Unique case of Helicobacter sp. osteomyelitis in an immunocompetent child diagnosed by broad-range 16S PCR

Diagnostic yield of broad-range 16s rRNA gene PCR varies by sample type and is improved by the addition of qPCR panels targeting the most common causative organisms

Introduction. Molecular techniques are used in the clinical microbiology laboratory to support culture-based diagnosis of infection and are particularly useful for detecting difficult to culture bacteria or following empirical antimicrobial treatment.Hypothesis/Gap Statement. Broad-range 16S rRNA PCR is a valuable tool that detects a wide range of bacterial species. Diagnostic yield is low for some sample types but can be improved with the addition of qPCR panels targeting common bacterial pathogens.Aim. To evaluate the performance of a broad-range 16S rRNA gene PCR and the additional diagnostic yield of targeted qPCR applied to specimens according to a local testing algorithm.Methodology. In total, 6130 primary clinical samples were collected as part of standard clinical practice from patients with suspected infection during a 17 month period. Overall, 5497 samples were tested by broad-range 16S rRNA gene PCR and a panel of targeted real-time qPCR assays were performed on selected samples according to a local testing algorithm. An additional 633 samples were tested by real-time qPCR only. The 16S rRNA gene PCR was performed using two assays targeting different regions of the 16S rRNA gene. Laboratory developed qPCR assays for seven common bacterial pathogens were also performed. Data was extracted retrospectively from Epic Beaker Laboratory Information Management System (LIMS).Results. Broad-range 16S rRNA gene PCR improves diagnostic yield in culture-negative samples and detects a large range of bacterial species. Streptococcus spp., Staphylococcus spp. and the Enterobacteriaceae family are detected the most frequently in samples with a single causative organism, but mixed samples frequently contained anaerobic species. The highest diagnostic yield was obtained from abscess, pus and empyema samples; 44.9 % were positive by 16S and 61 % were positive by the combined 16S and targeted qPCR testing algorithm. Samples with a particularly low diagnostic yield were blood, with 3.3 % of samples positive by 16S and CSF with 4.8 % of samples positive by 16S. The increased diagnostic yield of adding targeted qPCR is largest (~threefold) in these two sample types.Conclusion. Broad-range PCR is a powerful technique that can detect a very large range of bacterial pathogens but has limited diagnostic sensitivity. The data in this report supports a testing strategy that combines broad-range and targeted bacterial PCR assays for maximizing diagnosis of infection in culture-negative specimens. This is particularly justified for blood and CSF samples. Alternative approaches, such as metagenomic sequencing, are needed to provide the breadth of broad-range PCR and the sensitivity of targeted qPCR panels.

Tuberculosis Caused by Mycobacterium bovis in a Capybara (Hydrochoerus hydrochaeris)

Tuberculosis, associated with Mycobacterium bovis, was diagnosed post mortem in an adult female capybara (Hydrochoerus hydrochaeris), kept at the Pampulha Ecological Park, Belo Horizonte, Brazil, in a large metropolitan area. On post-mortem examination, there were numerous firm white nodules scattered throughout all lobes of both lungs. Tissue samples were collected for histological and microbiological examination. Microscopically, the pulmonary nodules were multifocal to coalescing granulomas and intralesional acid-fast bacilli were evident in Ziehl-Neelsen-stained sections of the lung and spleen. Colonies with morphological features of Mycobacterium spp. were isolated from lung samples and conventional polymerase chain reaction (PCR) with genomic DNA from the isolates was positive for M. bovis; sequencing indicated 100% identity with the region of difference 4 (RD4) of M. bovis. In addition, M. bovis DNA was detected in the lung by quantitative PCR. The finding of M. bovis in a capybara indicates a potential public health risk in a zoological collection.

Escherichia coli Vertebral Osteomyelitis Diagnosed According to Broad-range 16S rRNA Gene Polymerase Chain Reaction (PCR)

Identifying the causative agent of pyogenic osteomyelitis is often challenging, especially when antibiotics are administered before a biopsy. We herein present a case of osteomyelitis in the cervical vertebrae presenting with progressive paralytic symptoms, in which we successfully identified Escherichia coli from a biopsy specimen using broad-range 16S rRNA gene polymerase chain reaction (PCR) even though sensitive antibiotics had been used for more than 50 days before the biopsy. Broad-range 16S rRNA gene PCR is a useful diagnostic method, especially when prebiopsy antibiotics are unavoidably used for a clinically unstable state.

