Evidence of members of the Chlamydiales in bovine abortions in England and Wales

Machine learning modeling to predict causes of infectious abortions and perinatal mortalities in cattle

A plethora of infectious and non-infectious causes of bovine abortions and perinatal mortalities (APM) have been reported in literature. However, due to financial limitations or a potential zoonotic impact, many laboratories only offer a standard analytical panel, limited to a preestablished number of pathogens. To improve the cost-efficiency of laboratory diagnostics, it could be beneficial to design a targeted analytical approach for APM cases, based on maternal and environmental characteristics associated with the prevalence of specific abortifacient pathogens. The objective of this retrospective observational study was to implement a machine learning pipeline (MLP) to predict maternal and environmental factors associated with infectious APM. Our MLP based on a greedy ensemble approach incorporated a standard tuning grid of four models, applied on a dataset of 1590 APM cases with a positive diagnosis that was achieved by analyzing an extensive set of abortifacient pathogens. Production type (dairy/beef), gestation length, and season were successfully predicted by the greedy ensemble, with a modest prediction capacity which ranged between 63 and 73 %. Besides the predictive accuracy of individual variables, our MLP hierarchically identified predictor importance causes of associated environmental/maternal characteristics of APM. For instance, in APM cases that happened in beef cows, season at APM (spring/summer) was the most important predictor with a relative importance of 24 %. Furthermore, at the last trimester of gestation Trueperella pyogenes and Neospora caninum were the most important predictors of APM with a relative importance of 22 and 17 %, respectively. Interestingly, herd size came out as the most relevant predictor for APM in multiparous dams, with a relative importance of 12 %. Based on these and other mix of predicted environmental/maternal and pathogenic potential causes, it could be concluded that implementing our MLP may be beneficial to design a more cost-effective, case-specific diagnostic approach for bovine APM cases at the diagnostic laboratory level.

The role of chlamydiales in adverse pregnancy outcome: a community-based nested case-control study

OBJECTIVES

Over the last decades, the Chlamydiales order has expanded and a new group of Chlamydia-related bacteria has emerged, covering species like Waddlia (W.) chondrophila associated with bovine abortion. However, it is unknown whether they compromise human reproduction like Chlamydia (C.) trachomatis. We therefore aimed to investigate the association between vaginal colonisation of selected species of the Chlamydiales order with spontaneous abortion, preterm birth, and, animal exposure.

METHODS

Pregnant women were enrolled at the nuchal translucency scan or when admitted for suspected miscarriage at Aarhus University Hospital, Denmark. Cases were defined as spontaneous abortion <22 weeks and preterm birth <37 weeks. Controls were defined as term birth ≥37 weeks. Vaginal samples from 1203 women were assessed using C.trachomatis, W.chondrophila and pan-Chlamydiales specific real-time PCRs targeting the 16S rRNA gene.

RESULTS

A total of 1120 women of primarily Caucasian ancestry were enrolled, including 193 spontaneous abortions, 88 preterm births, and 839 term births. After sequencing for verification, the prevalence of Chlamydiales was 3/193 (1.6%, 95%CI 0.5-4.8) in women experiencing spontaneous abortion, 2/88 (2.3%, 95%CI 0.6-8.9) in women with preterm birth, and 20/839 (2.4%, 95%CI 1.6-3.7) in women giving birth at term. Thus, Chlamydiales infection was neither significantly associated with spontaneous abortion (OR 0.68, 95%CI 0.15-2.01) nor preterm birth (OR 1.02, 95%CI 0.15-3.60) compared to women giving birth at term. Amplicons from the pan-Chlamydiales assay revealed close sequence homology and were primarily identified as uncultured Chlamydiales bacteria.

CONCLUSIONS

Among Danish pregnant women, the prevalence of Chlamydiales was low and not associated with adverse pregnancy outcomes.

