Weissella confusa: an unexpected cause of vancomycin-resistant gram-positive bacteremia in immunocompromised hosts

A Case of Weissella confusa Isolated from Blood of a Patient with Coronary Heart Disease Complicated with Gastrointestinal Bleeding

Introduction

W. confusa has been known to cause various human infections. It is naturally resistant to vancomycin and is difficult to identify using traditional methods, which may lead to misidentification and delay treatment.

Case Presentation

We present a case of a 42-year-old male patient with gastrointestinal bleeding and coronary heart disease who developed sepsis caused by Weissella confusa. The patient's blood cultures showed the presence of gram-positive coccobacilli, later identified as W. confusa through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Antimicrobial susceptibility testing revealed that W. confusa had low minimum inhibitory concentrations (MICs) for some drugs (eg, ampicillin) and higher MICs for others (eg, cefotaxime). Empirical treatment with vancomycin was initially started, but after obtaining the identification and susceptibility results, the treatment was switched to meropenem combined with daptomycin, resulting in a successful outcome.

Conclusion

Weissella confusa bacteremia is relatively rare, and accurate pathogenic diagnosis is essential for effective clinical treatment.

The Weissella Genus: Clinically Treatable Bacteria with Antimicrobial/Probiotic Effects on Inflammation and Cancer

Weissella is a genus earlier considered a member of the family Leuconostocaceae, which was reclassified into the family Lactobacillaceae in 1993. Recently, there have been studies emphasizing the probiotic and anti-inflammatory potential of various species of Weissella, of which W. confusa and W. cibaria are the most representative. Other species within this genus include: W. paramesenteroides, W. viridescens, W. halotolerans, W. minor, W. kandleri, W. soli, W. ghanensis, W. hellenica, W. thailandensis, W. fabalis, W. cryptocerci, W. koreensis, W. beninensis, W. fabaria, W. oryzae, W. ceti, W. uvarum, W. bombi, W. sagaensis, W. kimchi, W. muntiaci, W. jogaejeotgali, W. coleopterorum, W. hanii, W. salipiscis, and W. diestrammenae. Weissella confusa, W. paramesenteroides, W. koreensis, and W. cibaria are among the few species that have been isolated from human samples, although the identification of these and other species is possible using metagenomics, as we have shown for inflammatory bowel disease (IBD) and healthy controls. We were able to isolate Weissella in gut-associated bacteria (post 24 h food deprivation and laxatives). Other sources of isolation include fermented food, soil, and skin/gut/saliva of insects/animals. With the potential for hospital and industrial applications, there is a concern about possible infections. Herein, we present the current applications of Weissella on its antimicrobial and anti-inflammatory mechanistic effects, the predisposing factors (e.g., vancomycin) for pathogenicity in humans, and the antimicrobials used in patients. To address the medical concerns, we examined 28 case reports focused on W. confusa and found that 78.5% of infections were bacteremia (of which 7 were fatal; 1 for lack of treatment), 8 were associated with underlying malignancies, and 8 with gastrointestinal procedures/diseases of which 2 were Crohn’s disease patients. In cases of a successful resolution, commonly administered antibiotics included: cephalosporin, ampicillin, piperacillin-tazobactam, and daptomycin. Despite reports of Weissella-related infections, the evolving mechanistic findings suggest that Weissella are clinically treatable bacteria with emerging antimicrobial and probiotic benefits ranging from oral health, skin care, obesity, and inflammatory diseases to cancer.

