The Spirochete Brachyspira pilosicoli, Enteric Pathogen of Animals and Humans

Pathogen Detection and Resistome Analysis in Healthy Shelter Dogs Using Whole Metagenome Sequencing

According to the Humane Society, 25 to 40 percent of pet dogs in the United States are adopted from animal shelters. Shelter dogs can harbor bacterial, viral, fungal, and protozoal pathogens, posing risks to canine and human health. These bacterial pathogens may also carry antibiotic resistance genes (ARGs), serving as a reservoir for antimicrobial resistance (AMR) transmission. This study aimed to utilize whole metagenome sequencing (WMS) to screen for microbial pathogens and assess the resistome in healthy shelter dogs. Fecal samples from 58 healthy shelter dogs across 10 shelters in Kentucky, Tennessee, and Virginia were analyzed using WMS. Genomic DNA was extracted, and bioinformatics analyses were performed to identify pathogens and ARGs. The WMS detected 53 potentially zoonotic or known pathogens including thirty-eight bacterial species, two protozoa, five yeast species, one nematode, four molds, and three viruses. A total of 4560 ARGs signatures representing 182 unique genes across 14 antibiotic classes were detected. Tetracycline resistance genes were most abundant (49%), while β-lactam resistance genes showed the highest diversity with 75 unique ARGs. ARGs were predominantly detected in commensal bacteria; however, nearly half (18/38, 47.4%) of known bacterial pathogens detected in this study carried ARGs for resistance to one or more antibiotic classes. This study provides evidence that healthy shelter dogs carry a diverse range of zoonotic and antibiotic-resistant pathogens, posing a transmission risk through fecal shedding. These findings highlight the value of WMS for pathogen detection and AMR surveillance, informing therapeutic and prophylactic strategies to mitigate the transmission of pathogens among shelter dog populations and the risk associated with zoonoses.

Metabarcoding study of potential pathogens and zoonotic risks associated with dog feces in Seoul, South Korea

BACKGROUND

A significant portion of South Korea's population, approximately a quarter, owns pets, with dogs being the most popular choice among them. However, studies analyzing the fecal organism communities of dogs in South Korea are lacking, and limited efforts have been exerted to identify pathogens with potential zoonotic implications. Therefore, this study aimed to investigate potential pathogens using metabarcoding analysis and evaluate the risk of zoonotic diseases in dog feces in Seoul, South Korea.

METHODOLOGY

Fecal samples were collected from both pet and stray dogs in the Mapo district of Seoul. Next-generation sequencing (NGS) was utilized, employing 16S rRNA amplicon sequencing to identify prokaryotic pathogens, and 18S rRNA amplicon sequencing for eukaryotic pathogens. The data obtained from the QIIME2 pipeline were subjected to various statistical analyses to identify different putative pathogens and their compositions.

PRINCIPAL FINDINGS

Significant variations in microbiota composition were found between stray and pet dogs, and putative prokaryotic and eukaryotic pathogens were identified. The most prevalent putative bacterial pathogens were Fusobacterium, Helicobacter, and Campylobacter. The most prevalent putative eukaryotic pathogens were Giardia, Pentatrichomonas, and Cystoisospora. Interestingly, Campylobacter, Giardia, and Pentatrichomonas were found to be significantly more prevalent in stray dogs than in pet dogs. The variation in the prevalence of potential pathogens in dog feces could be attributed to environmental factors, including dietary variances and interactions with wildlife, particularly in stray dogs. These factors likely contributed to the observed differences in pathogen occurrence between stray and pet dogs.

CONCLUSIONS/SIGNIFICANCE

This study offers valuable insights into the zoonotic risks associated with dog populations residing in diverse environments. By identifying and characterizing putative pathogens in dog feces, this research provides essential information on the impact of habitat on dog-associated pathogens, highlighting the importance of public health planning and zoonotic risk management.

Detection of Serum IgG Specific for Brachyspira pilosicoli and "Brachyspira canis" in Dogs

Brachyspira pilosicoli (B. pilosicoli) is a pathogen in pigs, poultry, and humans causing colitis, diarrhea, and poor growth rates. Its role as a canine pathogen is controversial, and the seroprevalence of specific IgG antibodies against B. pilosicoli in dogs is unknown. A further, not yet officially recognized Brachyspira species in dogs is "Brachyspira canis" ("B. canis"), which is proposed to be apathogenic. This study evaluates enzyme-linked immunosorbent assays (ELISAs) measuring serum IgG antibodies specific for B. pilosicoli or "B. canis" and investigates levels of specific IgG antibodies against B. pilosicoli and "B. canis" in a cohort of clinical patients presented at an animal referral clinic. These ELISAs use detergent-extracted antigens from B. pilosicoli and "B. canis". To increase analytic specificity, we precipitated the antigens with trichloroacetic acid (TCA) to isolate and concentrate the respective protein fraction. Our results indicate that a large number of serum IgG antibodies bind to shared epitopes of detergent-extracted antigens of the two spirochaetes. Our data also suggest that dogs might not only carry B. pilosicoli but also have "B. canis"-specific serum IgG antibodies.

Human intestinal spirochetosis: an entity associated with sexual transmitted infections

INTRODUCTION

Human intestinal spirochetosis (HIE) is a poorly studied clinical entity with variable clinical manifestations. However, in recent years it has gained special relevance because an increasing number of cases have been described in people living with HIV (PWH) and in patients with a history of sexually transmitted infections (STI) or immunosuppression.

