Identification of Campylobacter spp. and discrimination from Helicobacter and Arcobacter spp. by direct sequencing of PCR-amplified cpn60 sequences and comparison to cpnDB, a chaperonin reference sequence database

Determinants of Campylobacter species diversity in infants and association with family members, livestock, and household environments in rural Eastern Ethiopia

Background

Campylobacter infections pose a significant challenge in low- and middle-income countries, contributing to child mortality. Campylobacter is linked to acute gastrointestinal illness and severe long-term consequences, including environmental enteric dysfunction (EED) and stunting. In 2018, our cross-sectional study in Ethiopia detected Campylobacter in 88% of stools from children aged 12-15 months, with an average of 11 species per stool using meta-total RNA sequencing. Building on these findings, we conducted a longitudinal study (December 2020-June 2022) to investigate Campylobacter colonization of infants and identify reservoirs and risk factors in rural eastern Ethiopia.

Results

After a preliminary screening of 15 Campylobacter species using species-specific quantitative PCR, we analyzed four target species in 2,045 samples from infants (first month to just one year of life) and biannual samples from mothers, siblings, and livestock (goats, cattle, sheep, and chickens). Candidatus C. infans (41%), C. jejuni (26%), and C. upsaliensis (13%) were identified as the predominant in the infant gut. Colonization of C. infans and C.jejuni increased (C. infans: 0.85%, C. jejuni-0.98% increase/ day in the odds of colonization) and abundance (P = 0.027, 0.024) with age. Enteric symptoms were strongly associated with C. infans (diarrhea: OR = 2.02 [95%CI: 35%,100%]; fever: OR = 1.62 [95%CI: 14%, 83%]) and C. jejuni (diarrhea: OR = 2.29 [95%CI: 46%,100%], fever: OR = 2.53 [95%CI: 56%,100%]). Based on linear mixed models, we found elevated cumulative loads of C. infans load in infants (especially females OR = 1.5 [95%CI: 10%, 67%]), consuming raw milk (OR = 2.3 [95%CI: 24%,100%]) or those exposed to areas contaminated with animal droppings (OR = 1.6 [95%CI: 7%,93%]), while C. jejuni cumulative loads were higher in infants ingesting soil or animal feces (OR = 2.2 [95%CI: 23%,100%]). C. infans was also prevalent in siblings (56%) and mothers (45%), whereas C. jejuni was common in chickens (38%) and small ruminants (goats 27%, sheep 21%).

Conclusions

Campylobacter was highly prevalent in rural Ethiopian infants. C. infans was primarily associated with human hosts, and C. jejuni was mainly linked to zoonotic sources. Our findings emphasize the need for targeted interventions addressing environmental, dietary, and behavioral factors to reduce Campylobacter transmission in resource-limited settings.

The epidemiology and impact of persistent Campylobacter infections on childhood growth among children 0-24 months of age in resource-limited settings

Background

Campylobacter is the leading cause of bacterial gastroenteritis worldwide. It is generally associated with an acute gastrointestinal infection causing a self-limiting diarrheal episode. However, there is evidence that persistent/recurrent carriage of Campylobacter also occurs. In hyperendemic settings the epidemiology and consequences of persistent Campylobacter enteric infections is poorly studied.

Methods

Risk factors for and growth consequences of persistent Campylobacter infections detected by polymerase chain reaction (qPCR) were evaluated with data from the MAL-ED birth cohort study in children 0-24 months of age between November 2009 and February 2012. A persistent Campylobacter infection was defined as three or more consecutive Campylobacter positive monthly stools.

Findings

Across all study sites, 45.5% (781/1715) of children experienced at least one persistent Campylobacter episode. The average cumulative duration of days in which children with persistent Campylobacter were positive for Campylobacter spp. was 150 days (inter-quartile range: 28-236 days). Children who experienced a persistent Campylobacter episode had an attained 24-month length-for-age (LAZ) score that was 0.23 (95% (CI): -0.31, -0.15) less than children without a persistent Campylobacter episode. Among children who had at least one episode of Campylobacter over a 3-month or 9-month window, persistent episodes were not significantly associated with poorer 3-month weight gain (-28.7 g, 95% CI: -63.4 g, 6.0 g) but were associated with poorer 9-month linear growth (-0.134 cm 95% CI: -0.246, -0.022) compared to children with an episode that resolved within 31 days.

Interpretation

Persistent/recurrent Campylobacter infection is common among children and has a measurable negative impact on linear growth in early childhood.

Funding

Funding for this study was provided by the Bill and Melinda Gates Foundation (OPP1066146 and OPP1152146), the National Institutes of Health United States (R01AI158576 and R21AI163801 to MNK and CTP; K43TW012298 to FS; K01AI168493 to JMC; GOL was supported by K01AI145080. This research was also supported in part by USDA-ARS CRIS project 2030-42000-055-00D. The funders had no role in study design, study implementation, data analysis, or interpretation of the results.

Prevalence, Diversity, and Virulence of Campylobacter Carried by Migratory Birds at Four Major Habitats in China

Campylobacter species, especially C. jejuni and C. coli, are the main zoonotic bacteria causing human gastroenteritis. A variety of Campylobacter species has been reported in wild birds, posing a potential avian-human transmission pathway. Currently, there has been little surveillance data on Campylobacter carriage in migratory birds in China. In the current work, fresh fecal droppings from individual migratory birds were collected at four bird wintering/stopover sites in China from May 2020 to March 2021. Nucleic acid was extracted and tested for Campylobacter with PCR-based methods. Overall, 73.8% (329/446) of the samples were positive for Campylobacter, demonstrating location and bird host specificity. Further speciation revealed the presence of C. jejuni, C. coli, C. lari, C. volucris, and an uncharacterized species, which all harbored a variety of virulence factors. Phylogenetic analysis performed on concatenated 16S rRNA-atpA-groEL genes elucidated their genetic relationship, demonstrating both inter- and intra-species diversity. The wide distribution and high diversity of Campylobacter spp. detected in migratory birds in China indicated potential transmission across territories. The existence of virulence factors in all of these species highlighted their public health importance and the necessity of monitoring and controlling Campylobacter and other pathogens carried by migratory birds.

Helicobacter ibis sp. nov., isolated from faecal droppings of black-faced ibis (Theristicus melanopis)

As part of a larger study on Epsilonproteobacteria carried by wild birds in the city of Valdivia (southern Chile), two curved rod-shaped Gram-stain-negative strains (A82T and WB-40) were recovered from faecal samples and subjected to a taxonomic study. Results of a genus-specific PCR showed that these isolates belonged to the genus Helicobacter. Further identification by 16S rRNA and hsp60 (60 kDa heat-shock protein) gene sequence analysis revealed that they formed a separate phylogenetic clade, different from other known Helicobacter species with 'Helicobacter burdigaliensis' CNRCH 2005/566HT and Helicobacter valdiviensis WBE14T being the most closely related species. This was confirmed by core-genome phylogeny as well as digital DNA-DNA hybridization and average nucleotide identity analyses between the genomes of strains A82T and WB-40 and all other Helicobacter species. The draft genome sequences of A82T and WB-40, obtained by Illumina NextSeq 2000 sequencing, consisted of 1.6 Mb with a G+C content of 31.9-32.0 mol%. The results obtained from the phylogenetic and genomic characterization, together with their different morphological and biochemical features, revealed that these two strains represent a novel species, for which we propose the name Helicobacter ibis sp. nov. with A82T (=LMG 32718T=CCCT 22.04T) as the type strain.

