COVID-19 influences lung microbiota dynamics and favors the emergence of rare infectious diseases: A case report of Hafnia Alvei pneumonia.

The coronavirus disease 2019 causes a wide degree of organ dysfunction and is associated with bacterial secondary infections. We reported lung microbiota dynamics in a critically ill patient with coronavirus disease 2019, who developed severe Hafnia alvei ventilator-associated pneumonia and required extracorporeal membrane oxygenation support.

Microbiología de Hafnia alvei / Microbiology of Hafnia alvei

Hafnia alvei es un bacilo gramnegativo facultativamente anaeróbico que constituye parte de la flora intestinal humana. Hasta hace poco, las cepas de H. alvei, que se identificaban por métodos convencionales, por miniaturización o por sistemas automáticos, podían confundirse fácilmente con miembros de los géneros Serratia, Escherichia, Citrobacter, Yokenella, Obesumbacterium o Salmonella, por lo que era necesario realizar técnicas moleculares para su identificación definitiva en la práctica clínica. Además, recientemente se ha introducido una nueva especie de Hafnia, H. paralvei, que sin duda incluye a muchas de las cepas previamente identificadas en la literatura como H. alvei. Aunque el aislamiento de H. alvei de muestras clínicas humanas sigue siendo poco frecuente, han aumentado los artículos científicos que evidencian un aumento de la resistencia a los antibióticos en esta especie y es probable que este organismo gane cada vez más importancia en el futuro. Además, aunque H. alvei comparte algunos mecanismos de virulencia con otros enteropatógenos gramnegativos, se sabe poco sobre los factores que contribuyen a su patogénesis en humanos. El presente artículo revisa los métodos de identificación actuales, la resistencia a los antimicrobianos y los factores de virulencia de esta bacteria

Hafnia alvei is a Gram-negative facultatively anaerobic bacillus that constitutes part of the human gut flora. Until recently, H. alvei strains could be mistakenly identified by conventional methods, miniaturisation or automatic systems as members of the Serratia, Escherichia, Citrobacter, Yokenella, Obesumbacterium or Salmonella genera. Consequently, molecular techniques were required for their definitive identification in the clinical laboratory. In addition, a new Hafnia species, H. paralvei, has recently appeared, which undoubtedly includes many of the strains reported in the literature as H. alvei. Alrhough H. alvei isolation from human clinical specimens remains uncommon, the development of drug resistance due to this species is emerging and it is likely that this organism will gain increasing importance in the future. Moreover, although H. alvei shares some virulence mechanisms with other Gram-negative enteropathogens, little is known about the factors that contribute to its pathogenesis in humans. The present article reviews the current identification methods, antimicrobial resistance and virulence factors of this bacterium

Hafnia alvei pneumonia: a rare cause of infection in the multimorbid or immunocompromised.

Hafnia alvei is a rare, poorly understood commensal bacterium which has, on occasion, been shown to infect humans. We present two cases. The first patient presented with a 1-week history of dyspnoea, pleurisy and a productive cough, and the second with a prodrome of fatigue and night sweats. The former had a history of severe chronic obstructive pulmonary disease and the latter had a history of Crohn's disease. Both patients had underlying comorbidities and immunosuppression, but differed in presentation, radiological findings and recovery. This case series aims to remind readers of the broad differential of pathogens that can lead to disease in the immunocompromised and that one should not dismiss atypical cultured bacteria as commensal too hastily.

Design of microbial consortia for the fermentation of pea-protein-enriched emulsions.

In order to encourage Western populations to increase their consumption of vegetables, we suggest turning legumes into novel, healthy foods by applying an old, previously widespread method of food preservation: fermentation. In the present study, a total of 55 strains from different microbial species (isolated from cheese or plants) were investigated for their ability to: (i) grow on a emulsion containing 100% pea proteins and no carbohydrates or on a 50:50 pea:milk protein emulsion containing lactose, (ii) increase aroma quality and reduce sensory off-flavors; and (iii) compete against endogenous micro organisms. The presence of carbohydrates in the mixed pea:milk emulsion markedly influenced the fermentation by strongly reducing the pH through lactic fermentation, whereas the absence of carbohydrates in the pea emulsion promoted alkaline or neutral fermentation. Lactic acid bacteria assigned to Lactobacillus plantarum, Lactobacillus rhamnosus, Lactococcus lactis and Lactobacillus casei species grew well in both the pea and pea:milk emulsions. Most of the fungal strains tested (particularly those belonging to the Mucor and Geotrichum genera) were also able to grow on both emulsions. Although most Actinobacteria and Proteobacteria did not compete with endogenous microbiota (Bacillus), some species such as Hafnia alvei, Acinetobacter johnsonii and Glutamicibacter arilaitensis grew strongly and appeared to restrict the development of the endogenous microbiota when the pea emulsion was inoculated with a combination of three to nine strains. In the mixed emulsions, lactic fermentation inhibited Actinobacteria and Proteobacteria (e.g. Brevibacterium casei, Corynebacterium casei, Staphylococcus lentus) to the greatest extent but also inhibited Bacillus (e.g. Bacillus subtilis and Bacillus licheniformis). Overall, this procedure enabled us to select two microbial consortia able to colonize pea-based products and positively influence the release of volatile compounds by generating a roasted/grilled aroma for the 100% pea emulsion, and a fruity, lactic aroma for the 50:50 pea:milk emulsion. Moreover, the fermentation in the pea-based emulsions reduced the level of hexanal, which otherwise leads to an undesired green pea aroma. Our present results show how the assembly of multiple microbial cultures can help to develop an innovative food product.