METHODS

Retrospective review of all HIE cases identified in a tertiary level hospital (Hospital Universitario la Paz, Madrid) between 2014 and 2021.

RESULTS

36 Cases of HIE were identified. Most cases corresponded to males (94%) with a median age of 45 years. 10 patients (29.4%) were PWH and 20 (56%) were men who had sex with men. Although the clinical manifestations were very heterogeneous, the most frequent was chronic diarrhea (47%), and up to 25% of the subjects had clinical proctitis. 39% percent of patients had been diagnosed with an STI in the previous two years, this characteristic being more frequent in PWH (90% vs. 28%; p < 0.01) than in patients without HIV infection. The STI most frequently associated with a diagnosis of HIE was syphilis (31%).

CONCLUSION

HIE is frequently diagnosed with other STIs and affects mostly men who have sex with men, which supports that this entity could be considered as a new STI.

Brachyspira in dogs: risk factors of shedding in central Germany and longitudinal study of an infected kennel

BACKGROUND

Brachyspira (B.) pilosicoli is a zoonotic pathogen, able to infect different animal species such as pigs, poultry, and rodents, causing intestinal spirochetosis. An association of gastrointestinal clinical signs, such as diarrhea, with the isolation of B. pilosicoli from fecal samples or rectal swabs has not been proven in dogs. Other Brachyspira species commonly isolated from dogs, such as "B. canis" and "B. pulli", are considered commensals. This study investigated the occurrence of different Brachyspira species in rectal swabs and fecal samples in an independent canine cohort in central Germany. These included samples from shelter dogs, hunting dogs, and dogs presenting at regional small animal practices with various clinical signs. Data about the dogs, including potential risk factors for Brachyspira isolation, were obtained using a standardized questionnaire. The study also longitudinally investigated a colony of Beagle dogs for Brachyspira over 5 years.

RESULTS

The rate of Brachyspira spp. isolation was 11% and included different Brachyspira species ("B. canis", "B. pulli", and B. pilosicoli). "B. canis" was detected in 18 dogs, whereas B. pilosicoli was only isolated from 1 dog in the independent cohort (not including the Beagle colony). Risk factors for shedding Brachyspira and "B. canis" were being less than 1 year of age and shelter origin. Gastrointestinal signs were not associated with the shedding of Brachyspira. B. pilosicoli and "B. canis" were isolated from several dogs of the same Beagle colony in 2017 and again in 2022, while Brachyspira was not isolated at multiple sampling time points in 2021.

CONCLUSIONS

Shedding of B. pilosicoli in dogs appears to be uncommon in central Germany, suggesting a low risk of zoonotic transmission from dogs. Commensal status of "B. canis" and "B. pulli" is supported by the results of this study. Findings from the longitudinal investigation of the Beagle colony agree with an asymptomatic long-term colonization of dogs with "B. canis" and B. pilosicoli and suggest that introducing new animals in a pack can trigger an increased shedding of B. pilosicoli.

Colonizing the Unlikely: Brachyspira in an Immunocompetent Patient

Chronic diarrhea is a common condition that medical professionals often encounter. We present an unusual case of chronic diarrhea in a relatively young, immunocompetent man that was attributed to Brachyspira. The patient's clinical presentation was not specific, and he underwent workup for common infectious, inflammatory, and autoimmune causes, all unrevealing. During colonoscopy, no abnormalities were detected; however, histopathology revealed the presence of Brachyspira. Following a course of metronidazole, the patient showed marked improvement in his diarrhea. It is worth noting that the patient's social history did not align with the established risk factors mentioned in the existing literature.

Identification of Terminal βGlcNAc on Brachyspira Species in Human Intestinal Spirochetosis

Human intestinal spirochetosis (HIS) is a colorectal bacterial infection caused by the Brachyspira species. Griffonia simplicifolia-II (GS-II) is a lectin specific to terminal α/βGlcNAc residues. Here, we investigated terminal βGlcNAc residues in the context of HIS infection using GS-II-horseradish peroxidase staining and HIK1083 immunostaining specific to terminal αGlcNAc residues. Fourteen of 15 HIS cases were GS-II-positive on the bacterial body. No cases showed HIK1083 positivity. The percentage of bacterial bodies staining positively for GS-II based on comparison with anti-Treponema immunostaining was ≤30% in seven cases, 30-70% in two, and >70% in six. Of 15 HIS cases analyzed, none were comorbid with tubular adenomas, and three were comorbid with sessile serrated lesions (SSLs). To determine the species of spirochete infected, the B. aalborgi-specific or B. pilosicoli-specific NADPH oxidase genes were amplified by PCR. After direct sequencing of the PCR products, all nine cases in which PCR products were observed were found to be infected with B. aalborgi alone. These results indicate that the HIS bacterial body, especially of B. aalborgi, is characterized by terminal βGlcNAc and also indicate that terminal βGlcNAc on the HIS bacterial body is associated with HIS preference for SSLs.