Presence of DNA from Chlamydia-like organisms in the nasal cavities of grey seal pups (Halichoerus grypus) and three different substrates present in a breeding colony

Background

Chlamydia-like organisms (CLO) have been found to be present in many environmental niches, including human sewage and agricultural run-off, as well as in a number of aquatic species worldwide. Therefore, monitoring their presence in sentinel wildlife species may be useful in assessing the wider health of marine food webs in response to habitat loss, pollution and disease. We used nasal swabs from live (n = 42) and dead (n = 50) pre-weaned grey seal pups and samples of differing natal substrates (n = 8) from an off-shore island devoid of livestock and permanent human habitation to determine if CLO DNA is present in these mammals and to identify possible sources.

Results

We recovered CLO DNA from 32/92 (34.7%) nasal swabs from both live (n = 17) and dead (n = 15) seal pups that clustered most closely with currently recognised species belonging to three chlamydial families: Parachlamydiaceae (n = 22), Rhabdochlamydiaceae (n = 6), and Simkaniaceae (n = 3). All DNA positive sediment samples (n = 7) clustered with the Rhabdochlamydiaceae. No difference was found in rates of recovery of CLO DNA in live versus dead pups suggesting the organisms are commensal but their potential as opportunistic secondary pathogens could not be determined.

Conclusion

This is the first report of CLO DNA being found in marine mammals. This identification warrants further investigation in other seal populations around the coast of the UK and in other areas of the world to determine if this finding is unique or more common than shown by this data. Further investigation would also be warranted to determine if they are present as purely commensal organisms or whether they could also be opportunistic pathogens in seals, as well as to investigate possible sources of origin, including whether they originated as a result of anthropogenic impacts, including human waste and agricultural run-off.

Retrospective study of factors associated with bovine infectious abortion and perinatal mortality

Abortion and perinatal mortality, leading causes of economic loss in cattle industry, are the consequence of both non-infectious and a wide range of infectious causes. However, the relative contribution of pathogens to bovine abortion and perinatal mortality is poorly documented, since available studies involved only a limited number of pathogens. Therefore, the objectives of the present monitoring study were to determine the prevalence of infectious agents associated with bovine abortion and perinatal mortality, and to identify differences in production type, gestation length, parity and seasonality by using mixed effect models (logistic regression). A pre-established sampling protocol based on the collection of the aborted fetus/calf and a corresponding maternal blood sample, involving diagnostic testing for 10 pathogens, was performed. At least one potential causal agent of the abortion or perinatal mortality was detected in 39 % of cases. In these diagnosed cases, Neospora caninum was the most detected pathogen, followed by Trueperella pyogenes, BVDv, Escherichia coli, and Aspergillus fumigatus. Neospora caninum [odds ratio (OR): 0.4; 95 % confidence interval (CI): 0.3-0.7] and Aspergillus fumigatus (OR: 0.1; 95 % CI: 0.1-0.3) were detected less in late versus early gestation. Aspergillus fumigatus was less common in dairy in comparison to beef abortion cases (OR: 0.2; 95 % CI: 0.1-0.6). Winter was associated with a lower positivity for Neospora caninum and BVDv in comparison to warmer seasons. Despite extensive diagnostic testing, an etiological diagnosis was not reached in 61 % of cases, highlighting the need for even more extensive (non-)infectious disease testing or more accurate tests.

Role of Infection and Immunity in Bovine Perinatal Mortality: Part 1. Causes and Current Diagnostic Approaches

While non-infectious causes are more commonly diagnosed in cases of bovine perinatal mortality (PM), the proportion caused by infections is highly variable between studies (~5-35%); the reasons for this variation, and possible underestimation, are discussed. The most important pathogen-specific infectious causes of PM are bacteria (in particular, Bacillus licheniformis and Leptospira spp.), viruses (in particular BVDv) and a parasite (Neospora caninum). However, co-infection may occur in a small proportion of cases and in many cases no single pathogen is detected but gross or microscopic lesions of an inflammatory response are identified. Diagnosis is complicated by the criteria required to establish exposure, infection and causation. Additionally, pathogens can be classified as primary or secondary though such differentiation can be arbitrary. The majority of infectious cases of PM are due to in utero infections but postnatal infections (0-2 days) can also cause PM. Diagnosis of infectious PM is based on a systematic investigation of the herd health history and dam and cohort sampling and examination of the perinate and its placenta. Gross and histopathologic examinations and maternal/herd and perinate serology form the basis of current infectious PM investigations.

