Comprehensive evaluation of complex polymicrobial specimens using next generation sequencing and standard microbiological culture

The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids

The prolonged incubation period of traditional culture methods leads to a delay in diagnosing invasive infections. Nanopore 16S rRNA gene sequencing (Nanopore 16S) offers a potential rapid diagnostic approach for directly identifying bacteria in infected body fluids. To evaluate the clinical utility of Nanopore 16S, we conducted a study involving the collection and sequencing of 128 monomicrobial samples, 65 polymicrobial samples, and 20 culture-negative body fluids. To minimize classification bias, taxonomic classification was performed using 3 analysis pipelines: Epi2me, Emu, and NanoCLUST. The result was compared to the culture references. The limit of detection of Nanopore 16S was also determined using simulated bacteremic blood samples. Among the three classifiers, Emu demonstrated the highest concordance with the culture results. It correctly identified the taxon of 125 (97.7%) of the 128 monomicrobial samples, compared to 109 (85.2%) for Epi2me and 102 (79.7%) for NanoCLUST. For the 230 cultured species in the 65 polymicrobial samples, Emu correctly identified 188 (81.7%) cultured species, compared to 174 (75.7%) for Epi2me and 125 (54.3%) for NanoCLUST. Through ROC analysis on the monomicrobial samples, we determined a threshold of relative abundance at 0.058 for distinguishing potential pathogens from background in Nanopore 16S. Applying this threshold resulted in the identification of 107 (83.6%), 117 (91.4%), and 114 (91.2%) correctly detected samples for Epi2me, Emu, and NanoCLUST, respectively, in the monomicrobial samples. Nanopore 16S coupled with Epi2me could provide preliminary results within 6 h. However, the ROC analysis of polymicrobial samples exhibited a random-like performance, making it difficult to establish a threshold. The overall limit of detection for Nanopore 16S was found to be about 90 CFU/ml.

In vitro evaluation of the effect of transport medium, temperature, and time on the recovery of Mannheimia haemolytica and Pasteurella multocida

Appropriate sample collection, storage conditions, and time for transport to the laboratory are important for an accurate diagnostic result. We evaluated the effects of transport storage medium type, time of storage, and storage temperatures on Mannheimia haemolytica (MH) and Pasteurella multocida (PM) recovery using an in vitro model simulation. A quantitative culture method, using colony-forming units per milliliter, was used to recover MH or PM by an in vitro model with cotton swabs. Three independent trials were conducted, in which cotton swabs were inoculated with MH or PM and placed in either (1) a sterile 15-mL polypropylene tube without transport medium (dry), (2) Amies culture medium with charcoal (ACM), or (3) Cary-Blair transport agar (CBA). Swabs were evaluated for recovery of MH or PM when stored at 3 temperatures (4°C, 23°C, or 36°C) and after storage for 8 h, 24 h, or 48 h. From all study group combinations, a total of 162 individual independent swabs were evaluated. The nonparametric Dunn all-pairs approach was used to compare the proportion of culturable bacteria, between the various storage media, temperature, and time point combinations. The proportion of MH in samples stored at 4°C was significantly higher for ACM and CBA than dry storage at 24 and 48 h. The MH samples stored at 36°C had a significantly higher proportion for ACM and CBA than dry storage at 24 h. The proportion of PM in samples stored at 4°C was significantly lower for ACM compared with dry at 8 h but significantly higher at 48 h. The PM samples stored at 23°C in ACM had a significantly higher proportion than dry samples at 24 h, and, at 48 h, ACM and CBA had a significantly higher proportion than the dry group. All swabs stored at 36°C for 48 h had a proportion close to zero, indicating decreasing diagnostic efficacy. These results support the use of transport media such as ACM and CBA for increasing the detection of PM and MH from samples, especially when samples are exposed to high temperatures. The combination of longer periods from collection of samples to diagnostic evaluation (>24 h) and higher storage temperatures (>23°C) were shown to significantly impair diagnostic accuracy.