BPP43_05035 is a Brachyspira pilosicoli cell surface adhesin that weakens the integrity of the epithelial barrier during infection

The anaerobic spirochete Brachyspira causes intestinal spirochetosis, characterized by the intimate attachment of bacterial cells to the colonic mucosa, potentially leading to symptoms such as diarrhea, abdominal pain, and weight loss. Despite the clinical significance of Brachyspira infections, the mechanism of the interaction between Brachyspira and the colon epithelium is not known. We characterized the molecular mechanism of the B. pilosicoli-epithelium interaction and its impact on the epithelial barrier during infection. Through a proteomics approach, we identified BPP43_05035 as a candidate B. pilosicoli surface protein that mediates bacterial attachment to cultured human colonic epithelial cells. The crystal structure of BPP43_05035 revealed a globular lipoprotein with a six-bladed beta-propeller domain. Blocking the native BPP43_05035 on B. pilosicoli, either with a specific antibody or via competitive inhibition, abrogated its binding to epithelial cells, which required cell surface-exposed N-glycans. Proximity labeling and interaction assays revealed that BPP43_05035 bound to tight junctions, thereby increasing the permeability of the epithelial monolayer. Extending our investigation to humans, we discovered a downregulation of tight junction and brush border genes in B. pilosicoli-infected patients carrying detectable levels of epithelium-bound BPP43_05035. Collectively, our findings identify BPP43_05035 as a B. pilosicoli adhesin that weakens the colonic epithelial barrier during infection.

Fast detection of slender bodies in high density microscopy data

Computer-aided analysis of biological microscopy data has seen a massive improvement with the utilization of general-purpose deep learning techniques. Yet, in microscopy studies of multi-organism systems, the problem of collision and overlap remains challenging. This is particularly true for systems composed of slender bodies such as swimming nematodes, swimming spermatozoa, or the beating of eukaryotic or prokaryotic flagella. Here, we develop a end-to-end deep learning approach to extract precise shape trajectories of generally motile and overlapping slender bodies. Our method works in low resolution settings where feature keypoints are hard to define and detect. Detection is fast and we demonstrate the ability to track thousands of overlapping organisms simultaneously. While our approach is agnostic to area of application, we present it in the setting of and exemplify its usability on dense experiments of swimming Caenorhabditis elegans. The model training is achieved purely on synthetic data, utilizing a physics-based model for nematode motility, and we demonstrate the model's ability to generalize from simulations to experimental videos.

Effect of Panax ginseng and Fructus Mume on Intestinal Barrier and Gut Microbiota in Rats with Diarrhea

Panax ginseng and Fructus mume (Renshen Wumei in Chinese, RW) are natural medicines with high nutritional and pharmacological value. They have been widely used together in China to treat gastrointestinal diseases, especially persistent diarrhea, but the potential mechanisms remain elusive. In this study, a diarrhea model was established in rats using a 30% aqueous extract of senna. The therapeutic effects of RW were evaluated by recording the prevalence of loose stools, the diarrhea index, and histopathological changes in colon tissue. The levels of mucins, tight junction (TJ) proteins, inflammatory cytokines, and phosphoinositide 3-kinase/Akt/nuclear factor-κB (PI3K/Akt/NF-κB) signaling pathway proteins were measured. Metagenomic sequencing was used to analyze the gut microbiota. Treatment with RW alleviated injury to the intestinal barrier in rats with diarrhea and also upregulated levels of Muc2 and TJ proteins, such as occludin, zonula occludens-1, and claudin-1. Administration of RW regulated the structure of the gut microbiota in diarrheal rats. Furthermore, RW suppressed levels of interleukin (IL), tumor necrosis factor (TNF)-α, IL-1, PI3K, Akt, and p-NF-κB p65 and also increased IL-4 levels. Our study indicates that P. ginseng and Fructus mume help improve the symptoms of diarrhea, possibly by alleviating the intestinal barrier injury, regulating intestinal flora composition, and inhibiting the PI3K/Akt/NF-κB signaling pathway.

JMM Profile: Brachyspira species: the causative agent of Avian Intestinal Spirochaetosis

The genus Brachyspira includes nine officially recognised species, several of which are pathogenic to mammals and birds. B. pilosicoli, B. intermedia, and B. alvinipulli are the causative agents of avian intestinal spirochaetosis (AIS), a gastrointestinal disease in poultry caused by the colonisation of the caeca and/ or colo-rectum by Brachyspira. AIS primarily affects layer hens and broiler breeders over the age of 15 weeks. The severity of symptoms can vary but typically presents as reduced growth rates, delayed onset of lay, reduced egg production, faecally stained eggs, and diarrhoea. This disease is estimated to cost the UK laying industry £18 million per annum. Brachyspira colonisation in humans is common in populations from developing countries and HIV-positive patients; however, it is rarely investigated as a human pathogen.

Human intestinal spirochetosis, irritable bowel syndrome, and colonic polyps: A systematic review and meta-analysis

Human colonic spirochetosis (CS) is usually due toBrachyspira pilosicolior Brachyspira aalborgiinfection. While traditionally considered to be commensal bacteria, there are scattered case reports and case series of gastrointestinal (GI) symptoms in CS and reports of colonic polyps with adherent spirochetes. We performed a systematic review and meta-analysis investigating the association between CS and GI symptoms and conditions including the irritable bowel syndrome (IBS) and colonic polyps. Following PRISMA 2020 guidelines, a systematic search of Medline, CINAHL, EMBASE, and Web of Science was performed using specific keywords for CS and GI disease. Pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using a random-effects model. Of 75 studies identified in the search, 8 case-control studies met the inclusion criteria for meta-analysis and 67 case series studies met the inclusion criteria for pooled prevalence analysis. CS was significantly associated with diarrhea (n = 141/127, cases/controls, OR: 4.19, 95% CI: 1.72-10.21, P = 0.002) and abdominal pain (n = 64/65, OR: 3.66, 95% CI: 1.43-9.35, P = 0.007). CS cases were significantly more likely to have Rome III-diagnosed IBS (n = 79/48, OR: 3.84, 95% CI: 1.44-10.20, P = 0.007), but not colonic polyps (n = 127/843, OR: 8.78, 95% CI: 0.75-103.36, P = 0.084). In conclusion, we found evidence of associations between CS and both diarrhea and IBS, but not colonic polyps. CS is likely underestimated due to suboptimal diagnostic methods and may be an overlooked risk factor for a subset of IBS patients with diarrhea.