Descriptivo de Hafnia alvei aisladas en coprocultivo: aproximación a su valoración en clínica / A descriptive study of Hafnia alvei isolated from stool samples: an approach to its clinical assessment

Introducción. El papel de Hafnia alvei en la etiología de diarrea en humanos es todavía muy controvertido; el objetivo del estudio fue describir la población en cuyos coprocultivos se aisló H. alvei y el manejo terapéutico de estos casos en nuestro Área de Salud. Material y métodos. Para ello se realizó un estudio descriptivo retrospectivo de 2014 y 2015. Se recogieron en la historia clínica informatizada, variables epidemiológicas, clínicas, tratamiento y evolución. Resultados. Se procesaron 7.290 coprocultivos, 3.321 en 2014, 58 (1,7%) en los que se aisló H. alvei y 3.969 en 2015, 53 (1,3%) positivos. El 60,4% de las muestras fueron aisladas en mujeres. La edad media fue de 38,68 años. El 68,5% provenían de Atención Primaria. En el 71,2% se recogió clínica asociada, siendo el más frecuente la diarrea en el 57,7%. En el 75,7% de los casos no existía patología de base asociada. El 43,2% de los casos recibió tratamiento de los cuales el 66,7% de los pacientes procedían de Atención Primaria. La duración media del tratamiento fue de 8 días. En el 85,4% de los casos tratados, la evolución fue favorable. Todas las cepas fueron sensibles a ciprofloxacino y trimetoprim/sulfametoxazol. Conclusiones. Faltan estudios que establezcan de forma concluyente la enteropatogenicidad o no de H. alvei (AU)

Introduction. The importance in human diarrhoeal disease of Hafnia alvei is unclear. The objective of the study was to describe the population which was isolated H. alvei in stool cultures and the therapeutic management of these cases in our Health Area. Material and methods. A descriptive retrospective study was carried out in 2014 and 2015. Epidemiological, clinical, treatment and evolution variables were collected in the computerized clinical history. Result. A collection of 7,290 stool specimens were processed, 3,321 in 2014 and 3,969 in 2015, of which 58 (1.7%) and 53 (1.3%) were positive for H. alvei, respectively. A 60.4% of samples were isolated in women. The mean age was 38.68 years. A 68.5% of samples were from primary care. In 71.2% there was related clinic, diarrhoea in 57.7%. In 75.7% of the cases there was not associated underlying disease. A 43.2% of the cases received treatment. A 66.7% of treated patients came from Primary Care. The mean duration of treatment was 8 days. The evolution was favourable in 85.4% of the cases treated. All strains were susceptible to ciprofloxacin and trimethoprim/sulfamethoxazole. Conclusions. More evidence is needed to support H. alvei as a cause of gastroenteritis (AU)

Human norovirus binding to select bacteria representative of the human gut microbiota.

