New molecular tools for meningitis diagnostics in Ethiopia - a necessary step towards improving antimicrobial prescription.

BACKGROUND: Meningitis remains a top cause of premature death and loss of disability-adjusted life years in low-income countries. In resource-limited settings, proper laboratory diagnostics are often scarce and knowledge about national and local epidemiology is limited. Misdiagnosis, incorrect treatment and overuse of antibiotics are potential consequences, especially for viral meningitis. METHODS: A prospective study was conducted over three months in a teaching hospital in Ethiopia with limited laboratory resources. Cerebrospinal fluid (CSF) samples from patients with suspected meningitis were analysed using a multiplex PCR-based system (FilmArray, BioFire), in addition to basic routine testing with microscopy and culture. Clinical data, as well as information on treatment and outcome were collected. RESULTS: Two hundred and eighteen patients were included; 117 (54%) neonates (0-29 days), 63 (29%) paediatrics (1 month-15 years) and 38 (17%) adults (≥16 years). Of 218 CSF samples, 21 (10%) were PCR positive; 4% in neonates, 14% in paediatrics and 18% in adults. Virus was detected in 57% of the PCR positive samples, bacteria in 33% and fungi in 10%. All CSF samples that were PCR positive for a bacterial agent had a white cell count ≥75 cells/mm3 and/or turbid appearance. The majority (90%) of patients received more than one antibiotic for treatment of the meningitis episode. There was no difference in the mean number of different antibiotics received or in the cumulative number of days with antibiotic treatment between patients with a microorganism detected in CSF and those without. CONCLUSIONS: A rapid molecular diagnostic system was successfully implemented in an Ethiopian setting without previous experience of molecular diagnostics. Viral meningitis was diagnosed for the first time in routine clinical practice in Ethiopia, and viral agents were the most commonly detected microorganisms in CSF. This study illustrates the potential of rapid diagnostic tests for reducing antibiotic usage in suspected meningitis cases. However, the cost of consumables for the molecular diagnostic system used in this study limits its use in low-income countries.

Prevalence of udder pathogens in milk samples from Norwegian dairy cows recorded in a national database in 2019 and 2020.

BACKGROUND: Identification of aetiological agents of mastitis in dairy cattle is important for herd management of udder health. In Norway, results from mastitis diagnostics are systematically recorded in a central database, so that the dairy industry can follow trends in the recorded frequency of udder pathogens and antimicrobial resistance patterns at national level. However, bacteriological testing of milk samples is based on voluntary sampling, and data are therefore subject to some bias. The aim of this study was to examine the prevalence of udder pathogens in Norwegian dairy cows by analysing data from the national routine mastitis diagnostics and to explore how routines for sampling and diagnostic interpretations may affect the apparent prevalence of different bacterial pathogens. We also assessed associations between udder pathogen findings and the barn- and milking systems of the herds. RESULTS: The most frequently detected major udder pathogens among all milk samples submitted for bacterial culture (n = 36,431) were Staphylococcus aureus (24.5%), Streptococcus dysgalactiae (13.3%) and Streptococcus uberis (9.0%). In the subset of samples from clinical mastitis (n = 7598); Escherichia coli (14.5%) was the second most frequently detected pathogen following S. aureus (27.1%). Staphylococcus epidermidis (10.0%), Corynebacterium bovis (9.4%), and Staphylococcus chromogenes (6.0%) dominated among the minor udder pathogens. Non-aureus staphylococci as a group, identified in 39% of the sampling events, was the most frequently identified udder pathogen in Norway. By using different definitions of cow-level bacterial diagnoses, the distribution of minor udder pathogens changed. Several udder pathogens were associated with the barn- and milking system but the associations were reduced in strength when data were analysed from farms with a comparable herd size. S. aureus was associated with tiestall housing, E. coli and S. dysgalactiae were associated with freestall housing, and S. epidermidis was associated with automatic milking systems. Only 2.5% of the 10,675 tested S. aureus isolates were resistant to benzylpenicillin. Among the 2153 tested non-aureus staphylococci, altogether 34% were resistant to benzylpenicillin. CONCLUSIONS: This study presents the recorded prevalence of udder pathogens in Norway over a two-year period and assesses the possible impact of the sampling strategies, diagnostic methods and diagnostic criteria utilized in Norway, as well as associations with different housing and milking systems. The national database with records of results from routine mastitis diagnostics in Norway provides valuable information about the aetiology of bovine mastitis at population level and can reveal shifts in the distribution and occurrence of udder pathogens.