Prevalence and Load of the Campylobacter Genus in Infants and Associated Household Contacts in Rural Eastern Ethiopia: a Longitudinal Study from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project

In our previous cross-sectional study, multiple species of Campylobacter were detected (88%) in stool samples from children (12 to 14 months of age) in rural eastern Ethiopia. This study assessed the temporal fecal carriage of Campylobacter in infants and identified putative reservoirs associated with these infections in infants from the same region. The prevalence and load of Campylobacter were determined using genus-specific real-time PCR. Stool samples from 106 infants (n = 1,073) were collected monthly from birth until 376 days of age (DOA). Human stool samples (mothers and siblings), livestock feces (cattle, chickens, goats, and sheep), and environmental samples (soil and drinking water) from the 106 households were collected twice per household (n = 1,644). Campylobacter was most prevalent in livestock feces (goats, 99%; sheep, 98%; cattle, 99%; chickens, 93%), followed by human stool samples (siblings, 91%; mothers, 83%; infants, 64%) and environmental samples (soil, 58%; drinking water, 43%). The prevalence of Campylobacter in infant stool samples significantly increased with age, from 30% at 27 DOA to 89% at 360 DOA (1% increase/day in the odds of being colonized) (P < 0.001). The Campylobacter load increased linearly (P < 0.001) with age from 2.95 logs at 25 DOA to 4.13 logs at 360 DOA. Within a household, the Campylobacter load in infant stool samples was positively correlated with the load in mother stool samples (r2 = 0.18) and soil collected inside the house (r2 = 0.36), which were in turn both correlated with Campylobacter loads in chicken and cattle feces (0.60 < r2 < 0.63) (P < 0.01). In conclusion, a high proportion of infants are infected with Campylobacter in eastern Ethiopia, and contact with the mother and contaminated soil may be associated with early infections. IMPORTANCE A high Campylobacter prevalence during early childhood has been associated with environmental enteric dysfunction (EED) and stunting, especially in low-resource settings. Our previous study demonstrated that Campylobacter was frequently found (88%) in children from eastern Ethiopia; however, little is known about potential Campylobacter reservoirs and transmission pathways leading to infection of infants by Campylobacter during early growth. In the longitudinal study presented here, Campylobacter was frequently detected in infants within the 106 surveyed households from eastern Ethiopia, and the prevalence was age dependent. Furthermore, preliminary analyses highlighted the potential role of the mother, soil, and livestock in the transmission of Campylobacter to the infant. Further work will explore the species and genetic composition of Campylobacter in infants and putative reservoirs using PCR and whole-genome and metagenomic sequencing. The findings from these studies can lead to the development of interventions to minimize the risk of transmission of Campylobacter to infants and, potentially, EED and stunting.

Maternal vaginal microbiome composition does not affect development of the infant gut microbiome in early life

Birth mode has been implicated as a major factor influencing neonatal gut microbiome development, and it has been assumed that lack of exposure to the maternal vaginal microbiome is responsible for gut dysbiosis among caesarean-delivered infants. Consequently, practices to correct dysbiotic gut microbiomes, such as vaginal seeding, have arisen while the effect of the maternal vaginal microbiome on that of the infant gut remains unknown. We conducted a longitudinal, prospective cohort study of 621 Canadian pregnant women and their newborn infants and collected pre-delivery maternal vaginal swabs and infant stool samples at 10-days and 3-months of life. Using cpn60-based amplicon sequencing, we defined vaginal and stool microbiome profiles and evaluated the effect of maternal vaginal microbiome composition and various clinical variables on the development of the infant stool microbiome. Infant stool microbiomes showed significant differences in composition by delivery mode at 10-days postpartum; however, this effect could not be explained by maternal vaginal microbiome composition and was vastly reduced by 3 months. Vaginal microbiome clusters were distributed across infant stool clusters in proportion to their frequency in the overall maternal population, indicating independence of the two communities. Intrapartum antibiotic administration was identified as a confounder of infant stool microbiome differences and was associated with lower abundances of Escherichia coli, Bacteroides vulgatus, Bifidobacterium longum and Parabacteroides distasonis. Our findings demonstrate that maternal vaginal microbiome composition at delivery does not affect infant stool microbiome composition and development, suggesting that practices to amend infant stool microbiome composition focus factors other than maternal vaginal microbes.

Unravelling the reservoirs for colonisation of infants with Campylobacter spp. in rural Ethiopia: protocol for a longitudinal study during a global pandemic and political tensions

INTRODUCTION

Undernutrition is an underlying cause of mortality in children under five (CU5) years of age. Animal-source foods have been shown to decrease malnutrition in CU5. Livestock are important reservoirs for Campylobacter bacteria, which are recognised as risk factors for child malnutrition. Increasing livestock production may be beneficial for improving nutrition of children but these benefits may be negated by increased exposure to Campylobacter and research is needed to evaluate the complex pathways of Campylobacter exposure and infection applicable to low-income and middle-income countries. We aim to identify reservoirs of infection with Campylobacter spp. of infants in rural Eastern Ethiopia and evaluate interactions with child health (environmental enteric dysfunction and stunting) in the context of their sociodemographic environment.

METHODS AND ANALYSIS

This longitudinal study involves 115 infants who are followed from birth to 12 months of age and are selected randomly from 10 kebeles of Haramaya woreda, East Hararghe zone, Oromia region, Ethiopia. Questionnaire-based information is obtained on demographics, livelihoods, wealth, health, nutrition and women empowerment; animal ownership/management and diseases; and water, sanitation and hygiene. Faecal samples are collected from infants, mothers, siblings and livestock, drinking water and soil. These samples are analysed by a range of phenotypic and genotypic microbiological methods to characterise the genetic structure of the Campylobacter population in each of these reservoirs, which will support inference about the main sources of exposure for infants.

ETHICS AND DISSEMINATION

Ethical approval was obtained from the University of Florida Internal Review Board (IRB201903141), the Haramaya University Institutional Health Research Ethics Committee (COHMS/1010/3796/20) and the Ethiopia National Research Ethics Review Committee (SM/14.1/1059/20). Written informed consent is obtained from all participating households. Research findings will be disseminated to stakeholders through conferences and peer-reviewed journals and through the Feed the Future Innovation Lab for Livestock Systems.

Campylobacter jejuni and Other Emerging Campylobacteraceae in Retail Beef Liver - An Underestimated Potential Source?

Bovine by-products, such as liver, could be an underestimated source of Campylobacter jejuni. Therefore, our aims were to evaluate the occurrence of C. jejuni and other Campylobacteraceae in retail beef liver and characterize their antibiotic resistance (ciprofloxacin, tetracycline, erythromycin, and gentamicin) and potential genetic relationship by flagellin gene Restriction Fragment Length Polymorphism (flaA-RFLP) and Multilocus Sequence Typing (MLST) with clinical strains. Seventy-six out of 206 samples (36.9%) were positive for Campylobacter and related organisms. Arcobacter butzleri was the most frequently isolated species (21.8%), followed by C. jejuni (9.7%), C. fetus (7.8%) and C. coli (1%). The C. jejuni strains showed resistance to tetracycline (17.2%) or ciprofloxacin (6.9%), with only one strain resistant to both antibiotics. Meanwhile, 8.3% of ciprofloxacin resistance was observed in C. fetus. The other species showed no resistance. Most of the clonal complexes (CC) in which the C. jejuni genotypes were grouped (CC-21, 42, 48 and 52), coincided with genotypes of clinical strains previously reported in Chile. As such, this study provides evidence that beef liver could be an underestimated route for resistant C. jejuni to humans. Further studies should assess whether this food could play a role in the transmission of other emerging Campylobacteraceae such as those reported here.

cpn60 barcode sequences accurately identify newly defined genera within the Lactobacillaceae

The cpn60 barcode sequence is established as an informative target for microbial species identification. Applications of cpn60 barcode sequencing are supported by the availability of "universal" PCR primers for its amplification and a curated reference database of cpn60 sequences, cpnDB. A recent reclassification of lactobacilli involving the definition of 23 new genera provided an opportunity to update cpnDB and to determine if the cpn60 barcode could be used for accurate identification of species consistent with the new framework. Analysis of 275 cpn60 sequences representing 258/269 of the validly named species in Lactobacillus, Paralactobacillus and the 23 newer genera showed that cpn60-based sequence relationships were generally consistent with the whole-genome-based phylogeny. Aligning or mapping full length barcode sequences or a 150 bp subsequence resulted in accurate and unambiguous species identification in almost all cases. Taken together, our results show that the combination of available reference sequence data, "universal" barcode amplification primers, and the inherent sequence diversity within the cpn60 barcode make it a useful target for the detection and identification of lactobacilli as defined by the latest taxonomic framework.