Bartonella spp. Infections Identified by Molecular Methods, United States

Molecular methods can enable rapid identification of Bartonella spp. infections, which are difficult to diagnose by using culture or serology. We analyzed clinical test results of PCR that targeted bacterial 16S rRNA hypervariable V1-V2 regions only or in parallel with PCR of Bartonella-specific ribC gene. We identified 430 clinical specimens infected with Bartonella spp. from 420 patients in the United States. Median patient age was 37 (range 1-79) years; 62% were male. We identified B. henselae in 77%, B. quintana in 13%, B. clarridgeiae in 1%, B. vinsonii in 1%, and B. washoensis in 1% of specimens. B. quintana was detected in 83% of cardiac specimens; B. henselae was detected in 34% of lymph node specimens. We detected novel or uncommon Bartonella spp. in 9 patients. Molecular diagnostic testing can identify Bartonella spp. infections, including uncommon and undescribed species, and might be particularly useful for patients who have culture-negative endocarditis or lymphadenitis.

Antibiotic Resistance in Patients with Cystic Fibrosis: Past, Present, and Future

Patients with cystic fibrosis (CF) are repeatedly exposed to antibiotics, especially during the pulmonary exacerbations of the disease. However, the available therapeutic strategies are frequently inadequate to eradicate the involved pathogens and most importantly, facilitate the development of antimicrobial resistance (AMR). The evaluation of AMR is demanding; conventional culture-based susceptibility-testing techniques cannot account for the lung microenvironment and/or the adaptive mechanisms developed by the pathogens, such as biofilm formation. Moreover, features linked to modified pharmaco-kinetics and pulmonary parenchyma penetration make the dosing of antibiotics even more challenging. In this review, we present the existing knowledge regarding AMR in CF, we shortly review the existing therapeutic strategies, and we discuss the future directions of antimicrobial stewardship. Due to the increasing difficulty in eradicating strains that develop AMR, the appropriate management should rely on targeting the underlying resistance mechanisms; thus, the interest in novel, molecular-based diagnostic tools, such as metagenomic sequencing and next-generation transcriptomics, has increased exponentially. Moreover, since the development of new antibiotics has a slow pace, the design of effective treatment strategies to eradicate persistent infections represents an urgency that requires consorted work. In this regard, both the management and monitoring of antibiotics usage are obligatory and more relevant than ever.

Treatment and outcomes of peritonitis due to Rothia species in patients on peritoneal dialysis: A systematic review and multicentre registry analysis

Peritoneal dialysis (PD)-associated peritonitis remains a severe complication of PD. Although peritonitis due to Rothia spp. is rare, the treatment recommendations and outcomes are uncertain. Our study aims to review (1) published literature on peritonitis caused by Rothia spp. and (2) reported cases of peritonitis due to Rothia spp. in patients on PD in Australia and New Zealand. A literature search of PubMed, Scopus, Embase and Google Scholar for articles published between January 1949 and February 2022 was conducted. To be eligible, articles had to describe antibiotic therapy and treatment outcomes in all PD patients for peritonitis caused by Rothia or Stomatococcus spp. Data from the Australia and New Zealand Dialysis and Transplant (ANZDATA) registry of PD patients who developed peritonitis due to Rothia spp. between July 2011 and May 2020 were also reviewed. A total of 12 articles and 28 episodes were identified from the literature search and ANZDATA registry analysis, respectively. Over 60% of the peritonitis cases due to Rothia spp. were from the Rothia mucilaginosa species (8/12 and 17/28, respectively), while Rothia dentocariosa was the second most commonly identified species in both the literature search and the ANZDATA registry analysis (4/12 and 5/28, respectively). A majority 8 (66.7%) of the articles in the literature search employed a combination antibiotic regimen, while the remaining 4 (33.3%) used a single antibiotic regimen. In contrast, most of the episodes, 22 (78.6%) described in the ANZDATA registry analysis, employed a single antibiotic regimen, and only 6 (21.4%) episodes were treated with a combination antibiotic regimen. The duration of antibiotic therapy ranged from 2 to 3 weeks in the literature search, and 1 to 3 weeks in the ANZDATA registry. While no deaths within 30 days of developing peritonitis were reported, catheter removal was reported in three (25%) and two (7.1%) episodes in both the literature search and the ANZDATA registry analysis, respectively, of which the majority occurred in patients treated for ≤2 weeks. PD-associated peritonitis due to Rothia spp. is uncommon and associated with relatively good outcomes. Antibiotic treatment for 3 weeks is associated with better outcomes.

