RNA polymerase β-subunit gene (rpoB) sequence analysis for the identification of Bacteroides spp

A Globally Distributed Bacteroides caccae Strain Is the Most Prevalent Mother-Child Shared Bacteroidaceae Strain in a Large Scandinavian Cohort

Bacteroides and Phocaeicola, members of the family Bacteroidaceae, are among the first microbes to colonize the human infant gut. While it is known that these microbes can be transmitted from mother to child, our understanding of the specific strains that are shared and potentially transmitted is limited. In this study, we aimed to investigate the shared strains of Bacteroides and Phocaeicola in mothers and their infants. We analyzed fecal samples from pregnant woman recruited at 18 weeks of gestation from the PreventADALL study, as well as offspring samples from early infancy, including skin swab samples taken within 10 min after birth, the first available fecal sample (meconium), and fecal samples at 3 months of age. We screened 464 meconium samples for Bacteroidaceae, with subsequent selection of 144 mother-child pairs for longitudinal analysis, based on the presence of Bacteroidaceae, longitudinal sample availability, and delivery mode. Our results showed that Bacteroidaceae members were mainly detected in samples from vaginally delivered infants. We identified high prevalences of Phocaeicola vulgatus, Phocaeicola dorei, Bacteroides caccae, and Bacteroides thetaiotaomicron in mothers and vaginally born infants. However, at the strain level, we observed high prevalences of only two strains: a B. caccae strain and a P. vulgatus strain. Notably, the B. caccae strain was identified as a novel component of mother-child shared strains, and its high prevalence was also observed in publicly available metagenomes worldwide. Our findings suggest that mode of delivery may play a role in shaping the early colonization of the infant gut microbiota, in particular the colonization of Bacteroidaceae members. IMPORTANCE Our study provides evidence that Bacteroidaceae strains present on infants' skin within 10 min after birth, in meconium samples, and in fecal samples at 3 months of age in vaginally delivered infants are shared with their mothers. Using strain resolution analyses, we identified two strains, belonging to Bacteroides caccae and Phocaeicola vulgatus, as shared between mothers and their infants. Interestingly, the B. caccae strain showed a high prevalence worldwide, while the P. vulgatus strain was less common. Our findings also showed that vaginal delivery was associated with early colonization of Bacteroidaceae members, whereas cesarean section delivery was associated with delayed colonization. Given the potential for these microbes to influence the colonic environment, our results suggest that understanding the bacterial-host relationship at the strain level may have implications for infant health and development later in life.

Development and Clinical Application of a Multilocus Sequence Typing Scheme for Bacteroides fragilis Based on Whole-Genome Sequencing Data

Bacteroides fragilis is among the most abundant and pathogenic bacterial species in the gut microbiota and is associated with diarrheal disease in children, inflammatory bowel disease, and the development of colorectal cancer. It is increasingly resistant to potent antimicrobial agents such as carbapenems and metronidazole, making it among the most resistant anaerobic bacteria. These factors combined call for increased monitoring of B. fragilis and its population structure on a worldwide scale. Here, we present a possible solution through the development of a multilocus sequence typing scheme (MLST). The scheme is based on seven core gene fragments: groL (hsp60), rpoB, recA, dnaJ, rprX, prfA, and fusA. These gene fragments possess high discriminatory power while retaining concordance with whole core genome-based phylogenetic analysis. The scheme proved capable of differentiating B. fragilis isolates at the strain level. It offers a standardized method for molecular typing and can be applied to isolates from various sampling backgrounds, such as patient isolates, environmental samples, and strains obtained from food and animal sources. In total, 567 B. fragilis genomes were sequence typed and their isolate data collected. The MLST scheme clearly divided the B. fragilis population into two divisions based on the presence of the cfiA and cepA resistance genes. However, no other specific subpopulations within the analyzed genomes were found to be associated with any specific diseases or geographical location. With this MLST scheme, we hope to provide a powerful tool for the study and monitoring of B. fragilis on an international scale. IMPORTANCE Here, we present the first MLST scheme for Bacteroides fragilis, one of the most abundant pathogenic bacteria in the human gut microbiota. The scheme enables standard classification and monitoring of B. fragilis on a worldwide scale and groups the majority of current isolate data in one place. A more unified approach to the collection and analysis of B. fragilis data could provide crucial insights into how the pathogen operates and develops as a species. Close monitoring of B. fragilis is especially relevant, as it is increasingly resistant to potent antimicrobial agents and engages in horizontal gene transfer with other bacteria. Hopefully, this approach will guide new discoveries into how B. fragilis evolves and interacts with its human host. Additionally, the scheme could potentially be applied to other species of the genus Bacteroides.