Investigation of bovine abortion and stillbirth/perinatal mortality - similar diagnostic challenges, different approaches

This pracademic paper reviews current bovine foetopathy (abortion and stillbirth) case definitions, reporting and triage, and causes and time-of-death and proposes veterinary practitioner-focused investigative standard operating procedures (SOPs). Issues of under- and over-triage and intra-institutional SOP harmonisation are also discussed. It is proposed that an ‘observable abortion’ (120–260 days of gestation) is a more practitioner-friendly definition of abortion for reporting and benchmarking purposes and that the term ‘peristillbirth’ can replace stillbirth and perinatal mortality. Diagnosis of bovine foetopathy involves an investigative triad of the farmer, veterinary practitioner and the veterinary diagnostic laboratory. However, the poor sensitivity of abortion reporting undermines the value of currently adopted scanning/passive surveillance; parallel active surveillance/sentinel herd models should also be employed. The approach to abortion investigation differs from that of peristillbirth. The former should include collecting a herd and case history, examination and sampling of dam and cohorts and sampling of the foetus and placenta. A sample selection decision tree is provided to assist test selection. In peristillbirths, non-infectious and periparturient causes-of-death are more important hence the anamnesis must focus on peristillbirth risk factors and calving management. The foetopsy, while including the sampling menu appropriate to aborted foetuses, must also include a detailed internal and external examination of the carcass for lesions indicative of periparturient causes-of-death. In addition, for aborted foetuses the time-of-death is not important as the foetus is generally not viable; however, for the peristillbirth the time-of-death is critical as it provides useful information for the farmer to address modifiable risk factors and to alter their perinatal management. Reporting of the ultimate cause-of-death is more useful to prevent future abortions and peristillbirths though the proximate cause-of-death is often reported in the absence of a complete clinical anamnesis. Finally, the common reasons for diagnosis not reached (DNR) and the limitations of current investigative approaches are discussed.

Sero-Epidemiological Study of Selected Zoonotic and Abortifacient Pathogens in Cattle at a Wildlife-Livestock Interface in South Africa

A cross sectional sero-epidemiological study was conducted on cattle in a communal farming area adjacent to Kruger National Park at a wildlife-livestock interface in South Africa. A total of 184 cattle were screened for exposure to 5 abortifacient or zoonotic pathogens, namely Coxiella burnetii, Toxoplasma gondii, Chlamydophila abortus, Neospora caninum, and Rift Valley fever virus (RVFV) using enzyme-linked immunosorbent assays. In addition, the virus neutralization test was used to confirm the presence of antibodies to RVFV. The seroprevalence of C. burnetii, T. gondii, C. abortus, N. caninum, and RVFV antibodies was 38.0%, 32.6%, 20.7%, 1.6%, and 0.5%, respectively, and varied between locations (p < 0.001). Seroprevalence of C. burnetii and T. gondii was highly clustered by location (intraclass correlation coefficient [ICC] = 0.57), and that of C. abortus moderately so (ICC = 0.11). Seroprevalence was not associated with sex or age for any pathogen, except for C. abortus, for which seroprevalence was positively associated with age (p = 0.01). The predominant mixed infections were C. burnetii and T. gondii (15.2%) and C. burnetii, T. gondii, and C. abortus (13.0%). The serological detection of the five abortifacient pathogens in cattle indicates the potential for economic losses to livestock farmers, health impacts to domestic animals, transmission across the livestock-wildlife interface, and the risk of zoonotic transmission. This is the first documentation of T. gondii infection in cattle in South Africa, while exposure to C. burnetii, C. abortus, and N. caninum infections is being reported for the first time in cattle in a wildlife-livestock interface in the country.