Safety demonstration of a microbial species for use in the food chain: Weissella confusa

Due to their traditional use in food fermentation process for centuries, microbial food cultures are considered to have a safe history of use. A specific microbial risk assessment is therefore rarely conducted for fermented foods and their food cultures, inoculated or naturally present. Some of those food cultures have been also considered for their potential health effect as probiotic strain candidates, for which a specific safety demonstration process has been proposed by a joint expert report of FAO and WHO. The European Food Safety Authority (EFSA) Biohazard panel also provides an approach for evaluating the safety of a strain to be added in the food chain, the Qualified Presumption of Safety (QPS). Weissella confusa, former taxon Lactobacillus confusus, is a food culture characterized in the fermentation process of sourdough. Some strains have been recently proposed for their probiotic potential. The species is also documented in recent infection case reports. It is considered nevertheless to be opportunistic as underlying factors have been suggested to explain the infection. We report here the microbial risk assessment of the species, by studying a collection of 26 food and 17 clinical isolates of Weissella confusa. The phenotypic study, genomic characterization and bibliographical survey will allow us to conclude about the safety of the species and confirm its use for food fermentation and consider specific strains for demonstration of their respective health effects as probiotic candidates.

A case report of polymicrobial bacteremia with Weissella confusa and comparison of previous treatment for successful recovery with a review of the literature

Weissella confusa is a Gram-positive coccus and a commensal bacterium of the human gastrointestinal tract with a potential to cause invasive infections. We report the presence of W. confusa in the blood of a 25-year-old male patient with Crohn’s disease, short bowel syndrome treated with home parenteral nutrition, and a history of recurrent bloodstream infections, admitted to our hospital with fever and malaise. A polymicrobial culture of W. confusa and Aeromonas hydrophila was identified from blood, for which treatment with meropenem and metronidazole was initiated. The literature was searched for previous cases of infection with W. confusa. In total, 14 reports describing infection of 28 patients were found, most cases presenting with bacteremia. The previous reports have described variable susceptibility to antibiotics; however, all were reported to be vancomycin resistant. Because of its similarities to other vancomycin-resistant cocci, isolates of W. confusa might be difficult to identify with traditional methods. Infection may be facilitated by its natural vancomycin resistance, leading to severe infection in hosts with underlying diseases. We describe the treatment of previous cases of infection and suggest treatment methods shown effective in other cases. Vancomycin is often used as treatment of infection with Gram-positive organisms, but this may need to be reevaluated, as several pathogenic bacteria are intrinsically vancomycin resistant. A review on reported treatments of bacteremia by W. confusa suggests the use of daptomycin, amoxicillin-clavulanate or piperacillin/tazobactam as recommendable antibiotic regimens.

Genome Sequence of a Weissella confusa Strain Isolated from the First Reported Case of Neonatal Sepsis in an Equid

The genome of a Weissella confusa strain isolated from a foal with sepsis is reported. Weissella confusa inhabits feces and causes disease in immunocompromised humans and animals. It is important for veterinarians to be aware of the pathogenic ability of these bacteria due to the unknown potential for zoonotic transmission.

The genome of a Weissella confusa strain isolated from a foal with sepsis is reported. Weissella confusa inhabits feces and causes disease in immunocompromised humans and animals. It is important for veterinarians to be aware of the pathogenic ability of these bacteria due to the unknown potential for zoonotic transmission.

Literature-based safety assessment of an agriculture- and animal-associated microorganism: Weissella confusa

Although Weissella confusa was established as a species over 25 years ago, it has been understudied until very recently. Several independent observations have driven the recent interest in this important microorganism. First, this Leuconostoc-like species of Lactic Acid Bacteria is associated with agricultural environments, many spontaneous food fermentations-especially carbohydrate-rich vegetable fermentations-and silage. Second, Weissella confusa are members of the autochthonous microbiota of healthy humans and livestock. Third, Weissella confusa-in a strain-specific fashion-are postulated to be good candidates for the development of novel direct-fed microbial products. Fourth, Weissella confusa-in a strain-specific fashion-have been described as opportunistic pathogens-especially in immunocompromised individuals. Last, a distantly related species (Weissella ceti) is the etiologic agent of weissellosis, a disease that affects farmed fish that are important for commercial aquaculture. The purpose of this literature-based safety assessment is to consolidate findings from primary research related to Weissella confusa and its natural associations with and effects on animals, humans, and their agricultural environments. Based on these assessments, it is reasonable to conclude that many Weissella confusa are safe for use in direct-fed microbial products for poultry.