Closed Genome Sequences of Providencia alcalifaciens Isolates from Dogs.

Eight Providencia alcalifaciens isolates from eight different dogs in Norway with acute hemorrhagic diarrhea were sequenced. Based on Illumina and Oxford Nanopore Technologies sequencing, all of the genomes were complete and closed after hybrid assembly.

Whole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.

Streptococcus dysgalactiae (SD) is an emerging pathogen in human and veterinary medicine, and is associated with several host species, disease phenotypes and virulence mechanisms. SD has traditionally been divided into the subspecies dysgalactiae (SDSD) and subsp. equisimilis (SDSE), but recent molecular studies have indicated that the phylogenetic relationships are more complex. Moreover, the genetic basis for the niche versatility of SD has not been extensively investigated. To expand the knowledge about virulence factors, phylogenetic relationships and host-adaptation strategies of SD, we analyzed 78 SDSD genomes from cows and sheep, and 78 SDSE genomes from other host species. Sixty SDSD and 40 SDSE genomes were newly sequenced in this study. Phylogenetic analysis supported SDSD as a distinct taxonomic entity, presenting a mean value of the average nucleotide identity of 99%. Bovine and ovine associated SDSD isolates clustered separately on pangenome analysis, but no single gene or genetic region was uniquely associated with host species. In contrast, SDSE isolates were more heterogenous and could be delineated in accordance with host. Although phylogenetic clustering suggestive of cross species transmission was observed, we predominantly detected a host restricted distribution of the SD-lineages. Furthermore, lineage specific virulence factors were detected, several of them located in proximity to hotspots for integration of mobile genetic elements. Our study indicates that SD has evolved to adapt to several different host species and infers a potential role of horizontal genetic transfer in niche specialization.

Longitudinal Study of the Bulk Tank Milk Microbiota Reveals Major Temporal Shifts in Composition.

Introduction of microbial contaminations in the dairy value chain starts at the farm level and the initial microbial composition may severely affect the production of high-quality dairy products. Therefore, understanding the farm-to-farm variation and longitudinal shifts in the composition of the bulk tank milk microbiota is fundamental to increase the quality and reduce the spoilage and waste of milk and dairy products. In this study, we performed a double experiment to study long- and short-term longitudinal shifts in microbial composition using 16S rRNA gene amplicon sequencing. We analyzed milk from 37 farms, that had also been investigated two years earlier, to understand the stability and overall microbial changes over a longer time span. In addition, we sampled bulk tank milk from five farms every 1-2 weeks for up to 7 months to observe short-term changes in microbial composition. We demonstrated that a persistent and farm-specific microbiota is found in bulk tank milk and that changes in composition within the same farm are mostly driven by bacterial genera associated with mastitis (e.g., Staphylococcus and Streptococcus). On a long-term, we detected that major shift in milk microbiota were not correlated with farm settings, such as milking system, number of cows and quality of the milk but other factors, such as weather and feeding, may have had a greater impact on the main shifts in composition of the bulk tank milk microbiota. Our results provide new information regarding the ecology of raw milk microbiota at the farm level.

Molecular detection and genotype characterization of Streptococcus dysgalactiae from sheep flocks with outbreaks of infectious arthritis.