Systematic PCR detection in culture-negative osteoarticular infections

BACKGROUND

Identification of microorganisms is crucial for the successful treatment of osteoarticular infections. Molecular methods are more sensitive than culture-dependent methods but may suffer from lack of specificity.

METHODS

We studied a large series of 3840 bone and joint culture-negative samples collected from 2308 patients hospitalized in Marseille University Hospitals from November 2007 to October 2009. The samples were systematically cultured for 15 days, and conventional broad-range polymerase chain reaction (PCR) (16S rDNA and 18S rDNA) as well as real-time PCR assays targeting human Bglobin, Staphylococcus aureus, and Kingella kingae were realized on one culture-negative specimen.

RESULTS

Specimens from 741 patients (32.1%) tested positive by culture, including 38 in which bacteria grew only after 6 days of incubation. PCR was positive in 141 (9%) culture-negative specimens. Microorganisms identified by PCR were classified into 2 groups: fastidious bacteria (n = 35), mostly anaerobes in adult patients, and K. kingae in children; and nonfastidious bacteria (n = 106), mostly S. aureus (32.7%). A discrepancy between a positive PCR result for S. aureus and a negative culture were explained by previous antibiotherapy in 31.4% of cases. Our study highlights the usefulness of systematic 16S rDNA gene PCR for the diagnosis of bone and joint infections in culture-negative patients, thus enabling the administration of specific antibiotic treatments.

CONCLUSIONS

We recommend the use of conventional broad-range PCR for culture-negative bone and joint specimens, as well as S. aureus-specific PCR for adults and K. kingae-specific PCR for children. 18S rDNA PCR should be reserved only for specific cases.

Short communication: Evidence that microbial translocation occurs in HIV-infected children in the United Kingdom

Microbial translocation (MT) from the gut is implicated in driving immune activation, increasing morbidity and mortality in HIV. We used bacterial 16S rDNA PCR, Sanger sequencing, and high-throughput sequencing to identify microbial DNA in the bloodstream of HIV-infected children in London, United Kingdom. Blood samples were collected from sequential children attending the HIV clinic at Great Ormond Street Hospital, London. DNA extraction, broad range 16S rDNA PCR, and standard Sanger sequencing were carried out. A subset of positive samples was analyzed by high-throughput sequencing (Roche 454 platform). Of 105 samples collected from sequential children, nine were positive using broad range 16S rDNA PCR (8.6%; 95% CI 4.4-16%). From three amplicons, 16S rDNA sequences were identified as Streptococcus, Propionibacterium acnes, and coagulase-negative Staphylococcus. Four positive samples were analyzed by high-throughput sequencing. In the three samples in which organisms were identified by Sanger sequencing, the same species were identified. Further species, in differing proportions, were identified in all four samples. The identified organisms included known gut orders Bifidobacteriaceae, Lactobacillaceae, Bacteroidales, and Clostridiales. In immunocompetent children of equivalent age, no bacterial DNA was detected in blood using this approach. This is the first study to our knowledge using molecular techniques to identify MT in children in the developed world. Our data indicate that 16S rDNA is detectable in 8.6% of HIV-infected children. Levels of DNA were low and from multiple bacterial species. Further studies are needed to ascertain the importance of MT in HIV-infected children.

The increasing role of DNA molecular technologies in infection control-related medical bacteriology: what the infection prevention specialist needs to know

Molecular biology has the potential to revolutionise the way in which diagnostic tests are delivered in order to optimise care of infected patients, whether they are in hospital or in the community. Many routine hospital diagnostic laboratories are now beginning to adopt commercial molecular kits, which have dramatically expanded the availability of such tests into hospitals, which previously would not have used them. This has created a need among infection prevention specialists, microbiologists and infection control doctors as to what these tests mean, and how to formulate policy around them, so that there is added value for their use in the infection prevention scenario. This review wishes to explore their basis, their application in the infection prevention setting, their interpretation, as well as their advantages and disadvantages, in order to better inform infection prevention specialists.