A Review on Chlamydial Diseases in Animals: Still a Challenge for Pathologists?

Chlamydiae have a worldwide distribution causing a wide range of diseases in human hosts, livestock, and companion animals as well as in wildlife and exotic species. Moreover, they can persist in their hosts as asymptomatic infections for extended periods of time. The introduction of molecular techniques has revolutionized the Chlamydia field by expanding the host range of known chlamydial species but also by discovering new species and even new families of bacteria in the broader order Chlamydiales. The wide range of hosts, diseases, and tissues affected by chlamydiae complicate the diagnosis such that standard diagnostic approaches for these bacteria are rare. Bacteria of the Chlamydiales order are small and their inclusions are difficult to detect by standard microscopy. With the exception of avian and ovine chlamydiosis, macroscopic and/or histologic changes might not be pathognomic or indicative for a chlamydial infection or even not present at all. Moreover, detection of chlamydial DNA in specimens in the absence of other methods or related pathological lesions questions the significance of such findings. The pathogenic potential of the majority of recently identified Chlamydia-related bacteria remains largely unknown and awaits investigation through experimental or natural infection models including histomorphological characterization of associated lesions. This review aims to summarize the historical background and the most important developments in the field of animal chlamydial research in the past 5 years with a special focus on pathology. It will summarize the current nomenclature, present critical thoughts about diagnostics, and give an update on chlamydial infections in domesticated animals such as livestock, companion animals and birds, as well as free-ranging and captive wild animals such as reptiles, fish, and marsupials.

Amplicon sequencing of bacterial microbiota in abortion material from cattle

Abortions in cattle have a significant economic impact on animal husbandry and require prompt diagnosis for surveillance of epizootic infectious agents. Since most abortions are not epizootic but sporadic with often undetected etiologies, this study examined the bacterial community present in the placenta (PL, n = 32) and fetal abomasal content (AC, n = 49) in 64 cases of bovine abortion by next generation sequencing (NGS) of the 16S rRNA gene. The PL and AC from three fetuses of dams that died from non-infectious reasons were included as controls. All samples were analyzed by bacterial culture, and 17 were examined by histopathology. We observed 922 OTUs overall and 267 taxa at the genus level. No detectable bacterial DNA was present in the control samples. The microbial profiles of the PL and AC differed significantly, both in their composition (PERMANOVA), species richness and Chao-1 (Mann-Whitney test). In both organs, Pseudomonas was the most abundant genus. The combination of NGS and culture identified opportunistic pathogens of interest in placentas with lesions, such as Vibrio metschnikovii, Streptococcus uberis, Lactococcus lactis and Escherichia coli. In placentas with lesions where culturing was unsuccessful, Pseudomonas and unidentified Aeromonadaceae were identified by NGS displaying high number of reads. Three cases with multiple possible etiologies and placentas presenting lesions were detected by NGS. Amplicon sequencing has the potential to uncover unknown etiological agents. These new insights on cattle abortion extend our focus to previously understudied opportunistic abortive bacteria.

Herd-level prevalence of selected endemic infectious diseases of dairy cows in Great Britain