Early Neonatal Meconium Does Not Have a Demonstrable Microbiota Determined through Use of Robust Negative Controls with cpn60-Based Microbiome Profiling

Detection of bacterial DNA within meconium is often cited as evidence supporting in utero colonization. However, many studies fail to adequately control for contamination. We aimed to define the microbial content of meconium under properly controlled conditions. DNA was extracted from 141 meconium samples and subjected to cpn60-based microbiome profiling, with controls to assess contamination throughout. Total bacterial loads of neonatal meconium, infant stool, and controls were compared by 16S rRNA quantitative PCR (qPCR). Viable bacteria within meconium were cultured, and isolate clonality was assessed by pulsed-field gel electrophoresis (PFGE). Meconium samples did not differ significantly from controls with respect to read numbers or taxonomic composition. Twenty (14%) outliers with markedly higher read numbers were collected significantly later after birth and appeared more like transitional stool than meconium. Total bacterial loads were significantly higher in stool than in meconium, which did not differ from that of sequencing controls, and correlated well with read numbers. Cultured isolates were most frequently identified as Staphylococcus epidermidis, Enterococcus faecalis, or Escherichia coli, with PFGE indicating high intraspecies diversity. Our findings highlight the importance of robust controls in studies of low microbial biomass samples and argue against meaningful bacterial colonization in utero. Given that meconium microbiome profiles could not be distinguished from sequencing controls, and that viable bacteria within meconium appeared uncommon and largely consistent with postnatal skin colonization, there does not appear to be a meconium microbiota.

IMPORTANCE Much like the recent placental microbiome controversy, studies of neonatal meconium reporting bacterial communities within the fetal and neonatal gut imply that microbial colonization begins prior to birth. However, recent work has shown that placental microbiomes almost exclusively represent contamination from lab reagents and the environment. Here, we demonstrate that prior studies of neonatal meconium are impacted by the same issue, showing that the microbial content of meconium does not differ from negative controls that have never contained any biological material. Our culture findings similarly supported this notion and largely comprised bacteria normally associated with healthy skin. Overall, our work adds to the growing body of evidence against the in utero colonization hypothesis.

Enterohepatic Helicobacter species - clinical importance, host range, and zoonotic potential

The genus Helicobacter defined just over 30 years ago, is a highly diverse and fast-growing group of bacteria that are able to persistently colonize a wide range of animals. The members of this genus are subdivided into two groups with different ecological niches, associated pathologies, and phylogenetic relationships: the gastric Helicobacter (GH) and the enterohepatic Helicobacter (EHH) species. Although GH have been mostly studied, EHH species have become increasingly important as emerging human pathogens and potential zoonotic agents in the last years. This group of bacteria has been associated with the development of several diseases in humans from acute pathologies like gastroenteritis to chronic pathologies that include inflammatory bowel disease, and liver and gallbladder diseases. However, their reservoirs, as well as their routes of transmission, have not been well established yet. Therefore, this review summarizes the current knowledge of taxonomy, epidemiology, and clinical role of the EHH group.

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.

Exploring the role of healthy dogs as hosts of enterohepatic Helicobacter species using cultivation-dependent and -independent approaches

Enterohepatic Helicobacter (EHH) species have been increasingly associated with acute gastroenteritis, inflammatory bowel disease and hepatobiliary diseases in humans. However, their host range and transmission routes are poorly understood. Therefore, the aim of this study was to determine the presence of EHH in healthy dogs using both cultivation-dependent and -independent methods. Three hundred and ninety faecal samples from domestic dogs without gastrointestinal symptoms were analysed between June 2018 and July 2019 in Valdivia (South of Chile). Samples were inoculated on selective medium and in parallel were filtrated over an antibiotic-free blood agar. Both media were incubated in a microaerobic atmosphere at 37°C for 7 days. Colonies were identified by PCR and phylogenetic analysis. A subset of 50 samples (half of them positive for EHH by cultivation and the remaining half negative) was analysed by PCR-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) for direct detection. Cultivation method detected EHH in 15.4% (60/390) of the samples, being the most prevalent species H. canis (5.8%, 23/390) and H. canicola (5.1%, 20/390), followed by H. bilis (3.6%, 14/390) and 'H. winghamensis' (1.3%, 5/390). In contrast, PCR-DGGE method detected Helicobacter DNA in almost all (96%, 48/50) tested samples. On the other hand, the method used also allowed to isolate other Campylobacterales, in fact 44.3% (173/390) of the samples were positive for Campylobacter upsaliensis (43.3%, 169/390) followed by C. jejuni (2.0%, 8/390). Moreover, two strains that presented Campylobacter-like morphology were finally identified as Anaerobiospirillum succiniciproducens. Our results indicate that healthy domestic dogs commonly carry EHH and other Campylobacter species. However, further studies are needed to determine whether and how these Helicobacter and Campylobacter species can be transmitted to humans.

Identification of Brachyspira species by cpn60 universal target sequencing is superior to NADH oxidase gene sequencing

The pig colon is the habitat of diverse Brachyspira species, of which only a few are of clinical importance. Methods for identification have shifted from phenotypic to molecular testing over the last two decades. Following the emergence of B. hampsonii it became evident that relying on species-specific PCRs carries the risk of overlooking important new species. Consequently, sequencing was proposed as an unbiased alternative for identification of isolates. So far, the main target for identification across species has been the NADH oxidase gene (nox). However, multiple copies of this gene in the genome and potential lateral gene transfer reduce confidence when using this gene. This study compared identification and phylogentic relationship inferred from nox sequencing to that inferred from sequencing of the cpn60 universal target using a collection of 168 isolates from different Brachyspira species. The majority of isolates had an identical identification with both methods. There were a few outliers in the trees with uncertain assignment to a species by BLAST analysis. A few major discrepancies pertained to the pathogenic species B. hampsonii (2), B. pilosicoli (1) and B. suanatina (1). Weakly haemolytic variants of B. hyodysenteriae were assigned to the correct species by both methods. Some of the isolates identified as B. hampsonii also had a weakly haemolytic phenotype.

The role of Campylobacter spp. in chronic enteropathy in dogs

The aim of the study was to identifyCampylobacterspecies in a group of patients with chronic gastrointestinal problems and to investigate the relationship between the presence ofCampylobacterspp. in stool samples and as well as the severity of chronic enteropathy. Twenty-six dogs with chronic gastrointestinal problems were included in the prospective study. Each research subject had their stomach, duodenum, ileum, and colon examined endoscopically. A histopathological examination of the obtained biopsy samples was then performed, excluding other potential diseases. Stool samples were collected and then examined for the presence ofCampylobacterspp. To evaluate the relationship betweenCampylobacterspp. occurrence and the intensity of chronic enteropathy, patients were divided into two groups; animals in the first group presented with no to mild inflammation whereas research subjects in the second group suffered from moderate to severe inflammation. Subsequently, the patients were divided based on positive or negative test results forCampylobacterspp. cultures. No significant relationship between the presence ofCampylobacterspp. in stool samples and chronic enteropathy was found. In contrast to other previously published papers, our study showed a lower occurrence ofCampylobacter upsaliensis.

The applicability of gene sequencing and MALDI-TOF to identify less common gram-negative rods (Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium) from environmental isolates

Our aim was to identify less common non-fermenting gram-negative rods during the bioremediation process. Five genera were found: Advenella, Castellaniella, Kaistia, Pusillimonas and Sphingobacterium, for a total of 15 isolates. Therefore, we evaluated the applicability of four methods currently available for bacteria identification: (1) conventional biochemical methods, (2) the VITEK^®-2 system, (3) MALDI-TOF mass spectrometry and (4) 16S rRNA gene sequencing. The biochemical methods and the VITEK^®-2 system were reliable only for the Sphingobacterium isolate and solely at the genus level. Both MALDI-TOF mass spectrometry platforms (Bruker and VITEK^® MS) did not achieve reliable identification results for any of these genera. 16S rRNA gene sequencing identified eight isolates to the species level but not to the subspecies level, when applicable. The remaining seven isolates were reliably identified through 16S rRNA gene sequencing to the genus level only. Our findings suggest that the detection and identification of less common genera (and species) that appeared at certain moments during the bioremediation process can be a challenge to microbiologists considering the most used techniques. In addition, more studies are required to confirm our results.

Update on cpnDB: a reference database of chaperonin sequences

cpnDB was established in 2004 to provide a manually curated database of type I (60 kDa chaperonin, CPN60, also known as GroEL or HSP60) and type II (CCT, TRiC, thermosome) chaperonin sequences and to support chaperonin sequence-based applications including microbial species identification, detection and quantification, phylogenetic investigations and microbial community profiling. Since its establishment, cpnDB has grown to over 25 000 sequence records including over 4 000 records from bacterial type strains. The updated cpnDB webpage (www.cpndb.ca) provides tools for text- or sequence-based searches and links to protocols, and selected reference data sets are available for download. Here we present an updated description of the contents and taxonomic coverage of cpnDB and an analysis of cpn60 sequence diversity.