The Changes in Epidemiology of Imipenem-Resistant Acinetobacter baumannii Bacteremia in a Pediatric Intensive Care Unit for 17 Years

BACKGROUND

Acinetobacter baumannii infections cause high morbidity and mortality in intensive care unit (ICU) patients. However, there are limited data on the changes of long-term epidemiology of imipenem resistance in A. baumannii bacteremia among pediatric ICU (PICU) patients.

METHODS

A retrospective review was performed on patients with A. baumannii bacteremia in PICU of a tertiary teaching hospital from 2000 to 2016. Antimicrobial susceptibility tests, multilocus sequence typing (MLST), and polymerase chain reaction for antimicrobial resistance genes were performed for available isolates.

RESULTS

A. baumannii bacteremia occurred in 27 patients; imipenem-sensitive A. baumannii (ISAB, n = 10, 37%) and imipenem-resistant A. baumannii (IRAB, n = 17, 63%). There was a clear shift in the antibiogram of A. baumannii during the study period. From 2000 to 2003, all isolates were ISAB (n = 6). From 2005 to 2008, both IRAB (n = 5) and ISAB (n = 4) were isolated. However, from 2009, all isolates were IRAB (n = 12). Ten isolates were available for additional test and confirmed as IRAB. MLST analysis showed that among 10 isolates, sequence type 138 was predominant (n = 7). All 10 isolates were positive for OXA-23-like and OXA-51-like carbapenemase. Of 27 bacteremia patients, 11 were male (41%), the median age at bacteremia onset was 5.2 years (range, 0-18.6 years). In 33% (9/27) of patients, A. baumannii was isolated from tracheal aspirate prior to development of bacteremia (median, 8 days; range, 5-124 days). The overall case-fatality rate was 63% (17/27) within 28 days. There was no statistical difference in the case fatality rate between ISAB and IRAB groups (50% vs. 71%; P = 0.422).

CONCLUSION

IRAB bacteremia causes serious threat in patients in PICU. Proactive infection control measures and antimicrobial stewardship are crucial for managing IRAB infection in PICU.

Bacteroides pyogenes isolated from appendiceal abscess in a patient without animal contact

Bacteroides pyogenes is a member of the oral flora of cats and dogs. We report a case of B. pyogenes isolated from an appendiceal abscess in a patient without a history of animal contact. This species was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and sequencing of 16S rRNA, rpoB, gyrB and hsp60 genes.

Occupational exposure to anaerobic bacteria in a waste sorting plant

The study focused on exposure assessment to bacterial aerosols and organic dust in waste sorting plant. Samples were collected at different workplaces of waste sorting cycle i.e.: waste press, reloading area, loading of conveyor belt, sorting cabin, sorting hall, and control room. A quantitative analysis of aerobic and anaerobic bacteria was supplemented by qualitative analysis of anaerobic biota with the use of culture-based methods and biochemical tests. In addition, inhalable dust concentrations were also evaluated. To confirm the presence of Clostridium genus, the PCR reaction with specific primers (Chis150f and ClostIr) was performed. The average concentration of total bacteria in waste sorting plant was 4347 CFU m^-3 (SD = 2439), of which 66% were anaerobic strains (2852 CFU m^-3; SD = 2127). It was found that about 24% of anaerobic bacteria belonged to Clostridium genus (682 CFU m^-3; SD = 633). The highest contamination with anaerobic bacteria was observed near the waste reloading plant (3740 CFU m^-3), and the lowest in the control room (850 CFU m^-3). The average concentration of inhalable dust in the waste sorting plant was 0.81 mg m^-3 (SD = 0.59). The correlation analysis showed that the presence of anaerobic bacteria, including clostridia was significantly determined by the microclimate parameters. Qualitative analysis showed the presence of 16 anaerobic species belonging to 9 genera, of which Actinomyces, Clostridium, and Gemella were present at all workplaces. The molecular analysis confirmed the presence of Clostridium genus in both bioaerosol and settled dust samples.Implications: The study showed that anaerobic bacteria should be taken into account as an important component of this microbiota when assessing the exposure of waste sorting workers to biological agents. However, future studies should investigate more precisely how the composition of sorted waste as well as the season can affect the diversity of anaerobic bacteria in this working environment. More attention should be paid to regular cleaning of equipment surfaces in the plant, as deposited organic dust is an important reservoir of anaerobic bacteria, including those of a potentially pathogenic nature.