To implement appropriate and effective disease control programs at the national level, up-to-date and unbiased information on disease frequency is needed. The aim of this study was to estimate the prevalence of selected endemic infectious diseases in the population of dairy herds in Great Britain. Bulk milk tank (BMT) samples from 225 randomly selected dairy farms, stratified by region and herd size, were tested for antibodies against bovine viral diarrhea virus (BVDV), bovine herpesvirus type 1, Mycobacterium avium ssp. paratuberculosis, Leptospira Hardjo, Salmonella spp., Coxiella burnetii, Fasciola hepatica, Neospora caninum, and Ostertagia ostertagi. Furthermore, the presence of BVDV, C. burnetii, and Chlamydia-like organisms was determined by PCR. The apparent herd prevalence was estimated as a weighted proportion of positive herds. The true prevalence was calculated when a test was used with known test characteristics for the cut-off value used. Among unvaccinated herds, the true prevalence of BMT antibodies against BVDV was estimated at 66% [95% confidence interval (CI): 56-77%], M. avium ssp. paratuberculosis 68% (95% CI: 59-77%), bovine herpesvirus type 1 62% (95% CI: 52-73%), Leptospira Hardjo 47% (95% CI: 34-60%), and Salmonella spp. 48% (95% CI: 39-56%). The apparent prevalence of BMT antibodies against C. burnetii was 80% (95% CI: 75-85%), F. hepatica 55% (95% CI: 48-62%), N. caninum 46% (95% CI: 38-54%), and O. ostertagi 95% (95% CI: 91-98%). The BVDV, C. burnetii, and Chlamydia-like antigens were detected in 5 (95% CI: 2-9%), 29 (95% CI: 21-36%), and 31% (95% CI: 24-38%) of herds, respectively. Our results show that dairy cows across GB are frequently exposed to the studied pathogens, which are endemic at high levels with some geographical variations. These prevalence estimates provide a much-needed basis to assess whether nationwide control programs for the studied pathogens are justified by their potential economic, environmental, and public health implications. Should surveillance and control programs be initiated, the estimates presented here are a baseline against which progress can be assessed.

Chlamydia related bacteria (Chlamydiales) in early pregnancy: community-based cohort study

Objectives

Serological case–control studies suggest that certain chlamydia-related bacteria (Chlamydiales) which cause cows to abort may do the same in humans. Chlamydiales include Waddlia chondrophila, Chlamydia abortus and Chlamydia trachomatis. Data on prevalence of Chlamydiales in pregnancy are sparse. Using stored urine samples from a carefully characterised cohort of 847 newly pregnant women recruited from 37 general practices in London, UK, we aimed to investigate the prevalence and types of Chlamydiales infections. We also explored possible associations with miscarriage or spontaneous preterm birth.

Methods

Samples were tested using W. chondrophila and pan-Chlamydiales specific real-time PCRs targeting the 16S rRNA gene. Samples positive on either PCR were subjected to DNA sequencing and C. trachomatis PCR.

Results

The overall prevalence of Chlamydiales was 4.3% (36/847, 95% CI 3.0% to 5.8%). The prevalence of W. chondrophila was 0.6% (n = 5), C. trachomatis 1.7% (n = 14), and other Chlamydiales species 2.0% (n = 17). Infection with C. trachomatis was more common in women aged <25, of black ethnicity or with bacterial vaginosis, but this did not apply to W. chondrophila or other Chlamydiales.

Follow up was 99.9% at 16 weeks gestation and 90% at term. No infection was significantly associated with miscarriage at ≤12 weeks (prevalence 10%, 81/827) or preterm birth <37 weeks (prevalence 4%, 23/628). Of 25 samples sequenced, seven (28%) were positive for Chlamydiales bacterium sequences associated with respiratory tract infections in children.

Conclusion

In the first study to use the pan-Chlamydiales assay on female urine samples, 4% of pregnant women tested positive for Chlamydiales, including species known to be pathogenic in mothers and neonates.

Rhabdochlamydia spp. in an Oregon raptor

PCR-based approach was used to examine the rate of Chlamydia positivity in raptors from wild bird rehabilitation centers in Oregon. Three of 82 birds were identified as positive for Chlamydia with this PCR. Sequence analysis of 16S ribosomal DNA from 2 of these birds confirmed the presence of DNA from phylum Chlamydiae. One bird was positive for Chlamydia psittaci in both choanal and cloacal swabs. The second bird, a louse-infested red-tailed hawk, had evidence of choanal colonization by "Candidatus Rhabdochlamydia" spp. Our study describes evidence of this Chlamydia-like organism in the United States. This survey also suggests that the carriage rate of C. psittaci is low in raptors in Oregon wild bird rehabilitation centers, and that care must be taken in the design of PCR primers for phylum Chlamydiae such that colonization by insect endosymbionts is not mistaken for an infection by known chlamydial pathogens.