Emerging and reemerging infectious diseases of nonhuman primates in the laboratory setting

Despite numerous advances in the diagnosis and control of infectious diseases of nonhuman primates in the laboratory setting, a number of infectious agents continue to plague colonies. Some, such as measles virus and Mycobacterium tuberculosis, cause sporadic outbreaks despite well-established biosecurity protocols, whereas others, such as retroperitoneal fibromatosis-associated herpesvirus, have only recently been discovered, often as a result of immunosuppressive experimental manipulation. Owing to the unique social housing requirements of nonhuman primates, importation of foreign-bred animals, and lack of antemortem diagnostic assays for many new diseases, elimination of these agents is often difficult or impractical. Recognition of these diseases is therefore essential because of their confounding effects on experimental data, impact on colony health, and potential for zoonotic transmission. This review summarizes the relevant pathology and pathogenesis of emerging and reemerging infectious diseases of laboratory nonhuman primates.

Direct 16S rRNA gene sequencing from clinical specimens, with special focus on polybacterial samples and interpretation of mixed DNA chromatograms

RipSeq (iSentio, Bergen, Norway) is a web-based application for the analysis of mixed DNA chromatograms. It opens the possibility to analyze chromatograms obtained by direct 16S rRNA gene sequencing from polybacterial human clinical samples. In this study, we used direct 16S rRNA gene sequencing to investigate 264 samples from a wide range of suspected human bacterial infections. The sequence-based identification was compared with the results from routine culture-based identification. A total of 151 samples were positive by the first PCR, producing 85 pure and 66 mixed DNA chromatograms. All mixed chromatograms were analyzed by RipSeq, although seven were so complex that only the dominant bacterial sequences could be identified. In general, sequence-based identification detected a larger number of species than did culture for samples from patients who had received antibiotics prior to sample collection and for samples containing anaerobic bacteria. RipSeq made it possible to apply this supplementary diagnostic tool to typical polybacterial specimens, such as internal abscesses, pleural fluids, and bile.

Identification of Bartonella henselae in an aborted equine fetus

This report describes the characterization of a Bartonella henselae abortion in an equine fetus by gross, histologic, immunohistochemical, ultrastructural, and molecular methods. Bartonella henselae can cause cat scratch disease, bacillary angiomatosis, bacillary peliosis, and endocarditis in humans and other animals. The bacterium has been isolated from several mammalian species but only recently from equids; however, it has not been linked to abortion in equids. An aborted equine fetus exhibited necrosis and vasculitis in multiple tissues, with intralesional Gram-negative short-to-spirillar bacteria. Nucleotide sequence analysis of the bacterial 16S rRNA gene amplified from the DNA extracted from fetal tissues revealed 99.9% homology to that of B. henselae. The presence of B. henselae in the fetal tissues was further confirmed by polymerase chain reaction amplification and nucleotide sequence analysis of other Bartonella species-specific genes. Microorganisms were immunohistochemically labeled with a monoclonal antibody to B. henselae and were ultrastructurally characterized. Attempts to detect known causative agents of equine abortion were unsuccessful. Given the severity of vasculitis and the presence of intralesional bacteria, we concluded that B. henselae infection caused the abortion of this foal.

Usefulness of broad-range PCR for the diagnosis of osteoarticular infections

PURPOSE OF REVIEW

Conventional methods such as microbiological cultures may lack the sensitivity and specificity to establish definitive diagnosis of osteoarticular infections. Herein, we review the general principles and the usefulness of broad-range PCR to improve the etiological diagnosis of osteoarticular infections.

RECENT FINDINGS

Broad-range PCR followed by sequencing has been successfully developed to identify microorganisms involved in infections when patients have previously received antibiotics or in the presence of slow-growing or intracellular microorganisms. For osteoarticular infections, the studies have shown that the use of this molecular tool increased mainly the identification of Kingella kingae, anaerobic bacteria, and Streptococcus spp. However, it is very important to underline that the interpretation of this molecular tool is critical because of several pitfalls, including contamination causing false-positive results.

