADAMTS3 variant and found that it is enriched in the Norwich Terrier, Bulldog and French Bulldog. This discovery changes how we view respiratory disease predisposition in the dog, offers potential genetic screens and highlights a new biological function for ADAMTS3.

Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

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.

Occurrence and characterisation of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) in sheep in the federal state of Thuringia, Germany

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.