Maternal fecal microbiome predicts gestational age, birth weight and neonatal growth in rural Zimbabwe

BACKGROUND

Preterm birth and low birth weight (LBW) affect one in ten and one in seven livebirths, respectively, primarily in low-income and middle-income countries (LMIC) and are major predictors of poor child health outcomes. However, both have been recalcitrant to public health intervention. The maternal intestinal microbiome may undergo substantial changes during pregnancy and may influence fetal and neonatal health in LMIC populations.

METHODS

Within a subgroup of 207 mothers and infants enrolled in the SHINE trial in rural Zimbabwe, we performed shotgun metagenomics on 351 fecal specimens provided during pregnancy and at 1-month post-partum to investigate the relationship between the pregnancy gut microbiome and infant gestational age, birth weight, 1-month length-, and weight-for-age z-scores using extreme gradient boosting machines.

FINDINGS

Pregnancy gut microbiome taxa and metabolic functions predicted birth weight and WAZ at 1 month more accurately than gestational age and LAZ. Blastoscystis sp, Brachyspira sp and Treponeme carriage were high compared to Western populations. Resistant starch-degraders were important predictors of birth outcomes. Microbiome capacity for environmental sensing, vitamin B metabolism, and signalling predicted increased infant birth weight and neonatal growth; while functions involved in biofilm formation in response to nutrient starvation predicted reduced birth weight and growth.

INTERPRETATION

The pregnancy gut microbiome in rural Zimbabwe is characterized by resistant starch-degraders and may be an important metabolic target to improve birth weight.

FUNDING

Bill and Melinda Gates Foundation, UK Department for International Development, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, and UNICEF.

Association between Brachyspira and irritable bowel syndrome with diarrhoea

OBJECTIVE

The incidence of IBS increases following enteric infections, suggesting a causative role for microbial imbalance. However, analyses of faecal microbiota have not demonstrated consistent alterations. Here, we used metaproteomics to investigate potential associations between mucus-resident microbiota and IBS symptoms.

DESIGN

Mucus samples were prospectively collected from sigmoid colon biopsies from patients with IBS and healthy volunteers, and their microbial protein composition analysed by mass spectrometry. Observations were verified by immunofluorescence, electron microscopy and real-time PCR, further confirmed in a second cohort, and correlated with comprehensive profiling of clinical characteristics and mucosal immune responses.

RESULTS

Metaproteomic analysis of colon mucus samples identified peptides from potentially pathogenic Brachyspira species in a subset of patients with IBS. Using multiple diagnostic methods, mucosal Brachyspira colonisation was detected in a total of 19/62 (31%) patients with IBS from two prospective cohorts, versus 0/31 healthy volunteers (p<0.001). The prevalence of Brachyspira colonisation in IBS with diarrhoea (IBS-D) was 40% in both cohorts (p=0.02 and p=0.006 vs controls). Brachyspira attachment to the colonocyte apical membrane was observed in 20% of patients with IBS and associated with accelerated oro-anal transit, mild mucosal inflammation, mast cell activation and alterations of molecular pathways linked to bacterial uptake and ion-fluid homeostasis. Metronidazole treatment paradoxically promoted Brachyspira relocation into goblet cell secretory granules-possibly representing a novel bacterial strategy to evade antibiotics.

CONCLUSION

Mucosal Brachyspira colonisation was significantly more common in IBS and associated with distinctive clinical, histological and molecular characteristics. Our observations suggest a role for Brachyspira in the pathogenesis of IBS, particularly IBS-D.

Retrospective analysis of necrotizing typhlitis cases associated with Brachyspira spp. in British rheas

This paper describes a retrospective analysis of necrotizing typhlitis in common rheas (Rhea americana) diagnosed in the United Kingdom by the Animal & Plant Health Agency (APHA). From January 2008 to January 2020, seven cases of spirochaetal typhlitis associated with Brachyspira spp. were identified using the Veterinary Investigation Diagnosis Analysis database. Gross examination was combined with selective anaerobic culture, polymerase chain reaction, and histopathology to diagnose typhlitis associated with spirochaetal infection. Whole-genome sequencing was subsequently utilized on archived isolates from six of the seven submissions, overcoming issues with traditional testing methods and yielded gains in the identification of Brachyspira to species level. Brachyspira hyodysenteriae, an organism traditionally associated with typhlitis in rheas, was isolated in three sequenced submissions. One of these also demonstrated co-infection with Brachyspira intermedia. Brachyspira suanatina, Brachyspira hampsonii, and Brachyspira alvinipulli were identified by sequencing as single infections in the remaining three animals. This report demonstrates the ability of Brachyspira species other than B. hyodysenteriae to colonize the caeca of rheas presenting with typhlitis. Additionally, the B. alvinipulli isolate harboured a tva(A) gene, indicating higher potential pleuromutilin resistance, which has not previously been described in this Brachyspira species. This study discusses the epidemiology of examined cases and examines the potential role other species may play in these outbreaks.

Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli

The enteric, pathogenic spirochaete Brachyspira pilosicoli colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several in silico techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus Brachyspira. Our study revealed that an additional isolate that was unable to be species typed against any other Brachyspira lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the B. pilosicoli as random mutation (r/m=1.02). Comparative genomics has informed Brachyspira diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.

Spirochetes isolated from arthropods constitute a novel genus Entomospira genus novum within the order Spirochaetales

Spirochetal bacteria were successfully isolated from mosquitoes (Culex pipiens, Aedes cinereus) in the Czech Republic between 1999 and 2002. Preliminary 16S rRNA phylogenetic sequence analysis showed that these strains differed significantly from other spirochetal genera within the family Spirochaetaceae and suggested a novel bacterial genus in this family. To obtain more comprehensive genomic information of these isolates, we used Illumina MiSeq and Oxford Nanopore technologies to sequence four genomes of these spirochetes (BR151, BR149, BR193, BR208). The overall size of the genomes varied between 1.68 and 1.78 Mb; the GC content ranged from 38.5 to 45.8%. Draft genomes were compared to 36 publicly available genomes encompassing eight genera from the class Spirochaetes. A phylogeny generated from orthologous genes across all taxa and the percentage of conserved proteins (POCP) confirmed the genus status of these novel spirochetes. The genus Entomospira gen. nov. is proposed with BR151 selected as type species of the genus. For this isolate and the closest related isolate, BR149, we propose the species name Entomospira culicis sp. nov. The two other isolates BR208 and BR193 are named Entomospira nematocera sp. nov. (BR208) and Entomospira entomophilus sp. nov. (BR193). Finally, we discuss their interesting phylogenetic positioning.

Functional diversity of microbial ecologies estimated from ancient human coprolites and dental calculus

Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770–1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400–850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter–gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution.

This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.

Identification of Widespread Antibiotic Exposure in Patients With Cholera Correlates With Clinically Relevant Microbiota Changes

BACKGROUND

A first step to combating antimicrobial resistance in enteric pathogens is to establish an objective assessment of antibiotic exposure. Our goal was to develop and evaluate a liquid chromatography-ion trap mass spectrometry (LC/MS) method to determine antibiotic exposure in patients with cholera.

METHODS

A priority list for targeted LC/MS was generated from medication-vendor surveys in Bangladesh. A study of patients with and those without cholera was conducted to collect and analyze paired urine and stool samples.

RESULTS

Among 845 patients, 11% (90) were Vibrio cholerae positive; among these 90 patients, analysis of stool specimens revealed ≥1 antibiotic in 86% and ≥2 antibiotics in 52%. Among 44 patients with cholera and paired urine and stool specimens, ≥1 antibiotic was detected in 98% and ≥2 antibiotics were detected in 84%, despite 55% self-reporting medication use. Compared with LC/MS, a low-cost antimicrobial detection bioassay lacked a sufficient negative predictive value (10%; 95% confidence interval, 6%-16%). Detection of guideline-recommended antibiotics in stool specimens did (for azithromycin; P = .040) and did not (for ciprofloxacin) correlate with V. cholerae suppression. A nonrecommended antibiotic (metronidazole) was associated with decreases in anaerobes (ie, Prevotella organisms; P < .001).

CONCLUSION

These findings suggest that there may be no true negative control group when attempting to account for antibiotic exposure in settings like those in this study.

Postweaning mortality in commercial swine production II: review of infectious contributing factors

Postweaning mortality is extremely complex with a multitude of noninfectious and infectious contributing factors. In the current review, our objective is to describe the current state of knowledge regarding infectious causes of postweaning mortality, focusing on estimates of frequency and magnitude of effect where available. While infectious mortality is often categorized by physiologic body system affected, we believe the complex multifactorial nature is better understood by an alternative stratification dependent on intervention type. This category method subjectively combines disease pathogenesis knowledge, epidemiology, and economic consequences. These intervention categories included depopulation of affected cohorts of animals, elimination protocols using knowledge of immunity and epidemiology, or less aggressive interventions. The most aggressive approach to control infectious etiologies is through herd depopulation and repopulation. Historically, these protocols were successful for Actinobacillus pleuropneumoniae and swine dysentery among others. Additionally, this aggressive measure likely would be used to minimize disease spread if either a foreign animal disease was introduced or pseudorabies virus was reintroduced into domestic swine populations. Elimination practices have been successful for Mycoplasma hyopneumoniae, porcine reproductive and respiratory syndrome virus, coronaviruses, including transmissible gastroenteritis virus, porcine epidemic diarrhea virus, and porcine deltacoronavirus, swine influenza virus, nondysentery Brachyspira spp., and others. Porcine circovirus type 2 can have a significant impact on morbidity and mortality; however, it is often adequately controlled through immunization. Many other infectious etiologies present in swine production have not elicited these aggressive control measures. This may be because less aggressive control measures, such as vaccination, management, and therapeutics, are effective, their impact on mortality or productivity is not great enough to warrant, or there is inadequate understanding to employ control procedures efficaciously and efficiently. Since there are many infectious agents and noninfectious contributors, emphasis should continue to be placed on those infectious agents with the greatest impact to minimize postweaning mortality.