Comparison of media and growth conditions for culturing enterohepatic Helicobacter species

This research aims to compare the culturing conditions for enterohepatic Helicobacter, evaluating culture media, incubation atmosphere and susceptibility to antimicrobials used to generate selective conditions. Four common media for the closely related genus Campylobacter (Columbia, Bolton, Brucella and CCDA agar), as well as the need for hydrogen in the microaerobic incubation atmosphere, were evaluated. Serial dilutions of 13 strains belonging to six species (H. apodemus, H. bilis, H. canicola, H. canis, H. equorum and Helicobacter sp.) were inoculated in each media and incubated at 37°C for 48 to 96 h using CampyGen (OXOID) and gaseous exchange (including hydrogen) in parallel. Columbia or Brucella agars were the most appropriate for culturing EHH (P < 0·05). However, there was no significant difference between the atmospheres evaluated (P = 0·13). In addition, minimal inhibitory concentration for six antibiotics showed that all isolates were resistant to trimethoprim, whereas for the rest of the antibiotics (cephalothin, cefoperazone, cefsulodin, teicoplanin and vancomycin) the inhibition range was between 8 and 64 μg ml^{- 1} . Our findings suggest that Columbia or Brucella media, regardless of the use of hydrogen, can be used for the EHH isolation. In addition, the concentration of antibiotics included in commercial campylobacteria supplements is suitable for EHH species recovery. SIGNIFICANCE AND IMPACT OF THE STUDY: Enterohepatic Helicobacter (EHH) infections have been associated with several diseases in humans such as acute gastroenteritis, inflammatory bowel disease and hepatobiliary diseases. Although they are frequently detected in clinical samples by molecular methods, only occasionally they are isolated using culture conditions described for the taxonomic related pathogen Campylobacter sp. This is because the optimal conditions for the isolation of EHH have not yet been described, which results in an underestimation of the prevalence and clinical importance of these emerging pathogens. Therefore, this study provides insight for culturing EHH species.

Campylobacter in recreational lake water in southern Quebec, Canada: presence, concentration, and association with precipitation and ruminant farm proximity

Campylobacter is an important cause of gastrointestinal illness and exposure to recreational water is one potential source of infection. The objective of this study was to investigate the presence and concentrations of Campylobacter, and determine the influence of agricultural activities and precipitation on their presence, at lake beaches used for water recreation in southern Quebec, Canada. A total of 413 water samples were collected from June to August, from 22 beaches, between 2011 and 2013. The overall proportion of positive water samples was estimated to be 33.9% (95% CI: 27.7, 40.1) for C. jejuni and 49.7% (95% CI: 41.8, 57.6) for Campylobacter spp. The concentrations of both thermotolerant Campylobacter spp. and C. jejuni ranged from 20 to 900 bacteria/L of water. Logistic regressions showed that the presence of C. jejuni and Campylobacter spp. was significantly associated with the year and season. Other significant predictors of C. jejuni, but not Campylobacter spp., included the presence of precipitation the day before sampling and the presence of ruminant farms within a 5 km radius of the beach. The present study provides insights into the risk of Campylobacter presence in recreational lake water for better understanding public health risks.

Antimicrobial resistant Helicobacter fennelliae isolated from non-diarrheal child stool sample in Battambang, Cambodia

Helicobacter fennelliae (H. fennelliae) is associated with human gastroenteritis; however, H. fennelliae was isolated and confirmed by phenotypic and genotypic identification from a non-diarrheal child stool sample in Cambodia. Antimicrobial susceptibility testing demonstrated that this isolate had a high minimal inhibitory concentration against macrolides and quinolones, which are first-line antibiotic treatment choices for Campylobacter infections. Consequently, macrolides and quinolones were likewise expected to be ineffective against Campylobacter-like organisms such as H. fennelliae. This isolate warranted further genetic characterization to better understand associated antibiotic resistance mechanisms. Resistant pathogens from asymptomatic diarrheal cases are likely underestimated, and as such colonized individuals may spread resistant organisms to local community members and the environment.

Cleaning and disinfection programs against Campylobacter jejuni for broiler chickens: productive performance, microbiological assessment and characterization

Detailed cleaning and disinfection programs aims to reduce infection pressure from microorganisms from one flock to the next. However, studies evaluating the benefits to poultry performance, the sanitary status of the facilities, and the sanitary quality of the meat are rarely found. Thus, this study was designed to evaluate 2 cleaning and disinfecting programs regarding their influence on productive performance, elimination of Campylobacter, and characterization of Campylobacter jejuni strains when applied to broiler chickens’ facilities. Two subsequent flocks with 960 birds each were distributed into 32 pens containing 30 birds each. In the first, the whole flock was inoculated with a known strain of Campylobacter jejuni in order to contaminate the environment. In the second flock, performance and microbiological evaluations were done, characterizing an observational study between 2 cleaning and disinfection programs, regular and proposed. The regular program consisted of sweeping facilities, washing equipment and environment with water and neutral detergent. The proposed cleaning program consisted of dry and wet cleaning, application of 2 detergents (one acid and one basic) and 2 disinfectants (250 g/L glutaraldehyde and 185 g/L formaldehyde at 0.5% and 210 g/L para-chloro-meta-cresol at 4%). Total microorganism count in the environment and Campylobacter spp. identification were done for the microbiological assessment of the environment and carcasses. The positive samples were submitted to molecular identification of Campylobacter spp. and posterior genetic sequencing of the species identified as Campylobacter jejuni. The birds housed in the facilities and submitted to the proposed treatment had better performance when compared to the ones in the regular treatment, most likely because there was a smaller total microorganism count on the floor, walls, feeders and drinkers. The proposed program also resulted in a reduction of Campylobacter spp. on floors, drinkers and birds. Moreover, it was possible to identify 6 different Campylobacter jejuni strains in the facilities. The proposed treatment resulted in a positive influence on the birds’ performance and reduction of environment contamination for broiler chickens.

Arcobacter: an emerging food-borne zoonotic pathogen, its public health concerns and advances in diagnosis and control - a comprehensive review

Arcobacter has emerged as an important food-borne zoonotic pathogen, causing sometimes serious infections in humans and animals. Newer species of Arcobacter are being incessantly emerging (presently 25 species have been identified) with novel information on the evolutionary mechanisms and genetic diversity among different Arcobacter species. These have been reported from chickens, domestic animals (cattle, pigs, sheep, horses, dogs), reptiles (lizards, snakes and chelonians), meat (poultry, pork, goat, lamb, beef, rabbit), vegetables and from humans in different countries. Arcobacters are implicated as causative agents of diarrhea, mastitis and abortion in animals, while causing bacteremia, endocarditis, peritonitis, gastroenteritis and diarrhea in humans. Three species including A. butzleri, A. cryaerophilus and A. skirrowii are predominantly associated with clinical conditions. Arcobacters are primarily transmitted through contaminated food and water sources. Identification of Arcobacter by biochemical tests is difficult and isolation remains the gold standard method. Current diagnostic advances have provided various molecular methods for efficient detection and differentiation of the Arcobacters at genus and species level. To overcome the emerging antibiotic resistance problem there is an essential need to explore the potential of novel and alternative therapies. Strengthening of the diagnostic aspects is also suggested as in most cases Arcobacters goes unnoticed and hence the exact epidemiological status remains uncertain. This review updates the current knowledge and many aspects of this important food-borne pathogen, namely etiology, evolution and emergence, genetic diversity, epidemiology, the disease in animals and humans, public health concerns, and advances in its diagnosis, prevention and control.