Recent reports describe the ability of select bacterial strains to bind human norovirus, although the specificity of such interactions is unknown. The purpose of this work was to determine if a select group of bacterial species representative of human gut microbiota bind to human norovirus, and if so, to characterize the intensity and location of that binding. The bacteria screened included naturally occurring strains isolated from human stool (Klebsiella spp., Citrobacter spp., Bacillus spp., Enterococcus faecium and Hafnia alvei) and select reference strains (Staphylococcus aureus and Enterobacter cloacae). Binding in PBS was evaluated to three human norovirus strains (GII.4 New Orleans 2009 and Sydney 2012, GI.6) and two surrogate viruses (Tulane virus and Turnip Crinkle Virus (TCV)) using a suspension assay format linked to RT-qPCR for quantification. The impact of different overnight culture media prior to washing on binding efficiency in PBS was also evaluated, and binding was visualized using transmission electron microscopy. All bacteria tested bound the representative human norovirus strains with high efficiency (<1 log10 of input virus remained unbound or <10% unbound and >90% binding efficiency) (p>0.05); there was selective binding for Tulane virus and no binding observed for TCV. Binding efficiency was highest when bacteria were cultured in minimal media (<1 log10 of input virus remained unbound, so >90% bound), but notably decreased when cultured in enriched media (1-3 log10 unbound or 0.01 -<90% bound)) (p<0.05). The norovirus-bacteria binding occurred around the outer cell surfaces and pili structures, without apparent localization. The findings reported here further elucidate and inform the dynamics between human noroviruses and enteric bacteria with implications for norovirus pathogenesis.

Risk of infection transmission in curvilinear array echoendoscopes: results of a prospective reprocessing and culture registry.

BACKGROUND AND AIMS: The complex design of the elevator mechanism in duodenoscopes has been recognized as a challenge for disinfection and recently implicated as a potential source of persistent bacterial contamination. Curvilinear array (CLA) echoendoscopes also have an elevator mechanism; however, there are no recommendations or data regarding the risk of persistent bacterial contamination of echoendoscopes. Here we hoped to determine the yield of microbial growth with routine bacterial surveillance cultures of reprocessed CLA echoendoscopes. METHODS: Beginning in February 2015 to February 2016, CLA echoendoscopes at a single tertiary care center underwent prospective bacterial surveillance cultures after reprocessing. Any growth of gram-negative bacilli was considered to be critical. Echoendoscopes with a positive result underwent quarantine followed by repeat disinfection and culture. RESULTS: During the study period, 540 cultures were obtained; 521 (96.5%) were primary cultures obtained from 18 CLA echoendoscopes. Twenty-two primary cultures (4.2%) were positive for gram-negative bacilli after high-level disinfection reprocessing. Eleven different bacteria were isolated: Klebsiella pneumoniae, Citrobacter freundii, Escherichia coli, Pseudomonas aeruginosa, Klebsiella oxytoca, Sphingomonas paucimobilis, Acinetobacter baumanii, Enterobacter cloacae, Hafnia alvei, Pseudomonas putida, and Stenotrophomonas maltophilia. Antibiotic sensitivity data on 19 of 24 bacteria (79.2%) isolated from positive primary cultures revealed no documented cases of carbapenem-resistant enterobacteriaceae, cephalosporin-resistant-Klebsiella, or multidrug-resistant Acinetobacter. There have been no documented cases of patient-to-patient transmission. CONCLUSIONS: After following standard high-level disinfection and reprocessing, CLA echoendoscopes can remain culture positive for high-concern organisms. Recommendations regarding infection risk should take into consideration elevator-containing echoendoscopes in addition to duodenoscopes to ensure patient safety and endoscope reprocessing efficacy.

Survival of cheese-ripening microorganisms in a dynamic simulator of the gastrointestinal tract.

A mixture of nine microorganisms (six bacteria and three yeasts) from the microflora of surface-ripened cheeses were subjected to in vitro digestive stress in a three-compartment "dynamic gastrointestinal digester" (DIDGI). We studied the microorganisms (i) grown separately in culture medium only (ii) grown separately in culture medium and then mixed, (iii) grown separately in culture medium and then included in a rennet gel and (iv) grown together in smear-ripened cheese. The yeasts Geotrichum candidum, Kluyveromyces lactis and Debaryomyces hansenii, were strongly resistant to the whole DIDGI process (with a drop in viable cell counts of less than <1 log CFU mL(-1)) and there were no significant differences between lab cultures and cheese-grown cultures. Ripening bacteria such as Hafnia alvei survived gastric stress less well when grown in cheese (with no viable cells after 90 min of exposure of the cheese matrix, compared with 6 CFU mL(-1) in lab cultures). The ability of Corynebacterium casei and Staphylococcus equorum to withstand digestive stress was similar for cheese and pure culture conditions. When grow in a cheese matrix, Brevibacterium aurantiacum and Arthrobacter arilaitensis were clearly more sensitive to the overall digestive process than when grown in pure cultures. Lactococcus lactis displayed poorer survival in gastric and duodenal compartments when it had been grown in cheese. In vivo experiments in BALB/c mice agreed with the DIDGI experiments and confirmed the latter's reliability.

Antibiotic resistance versus antimicrobial substances production by gram-negative foodborne pathogens isolated from minas frescal cheese: heads or tails?