Protein Secretion in Spirochetes

Spirochetes form a separate phylum of bacteria with two membranes but otherwise unusual morphologies and envelope structures. Distinctive common features of Borrelia, Leptospira, and Treponema include the sequestration of flagella to the periplasm and thin peptidoglycan cell walls that are more closely associated with the inner membrane. Outer membrane compositions differ significantly between the genera. Leptospira most closely track Gram-negative bacteria due to the incorporation of lipopolysaccharides. Treponema and Borrelia outer membranes lack lipopolysaccharide, with treponemes expressing only a few outer membrane proteins and Borrelia displaying a dizzying diversity of abundant surface lipoproteins instead. Phylogenetic and experimental evidence indicates that spirochetes have adapted various modules of bacterial export and secretion pathways to build and maintain their envelopes. Export and insertion pathways in the inner membrane appear conserved, while spirochetal experimentation with various envelope architectures over time has led to variations in secretion pathways in the periplasm and outer membrane. Classical type I to III secretion systems have been identified, with demonstrated roles in drug efflux and export of flagellar proteins only. Unique activities of periplasmic proteases, including a C-terminal protease, are involved in maturation of some periplasmic proteins. Proper lipoprotein sorting within the periplasm appears to be dependent on functional Lol pathways that lack the outer membrane lipoprotein insertase LolB. The abundance of surface lipoproteins in Borrelia and detailed protein sorting studies suggest a lipoprotein secretion pathway that either extends Lol through the outer membrane or bypasses it altogether. Proteins can be released from cells in outer membrane vesicles or, rarely, as soluble proteins.

First identification and characterisation of Brachyspira hyodysenteriae in pigs in Hong Kong

Swine dysentery (SD) is an important endemic disease of pigs throughout the world. The most common aetiological agent is the anaerobic intestinal spirochaete Brachyspira hyodysenteriae. The related spirochaete Brachyspira pilosicoli causes a milder form of colitis. We report the first isolation of B. hyodysenteriae and B. pilosicoli from a pig farm in Hong Kong. Faecal samples containing mucus or fresh blood were collected from the ground where finisher pigs had just been loaded into a truck for transport to the abattoir. The samples were subjected to selective anaerobic culture and PCR for B. hyodysenteriae and B. pilosicoli, and two isolates of both species were obtained. The B. hyodysenteriae isolates showed clinical resistance to tylosin and lincomycin, whilst the B. pilosicoli isolates were resistant to tylosin and showed intermediate susceptibility to lincomycin. The B. hyodysenteriae isolates were subjected to multilocus sequence typing and a single previously undescribed sequence type (ST250) was identified. Disease was not recorded in other pigs on the farm, but it may have been masked by the use of antimicrobials. Further work is required to examine the distribution of these two pathogens in this and other farms in Hong Kong and in adjoining mainland China.

Severe Human Intestinal Spirochetosis: An Unusual Cause of Diffuse Colonic Ulcerations in a Patient Living with HIV

We describe a case of a homosexual male with human immunodeficiency virus (HIV) and CD4 count of 246 presenting with acute severe bloody diarrhea. Infectious work up was negative, and colonoscopy revealed severe diffuse colonic ulcerations. Histopathologic analysis and Treponemal pallidum immunostaining confirmed the diagnosis of intestinal spirochetosis. There was no evidence of co-infection with other pathogens. His symptoms completely resolved after a 14-day course of metronidazole. This case is notable as colonic ulceration of any severity in patients living with HIV is rarely identified with intestinal spirochetosis. Hence, it should be considered in the differential diagnosis of colonic ulcerations.

Hiding in Plain Sight: Colonic Spirochetosis in Humans

In 1967, Harland and Lee made a startling discovery: in some humans, the colonic epithelium is covered with a "forest" of spirochetes (W. A. Harlan, and F. D. Lee, Br Med J 3:718-719, 1967, https://doi.org/10.1136/bmj.3.5567.718). In this issue of Journal of Bacteriology, Thorell et al. present a systematic analysis of the prevalence and diversity of the spirochetes Brachyspira aalborgi and Brachyspira pilosicoli in the human colon. These and prior studies provide avenues toward resolving important questions: what bacterial and host parameters contribute to this extensive colonization, and what impact does it have on human health?

Isolates from Colonic Spirochetosis in Humans Show High Genomic Divergence and Potential Pathogenic Features but Are Not Detected Using Standard Primers for the Human Microbiota

This is the first report of whole-genome analysis of clinical isolates from individuals with colonic spirochetosis. This characterization provides new opportunities in understanding the physiology and potentials of these bacteria that densely colonize the gut in the individuals infected. The observation that standard 16S amplicon primers fail to detect colonic spirochetosis may have major implications for studies searching for associations between members of the microbiota and clinical conditions such as irritable bowel syndrome (IBS) and should be taken into consideration in project design and interpretation of gastrointestinal tract microbiota in population-based and clinical settings.

Colonic spirochetosis, diagnosed based on the striking appearance in histological sections, still has an obscure clinical relevance, and only a few bacterial isolates from this condition have been characterized to date. In a randomized, population-based study in Stockholm, Sweden, 745 healthy individuals underwent colonoscopy with biopsy sampling. Of these individuals, 17 (2.3%) had colonic spirochetosis, which was associated with eosinophilic infiltration and a 3-fold-increased risk for irritable bowel syndrome (IBS). We aimed to culture the bacteria and perform whole-genome sequencing of the isolates from this unique representative population sample. From 14 out of 17 individuals with spirochetosis we successfully isolated, cultured, and performed whole-genome sequencing of in total 17 isolates, including the Brachyspira aalborgi type strain, 513A. Also, 16S analysis of the mucosa-associated microbiota was performed in the cases and nonspirochetosis controls. We found one isolate to be of the species Brachyspira pilosicoli; all remaining isolates were of the species Brachyspira aalborgi. Besides displaying extensive genetic heterogeneity, the isolates harbored several mucin-degrading enzymes and other virulence-associated genes that could confer a pathogenic potential in the human colon. We also showed that 16S amplicon sequencing using standard primers for human microbiota studies failed to detect Brachyspira due to primer incompatibility.