The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women

The vaginal microbiome plays an important role in maternal and neonatal health. Imbalances in this microbiota (dysbiosis) during pregnancy are associated with negative reproductive outcomes, such as pregnancy loss and preterm birth, but the underlying mechanisms remain poorly understood. Consequently a comprehensive understanding of the baseline microbiome in healthy pregnancy is needed. We characterized the vaginal microbiomes of healthy pregnant women at 11–16 weeks of gestational age (n = 182) and compared them to those of non-pregnant women (n = 310). Profiles were created by pyrosequencing of the cpn60 universal target region. Microbiome profiles of pregnant women clustered into six Community State Types: I, II, III, IVC, IVD and V. Overall microbiome profiles could not be distinguished based on pregnancy status. However, the vaginal microbiomes of women with healthy ongoing pregnancies had lower richness and diversity, lower prevalence of Mycoplasma and Ureaplasma and higher bacterial load when compared to non-pregnant women. Lactobacillus abundance was also greater in the microbiomes of pregnant women with Lactobacillus-dominated CSTs in comparison with non-pregnant women. This study provides further information regarding characteristics of the vaginal microbiome of low-risk pregnant women, providing a baseline for forthcoming studies investigating the diagnostic potential of the microbiome for prediction of adverse pregnancy outcomes.

Response a chronic effects of PBDE-47: Up-regulations of HSP60 and HSP70 expression in freshwater bivalve Anodonta woodiana

Heat shock proteins (HSPs) play an important role in adaption of environmental stress by protein folding, membrane translocation, degradation of misfolded proteins and other regulatory processes. Our previous study showed oxidative stress generated from polybrominated diphenyl ether-47 (PBDE-47) could cause an acute toxicity on freshwater bivalve Anodonta Woodiana, but the effect of chronic toxicity need to be elucidated. In order to further investigate the chronic effect of PBDE-47, clams A. Woodiana were randomly divided into the PBDE-47 treated group administrated with PBDE-47 at a concentration 3.36 μg/L and control group treated with a similar volume dimethyl sulfoxide. Two complete HSP sequences were isolated from A. Woodianaa and respectively named AwHSP60 and AwHSP70. They were widely distributed in foot, gill, hepatopancreas, adductor muscle, heart, hemocytes and mantle. Administration of PBDE-47 could result in a significant up-regulation of AwHSP60 and AwHSP70 expressions in the hepatopancreas, gill and hemocytes. In the hepatopancreas, compared with that of control group, mRNA level of AwHSP60 increased more than 89.9% (P < 0.05) from day 1-15, AwHSP70 increased more 2.79 times (P < 0.01). In the gill, during experiment observed, expression of AwHSP60 increased more 2.09 times (P < 0.01) in contrasted with that of control group. Significant up-regulation of AwHSP70 expression showed a reversed U shape. In the hemocytes, AwHSP60 and AwHSP70 expressions of PBDE-47 treated group respectively increased more 2.09 times (P < 0.05) and 1.81 times (P < 0.05) compared with that of control group. These results indicated that up-regulations of AwHSP60 and AwHSP70 expression are contribute to enhancing adaption of bivalve A. Woodiana exposed to PBDE-47 treatment.

Usefulness of Housekeeping Genes for the Diagnosis of Helicobacter pylori Infection, Strain Discrimination and Detection of Multiple Infection

BACKGROUND

Helicobacter pylori infects human stomachs of over half the world's population, evades the immune response and establishes a chronic infection. Although most people remains asymptomatic, duodenal and gastric ulcers, MALT lymphoma and progression to gastric cancer could be developed. Several virulence factors such as flagella, lipopolysaccharide, adhesins and especially the vacuolating cytotoxin VacA and the oncoprotein CagA have been described for H. pylori. Despite the extensive published data on H. pylori, more research is needed to determine new virulence markers, the exact mode of transmission or the role of multiple infection.

MATERIALS AND METHODS

Amplification and sequencing of six housekeeping genes (amiA, cgt, cpn60, cpn70, dnaJ, and luxS) related to H. pylori pathogenesis have been performed in order to evaluate their usefulness for the specific detection of H. pylori, the genetic discrimination at strain level and the detection of multiple infection. A total of 52 H. pylori clones, isolated from 14 gastric biopsies from 11 patients, were analyzed for this purpose.

RESULTS

All genes were specifically amplified for H. pylori and all clones isolated from different patients were discriminated, with gene distances ranged from 0.9 to 7.8%. Although most clones isolated from the same patient showed identical gene sequences, an event of multiple infection was detected in all the genes and microevolution events were showed for amiA and cpn60 genes.

CONCLUSIONS

These results suggested that housekeeping genes could be useful for H. pylori detection and to elucidate the mode of transmission and the relevance of the multiple infection.

DNA Barcoding for Efficient Species- and Pathovar-Level Identification of the Quarantine Plant Pathogen Xanthomonas

Genus Xanthomonas comprises many economically important plant pathogens that affect a wide range of hosts. Indeed, fourteen Xanthomonas species/pathovars have been regarded as official quarantine bacteria for imports in China. To date, however, a rapid and accurate method capable of identifying all of the quarantine species/pathovars has yet to be developed. In this study, we therefore evaluated the capacity of DNA barcoding as a digital identification method for discriminating quarantine species/pathovars of Xanthomonas. For these analyses, 327 isolates, representing 45 Xanthomonas species/pathovars, as well as five additional species/pathovars from GenBank (50 species/pathovars total), were utilized to test the efficacy of four DNA barcode candidate genes (16S rRNA gene, cpn60, gyrB, and avrBs2). Of these candidate genes, cpn60 displayed the highest rate of PCR amplification and sequencing success. The tree-building (Neighbor-joining), ‘best close match’, and barcode gap methods were subsequently employed to assess the species- and pathovar-level resolution of each gene. Notably, all isolates of each quarantine species/pathovars formed a monophyletic group in the neighbor-joining tree constructed using the cpn60 sequences. Moreover, cpn60 also demonstrated the most satisfactory results in both barcoding gap analysis and the ‘best close match’ test. Thus, compared with the other markers tested, cpn60 proved to be a powerful DNA barcode, providing a reliable and effective means for the species- and pathovar-level identification of the quarantine plant pathogen Xanthomonas.

First reported case of Campylobacter lanienae enteritis in a human

Introduction:

Campylobacters are the most frequently identified bacteria causing diarrhoea in humans worldwide. Campylobacter lanienae was isolated for the first time in 2000 from faecal samples of two asymptomatic abattoir workers in Switzerland during a routine hygiene screen, but has never been associated with human disease.

Case presentation:

At hospital admission, the patient reported diarrhoea, lower abdominal cramps, nausea, one episode of bilious vomiting and low-grade fever of 38 °C. The patient was having 10 or more diarrheic stools per day as well as during the night, and had noticed blood mixed with the stools on several occasions. Stool cultures were negative for species of Salmonella and Shigella, Escherichia coli O157:H7 and Yersinia enterocolitica, but were positive for C. lanienae. Identification was made by classical biochemical testing, as well as 16S rRNA gene and cpn60 sequencing. The patient slowly improved without antibiotic treatment and was discharged nine days after admission with complete resolution of symptoms.

Conclusion:

On the whole it seems very likely that C. lanienae was the causative agent. Clinical microbiologists should be aware of this micro-organism which can be identified by phenotypic and molecular methods. The real burden of C. lanienae infection in humans might be underestimated and should be further investigated as a potential cause of human diarrhoea disease.

Impact of enterovirus and other enteric pathogens on oral polio and rotavirus vaccine performance in Bangladeshi infants

BACKGROUND

Oral polio vaccine (OPV) and rotavirus vaccine (RV) exhibit poorer performance in low-income settings compared to high-income settings. Prior studies have suggested an inhibitory effect of concurrent non-polio enterovirus (NPEV) infection, but the impact of other enteric infections has not been comprehensively evaluated.

METHODS

In urban Bangladesh, we tested stools for a broad range of enteric viruses, bacteria, parasites, and fungi by quantitative PCR from infants at weeks 6 and 10 of life, coincident with the first OPV and RV administration respectively, and examined the association between enteropathogen quantity and subsequent OPV serum neutralizing titers, serum rotavirus IgA, and rotavirus diarrhea.

RESULTS

Campylobacter and enterovirus (EV) quantity at the time of administration of the first dose of OPV was associated with lower OPV1-2 serum neutralizing titers, while enterovirus quantity was also associated with diminished rotavirus IgA (-0.08 change in log titer per tenfold increase in quantity; P=0.037), failure to seroconvert (OR 0.78, 95% CI: 0.64-0.96; P=0.022), and breakthrough rotavirus diarrhea (OR 1.34, 95% CI: 1.05-1.71; P=0.020) after adjusting for potential confounders. These associations were not observed for Sabin strain poliovirus quantity.