SUMMARY

Broad-range PCR followed by sequencing offers several advantages when used to complement culture results for the diagnosis of fastidious bacteria and for patients taking antibiotics. However, its use should be restricted mainly for culture-negative cases when infection is suspected on the basis of clinical signs and symptoms or inflammatory syndrome. Future developments will include the use of real-time PCR in a closed system and pathogen-specific PCR for the molecular diagnosis of osteoarticular infections.

Metritis, valvular endocarditis, and septicemia by Actinobacillus equuli in a gilt in the United States

A 1-year-old pregnant Yorkshire gilt was found dead with no previous clinical signs. Gross findings included metritis, splenomegaly, and valvular endocarditis. Bacterial endocarditis (in the mitral and tricuspid valves) and metritis with dissemination to multiple organs was diagnosed by using histologic examination. Gram-negative coccobacillary organisms present in the valvular lesions were characterized as Actinobacillus equuli by using polymerase chain reaction examination on formalin-fixed, paraffin-embedded tissues (FFPE). A. equuli is rarely reported as a cause of septicemia in pigs in Europe. A. equuli in pigs in the United States has been reported only twice and not, to our knowledge, in the last 30 years. This is the first time that molecular techniques have been used to characterize this organism in FFPE porcine tissues.

Infection and musculoskeletal conditions: Osteomyelitis

Osteomyelitis can result from hematogenous or contiguous microbial seeding of the bone. Staphylococcus aureus is the most common infecting microorganism. Although any bone can potentially develop osteomyelitis, long-bone, vertebral, and foot osteomyelitis account for the majority of cases. Confirmatory diagnosis of osteomyelitis often depends on the results of a bone biopsy and bone cultures. Radiologic and laboratory studies are often helpful in leading to the diagnosis, determining the extent of the disease, and following up selected patients with osteomyelitis. Optimal therapy for osteomyelitis requires the collaboration of a multidisciplinary team of physicians. Debridement is often needed in contiguous osteomyelitis, whereas acute hematogenous and vertebral osteomyelitis can often be treated with a prolonged course of antimicrobial therapy.

Adherent and invasive Escherichia coli is associated with granulomatous colitis in boxer dogs

The mucosa-associated microflora is increasingly considered to play a pivotal role in the pathogenesis of inflammatory bowel disease. This study explored the possibility that an abnormal mucosal flora is involved in the etiopathogenesis of granulomatous colitis of Boxer dogs (GCB). Colonic biopsy samples from affected dogs (n = 13) and controls (n = 38) were examined by fluorescent in situ hybridization (FISH) with a eubacterial 16S rRNA probe. Culture, 16S ribosomal DNA sequencing, and histochemistry were used to guide subsequent FISH. GCB-associated Escherichia coli isolates were evaluated for their ability to invade and persist in cultured epithelial cells and macrophages as well as for serotype, phylogenetic group, genome size, overall genotype, and presence of virulence genes. Intramucosal gram-negative coccobacilli were present in 100% of GCB samples but not controls. Invasive bacteria hybridized with FISH probes to E. coli. Three of four GCB-associated E. coli isolates adhered to, invaded, and replicated within cultured epithelial cells. Invasion triggered a "splash"-type response, was decreased by cytochalasin D, genistein, colchicine, and wortmannin, and paralleled the behavior of the Crohn's disease-associated strain E. coli LF 82. GCB E. coli and LF 82 were diverse in serotype and overall genotype but similar in phylogeny (B2 and D), in virulence gene profiles (fyuA, irp1, irp2, chuA, fepC, ibeA, kpsMII, iss), in having a larger genome size than commensal E. coli, and in the presence of novel multilocus sequence types. We conclude that GCB is associated with selective intramucosal colonization by E. coli. E. coli strains associated with GCB and Crohn's disease have an adherent and invasive phenotype and novel multilocus sequence types and resemble E. coli associated with extraintestinal disease in phylogeny and virulence gene profile.