IMPORTANCE This is the first report of whole-genome analysis of clinical isolates from individuals with colonic spirochetosis. This characterization provides new opportunities in understanding the physiology and potentials of these bacteria that densely colonize the gut in the individuals infected. The observation that standard 16S amplicon primers fail to detect colonic spirochetosis may have major implications for studies searching for associations between members of the microbiota and clinical conditions such as irritable bowel syndrome (IBS) and should be taken into consideration in project design and interpretation of gastrointestinal tract microbiota in population-based and clinical settings.

A survey on the occurrence of Brachyspira pilosicoli and Brachyspira hyodysenteriae in growing-finishing pigs

Background: The major pathogenic intestinal spirochetes affecting pigs during the growing- finishing stage of production include Brachyspira hyodysenteriae and Brachyspira pilosicoli. Infections by these pathogens, which affect the economics of pig production, can result in mortality, growth rate losses and substantial antibiotic costs. The aim of this study was to assess the current occurrence of B. hyodysenteriae and B. pilosicoli in Polish pig herds. Moreover, associations between the presence of diarrhea or other intestinal pathogens and occurrence of B. hyodysenteriae and B. pilosicoli in pigs were investigated. Methods: Between January 2017 and August 2019, a total of 401 samples of pig feces from 95 different herds were submitted to the National Veterinary Research Institute of Poland. These samples were obtained from pigs older than 7 weeks. All the received fecal samples were examined for the presence of B. hyodysenteriae, B. pilosicoli and Lawsonia intracellularis by real-time PCR. Results: For B. pilosicoli, 4.5% (95% CI, 2.5-7.0%) of samples and 13.7% (95% CI, 7.5-22.3%) of herds were positive. Out of 12 samples, B. pilosicoli was detected simultaneously with L. intracellularis, B. hyodysenteriae and B. pilosicoli were detected alone in two samples each. In terms of B. hyodysenteriae, 7.0% of samples (95% CI, 4.7-9.9%) from 18.9% of herds (95% CI, 11.6-28.3%) were positive in real time PCR. The presence of B. hyodysenteriae in fecal samples was associated with the presence of diarrhea in pigs. Conclusions: This study confirmed that B. pilosicoli infections occur in Polish pig herds, but the prevalence is at a low level and the presence of B. pilosicoli is not associated with the development of diarrhea in pigs. B. hyodysenteriae is still a common cause of diarrhea among pigs from Polish herds.

A survey on the occurrence of Brachyspira pilosicoli and Brachyspira hyodysenteriae in growing-finishing pigs

Background: The major pathogenic intestinal spirochetes affecting pigs during the growing- finishing stage of production include Brachyspira hyodysenteriae and Brachyspira pilosicoli. The aim of this study was to assess the current occurrence of B. hyodysenteriae and B. pilosicoli in Polish pig herds. Moreover, associations between the presence of diarrhea or other intestinal pathogens and occurrence of B. hyodysenteriae and B. pilosicoli in pigs were investigated. Methods: Between January 2017 and August 2019, a total of 401 samples of pig feces from 95 different herds were submitted to the National Veterinary Research Institute of Poland. These samples were obtained from pigs older than 7 weeks. All the received fecal samples were examined for the presence of B. hyodysenteriae, B. pilosicoli and Lawsonia intracellularis by real-time PCR. Results: B. pilosicoli was detected in 4.5% (95% CI, 2.5-7.0%) (18/401) of pig fecal samples. At the herd level 13.7% (95% CI, 7.5-22.3%) (13/95) of herds were positive for B. pilosicoli. B. hyodysenteriae was detected in 7.0% (95% CI, 4.7-9.9%) (28/401) of pig fecal samples and 18.9% (95% CI, 11.6-28.3%) (18/95) of pig herds were positive. Out of 18 B. pilosicoli positive samples, this pathogen was detected alone in 5 samples; simultaneously with L. intracellularis in 9 samples; simultaneously with B. hyodysenteriae in 1 sample and in 3 samples was detected simultaneously with both of these bacteria. The presence of B. hyodysenteriae in fecal samples was associated with the presence of diarrhea in pigs. Conclusions: This study confirmed that B. pilosicoli infections occur in Polish pig herds, but the prevalence is at a low level and the presence of B. pilosicoli is not associated with the development of diarrhea in pigs. B. hyodysenteriae is still a common cause of diarrhea among pigs from Polish herds.