CONCLUSION

In this broad survey of enteropathogens and oral vaccine performance we find a particular association between EV carriage, particularly NPEV, and OPV immunogenicity and RV protection. Strategies to reduce EV infections may improve oral vaccine responses. ClinicalTrials.gov Identifier: NCT01375647.

Identification, characterization and description of Arcobacter faecis sp. nov., isolated from a human waste septic tank

A study on the taxonomic classification of Arcobacter species was performed on the cultures isolated from various fecal sources where an Arcobacter strain AF1078(T) from human waste septic tank near Ottawa, Ontario, Canada was characterized using a polyphasic approach. Genetic investigations including 16S rRNA, atpA, cpn60, gyrA, gyrB and rpoB gene sequences of strain AF1078(T) are unique in comparison with other arcobacters. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain is most closely related to Arcobacter lanthieri and Arcobacter cibarius. Analyses of atpA, cpn60, gyrA, gyrB and rpoB gene sequences suggested that strain AF1078(T) formed a phylogenetic lineage independent of other species in the genus. Whole-genome sequence, DNA-DNA hybridization, fatty acid profile and phenotypic analysis further supported the conclusion that strain AF1078(T) represents a novel Arcobacter species, for which the name Arcobacter faecis sp. nov. is proposed, with type strain AF1078(T) (=LMG 28519(T); CCUG 66484(T)).

A Side by Side Comparison of Bruker Biotyper and VITEK MS: Utility of MALDI-TOF MS Technology for Microorganism Identification in a Public Health Reference Laboratory

Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid, highly accurate, and cost-effective method for routine identification of a wide range of microorganisms. We carried out a side by side comparative evaluation of the performance of Bruker Biotyper versus VITEK MS for identification of a large and diverse collection of microorganisms. Most difficult and/or unusual microorganisms, as well as commonly encountered microorganisms were selected, including Gram-positive and negative bacteria, mycobacteria, actinomycetes, yeasts and filamentous fungi. Six hundred forty two strains representing 159 genera and 441 species from clinical specimens previously identified at the Laboratoire de santé publique du Québec (LSPQ) by reference methods were retrospectively chosen for the study. They included 254 Gram-positive bacteria, 167 Gram-negative bacteria, 109 mycobacteria and aerobic actinomycetes and 112 yeasts and moulds. MALDI-TOF MS analyses were performed on both systems according to the manufacturer’s instructions. Of the 642 strains tested, the name of the genus and / or species of 572 strains were referenced in the Bruker database while 406 were present in the VITEK MS IVD database. The Biotyper correctly identified 494 (86.4%) of the strains, while the VITEK MS correctly identified 362 (92.3%) of the strains (excluding 14 mycobacteria that were not tested). Of the 70 strains not present in the Bruker database at the species level, the Biotyper correctly identified 10 (14.3%) to the genus level and 2 (2.9%) to the complex/group level. For 52 (74.2%) strains, we obtained no identification, and an incorrect identification was given for 6 (8.6%) strains. Of the 178 strains not present in the VITEK MS IVD database at the species level (excluding 71 untested mycobacteria and actinomycetes), the VITEK MS correctly identified 12 (6.8%) of the strains each to the genus and to the complex/group level. For 97 (54.5%) strains, no identification was given and for 69 (38.7%) strains, an incorrect identification was obtained. Our study demonstrates that both systems gave a high level (above 85%) of correct identification for a wide range of microorganisms. However, VITEK MS gave more misidentification when the microorganism analysed was not present in the database, compared to Bruker Biotyper. This should be taken into account when this technology is used alone for microorganism identification in a public health laboratory, where isolates received are often difficult to identify and/or unusual microorganisms.

The GyrA encoded gene: A pertinent marker for the phylogenetic revision of Helicobacter genus

Phylogeny of Epsilonproteobacteria is based on sequencing of the 16S rRNA gene. However, this gene is not sufficiently discriminatory in Helicobacter species and alternative markers would be useful. In this study, the 16S rRNA, gyrA, hsp60, gyrB, and ureA-ureB gene sequences, as well as GyrA, HSP60 and GyrB protein sequences were analyzed as tools to support Helicobacter species phylogeny: 72 Helicobacter strains, belonging to 41 species of which 36 are validated species, were included. Results of the phylogenetic reconstructions of the GyrA gene encoded protein (approximately 730 residues) indicated the most stable trees to bootstrap resampling with a good separation of Helicobacter taxa, especially between gastric and enterohepatic species. Moreover, the GyrA tree revealed high similarity with that of the gyrB and ureA-ureB genes (restricted to urease-positive Helicobacter species). However, some differences in clustering were observed when compared to the hsp60 and 23S rRNA gene trees. Altogether, these revised phylogenies (except the 16S rRNA gene for enterohepatic Helicobacters) enabled reliable clustering of Helicobacter cinaedi and 'Flexispira' strains, determined a reliable position for Helicobacter mustelae (except the hsp60 gene) and for novel Helicobacter species proposed such as 'Helicobacter sanguini', 'Helicobacter apodemus' or 'Helicobacter winghamensis', and suggest that Helicobacter species MIT 09-6949 and MIT 05-5293 isolated from rodents constitute novel species. Although they are not commonly used to study the phylogeny of Epsilonproteobacteria, protein sequences and, in particular, the GyrA protein sequence may constitute pertinent phylogenetic markers for Helicobacter genus.

A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types

The vaginal microbiota is important in women’s reproductive and overall health. However, the relationships between the structure, function and dynamics of this complex microbial community and health outcomes remain elusive. The objective of this study was to determine the phylogenetic range and abundance of prokaryotes in the vaginal microbiota of healthy, non-pregnant, ethnically diverse, reproductive-aged Canadian women. Socio-demographic, behavioural and clinical data were collected and vaginal swabs were analyzed from 310 women. Detailed profiles of their vaginal microbiomes were generated by pyrosequencing of the chaperonin-60 universal target. Six community state types (CST) were delineated by hierarchical clustering, including three Lactobacillus-dominated CST (L. crispatus, L. iners, L. jensenii), two Gardnerella-dominated (subgroups A and C) and an “intermediate” CST which included a small number of women with microbiomes dominated by seven other species or with no dominant species but minority populations of Streptococcus, Staphylococcus, Peptoniphilus, E. coli and various Proteobacteria in co-dominant communities. The striking correspondence between Nugent score and deep sequencing CST continues to reinforce the basic premise provided by the simpler Gram stain method, while additional analyses reveal detailed cpn60-based phylogeny and estimated abundance in microbial communities from vaginal samples. Ethnicity was the only demographic or clinical characteristic predicting CST, with differences in Asian and White women (p = 0.05). In conclusion, this study confirms previous work describing four cpn60-based subgroups of Gardnerella, revealing previously undescribed CST. The data describe the range of bacterial communities seen in Canadian women presenting with no specific vaginal health concerns, and provides an important baseline for future investigations of clinically important cohorts.

Long-Lasting Outbreak of Erythromycin- and Ciprofloxacin-Resistant Campylobacter jejuni Subspecies jejuni From 2003 to 2013 in Men Who Have Sex With Men, Quebec, Canada

From January 2003 to December 2013, sexual transmission of 2 clades of Campylobacter jejuni subspecies jejuni isolates resulted in a prolonged outbreak among men who have sex with men living in Quebec, Canada. The outbreak isolates were acquired locally and were resistant to erythromycin and ciprofloxacin.

Arcobacter lanthieri sp. nov., isolated from pig and dairy cattle manure

A study was undertaken to determine the prevalence and diversity of species of the genus Arcobacter in pig and dairy cattle manure, which led to the identification of strains AF1440T, AF1430 and AF1581. Initially identified as Arcobacter butzleri based on colony morphology and initial PCR-confirmation tests, analyses of 16S rRNA gene sequences of these strains confirmed that they belonged to the genus Arcobacter and were different from all known species of the genus. The isolates formed a distinct group within the genus Arcobacter based on their 16S rRNA, gyrB, rpoB, cpn60, gyrA and atpA gene sequences and fatty acid profiles. Their unique species status was further supported by physiological properties and DNA-DNA hybridization that allowed phenotypic and genotypic differentiation of the strains from other species of the genus Arcobacter. The isolates were found to be oxidase, catalase and esterase positive and urease negative; they grew well at 30 °C under microaerophilic conditions and produced nitrite and acetoin. Based on their common origin and various physiological properties, it is proposed that the isolates are classified as members of a novel species with the name Arcobacter lanthieri sp. nov. The type strain is AF1440T ( = LMG 28516T = CCUG 66485T); strains AF1430 ( = LMG 28515 = CCUG 66486) and AF1581 ( = LMG 28517 = CCUG 66487) are reference strains.