Why Are Weissella spp. Not Used as Commercial Starter Cultures for Food Fermentation?

Among other fermentation processes, lactic acid fermentation is a valuable process which enhances the safety, nutritional and sensory properties of food. The use of starters is recommended compared to spontaneous fermentation, from a safety point of view but also to ensure a better control of product functional and sensory properties. Starters are used for dairy products, sourdough, wine, meat, sauerkraut and homemade foods and beverages from dairy or vegetal origin. Among lactic acid bacteria, Lactobacillus, Lactococcus, Leuconostoc, Streptococcus and Pediococcus are the majors genera used as starters whereas Weissella is not. Weissella spp. are frequently isolated from spontaneous fermented foods and participate to the characteristics of the fermented product. They possess a large set of functional and technological properties, which can enhance safety, nutritional and sensory characteristics of food. Particularly, Weissella cibaria and Weissella confusa have been described as high producers of exo-polysaccharides, which exhibit texturizing properties. Numerous bacteriocins have been purified from Weissella hellenica strains and may be used as bio-preservative. Some Weissella strains are able to decarboxylate polymeric phenolic compounds resulting in a better bioavailability. Other Weissella strains showed resistance to low pH and bile salts and were isolated from healthy human feces, suggesting their potential as probiotics. Despite all these features, the use of Weissella spp. as commercial starters remained non-investigated. Potential biogenic amine production, antibiotic resistance pattern or infection hazard partly explains this neglecting. Besides, Weissella spp. are not recognized as GRAS (Generally Recognized As Safe). However, Weissella spp. are potential powerful starters for food fermentation as well as Lactococcus, Leuconostoc or Lactobacillus species.

Bloodstream Infections

Bacteremia and sepsis are conditions associated with high mortality and are of great impact to health care operations. Among the top causes of mortality in the United States, these conditions cause over 600 fatalities each day. Empiric, broad-spectrum treatment is a common but often a costly approach that may fail to effectively target the correct microbe, may inadvertently harm patients via antimicrobial toxicity or downstream antimicrobial resistance. To meet the diagnostic challenges of bacteremia and sepsis, laboratories must understand the complexity of diagnosing and treating septic patients, in order to focus on creating algorithms that can help direct a more targeted approach to antimicrobial therapy and synergize with existing clinical practices defined in new Surviving Sepsis Guidelines. Significant advances have been made in improving blood culture media; as yet no molecular or antigen-based method has proven superior for the detection of bacteremia in terms of limit of detection. Several methods for rapid molecular identification of pathogens from blood cultures bottles are available and many more are on the diagnostic horizon. Ultimately, early intervention by molecular detection of bacteria and fungi directly from whole blood could provide the most patient benefit and contribute to tailored antibiotic coverage of the patient early on in the course of the disease. Although blood cultures remain as the best means of diagnosing bacteremia and candidemia, complementary testing with antigen tests, microbiologic investigations from other body sites, and histopathology can often aid in the diagnosis of disseminated disease, and application of emerging nucleic acid test methods and other new technology may greatly impact our ability to bacteremic and septic patients, particularly those who are immunocompromised.