In this study, 15 Gram-negative isolates from Minas Frescal cheese sold in commercial establishments in Rio de Janeiro, Brazil, were able to produce antimicrobial substances (AMSs). Seven, four, two, one, and one isolates identified as Yersinia, Acinetobacter, Enterobacter, Escherichia, and Hafnia genera, respectively, were considered potentially pathogenic. All 15 AMS(+) isolates were resistant to at least 1 antibiotic; however, 7 strains presented resistance to at least 3 antibiotics from different classes, exhibiting multiresistance profiles. The strains were also subjected to plasmid profile analysis. All isolates presented different plasmid forms with most ranging in size from 1 to 10 kb. Activity against various pathogens associated with food was tested and all 15 AMS(+) showed the same activity spectrum, inhibiting all Escherichia coli and Salmonella strains that were tested. Although restricted, the action spectrum of AMS-producing strains is extremely relevant to the food industry because Gram-negative bacteria such as E. coli and Salmonella spp. are most often associated with foodborne illnesses. The findings of this study reveal that even AMS produced by pathogens can have potential applications against other foodborne pathogens.

Quorum sensing activity of Hafnia alvei isolated from packed food.

Quorum sensing (QS) is a mechanism adopted by bacteria to regulate expression of genes according to population density. N-acylhomoserine lactones (AHLs) are a type of QS signalling molecules commonly found in Gram-negative bacteria which have been reported to play a role in microbial spoilage of foods and pathogenesis. In this study, we isolated an AHL-producing Hafnia alvei strain (FB1) from spherical fish pastes. Analysis via high resolution triple quadrupole liquid chromatography/mass spectrometry (LC/MS) on extracts from the spent supernatant of H. alvei FB1 revealed the existence of two short chain AHLs: N-(3-oxohexanoyl) homoserine lactone (3-oxo-C6-HSL) and N-(3-oxo- octanoyl) homoserine lactone (3-oxo-C8-HSL). To our knowledge, this is the first report of the production of AHLs, especially 3-oxo-C8-HSL, by H. alvei.

Recovery of Hafnia alvei from diseased brown trout, Salmo trutta L., and healthy noble crayfish, Astacus astacus (L.), in Bulgaria.

Hafnia alvei was isolated in Bulgaria from healthy noble crayfish, Astacus astacus (L.), and then from farmed diseased brown trout, Salmo trutta L., with signs of haemorrhagic septicaemia. The isolates were identified initially with conventional phenotyping and commercial Merlin Micronaut and API 20E rapid identification systems, followed by sequencing of the 16S rRNA gene. Hafnia alvei Bt1, Bt2 and Aa4 were of low virulence to rainbow trout and brown trout, although cytotoxicity was demonstrated by Bt1 and Bt2, but not by Aa4.

New complete structure of Hafnia alvei clinical isolate strain PCM 2670 semi-rough lipopolysaccharide.

Hafnia alvei strain PCM 2670 is a clinical isolate from a patient with chronic reproductive tract infection. The novel structure of the semi-rough lipopolysaccharide was established with the use of NMR spectroscopy and mass spectrometry as well as immunochemical techniques. According to the mass spectrometry data, heptose in the oligosaccharide is partially substituted by glycine. H. alvei PCM 2670 core structure encompasses the common core of H. alvei which is modified with two additional galactose units. [structure: see text]. The 6-substituted galactose is the O-antigen repeating unit substitution residue. The repeating unit consists of five monosaccharide residues and has the following structure: →2)-ß-Galp-(1→6)-α-Glcp-(1→6)-αGlcpNAc3OAc-(1→4)-α-GalpA-(1→3)-ß-GlcpNAc6OAc-(1→6)-core.

Hafnia alvei pyelonephritis in a renal transplant recipient: case report and review of an under-recognized nosocomial pathogen.

We describe the first case to our knowledge of Hafnia alvei pyelonephritis in a renal transplant recipient. Clinicians should consider this under-recognized pathogen when clinically evaluating immunosuppressed patients with a history of invasive procedures.

Improved selective and differential medium for isolation of Escherichia coli O157:H7.

GMAC, a modified version of Sorbitol MacConkey medium (SMAC), was produced with a reduced quantity of selective agents and incorporated gentiobiose. GMAC supported a higher recovery rate of heat- or acid-injured Escherichia coli O157:H7 cells than SMAC with cefixime and tellurite (CT-SMAC), while differentiating E. coli O157:H7 from sorbitol-nonfermenting Hafnia alvei.