Identification of uncultured bacteria from abscesses of exotic pet animals using broad-range nested 16S rRNA polymerase chain reaction and Sanger sequencing

Background:

The Sanger sequencing technique has been questioned and challenged by advanced high-throughput sequencing approaches. Sanger sequencing seems to be an obsolete technology. However, there are still research problems that could be answered using the Sanger sequencing technology. Fastidious obligate anaerobic bacteria are mostly associated with abscesses in animals. These bacteria are difficult to isolate from abscesses and are frequently excluded due to the bias of conventional bacterial culturing.

Aim:

This study demonstrated the usefulness of a broad-range polymerase chain reaction (PCR) with Sanger sequencing to identify the majority population of bacteria in abscesses from exotic pet animals.

Materials and Methods:

This study performed a pilot investigation of abscesses from 20 clinical cases (17 rabbits, 2 hedgehogs, and 1 sugar glider) using standard culture methods for both aerobes and anaerobes and broad-range nested PCR targeting the 16S rRNA gene followed by the Sanger sequencing technique.

Results:

The standard culture and PCR techniques detected bacteria in 9 and 17 of 20 samples, respectively. From the 17 sequencings of the 16S rRNA, 10 PCR products were found to be closely related with obligate anaerobes including Bacteroides spp., Fusobacterium spp., Prevotella spp. Phylogenetic analysis using the rpoB gene revealed that the species for the Bacteroides was thetaiotaomicron and for the Fusobacterium was varium and nucleatum. However, the amplification of the rpoB gene for the Prevotella spp. was unsuccessful. Correlations between the standard culture and PCR techniques were found in 9 (6 positive and 3 negative samples) of 20 samples. Eleven samples were discordant between the standard culture and PCR techniques which were composed of eight samples negative by culture but positive by PCR and three samples had different bacteria by the culture and PCR techniques.

Conclusion:

According to this study, broad-range PCR combined with Sanger sequencing might be useful for the detection of dominant anaerobic bacteria in abscesses that were overlooked based on conventional bacterial culture.

Anaerobic bacteria in wastewater treatment plant

Purpose

The objective of this study was to assess exposure to anaerobic bacteria released into air from sewage and sludge at workplaces from a wastewater treatment plant (WWTP).

Methods

Samples of both sewage and sludge were collected at six sampling points and bioaerosol samples were additionally collected (with the use of a 6-stage Andersen impactor) at ten workplaces covering different stages of the technological process. Qualitative identification of all isolated strains was performed using the biochemical API 20A test. Additionally, the determination of Clostridium pathogens was carried out using 16S rRNA gene sequence analysis.

Results

The average concentration of anaerobic bacteria in the sewage samples was 5.49 × 10⁴ CFU/mL (GSD = 85.4) and in sludge—1.42 × 10⁶ CFU/g (GSD = 5.1). In turn, the average airborne bacterial concentration was at the level of 50 CFU/m³ (GSD = 5.83) and the highest bacterial contamination (4.06 × 10³ CFU/m³) was found in winter at the bar screens. In total, 16 bacterial species were determined, from which the predominant strains belonged to Actinomyces, Bifidobacterium, Clostridium, Propionibacterium and Peptostreptococcus genera. The analysis revealed that mechanical treatment processes were responsible for a substantial emission of anaerobic bacteria into the air. In both the sewage and air samples, Clostridium perfringens pathogen was identified.

Conclusions

Anaerobic bacteria were widely present both in the sewage and in the air at workplaces from the WWTP, especially when the technological process was performed in closed spaces. Anaerobic bacteria formed small aggregates with both wastewater droplets and dust particles of sewage sludge origin and as such may be responsible for adverse health outcomes in exposed workers.