Identification of Weissella species by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Although some Weissella species play beneficial roles in food fermentation and in probiotic products, others such as Weissella confusa are emerging Gram-positive pathogens in immunocompromised hosts. Weissella species are difficult to identify by conventional biochemical methods and commercial automated systems and are easily misidentified as Lactobacillus and Leuconostoc species. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is increasingly being used for bacterial identification. Little, however, is known about the effectiveness of MALDI-TOF MS in identifying clinical isolates of Weissella to the species level. In this study, we evaluated whether the MALDI-TOF MS Bruker Biotyper system could accurately identify a total of 20 W. confusa and 2 W. cibaria blood isolates that had been confirmed by 16s rRNA sequencing analysis. The MALDI-TOF Biotyper system yielded no reliable identification results based on the current reference spectra for the two species (all score values <1.7). New W. confusa spectra were created by randomly selecting 3 W. confusa isolates and external validation was performed by testing the remaining 17 W. confusa isolates using the new spectra. The new main spectra projection (MSP) yielded reliable score values of >2 for all isolates with the exception of one (score value, 1.963). Our results showed that the MSPs in the current database are not sufficient for correctly identifying W. confusa or W. cibaria. Further studies including more Weissella isolates are warranted to further validate the performance of MALDI-TOF in identifying Weissella species.

Identification and significance of Weissella species infections

Weissella spp. are non-spore forming, catalase-negative, gram-positive coccobacilli. They are often misidentified by traditional and commercial phenotypic identification methods as Lactobacillus spp. or Lactobacillus-like organisms. Weissella spp. were previously grouped along with Lactobacillus spp., Leuconostoc spp., and Pediococcus spp. Utilization of more sensitive methods like DNA sequencing or Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) has facilitated identification of Weissella as a unique genus. Nineteen species have been identified to date. W. confusa, W. cibaria, and W. viridescens are the only species isolated from humans. The true prevalence of Weissella spp. continues to be probably underestimated. Weissella spp. strains have been isolated from a wide range of habitats including raw milk, feces, fermented cereals, and vegetables. Weisella is believed to be a rare cause of usually nonfatal infections in humans, and is often considered a contaminant. However, in recent years, Weissella spp. have been implicated in bacteremia, abscesses, prosthetic joint infections, and infective endocarditis. Alterations of the gut flora from surgery or chemotherapy are believed to facilitate translocation of Weissella spp. due to disruption of the mucosal barrier, predisposing the host to infection with this organism. Implications of the isolation of Weissella spp. from blood must be interpreted in context of underlying risk factors. Weissella spp. are inherently resistant to vancomycin. Therefore, early consideraton of the pathogenic role of this bacteria and choice of alternate therapy is important to assure better outcomes.

The controversial nature of the Weissella genus: technological and functional aspects versus whole genome analysis-based pathogenic potential for their application in food and health

Despite the use of several Weissella (W.) strains for biotechnological and probiotic purposes, certain species of this genus were found to act as opportunistic pathogens, while strains of W. ceti were recognized to be pathogenic for farmed rainbow trout. Herein, we investigated the pathogenic potential of weissellas based on in silico analyses of the 13 whole genome sequences available to date in the NCBI database. Our screening allowed us to find several virulence determinants such as collagen adhesins, aggregation substances, mucus-binding proteins, and hemolysins in some species. Moreover, we detected several antibiotic resistance-encoding genes, whose presence could increase the potential pathogenicity of some strains, but should not be regarded as an excluding trait for beneficial weissellas, as long as these genes are not present on mobile genetic elements. Thus, selection of weissellas intended to be used as starters or for biotechnological or probiotic purposes should be investigated regarding their safety aspects on a strain to strain basis, preferably also by genome sequencing, since nucleotide sequence heterogeneity in virulence and antibiotic resistance genes makes PCR-based screening unreliable for safety assessments. In this sense, the application of W. confusa and W. cibaria strains as starter cultures or as probiotics should be approached with caution, by carefully selecting strains that lack pathogenic potential.