A survey on the occurrence of Brachyspira pilosicoli and Brachyspira hyodysenteriae in growing-finishing pigs

Background: The major pathogenic intestinal spirochetes affecting pigs during the growing- finishing stage of production include Brachyspira hyodysenteriae and Brachyspira pilosicoli. The aim of this study was to assess the current occurrence of B. hyodysenteriae and B. pilosicoli in Polish pig herds. Moreover, associations between the presence of diarrhea or other intestinal pathogens and occurrence of B. hyodysenteriae and B. pilosicoli in pigs were investigated. Methods: Between January 2017 and August 2019, a total of 401 samples of pig feces from 95 different herds were submitted to the National Veterinary Research Institute of Poland. These samples were obtained from pigs older than 7 weeks. All the received fecal samples were examined for the presence of B. hyodysenteriae, B. pilosicoli and Lawsonia intracellularis by real-time PCR. Results: B. pilosicoli was detected in 4.5% (95% CI, 2.5-7.0%) (18/401) of pig fecal samples. At the herd level 13.7% (95% CI, 7.5-22.3%) (13/95) of herds were positive for B. pilosicoli. B. hyodysenteriae was detected in 7.0% (95% CI, 4.7-9.9%) (28/401) of pig fecal samples and 18.9% (95% CI, 11.6-28.3%) (18/95) of pig herds were positive. Out of 18 B. pilosicoli positive samples, this pathogen was detected alone in 5 samples; simultaneously with L. intracellularis in 9 samples; simultaneously with B. hyodysenteriae in 1 sample and in 3 samples was detected simultaneously with both of these bacteria. The presence of B. hyodysenteriae in fecal samples was associated with the presence of diarrhea in pigs. Conclusions: This study confirmed that B. pilosicoli infections occur in Polish pig herds, but the prevalence is at a low level and the presence of B. pilosicoli is not associated with the development of diarrhea in pigs. B. hyodysenteriae is still a common cause of diarrhea among pigs from Polish herds.

Ovarian abscess caused by Helicobacter cinaedi in a patient with endometriosis

Helicobacter cinaedi is a rarely encountered pathogen that easily induces bacteremia. Various foci of H. cinaedi infection have been reported; however, no case of adnexal abscess caused by H. cinaedi has been reported in the English literature. We herein report a case of ovarian abscess caused by H. cinaedi.

A 38-year-old nulligravid Japanese woman was admitted to our hospital with an adnexal abscess. Clinical findings included fever, leukocytosis, and elevated C-reactive protein. Laparoscopic right partial oophorectomy with abdominal lavage was performed. H. cinaedi was isolated from cultures of blood and ovarian abscess fluid after surgery. Intravenous ampicillin/sulbactam was administered for 2 weeks, followed by oral amoxicillin for an additional 2 weeks. The postoperative course was uneventful and clinical findings improved. There was no evidence of relapse. H. cinaedi can cause ovarian abscess and is likely an under-recognized pathogen.

Avian Toll-like receptor allelic diversity far exceeds human polymorphism: an insight from domestic chicken breeds

Immune genes show remarkable levels of adaptive variation shaped by pathogen-mediated selection. Compared to humans, however, population polymorphism in animals has been understudied. To provide an insight into immunogenetic diversity in birds, we sequenced complete protein-coding regions of all Toll-like receptor (TLR) genes with direct orthology between mammals and birds (TLR3, TLR4, TLR5 and TLR7) in 110 domestic chickens from 25 breeds and compared their variability with a corresponding human dataset. Chicken TLRs (chTLRs) exhibit on average nine-times higher nucleotide diversity than human TLRs (hTLRs). Increased potentially functional non-synonymous variability is found in chTLR ligand-binding ectodomains. While we identified seven sites in chTLRs under positive selection and found evidence for convergence between alleles, no selection or convergence was detected in hTLRs. Up to six-times more alleles were identified in fowl (70 chTLR4 alleles vs. 11 hTLR4 alleles). In chTLRs, high numbers of alleles are shared between the breeds and the allelic frequencies are more equal than in hTLRs. These differences may have an important impact on infectious disease resistance and host-parasite co-evolution. Though adaptation through high genetic variation is typical for acquired immunity (e.g. MHC), our results show striking levels of intraspecific polymorphism also in poultry innate immune receptors.

Vaccination of chickens with the 34 kDa carboxy-terminus of Bpmp72 reduces colonization with Brachyspira pilosicoli following experimental infection

The anaerobic intestinal spirochaete Brachyspira pilosicoli colonizes the large intestine of a variety of species of mammals and birds, and may result in colitis, diarrhoea and reductions in growth rate. Naturally occurring infections in chickens are largely confined to adult laying and breeding birds. In this study, the 34 kD carboxy-terminus of the prominent outer membrane protein Bmp72 of B. pilosicoli was expressed as a histidine-tagged recombinant protein and used to immunize two groups (B and C) of 15 individually housed layer chickens. Vaccination was with either 100 μg (B) or 1 mg (C) protein emulsified with Freund's incomplete adjuvant delivered into the pectoral muscles, followed three weeks later by 1 mg of protein in phosphate buffered saline delivered via crop tube. Two weeks later these and 15 non-vaccinated positive control birds (group A) housed in the same room were challenged via crop tube with B. pilosicoli avian strain CPS1. B. pilosicoli was detected in the faeces of all control birds and in 14 of the vaccinated birds in each vaccinated group at some point over the 30-day period following challenge. Colonization was delayed and the duration of excretion was significantly reduced (P = 0.0001) in both groups of vaccinated birds compared to the non-vaccinated control birds. Fewer immunized birds had abnormal caecal contents at post mortem examination compared to non-vaccinated birds, but the difference was not statistically significant. This study indicates that recombinant Bmp72 C-terminus has potential to be developed for use as a vaccine component to provide protection against B. pilosicoli infections. RESEARCH HIGHLIGHTS Laying chickens were immunized with recombinant Brachyspira pilosicoli membrane protein Bpmp72. Immunized birds had a highly significant reduction in the duration of colonization. Fewer immunized than control birds had abnormal caecal contents after infection. Bpmp72 showed potential for use as a novel vaccine component for B. pilosicoli.