Biogeography of Nocardiopsis strains from hypersaline environments of Yunnan and Xinjiang Provinces, western China

The genus Nocardiopsis is a widespread group within the phylum Actinobacteria and has been isolated from various salty environments worldwide. However, little is known about whether biogeography affects Nocardiopsis distribution in various hypersaline environments. Such information is essential for understanding the ecology of Nocardiopsis. Here we analyzed 16S rRNA, gyrB, rpoB and sodA genes of 78 Nocardiopsis strains isolated from hypersaline environments in Yunnan and Xinjiang Provinces of western China. The obtained Nocardiopsis strains were classified into five operational taxonomic units, each comprising location-specific phylo- and genotypes. Statistical analyses showed that spatial distance and environmental factors substantially influenced Nocardiopsis distribution in hypersaline environments: the former had stronger influence at large spatial scales, whereas the latter was more influential at small spatial scales.

Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses

BACKGROUND

Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported.

METHODS

The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains.

RESULTS

Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed.

CONCLUSION

Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3-100%. However, the inter-species similarities were relatively low, ranging from 68.7-97.9%. The housekeeping genes rpoB and gyrB1 were demonstrated to be alternative classification markers to the species level based on intra- and inter-species comparisons, whereas based on phylogenetic tree rpoB proved to be reliable phylogenetic marker for the genus Prevotella.

Falsiporphyromonas endometrii gen. nov., sp. nov., isolated from the post-partum bovine uterus, and emended description of the genus Porphyromonas Shah and Collins 1988

Two black-pigmented, anaerobic bacterial strains, designated LMM 40T and LMM 41, were isolated from the bovine post-partum endometrium of two Holstein cows. The 16S rRNA gene sequences of the two strains were identical and showed the highest similarity to the 16S rRNA gene sequence of the type strain of Porphyromonas crevioricanis (90.2 %) but only 85.1 % 16S rRNA gene sequence similarity to the type strain of the type species of the genus Porphyromonas , Porphyromonas asaccharolytica . The major fatty acid profiles of the two strains were similar to those of species of the genus Porphyromonas , containing iso-C15 : 0 as the major component and moderate amounts of anteiso-C15 : 0, iso-C13 : 0, C15 : 0 and C16 : 0. Hydroxylated fatty acids, such as iso-C14 : 0 3-OH, iso-C16 : 0 3-OH and iso-C17 : 0 3-OH, were also detected. The quinone profiles were dominated by the menaquinones MK-8 and MK-9, while spermidine was the major polyamine. The polar lipid profiles contained major amounts of phosphatidylethanolamine, an unidentified phospholipid, an unidentified aminophospholipid and two unidentified lipids and minor amounts of phosphatidylglycerol, an unidentified aminolipid, a second unidentified aminophospholipid and an unidentified glycolipid. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The genomic DNA G+C contents of LMM 40T and LMM 41 were 40.7 and 41.3 mol%, respectively. Based on a polyphasic approach, including phylogenetic analysis, physiological and biochemical tests as well as metabolic fingerprinting, it is proposed that the two strains are members of a novel genus and species, for which the name Falsiporphyromonas endometrii gen. nov., sp. nov. is proposed. The type strain of Falsiporphyromonas endometrii is LMM 40T ( = DSM 27210T = CCUG 64267T). An emended description of the genus Porphyromonas is also presented.

Identification and classification of the genus Bacteroides by multilocus sequence analysis

Multilocus sequence analysis (MLSA) was performed on representative species of the genus Bacteroides. Internal fragments of the genes selected, dnaJ, gyrB, hsp60, recA, rpoB and 16S rRNA, were amplified by direct PCR and then sequenced from 38 Bacteroides strains representing 35 species. Neighbour-joining (NJ), maximum-likelihood (ML) and maximum-parsimony (MP) phylogenies of the individual genes were compared. The data confirm that the potential for discrimination of Bacteroides species is greater using MLSA of housekeeping genes than 16S rRNA genes. Among the housekeeping genes analysed, gyrB was the most informative, followed by dnaJ. Analyses of concatenated sequences (4816 bp) of all six genes revealed robust phylogenetic relationships among different Bacteroides species when compared with the single-gene trees. The NJ, ML and MP trees were very similar, and almost fully resolved relationships of Bacteroides species were obtained, to our knowledge for the first time. In addition, analysis of a concatenation (2457 bp) of the dnaJ, gyrB and hsp60 genes produced essentially the same result. Ten distinct clades were recognized using the SplitsTree4 program. For the genus Bacteroides, we can define species as a group of strains that share at least 97.5% gene sequence similarity based on the fragments of five protein-coding housekeeping genes and the 16S rRNA gene. This study demonstrates that MLSA of housekeeping genes is a valuable alternative technique for the identification and classification of species of the genus Bacteroides.

hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes

hsp60 gene sequences were determined for members of the genus Bacteroides and sequence similarities were compared with those obtained for the 16S rRNA gene. Among the 29 Bacteroides type strains, the mean sequence similarity of the hsp60 gene (84.5 %) was significantly less than that of the 16S rRNA gene (90.7 %), indicating a high discriminatory power of the hsp60 gene. Species of the genus Bacteroides were differentiated well by hsp60 gene sequence analysis, except for Bacteroides pyogenes JCM 6294T, Bacteroides suis JCM 6292T and Bacteroides tectus JCM 10003T. The hsp60 gene sequence analysis and the levels of DNA–DNA relatedness observed demonstrated that these three type strains are a single species. Consequently, B. suis and B. tectus are heterotypic synonyms of B. pyogenes. This study suggests that the hsp60 gene is an alternative phylogenetic marker for the classification of species of the genus Bacteroides.

Differentiation of Bifidobacterium species using partial RNA polymerase {beta}-subunit (rpoB) gene sequences

Partial RNA polymerase β-subunit gene (rpoB) sequences (315 bp) were determined and used to differentiate the type strains of 23 species of the genus Bifidobacterium. The sequences were compared with those of the partial hsp60 (604 bp) and 16S rRNA genes (1475 or 1495 bp). The rpoB gene sequences showed nucleotide sequence similarities ranging from 84.1 % to 99.0 %, while the similarities of the hsp60 sequences ranged from 78.5 % to 99.7 % and the 16S rRNA gene sequence similarities ranged from 89.4 % to 99.2 %. The phylogenetic trees constructed from the sequences of these three genes showed similar clustering patterns, with the exception of several species. The Bifidobacterium catenulatum-Bifidobacterium pseudocatenulatum, Bifidobacterium pseudolongum subsp. pseudolongum-Bifidobacterium pseudolongum subsp. globosum and Bifidobacterium gallinarum-Bifidobacterium pullorum-Bifidobacterium saeculare groups were more clearly differentiated in the partial rpoB and hsp60 gene sequence trees than they were in the 16S rRNA gene tree. Based on sequence similarities and tree topologies, the newly determined rpoB gene sequences are suitable molecular markers for the differentiation of species of the genus Bifidobacterium and support various other molecular tools used to determine the relationships among species of this genus.

Molecular characterization of Capnocytophaga canimorsus and other canine Capnocytophaga spp. and assessment by PCR of their frequencies in dogs

Capnocytophaga canimorsus can be a virulent pathogen, whereas C. cynodegmi is of low virulence. Heterogeneity within these species, their frequency in dogs, and pathogenicity factors are largely unknown. Strains from blood cultures from patients presumptively identified as C. canimorsus (n = 25) and as C. cynodegmi by rrs analysis (n = 4), blood cultures from dogs (n = 8), blood cultures from cats (n = 2), and cultures from swabs from dog mouths (n = 53) were analyzed. PCR-restriction fragment length polymorphism (PCR-RFLP), a species-specific PCR on rpoB, and rrs sequencing were used. All 29 strains from human blood cultures could be grouped into three PCR-RFLP types. One included the C. canimorsus type strain, and the other types were closely related. Two canine strains were C. canimorsus and grouped into the least common RLFP pattern group. Five were C. cynodegmi and clustered with the reference strain. One canine and both feline strains were distinct. Four human strains that presumptively had been identified as C. cynodegmi by RNA gene sequence analysis clustered with the C. canimorsus strains by both PCR-RFLP and the sequence-specific PCR of the rpoB gene. C. canimorsus DNA was present in 73% (range, 61 to 85%) of dogs' mouths, and C. cynodegmi DNA was present in 96% (range, 94 to 100%) of dogs' mouths. As defined by rpoB PCR-RFLP and by PCRs using specific primers, all strains from human blood were C. canimorsus. The sequencing of rrs genes suggested the presence of different gene copies in a few strains, indicating that the method is less appropriate for species identification. Both species are present in the majority of dogs. Additional Capnocytophaga species occur in dogs' and cats' mouths.