The genus Weissella: taxonomy, ecology and biotechnological potential

Bacteria assigned to the genus Weissella are Gram-positive, catalase-negative, non-endospore forming cells with coccoid or rod-shaped morphology (Collins et al., 1993; Björkroth et al., 2009, 2014) and belong to the group of bacteria generally known as lactic acid bacteria. Phylogenetically, the Weissella belong to the Firmicutes, class Bacilli, order Lactobacillales and family Leuconostocaceae (Collins et al., 1993). They are obligately heterofermentative, producing CO2 from carbohydrate metabolism with either d(-)-, or a mixture of d(-)- and l(+)- lactic acid and acetic acid as major end products from sugar metabolism. To date, there are 19 validly described Weissella species known. Weissella spp. have been isolated from and occur in a wide range of habitats, e.g., on the skin and in the milk and feces of animals, from saliva, breast milk, feces and vagina of humans, from plants and vegetables, as well as from a variety of fermented foods such as European sourdoughs and Asian and African traditional fermented foods. Thus, apart from a perceived technical role of certain Weissella species involved in such traditional fermentations, specific Weissella strains are also receiving attention as potential probiotics, and strain development of particularly W. cibaria strains is receiving attention because of their high probiotic potential for controlling periodontal disease. Moreover, W. confusa and W. cibaria strains are known to produce copius amounts of novel, non-digestible oligosaccharides and extracellular polysaccharides, mainly dextran. These polymers are receiving increased attention for their potential application as prebiotics and for a wide range of industrial applications, predominantly for bakeries and for the production of cereal-based fermented functional beverages. On the detrimental side, strains of certain Weissella species, e.g., of W. viridescens, W. cibaria and W. confusa, are known as opportunistic pathogens involved in human infections while strains of W. ceti have been recently recongnized as etiological agent of "weissellosis," which is a disease affecting farmed rainbow trouts. Bacteria belonging to this species thus are important both from a technological, as well as from a medical point of view, and both aspects should be taken into account in any envisaged biotechnological applications.

A confusing case - Weissella confusa prosthetic joint infection: A case report and review of the literature

This article describes a case involving a 94-year-old woman with an infection of her knee, which had previously undergone total knee arthroplasty. Following culture of aspirate from the knee, the causative organism was tentatively identified as a Lactobacillus species. The infection was later determined to be caused by Weissella confusa. The authors discuss the difficulties in identifying W confusa and present a literature review of infections caused by the species.

The authors describe the first case of Weissella confusa infection of a prosthetic joint. Identification of the pathogen required 16S ribosomal RNA sequencing of isolates obtained on two separate occasions during the assessment of an elderly woman with a painful, swollen knee following total knee arthroplasty. A review of reported human infections due to W confusa are summarized, and risk factors and pitfalls in the application of empirical antimicrobial therapy pending definitive microbiological identification are discussed.

Weissella confusa: problems with identification of an opportunistic pathogen that has been found in fermented foods and proposed as a probiotic

Weissella confusa is found in fermented foods and has been suggested as a probiotic, but also causes sepsis and other serious infections in humans and animals. The incidence of human infections is underestimated partly due to confusion with viridans streptococci and partly due to difficulty making a definitive identification, even if the organism is recognized to belong to another genus, owing to the inability of commercial organism systems to identify it. We report our experiences identifying W. confusa isolated from two immune-compromised patients, both of whom developed sepsis with this organism. Two MicroScan gram positive combination panels, could not identify the organism because they did not have W. confusa in their data bases, but did not provide a false identification. Other laboratorians have reported failure to identify or false identifications of W. confusa with other commercial systems. W. confusa is in the data base of the RapID™ Str panel (Remel), which gave three incorrect, high probability results (≥95%). 16S rDNA sequencing identified the isolates as W. confusa. Maldi-Tof, performed by two of our reference laboratories, also correctly identified both isolates. Use of W. confusa as a probiotic should be approached with caution because its true incidence as an opportunisitic pathogen is unknown.

