The genus Hafnia: from soup to nuts

Revealing the genetic traits of the foodborne microbial genus hafnia: Implications for the human gut microbiome

The bacterial genus Hafnia has recently attracted attention due to its complex metabolic features and host-interaction capabilities, which are associated with health benefits, primarily weight loss. However, significant gaps remain in our understanding of the genomic characteristics of this emerging microbial group. In this study, we utilized all available high-quality genomes of Hafnia alvei and Hafnia paralvei to uncover the broad distribution of Hafnia in human and honeybee guts, as well as in dairy products, by analysing 1068 metagenomic datasets. We then investigated the genetic traits related to Hafnia's production of vitamins and short-chain fatty acids (SCFAs) through a comparative genomics analysis that included all dominant bacterial species in the three environments under study. Our findings underscore the extensive metabolic capabilities of Hafnia, particularly in the production of vitamins such as thiamine (B1), nicotinate (B3), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and menaquinone (K2). Additionally, Hafnia demonstrated a conserved genetic makeup associated with SCFA production, including acetate, propanoate, and butanoate. These metabolic traits were further confirmed using RNAseq analyses of a newly isolated H. paralvei strain T10. Overall, our study illuminates the ecological distribution and genetic attributes of this bacterial genus, which is of increasing scientific and industrial relevance.

Snapshot of resistome, virulome and mobilome in aquaculture

Aquaculture environments can be hotspots for resistance genes through the surrounding environment. Our objective was to study the resistome, virulome and mobilome of Gram-negative bacteria isolated in seabream and bivalve molluscs, using a WGS approach. Sixty-six Gram-negative strains (Aeromonadaceae, Enterobacteriaceae, Hafniaceae, Morganellaceae, Pseudomonadaceae, Shewanellaceae, Vibrionaceae, and Yersiniaceae families) were selected for genomic characterization. The species and MLST were determined, and antibiotic/disinfectants/heavy metals resistance genes, virulence determinants, MGE, and pathogenicity to humans were investigated. Our study revealed new sequence-types (e.g. Aeromonas spp. ST879, ST880, ST881, ST882, ST883, ST887, ST888; Shewanella spp. ST40, ST57, ST58, ST60, ST61, ST62; Vibrio spp. ST206, ST205). >140 different genes were identified in the resistome of seabream and bivalve molluscs, encompassing genes associated with β-lactams, tetracyclines, aminoglycosides, quinolones, sulfonamides, trimethoprim, phenicols, macrolides and fosfomycin resistance. Disinfectant resistance genes qacE-type, sitABCD-type and formA-type were found. Heavy metals resistance genes mdt, acr and sil stood out as the most frequent. Most resistance genes were associated with antibiotics/disinfectants/heavy metals commonly used in aquaculture settings. We also identified 25 different genes related with increased virulence, namely associated with adherence, colonization, toxins production, red blood cell lysis, iron metabolism, escape from the immune system of the host. Furthermore, 74.2 % of the strains analysed were considered pathogenic to humans. We investigated the genetic environment of several antibiotic resistance genes, including blaTEM-1B, blaFOX-18, aph(3″)-Ib, dfrA-type, aadA1, catA1-type, tet(A)/(E), qnrB19 and sul1/2. Our analysis also focused on identifying MGE in proximity to these genes (e.g. IntI1, plasmids and TnAs), which could potentially facilitate the spread of resistance among bacteria across different environments. This study provides a comprehensive examination of the diversity of resistance genes that can be transferred to both humans and the environment, with the recognition that aquaculture and the broader environment play crucial roles as intermediaries within this complex transmission network.

Host genetic background rather than diet-induced gut microbiota shifts of sympatric black-necked crane, common crane and bar-headed goose

Introduction

Gut microbiota of wild birds are affected by many factors, and host genetic background and diet are considered to be two important factors affecting their structure and function.

Methods

In order to clarify how these two factors influence the gut microbiota, this study selected the sympatric and closely related and similar-sized Black-necked Crane (Grus nigricollis) and Common Crane (Grus grus), as well as the distantly related and significantly different-sized Bar-headed Goose (Anser indicus). The fecal samples identified using sanger sequencing as the above three bird species were subjected to high-throughput sequencing of rbcL gene and 16S rRNA gene to identify the feeding types phytophagous food and gut microbiota.