Effect of polymicrobial interactions on antimicrobial resistance: an in vitro analysis in human ocular infections

Purpose: Investigate the effect of polymicrobial interactions on antimicrobial resistance (AMR) of ocular pathogens in polymicrobial settings, compared with monomicrobial infections. Methods: Polymicrobial interactions were labeled as antagonistic, synergistic or indifferent based on a reduction, an increase or no change, respectively, in antibiotics' MIC by the Vitek 2 compact system, compared with monomicrobial pathogens. Results: Staphylococcus epidermidis showed antagonistic polymicrobial interactions (22.6%); Pseudomonas aeruginosa showed synergistic interactions (62.5%); multidrug-resistant Acinetobacter baumannii showed increased susceptibility to select antibiotics; Serratia ficaria (inherently colistin resistant) became colistin-susceptible in polymicrobial combinations. Conclusion: Both antagonistic and synergistic interactions exist among human pathogens in polymicrobial settings. Gram-positive pathogens had significantly higher antagonistic polymicrobial interactions (increased MICs: 20.4%) compared with Gram-negative ones (synergistic: 59.4%).

Next-generation sequencing as an advanced supplementary tool for the diagnosis of pathogens in lower respiratory tract infections: An observational trial in Xi'an, China

The application of next-generation sequencing (NGS) in routine clinical analysis is still limited. The significance of NGS in the identification of pathogens of lower respiratory tract infection should be assessed as part of routine clinical bacterial examinations and chest imaging results. In the present study, the alveolar lavage fluid samples of 30 patients (25 males and 5 females, aged 19-92 years old, with a median age of 62) were examined by routine bacterial culture and NGS, and the results of pathogen detection and identification were compared. Chest imaging showed consolidation in all 30 patients (100%), and pleural effusion in 13 of the 30 patients (43.33%). The routine bacterial culture of the lavage solution was only positive in 14 of the 30 patients (46.6%), and negative in 16 patients (53.33%). However, the positive rate of NGS test results of the lavage fluid was 100%. A total of 12 cases (40%) were completely consistent with the routine bacterial culture test, with 56 other pathogens of mixed infection detected, accounting for the short comings of the routine bacterial examination. Although NGS cannot distinguish between live and dead bacteria, it is still a useful detection technology for accurate diagnosis of clinical infectious diseases. It is worthy of adaptation in the clinic for more effective clinical management and treatment of the lower respiratory airway infection in addition to the routine bacterial culture testing.

Using Plate-Wash PCR and High-Throughput Sequencing to Measure Cultivated Diversity for Natural Product Discovery Efforts

Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Sequence-based data indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete and more complex, understanding of which organisms were present compared to what was eventually detected during cultivation. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against an already multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.