Outbreaks of infectious arthritis in young lambs are a growing concern for the Norwegian sheep industry. In other countries, Streptococcus dysgalactiae subspecies dysgalactiae (SDSD) is a frequent cause of such outbreaks. The objectives of this study were to investigate the causes of outbreaks of infections arthritis in Norwegian sheep flocks, and describe the sources, colonization patterns and genetic diversity of SDSD in affected and healthy sheep flocks. Almost 2000 samples from joints, animal body sites and the indoor environment were analysed by qPCR and culturing for SDSD, which was detected in 27 of 30 flocks. The proportion of positive samples was greater in outbreak flocks compared to healthy flocks. Altogether, SDSD was detected in 48 % of the samples from lambs, 27 % of the samples from ewes and 48 % of environmental samples. A relatively high proportion (67 %) of ear tag wounds were SDSD positive. These wounds may provide a port of entry for SDSD. Whole genome sequencing revealed a clonal distribution of SDSD-isolates, and identified four different multi locus sequence types (STs), among which two STs, ST454 and ST531, dominated. These STs were found in geographically distant flocks. ST454 was almost exclusively found in outbreak flocks. The current study points to skin, wounds and mucous membranes of animals as the main reservoir of SDSD in sheep flocks. However, a significantly higher proportion of SDSD-positive environmental samples in outbreak flocks compared to healthy flocks suggests that also indirect transmission may play a role.

An Official Outbreak Investigation of Acute Haemorrhagic Diarrhoea in Dogs in Norway Points to Providencia alcalifaciens as a Likely Cause.

An outbreak investigation was initiated in September 2019, following a notification to the Norwegian Food Safety Authority (NFSA) of an unusually high number of dogs with acute haemorrhagic diarrhoea (AHD) in Oslo. Diagnostic testing by reporting veterinarians had not detected a cause. The official investigation sought to identify a possible common cause, the extent of the outbreak and prevent spread. Epidemiological data were collected through a survey to veterinarians and interviews with dog owners. Diagnostic investigations included necropsies and microbiological, parasitological and toxicological analysis of faecal samples and food. In total, 511 dogs with acute haemorrhagic diarrhoea were registered between 1 August and 1 October. Results indicated a common point source for affected dogs, but were inconclusive with regard to common exposures. A notable finding was that 134 of 325 faecal samples (41%) cultured positive for Providencia alcalifaciens. Whole genome sequencing (WGS) of 75 P. alcalifaciens isolates from 73 dogs revealed that strains from 51 dogs belonged to the same WGS clone. Findings point to P. alcalifaciens as implicated in the outbreak, but investigations are needed to reveal the pathogenic potential of P. alcalifaciens in dogs and its epidemiology.

Flock-level risk factors for outbreaks of infectious arthritis in lambs, Norway 2018.

BACKGROUND: Outbreaks of infectious arthritis in young lambs associated with Streptococcus dysgalactiae subspecies dysgalactiae (SDSD) lead to reduced animal welfare, increased use of antibiotics and economic losses for sheep farmers. Understanding risk factors is essential when developing strategies to prevent such outbreaks. This questionnaire-based cross-sectional study classified sheep flocks of respondents as cases or controls. Flock-level risk factors for outbreaks of infectious arthritis were assessed using a multivariable logistic regression model. RESULTS: Eighty-four of 1498 respondents (5.6%) experienced an outbreak of infectious arthritis in their flock in 2018, the year of study. Factors associated with a higher risk of outbreak were larger flock size (OR 1.3, 95% CI 1.1-1.4, per 100 lambs), plastic mesh flooring in the lambing pen (OR 3.0, 95% CI 1.7-5.3) and a lambing percentage greater than 200 (OR 2.0, 95% CI 1.1-3.5). Flocks where farmers observed infections around the ear tags of lambs also had an increased risk of outbreak (OR 2.6, 95% CI 1.6-4.3). CONCLUSIONS: The risk factors identified in this study are characteristic of modern and intensively managed sheep farms in Norway. A distinguishing feature of Norwegian sheep farming is winter housing and indoor lambing. One might expect that this in itself is a risk factor because of high stocking densities during lambing. However, outbreaks of infectious arthritis in young lambs are reported by the industry to be a more recent phenomenon. The current study indicates that intensification of indoor management systems with larger flocks and higher production per ewe may predispose to outbreaks. The results provide a basis for further studies on transmission dynamics of SDSD in sheep flocks with indoor lambing.

Experimental infection of cattle with ovine Dichelobacter nodosus isolates.