Results

The results showed significant differences in food diversity between black-necked cranes and Common Cranes, but no significant differences in gut microbiota, Potatoes accounted for approximately 50% of their diets. Bar-headed Geese mainly feed on medicinal plants such as Angelica sinensis, Alternanthera philoxeroides, and Ranunculus repens. Black-necked cranes and Common Cranes, which have a high-starch diet, have a similar degree of enrichment in metabolism and synthesis functions, which is significantly different from Bar-headed Geese with a high-fiber diet. The differences in metabolic pathways among the three bird species are driven by food. The feeding of medicinal plants promotes the health of Bar-headed Geese, indicating that food influences the functional pathways of gut microbiota. Spearman analysis showed that there were few gut microbiota related to food, but almost all metabolic pathways were related to food.

Conclusion

The host genetic background is the dominant factor determining the composition of the microbiota. Monitoring the changes in gut microbiota and feeding types of wild birds through bird feces is of great reference value for the conservation of other endangered species.

Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge

The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where such initial mobilization events of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes.

Could the Microbiota Be a Predictive Factor for the Clinical Response to Probiotic Supplementation in IBS-D? A Cohort Study

BACKGROUND

Increasing evidence suggests the beneficial effects of probiotics in irritable bowel syndrome (IBS), but little is known about how they can impact the gut microbiota. Our objective was to evaluate the effects of a multistrain probiotic on IBS symptoms, gut permeability and gut microbiota in patients with diarrhoea-predominant IBS (IBS-D).

METHODS

Adults with IBS-D were enrolled in an open-label trial to receive a multistrain probiotic for 4 weeks. Abdominal pain, stool frequency, quality of life, gut permeability, and the luminal and adherent microbiota from colonic biopsies were evaluated before and after supplementation.

RESULTS

Probiotics significantly improved symptoms and quality of life, despite having no impact on permeability in the global population. In the population stratified by the response, the diarrhoea responders displayed reduced colonic permeability after supplementation. The luminal and adherent microbiota were specifically altered depending on the patients' clinical responses regarding pain and diarrhoea. Interestingly, we identified a microbial signature in IBS-D patients that could predict a response or lack of response to supplementation.

CONCLUSIONS

The multistrain probiotic improved the symptoms of IBS-D patients and induced distinct effects on the gut microbiota according to the patient's clinical response and initial microbiota composition. Our study further supports the need to develop individualised probiotic-based approaches regarding IBS.

Short Communication: Low Prevalence of Clinically Important Antibiotic-Resistant Strains among Non-Pathogenic Genera of the Tribe Klebsielleae

Hafnia sp. and Serratia sp. belong to the Tribe Klebsielleae; although they are not considered pathogenic bacteria, there are many documented cases of diseases caused by these microorganisms. The aim of this study was to determine the antibiotic resistance profiles of strains belonging to the genus Hafnia and Serratia isolated from fish and shrimps. Phenotypic antibiotic resistance was determined using the semi-automatic Vitek 2 system (bioMérieux, Marcy-l’Étoile, France), while the presence of the extended-spectrum beta-lactamase, AmpC beta-lactamases, Klebsiella pneumoniae carbapenemases and Metallo-β-Lactamase producing strains were determined using the MIC Test Strip (Liofilchem, Roseto degli Abbruzzi, Italy). As a result of the conducted research, it was observed that a vast number of Hafnia sp. strains were resistant to cefalexin (84.61%), while Serratia sp. Strains to cefuroxime (79.41%) and nitrofurantoin (85.29%). In addition, it was observed that of all strains, only one had an ability to produce enzymes typical for β-lactamase-producing Enterobacterales. Although the strains of Hafnia sp. and Serratia sp. isolated from fish and shrimp are not characterized by frequent resistance to antibiotics, taking into account the constantly growing number of antibiotic-resistant strains, this may be a problem in the future, mainly due to gene transfer through mobile genetic elements and the acquisition of resistance expressed phenotypically through contact with stress factors. Therefore, studies monitoring the antibiotic resistance profile of these species should be carried out on a regular basis.