Comparison of Strategies for Isolating Anaerobic Bacteria from the Porcine Intestine

The isolation of bacteria that represent the diversity of autochthonous taxa in the gastrointestinal tract is necessary to fully ascertain their function, but the majority of bacterial species inhabiting the intestines of mammals are fastidious and thus challenging to isolate. The goal of the current study was to isolate a diverse assemblage of anaerobic bacteria from the intestine of pigs as a model animal and to comparatively examine various novel and traditional isolation strategies. Methods used included long-term enrichments, direct plating, a modified ichip method, as well as ethanol and tyndallization treatments of samples to select for endospore-forming taxa. A total of 234 taxa (91 previously uncultured) comprising 80 genera and 7 phyla were isolated from mucosal and luminal samples from the ileum, cecum, ascending colon, and spiral colon removed from animals under anesthesia. The diversity of bacteria isolated from the large intestine was less than that detected by next-generation sequence analysis. Long-term enrichments yielded the greatest diversity of recovered bacteria (Shannon's index [SI] = 4.7). Methods designed to isolate endospore-forming bacteria produced the lowest diversity (SI ≤ 2.7), with tyndallization yielding lower diversity than the ethanol method. However, the isolation frequency of previously uncultured bacteria was highest for ethanol-treated samples (41.9%) and the ichip method (32.5%). The goal of recovering a diverse collection of enteric bacteria was achieved. Importantly, the study findings demonstrate that it is necessary to use a combination of methods in concert to isolate bacteria that are representative of the diversity within the intestines of mammals.IMPORTANCE This work determined that using a combination of anaerobic isolation methods is necessary to increase the diversity of bacteria recovered from the intestines of monogastric mammals. Direct plating methods have traditionally been used to isolate enteric bacteria, and recent methods (e.g., diffusion methods [i.e., ichip] or differential isolation of endospore-forming bacteria) have been suggested to be superior at increasing diversity, including the recovery of previously uncultured taxa. We showed that long-term enrichment of samples using a variety of media isolated the most diverse and novel bacteria. Application of the ichip method delivered a diversity of bacteria similar to those of enrichment and direct plating methods. Methods that selected for endospore-forming bacteria generated collections that differed in composition from those of other methods with reduced diversity. However, the ethanol treatment frequently isolated novel bacteria. By using a combination of methods in concert, a diverse collection of enteric bacteria was generated for ancillary experimentation.

A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation

There is accumulating evidence that the lower airway microbiota impacts lung health. However, the link between microbial community composition and lung homeostasis remains elusive. We combine amplicon sequencing and bacterial culturing to characterize the viable bacterial community in 234 longitudinal bronchoalveolar lavage samples from 64 lung transplant recipients and establish links to viral loads, host gene expression, lung function, and transplant health. We find that the lung microbiota post-transplant can be categorized into four distinct compositional states, 'pneumotypes'. The predominant 'balanced' pneumotype is characterized by a diverse bacterial community with moderate viral loads, and host gene expression profiles suggesting immune tolerance. The other three pneumotypes are characterized by being either microbiota-depleted, or dominated by potential pathogens, and are linked to increased immune activity, lower respiratory function, and increased risks of infection and rejection. Collectively, our findings establish a link between the lung microbial ecosystem, human lung function, and clinical stability post-transplant.

Clinical Implications of Polymicrobial Synergism Effects on Antimicrobial Susceptibility

With the development of next generation sequencing technologies in recent years, it has been demonstrated that many human infectious processes, including chronic wounds, cystic fibrosis, and otitis media, are associated with a polymicrobial burden. Research has also demonstrated that polymicrobial infections tend to be associated with treatment failure and worse patient prognoses. Despite the importance of the polymicrobial nature of many infection states, the current clinical standard for determining antimicrobial susceptibility in the clinical laboratory is exclusively performed on unimicrobial suspensions. There is a growing body of research demonstrating that microorganisms in a polymicrobial environment can synergize their activities associated with a variety of outcomes, including changes to their antimicrobial susceptibility through both resistance and tolerance mechanisms. This review highlights the current body of work describing polymicrobial synergism, both inter- and intra-kingdom, impacting antimicrobial susceptibility. Given the importance of polymicrobial synergism in the clinical environment, a new system of determining antimicrobial susceptibility from polymicrobial infections may significantly impact patient treatment and outcomes.