Molecular diagnostic tools for detection and differentiation of phytoplasmas based on chaperonin-60 reveal differences in host plant infection patterns

Phytoplasmas (‘Candidatus Phytoplasma’ spp.) are insect-vectored bacteria that infect a wide variety of plants, including many agriculturally important species. The infections can cause devastating yield losses by inducing morphological changes that dramatically alter inflorescence development. Detection of phytoplasma infection typically utilizes sequences located within the 16S–23S rRNA-encoding locus, and these sequences are necessary for strain identification by currently accepted standards for phytoplasma classification. However, these methods can generate PCR products >1400 bp that are less divergent in sequence than protein-encoding genes, limiting strain resolution in certain cases. We describe a method for accessing the chaperonin-60 (cpn60) gene sequence from a diverse array of ‘Ca.Phytoplasma’ spp. Two degenerate primer sets were designed based on the known sequence diversity of cpn60 from ‘Ca.Phytoplasma’ spp. and used to amplify cpn60 gene fragments from various reference samples and infected plant tissues. Forty three cpn60 sequences were thereby determined. The cpn60 PCR-gel electrophoresis method was highly sensitive compared to 16S-23S-targeted PCR-gel electrophoresis. The topology of a phylogenetic tree generated using cpn60 sequences was congruent with that reported for 16S rRNA-encoding genes. The cpn60 sequences were used to design a hybridization array using oligonucleotide-coupled fluorescent microspheres, providing rapid diagnosis and typing of phytoplasma infections. The oligonucleotide-coupled fluorescent microsphere assay revealed samples that were infected simultaneously with two subtypes of phytoplasma. These tools were applied to show that two host plants, Brassica napus and Camelina sativa, displayed different phytoplasma infection patterns.

Description of Helicobacter valdiviensis sp. nov., an Epsilonproteobacteria isolated from wild bird faecal samples

Two Gram-stain-negative, gently curved rod-shaped isolates (WBE14T and WBE19), recovered from wild bird faecal samples in the city of Valdivia (Southern Chile) were subjected to a polyphasic taxonomic study. Results of a genus-specific PCR indicated that these isolates belonged to the genus Helicobacter . This was further confirmed by a phylogenetic analyses based on the 16S rRNA, 60 kDa heat-shock protein (cpn60) and gyrase subunit B (gyrB) genes, where both strains formed a novel phylogenetic line within this genus. The 16S rRNA gene sequence similarity of strain WBE14T to the type strains of all other species of the genus Helicobacter examined ranged from 89.4 to 97.0 %; Helicobacter brantae and Helicobacter pametensis were the most closely related species. However, on the basis of the protein-coding genes Helicobacter pullorum and Helicobacter canadensis are the most closely related species. These data, together with their different morphological and biochemical characteristics, revealed that these strains represent a novel species, for which the name Helicobacter valdiviensis sp. nov. is proposed, with the type strain WBE14T ( = CECT 8410T = LMG 27920T).

Campylobacter corcagiensis sp. nov., isolated from faeces of captive lion-tailed macaques (Macaca silenus)

An investigation of the prevalence of Campylobacter ureolyticus in a variety of animals led to the identification of the strain CIT 045(T), in the faeces of captive lion-tailed macaques (Macaca silenus). Originally, believed to be Campylobacter ureolyticus based on the colony morphology and positive urease test, analysis of 16S rRNA and hsp60 gene sequences of this isolate revealed that the strain differs significantly from other species of the genus Campylobacter described to date. Species-specific primers for 16S rRNA and hsp60 genes were designed and used to identify two additional strains isolated from faeces samples from other macaques. Nucleotide sequence analysis of the 16S rRNA and hsp60 genes revealed ≤95% and ≤82  % sequence similarity to recognized species of the genus Campylobacter respectively. All three isolates formed a distinct group within the genus Campylobacter based on their 16S rRNA and hsp60 sequences and matrix-assisted laser desorption/ionization time of flight (MALDI-TOF) profiles. The unique species status was further supported by phenotypic characteristics of the isolates. All isolates were found to be oxidase-, catalase- and urease-positive, they grew well at 37 °C and 42 °C and produced H2S on TSI (triple-sugar iron) and SIM (sulfide indole motility) media. The name Campylobacter corcagiensis sp. nov. is proposed for this novel species, with the strain CIT 045(T) as the type strain CIT 045(T) ( = LMG 27932(T), CCUG 64942(T)).

Antimicrobial susceptibility of Campylobacter jejuni and Campylobacter coli isolates obtained in Montreal, Quebec, Canada, from 2002 to 2013

From 2002 to 2013 in Montreal, Quebec, Canada, 38 Campylobacter coli isolates were more frequently erythromycin, tetracycline, and ciprofloxacin resistant than 440 Campylobacter jejuni subsp. jejuni isolates (18.4% versus 1.8%; P = 0.00005), of which the 148 isolates acquired abroad were more frequently erythromycin, tetracycline, and ciprofloxacin resistant than the 292 isolates acquired locally (5.4% versus 0%; P = 0.0001).

Isolation and characterization of Brachyspira spp. including "Brachyspira hampsonii" from lesser snow geese (Chen caerulescens caerulescens) in the Canadian Arctic

Brachyspira is associated with diarrhea and colitis in pigs, and control of these pathogens is complicated by their complex ecology. Identification of wildlife reservoirs of Brachyspira requires the discrimination of colonized animals and those simply contaminated through environmental exposure. Lesser snow geese (Chen caerulescens caerulescens) were sampled in the Canadian arctic during the summer of 2011, and cloacal swabs were cultured on selective media. Brachyspira isolates were obtained from 15/170 (8.8 %) samples, and 12/15 isolates were similar to isolates previously recovered from pigs, including "Brachyspira hampsonii", a recently characterized species associated with dysentery-like disease in pigs in North America. A pilot inoculation study with one strongly β-hemolytic B. hampsonii isolate resulted in fecal shedding of the isolate by inoculated pigs for up to 14 days post-inoculation, but no severe clinical disease. Results of this study indicate that lesser snow geese can be colonized by Brachyspira strains that can also colonize pigs. Millions of lesser snow geese (C. caerulescens caerulescens) travel through the major pork-producing areas of Canada and the USA during their annual migration, making them a potential factor in the continental distribution of these bacteria.

Campylobacter coli outbreak in men who have sex with men, Quebec, Canada, 2010-2011

During September 2010–November 2011, a cluster of erythromycin-susceptible, tetracycline- and ciprofloxacin-resistant Campylobacter coli pulsovar 1 infections was documented, involving 10 case-patients, in Montreal, Quebec, Canada. The findings suggested sexual transmission of an enteric infection among men who have sex with men.

Isolation rates of Campylobacter fetus subsp venerealis from bovine preputial samples via passive filtration on nonselective medium versus selective medium, with and without transport medium

OBJECTIVE

To compare the recovery rates of Campylobacter fetus subsp venerealis (Cfv) from preputial scrapings of infected bulls with passive filtration on selective medium versus nonselective medium, with and without transport medium.

SAMPLES

217 preputial scrapings from 12 bulls (4 naturally and 8 artificially infected with Cfv).

PROCEDURES

Preputial scrapings were collected in 2 mL of PBS solution and bacteriologically cultured directly on Skirrow medium or passively filtered through 0.65-μm filters onto blood agar, with or without 24 hour preincubation in modified Weybridge transport enrichment medium (TEM). After 72 hours, plates were examined for Cfv and bacterial and fungal contamination or overgrowth.

RESULTS

Passive filtration of fresh preputial scrapings onto blood agar yielded significantly higher recovery rates of Cfv (86%) than direct plating on Skirrow medium (32%), whereas recovery from TEM was poor for both media (35% and 40%, respectively). Skirrow cultures without TEM were significantly more likely to have fungal contamination than were cultures performed with any other technique, and fungal contamination was virtually eliminated by passive filtration onto blood agar. Bacterial contamination by Pseudomonas spp was significantly more common with Skirrow medium versus passive filtration on blood agar, regardless of TEM use.