[Report of four clinical cases of Hafnia alvei bacteremia in a pediatric cardiac surgery unit]. / Reporte de cuatro casos clínicos de bacteriemia por Hafnia alvei en una unidad cardio-quirúrgica pediátrica.

INTRODUCTION: The gram-negative bacillus Hafnia alvei is the only species of the genus Hafnia, family Enterobacteriaceae. It occasionally behaves as an opportunistic pathogen in humans, causing intestinal and respiratory infection and sepsis. It rarely causes bacteremia, usually of unknown focus. OBJECTIVE: To describe a nosocomial outbreak of four pediatric patients with bacteremia by Hafnia alvei. METHODS: Descriptive study using clinical records of pediatric patients diagnosed with Hafnia alvei bacteremia in a pediatric cardio surgical unit, in October 2008. RESULTS: The attack rate was 4/8 (50%), lethality rate 2/4 (50%) and mortality 2/8 (25%). The microbiological study and pulsed-field gel electrophoresis confirmed the same clonal bacterial strain. DISCUSSION: The source of bacteremia was identified only in two patients and was associated with central venous catheters. The other two cases had no known infectious source. Epidemiological surveillance of emerging agents must be maintained.

Reporte de cuatro casos clínicos de bacteriemia por Hafnia alvei en una unidad cardio-quirúrgica pediátrica / Report of four clinical cases of Hafnia alvei bacteremia in a pediatric cardiac surgery unit

Introduction: The gram-negative bacillus Hafnia alvei is the only species of the genus Hafnia, family Enterobacteriaceae. It occasionally behaves as an opportunistic pathogen in humans, causing intestinal and respiratory infection and sepsis. It rarely causes bacteremia, usually of unknown focus. Objective: To describe a nosocomial outbreak of four pediatric patients with bacteremia by Hafnia alvei. Methods: Descriptive study using clinical records of pediatric patients diagnosed with Hafnia alvei bacteremia in a pediatric cardio surgical unit, in October 2008. Results: The attack rate was 4/8 (50 percent), lethality rate 2/4 (50 percent) and mortality 2/8 (25 percent). The microbiological study and pulsed-field gel electrophoresis confirmed the same clonal bacterial strain. Discussion: The source of bacteremia was identified only in two patients and was associated with central venous catheters. The other two cases had no known infectious source. Epidemiological surveillance of emerging agents must be maintained.

Introducción: Hajhia alvei, bacilo Gram negativo, constituye la única especie del género Hajhia, familia Enterobacteriaceae. En el humano se comporta ocasionalmente como oportunista produciendo infección intestinal, respiratoria y sepsis. Es causa infrecuente de bacteriemias, generalmente de foco infeccioso desconocido. Objetivo: Describir un brote intrahospitalario de cuatro pacientes pediátricos con bacteriemias por Hajhia alvei. Método: Estudio descriptivo retrospectivo de los registros clínicos de cuatro pacientes pediátricos con diagnóstico de bacte-riemia por Hajhia alvei en una unidad cardioquirúrgica pediátrica identificados en octubre del 2008. Resultados: La tasa de ataque fue 4/8 (50 por ciento), tasa de letalidad 2/4 (50 por ciento) y de mortalidad de 2/8 (25 por ciento). El estudio micro-biológico y la electroforesis de campo pulsado confirman la misma cepa bacteriana clonal. Discusión: Se identificó el origen de la bacteriemia sólo en dos pacientes asociado a catéter venoso central. Los otros dos casos no tuvieron foco infeccioso conocido. Se debe mantener vigilancia epidemiológica de agentes emergentes.

Isolation of Hafnia species from kimchi.

Eight commercially packaged kimchi products were examined over 15 days of storage at 4 degrees to evaluate the occurrence of Hafnia alvei (H. alvei). Additionally, 7 saeujeot products, as a possible ingredient source, were analyzed to examine the bacteria's origin. Over the storage period, kimchi samples had decreasing pH levels, which stabilized at pH 4.2; acidity increased to 0.9+/-0.1%. Lactose-nonfermenting bacteria, which H. alvei belongs to, gradually reduced in numbers over the kimchi storage. However, the relative frequency of H. alvei to lactose-nonfermenting bacteria tended to increase. From the kimchi samples, 58 H. alvei-presumptive colonies were selected. Forty-three colonies turned out to be H. alvei and 15 colonies were identified as other strains or of uncertain identification when the API 20E system was used. From further test, 3 of the 43 colonies were H. alvei (-) against the phage test. Finally, H. alvei was isolated from saeujeot, indicating that this ingredient can be an originating source of H. alvei in kimchi.