Weissella confusa septicemia in a foal

Weissella confusa is a Gram-positive bacterium that has been identified in environmental and food samples from around the world. Rare cases of bacteremia in immunocompromised people have been reported. A 2-day-old foal was presented for weakness and suspected sepsis. Blood culture yielded pure growth of a Gram-positive coccobacillus, which was identified as W. confusa through sequencing of the 16S ribosomal DNA. Although the foal initially responded to antimicrobial therapy with ceftiofur and metronidazole, it later developed septic complications of the right tarsocrural joint and right digital flexor tendon sheath and was euthanized. Postmortem examination and histology revealed subcutaneous icterus, severe diffuse interstitial pneumonia, septic synovitis, necrotizing vasculitis with marked thrombosis and hemorrhage in the medial digital vessels of the right hind limb, and ischemic necrosis of the right hind hoof laminae. Gram-positive, coccobacilli were observed in the vascular lesion.

Targeting the microbiota to address diet-induced obesity: a time dependent challenge

Links between the gut microbiota and host metabolism have provided new perspectives on obesity. We previously showed that the link between the microbiota and fat deposition is age- and time-dependent subject to microbial adaptation to diet over time. We also demonstrated reduced weight gain in diet-induced obese (DIO) mice through manipulation of the gut microbiota with vancomycin or with the bacteriocin-producing probiotic Lactobacillus salivarius UCC118 (Bac(+)), with metabolic improvement achieved in DIO mice in receipt of vancomycin. However, two phases of weight gain were observed with effects most marked early in the intervention phase. Here, we compare the gut microbial populations at the early relative to the late stages of intervention using a high throughput sequencing-based analysis to understand the temporal relationship between the gut microbiota and obesity. This reveals several differences in microbiota composition over the intervening period. Vancomycin dramatically altered the gut microbiota composition, relative to controls, at the early stages of intervention after which time some recovery was evident. It was also revealed that Bac(+) treatment initially resulted in the presence of significantly higher proportions of Peptococcaceae and significantly lower proportions of Rikenellaceae and Porphyromonadaceae relative to the gut microbiota of L. salivarius UCC118 bacteriocin negative (Bac(-)) administered controls. These differences were no longer evident at the later time. The results highlight the resilience of the gut microbiota and suggest that interventions may need to be monitored and continually adjusted to ensure sustained modification of the gut microbiota.

Clinical impact of the use of 16S rRNA sequencing method for the identification of "difficult-to-identify" bacteria in immunocompromised hosts

Molecular method of 16S rRNA sequencing is reported to be helpful in the accurate identification of organisms with ambiguous phenotypic profiles. We analyzed the use of 16S rRNA sequencing method to identify clinically significant, "difficult-to-identify" bacteria recovered from clinical specimens, and evaluated its role in patient management and consequent clinical outcome. Among the 172 "difficult-to-identify" bacteria recovered over a 4-year period, 140 were gram-positive cocci or gram-negative bacilli; identification by 16S rRNA did not play a role in the management of patients infected with these bacteria. From 32 patients, 33 "difficult-to-identify" gram-positive bacilli were identified; the organisms were mycobacteria, Nocardia, Tsukamurella, Rhodococcus, and Gordonia. In 24 patients for whom clinical data were available, results from the 16S rRNA sequencing method led to treatment change in 14 immunocompromised patients (including 7 hematopoietic stem cell recipients and 1 liver transplant recipient). Therapy was modified in 9 patients, initiated in 3 patients, and discontinued in 2 patients. Most patients' therapy was switched to oral antibiotics with discontinuation of intravascular catheters, facilitating early hospital discharge. All 14 patients were alive 30 days after infection onset. The present study demonstrates the clinical application of 16S rRNA sequencing method to identify "difficult-to-identify" mycobacteria and other gram-positive bacilli in clinical specimens, particularly in immunocompromised hosts.

Weissella confusa: a rare cause of vancomycin-resistant Gram-positive bacteraemia

We describe a case of bacteraemia caused by Weissella confusa in a 48-year-old male who was operated on for adenocarcinoma of the gastro-oesophageal junction and maintained on total parenteral nutrition. Blood cultures were positive for a vancomycin-resistant streptococcus-like organism which was identified as W. confusa by 16S rRNA gene sequencing.