CONCLUSIONS AND CLINICAL RELEVANCE

The use of transport medium and the choice of culture medium had significant effects on Cfv recovery and culture contamination rates from clinical samples. Both factors should be considered when animals are tested for this pathogen.

[Application of restriction fragment length polymorphism-polymerase chain reaction-flaA and resistotype to identify potential undiagnosed outbreaks of campylobacteriosis in Spain]

INTRODUCTION

Outbreaks of campylobacteriosis are infrequent and usually involve a low number of patients, although it is estimated that many more remain undiagnosed. The most successful techniques for outbreak investigation in Campylobacter spp. (PFGE, MLST) have the drawback of being laborious and not available in many laboratories.

METHODS

During the year 2008, 352 isolates of C. jejuni and C. coli from 16 hospitals were received in our laboratory. All strains were genotyped by RFLP-PCR-flaA (flaA type) and phenotyped with their resistotype. It was established that the strains of the same species from the same hospital, isolated over a period of up to 11 days, with MIC values of±1 dilution with the same flaA type could belong to an outbreak. Strains that met these criteria would be later subtyped by KpnI-PFGE and MLST.

RESULTS

A total of 23 out of 352 isolates, distributed in 10 groups, met the criteria for being associated with putative undiagnosed outbreaks. The similarity of the PFGE-profiles in 8 groups was greater than 95% among the isolates from each group. In 7 of the groups, the sequence types (MLST) were coincident.

CONCLUSIONS

The use of 2 easy markers (resistotype and RFLP-PCR-flaA) may detect isolates probably belonging to an undiagnosed outbreak of campylobacteriosis. Accurate diagnosis requires other molecular markers and epidemiological data of each isolate. The study suggests that, as in other countries, the number of outbreaks of campylobacteriosis in Spain is probably underestimated.

The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data

Barcoding with molecular sequences is widely used to catalogue eukaryotic biodiversity. Studies investigating the community dynamics of microbes have relied heavily on gene-centric metagenomic profiling using two genes (16S rRNA and cpn60) to identify and track Bacteria. While there have been criteria formalized for barcoding of eukaryotes, these criteria have not been used to evaluate gene targets for other domains of life. Using the framework of the International Barcode of Life we evaluated DNA barcodes for Bacteria. Candidates from the 16S rRNA gene and the protein coding cpn60 gene were evaluated. Within complete bacterial genomes in the public domain representing 983 species from 21 phyla, the largest difference between median pairwise inter- and intra-specific distances (“barcode gap”) was found from cpn60. Distribution of sequence diversity along the ∼555 bp cpn60 target region was remarkably uniform. The barcode gap of the cpn60 universal target facilitated the faithful de novo assembly of full-length operational taxonomic units from pyrosequencing data from a synthetic microbial community. Analysis supported the recognition of both 16S rRNA and cpn60 as DNA barcodes for Bacteria. The cpn60 universal target was found to have a much larger barcode gap than 16S rRNA suggesting cpn60 as a preferred barcode for Bacteria. A large barcode gap for cpn60 provided a robust target for species-level characterization of data. The assembly of consensus sequences for barcodes was shown to be a reliable method for the identification and tracking of novel microbes in metagenomic studies.

Resolution and characterization of distinct cpn60-based subgroups of Gardnerella vaginalis in the vaginal microbiota

Bacterial vaginosis (BV), characterized by a shift of the vaginal microbiota from a Lactobacillus-dominated community to a dense biofilm containing a complex mixture of organisms, is an important risk factor in poor reproductive health outcomes. The Nugent score, based on Gram stain, is used to diagnose BV and Gardnerella vaginalis abundance in the sample is one factor determining Nugent score. A high Nugent score is indicative of BV but does not always correspond to the presence of clinical symptoms. G. vaginalis is recognized as a heterogeneous group of organisms, which can also be part of the normal, healthy vaginal microbiome. In addition, asymptomatic BV and non-Gardnerella types of BV are being recognized. In an attempt to resolve the heterogeneous group of G. vaginalis, a phylogenetic tree of cpn60 universal target sequences from G. vaginalis isolates was constructed that indicates the existence of four subgroups of G. vaginalis. This subdivision, supported by whole genome similarity calculation of representative strains using JSpecies, demonstrates that these subgroups may represent different species. The cpn60 subgroupings did not correspond with the Piot biotyping scheme, but did show consistency with ARDRA genotyping and sialidase gene presence. Isolates from all four subgroups produced biofilm in vitro. We also investigated the distribution of G. vaginalis subgroups in vaginal samples from Kenyan women with Nugent scores consistent with BV, Intermediate and Normal microbiota (n = 44). All subgroups of G. vaginalis were detected in these women, with a significant difference (z = −3.372, n = 39, p = 0.001) in frequency of G. vaginalis subgroup B between BV and Normal groups. Establishment of a quantifiable relationship between G. vaginalis subgroup distribution and clinical status could have significant diagnostic implications.

Selection, phenotyping and identification of acid and hydrogen peroxide producing bacteria from vaginal samples of Canadian and East African women

The common but poorly understood condition known as bacterial vaginosis (BV) increases vulnerability to HIV infection and is associated with the absence of H₂O₂-producing Lactobacillus. Vaginal lactic acid bacteria (LAB) produce anti-HIV factors such as organic acids and hydrogen peroxide (H₂O₂), and may bind and inactivate HIV particles during scavenging of mannose. These factors define potential criteria for initial selection of candidate probiotics to block heterosexual transmission of HIV. Therefore, the primary goal of this study was to characterize acid production on mannose and H₂O₂ production in vaginal isolates from Canadian adolescents (192 isolates, 16 individuals) and commercial sex workers in Nairobi, Kenya (576 isolates, 96 individuals). Selection of isolates from H₂O₂-detecting media suggested an idiosyncratic individual-level profile and extensive phenotypic diversity, including the identification of a subset of “double-strong” acid- and H₂O₂-producers with phenotypes similar to well-characterized probiotic strains. Molecular fingerprinting of all isolates by capillary electrophoresis of 16S-23S rRNA interspacer amplicons was coupled with chaperonin-60 universal target (cpn60 UT) sequencing in a subset, tentatively identifying 96% of isolates although only 19% were sequenced. Most isolates belonged to Lactobacillus, Streptococcus, Bifidobacterium or Gardnerella, with a total of 37 species in 15 genera, as well as 5 potentially novel organisms, identified in this study. This sensitivity was likely enhanced by phenotype-based selection on two chromogenic media formulations. Identification of double-strong isolates may provide a rational basis for selection and further characterization of vaginal probiotics, with potential application as part of HIV prevention initiatives in western Canada and East Africa.

A 'universal' type II chaperonin PCR detection system for the investigation of Archaea in complex microbial communities

Bacteria and Archaea are evolutionarily and biochemically distinct domains found together in many environments. Robust 'universal' PCR primer sets targeting both the bacterial 16S rRNA gene and the type I chaperonin gene have been established. However, 'universal' PCR primers for Archaea are currently limited to the 16S rRNA gene. We investigated the type II chaperonin (known as the thermosome, TF55, CCT or TCP-1) as a potential universal target (UT) for Archaea. Reproducible amplification of thermosome gene sequences from all major phyla tested was achieved through the application of a mixture or 'cocktail' of two forward and two reverse primers. Phylogenies based on the ∼750-bp thermosome UT were congruent with 16S rRNA gene phylogenies while exhibiting longer branch lengths, improving resolution of closely related taxa. 'Universal' thermosome primers were applied to profiling the archaeal community of dairy cow rumen and results compared with profiles based on the 16S rRNA gene and methyl co-enzyme M reductase (methanogen-specific) gene. Clone libraries generated from each target gene, as well as a pyrosequencing profile of one thermosome rumen library, revealed that all three targets consistently detected Methanobrevibacter smithii, Methanobrevibacter ruminantium and Methanosphaera stadtmanae as the dominant constituents; however, thermosome gene sequences were more diverse than either of the other targets providing a higher resolution description of the archaeal community. These findings demonstrate that a 'universal' thermosome PCR protocol is a powerful metagenomic tool for detecting and characterizing Archaea and archaeal communities.