Analysis of 525 samples to determine the usefulness of PCR amplification and sequencing of the 16S rRNA gene for diagnosis of bone and joint infections

The 16S rRNA gene PCR in the diagnosis of bone and joint infections has not been systematically tested. Five hundred twenty-five bone and joint samples collected from 525 patients were cultured and submitted to 16S rRNA gene PCR detection of bacteria in parallel. The amplicons with mixed sequences were also cloned. When discordant results were observed, culture and PCR were performed once again. Bacteria were detected in 139 of 525 samples. Culture and 16S rRNA gene PCR yielded identical documentation in 475 samples. Discrepancies were linked to 13 false-positive culture results, 5 false-positive PCR results, 9 false-negative PCR results, 16 false-negative culture results, and 7 mixed infections. Cloning and sequencing of 16S rRNA gene amplicons in 6 of 8 patients with mixed infections identified 2 to 8 bacteria per sample. Rarely described human pathogens such as Alcaligenes faecalis, Comamonas terrigena, and 21 anaerobes were characterized. We also detected, by 16S rRNA gene PCR, four previously identified bacteria never reported in human infection, Alkanindiges illinoisensis, dehydroabietic acid-degrading bacterium DhA-73, unidentified Hailaer soda lake bacterium, and uncultured bacterium clone HuCa4. Seven organisms representing new potential species were also detected. PCR followed by cloning and sequencing may help to identify new pathogens involved in mixed bone infection.

Empyema: the use of broad range 16S rDNA PCR for pathogen detection

BACKGROUND

An increase in the incidence of thoracic empyema in children has been reported. The causative pathogen is often unknown as pleural fluid is frequently sterile at the time of culture. The role of unusual organisms is unclear.

AIMS

(1) To compare the detection of organisms in pleural fluid from children with empyema using a molecular technique (16S rDNA polymerase chain reaction (PCR)) and bacterial culture. (2) To compare the concordance of organisms identified using the two techniques and the influence of prior antibiotic treatment on positive detection rate.

METHODS

Pleural fluid from children admitted with empyema between January 2000 and February 2002 was cultured and additionally analysed using broad range 16S rDNA PCR.

RESULTS

Pleural fluid was cultured from 32 patients, aged 1 month-16 years. Median duration of previous antibiotic therapy was 8 days (range 1-42 days). Six samples were culture positive and 22 were PCR positive. A causal organism was detected by PCR alone, after considering results from the local hospital, in 14 patients. There was complete concordance in organisms cultured and detected by PCR. Additional organisms detected by PCR were predominantly S pneumoniae, S pyogenes, and anaerobes.

CONCLUSIONS

Analysis of pleural fluid by broad range 16S rDNA PCR in addition to culture, increases organism identification in empyema.

Helicobacter pylori and extragastric diseases -- other helicobacters

The role of Helicobacter pylori infection is explored in more and more extragastric diseases without definite proof in most of the studies, except possibly some hematologic diseases. In cardiovascular diseases, including stroke, the presence of CagA positive strains may be involved. The possible role of helicobacters in hepatobiliary diseases goes beyond that of H. pylori to involve enterohepatic helicobacters. New Helicobacter species are regularly described and molecular methods are developed to improve their detection. Helicobacter felis remains the major species to be used in animal models of Helicobacter infection.

Development of broad-range 16S rDNA PCR for use in the routine diagnostic clinical microbiology service

The aim of the present study was to develop a broad-range PCR based on bacterial 16S rDNA for use in the routine diagnostic clinical microbiology service. The optimization and validation of the assay for use on clinical specimens from normally sterile sites is described, and preliminary results are reported on the use of the assay in the clinical diagnosis of bacterial infection in 382 paediatric specimens over a 2-year period. These results are compared to those obtained by standard culture techniques and show increased diagnosis of bacterial infection when both culture and PCR are used together; 16S rDNA PCR provided the sole evidence of pathogenic infection in 71 cases. Key stages in the assay development and potential pitfalls of the technique are highlighted and the improvement the assay offers in the diagnosis of infection in the paediatric setting is discussed.

Clinical significance of Helicobacter species other than Helicobacter pylori

The cultivation of Helicobacter pylori and the recognition of its clinical significance have served to stimulate interest in bacteria associated with the gastrointestinal and hepatobiliary tracts. Many novel Helicobacter species have been identified and are increasingly recognized in association with human disease, most of which is likely acquired as a zoonosis. Because their identification can be difficult by use of routine methods available in the clinical laboratory, awareness of methods for diagnosis and treatment of these Helicobacter species is important, particularly in the evaluation of immunocompromised patients.