BACKGROUND: Dichelobacter nodosus is the main causative agent of ovine footrot, and there are strong indications that the bacterium can be transferred to cattle grazing on the same pasture as sheep. The aim of this study was to investigate if benign and virulent D. nodosus strains isolated from sheep can be transferred to the interdigital skin of cattle under experimental conditions. Further, we wanted to observe the impact of such infection on bovine foot health, and test the effect of topical chlortetracycline (Cyclo spray(®): Eurovet) on the infection. FINDINGS: Six heifers were included in the study. After an initial 18-day maceration period, three heifers were inoculated on one single foot with a benign strain and three with a virulent strain by adding bacterial suspension in a bandage. The bandages were left on for 17 days, and when removed, D. nodosus was isolated from all six heifers. All six heifers developed interdigital dermatitis. In five of the heifers D. nodosus organisms were demonstrated within the epidermis. Twenty-four days after treatment with chlortetracycline all heifers were negative by cultivation, but tested positive for D. nodosus by polymerase chain reaction (PCR). Two of the six heifers still tested positive for D. nodosus by PCR 49 days after treatment. After 70 days, all heifers tested negative for D. nodosus. CONCLUSIONS: This study shows that both virulent and benign D. nodosus strains originating from sheep can be transferred to naïve heifers under experimental conditions. Further, the study supports the hypothesis that infections with virulent D. nodosus in cattle are associated with interdigital dermatitis. No conclusion regarding the treatment of D. nodosus infection with chlortetracycline was possible.

Possible cross-infection of Dichelobacter nodosus between co-grazing sheep and cattle.

BACKGROUND: The aim of this study was to investigate possible cross-infection of Dichelobacter nodosus in Norwegian farms practising co-grazing of sheep and cattle. METHODS: Thirteen farms practising co-grazing of sheep and cattle were included in this descriptive study: five farms with a history of severe ovine footrot (Group I) and eight farms with free-stall housing of cattle and signs of mild or no footrot in sheep (Group II). Sampling for PCR detection of D. nodosus was performed from animals in all farms, and clinical claw examination of sheep and cattle was performed in Group II. D. nodosus positive samples were analysed by a multiplex PCR method that detects variants of the fimA gene corresponding to D. nodosus serogroups A through I. RESULTS: D. nodosus serogroup A was identified more frequently in sheep from farms with a history of severe footrot (Group I) versus from Group II, and in most of the farms with a history of severe footrot there was a coexistence of D. nodosus serogroup A in sheep and cattle. In one farm heel horn erosion and dermatitis emerged in cattle after co-grazing with sheep suffering from severe footrot where D. nodosus serogroup A was detected. Six months later heel horn erosion and dermatitis were still diagnosed, and D. nodosus serogroup A was identified. Out of the 16 D. nodosus positive sheep samples from Group II, ten of the samples were positive by the fimA serogrouping PCR. Among these 10 samples all serogroups except G were detected. All the D. nodosus serogroups detected in sheep were also present in the corresponding cattle herds. CONCLUSION: The clinical findings and the coexistence of the same serogroups in co-grazing sheep and cattle could indicate cross-infection. However, further research including isolation of the bacterial strains, virulence-testing and genetic identification, is needed.

An outbreak of Escherichia coli O103:H25 - bacteriological investigations and genotyping of isolates from food.

During the spring of 2006, a national disease outbreak caused by Shiga toxin-producing Escherichia coli (STEC) O103:H25 was investigated in Norway. At the time of the outbreak the Norwegian School of Veterinary Science was the national reference laboratory for E. coli O157 in food, and the microbiological investigations to identify the food source were performed there. Food- and environmental samples (n=931) were collected by the Norwegian Food Safety Authorities following two different hypotheses i) that minced meat was the source of STEC, and ii) that fermented sausage was the source of STEC. Twenty seven food samples, all collected following the latter hypothesis contained eae-positive E. coli O103:H25, but none of these were stx-positive. By PFGE it was shown that isolates from one particular type of fermented sausage "morr sausage 1" were identical to the isolates from patients. Samples of sheep meat that were linked epidemiologically to meat used for sausage production also contained isolates identical or closely related to patient strains. The presented study underpins epidemiological indications that fermented sausage was the source of the outbreak, but points specifically to one particular brand of sausage as the source.