Genomic analysis of a novel active prophage of Hafnia paralvei

Little is known about the prophages in Hafniaceae bacteria. A novel Hafnia phage, yong2, was induced from Hafnia paralvei by treatment with mitomycin C. The phage has an elliptical head with dimensions of approximately 45 × 38 nm and a long noncontractile tail of approximately 157 × 4 nm. The complete genome of Hafnia phage yong2 is a 39,546-bp double-stranded DNA with a G+C content of 49.9%, containing 59 open reading frames (ORFs) and having at least one fixed terminus (GGGGCAGCGACA). In phylogenetic analysis, Hafnia phage yong2 clustered with four predicted Hafnia prophages and one predicted Enterobacteriaceae prophage. These prophages and members of the family Drexlerviridae together formed two distinct subclades nested within a clade, suggesting the existence of a novel class of prophages with conserved sequences and a unique evolutionary status not yet studied before in Hafniaceae and Enterobacteriaceae bacteria.

Transitional genomes and nutritional role reversals identified for dual symbionts of adelgids (Aphidoidea: Adelgidae)

Many plant-sap-feeding insects have maintained a single, obligate, nutritional symbiont over the long history of their lineage. This senior symbiont may be joined by one or more junior symbionts that compensate for gaps in function incurred through genome-degradative forces. Adelgids are sap-sucking insects that feed solely on conifer trees and follow complex life cycles in which the diet fluctuates in nutrient levels. Adelgids are unusual in that both senior and junior symbionts appear to have been replaced repeatedly over their evolutionary history. Genomes can provide clues to understanding symbiont replacements, but only the dual symbionts of hemlock adelgids have been examined thus far. Here, we sequence and compare genomes of four additional dual-symbiont pairs in adelgids. We show that these symbionts are nutritional partners originating from diverse bacterial lineages and exhibiting wide variation in general genome characteristics. Although dual symbionts cooperate to produce nutrients, the balance of contributions varies widely across pairs, and total genome contents reflect a range of ages and degrees of degradation. Most symbionts appear to be in transitional states of genome reduction. Our findings support a hypothesis of periodic symbiont turnover driven by fluctuating selection for nutritional provisioning related to gains and losses of complex life cycles in their hosts.

First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism

A unique lytic phage infecting Hafnia paralvei was isolated and identified. Hafnia phage Ca belongs to the family Autographiviridae, possessing an icosahedral head with a diameter of 55 nm and a short non-contractile tail. Unusually, the burst size of Hafnia phage Ca of 10,292 ± 1,097 plaque-forming units (PFUs)/cell is much larger than other dsDNA phages reported before. Compared to the genome of the related phage, Hafnia phage Ca genome contains extra genes including DNA mimic ocr, dGTP triphosphohydrolase inhibitor, endonuclease, endonuclease VII, and HNH homing endonuclease gene. Extraordinarily, the phage developed different sizes of plaques when a single plaque was picked out and inoculated on a double-layer Luria broth agar plate with its host. Furthermore, varied packaging tightness for the tails of Hafnia phage Ca was observed (tail length: 4.35–45.92 nm). Most of the tails appeared to be like a cone with appendages, some were dot-like, bun-like, table tennis racket handle-like, and ponytail-like. Although the complete genome of Hafnia phage Ca is 40,286 bp, an incomplete genome with a deletion of a 397-bp fragment, containing one ORF predicted as HNH homing endonuclease gene (HEG), was also found by high throughput sequencing. Most of the genome of the virus particles in large plaques is complete (>98%), while most of the genome of the virus particles in small plaques is incomplete (>98%), and the abundance of both of them in medium-sized plaques is similar (complete, 40%; incomplete, 60%). In an experiment to see if the phage could be protective to brocade carps intramuscularly injected with H. paralvei LY-23 and phage Ca, the protection rate of Hafnia phage Ca to brocade carp (Cyprinus aka Koi) against H. paralvei was 33.38% (0.01 < p < 0.05). This study highlights some new insights into the peculiar biological and genomic characteristics of phage.

Induction and Genomic Analysis of a Lysogenic Phage of Hafnia paralvei

Hafnia paralvei is a bacterium that can cause zoonoses. No research has been reported on H. paralvei prophage. In this study, a Hafnia phage yong1 was induced from pathogenic H. paralvei LY-23 by mitomycin C. The phage showed a Myoviridae-like morphology having a hexagonal head of approximately 65 nm in diameter and a contractile tail of approximately 95 nm in length and 17 nm in width. Its genome was sequenced by using the Illumina Miseq platform. The complete genome of Hafnia phage yong1 is 43,329 bp with a G + C content of 47.65%. BLASTn analysis revealed that Hafnia phage yong1 had the highest sequence similarity with the predicted prophages of Enterobacter chengduensis strain WCHECl-C4 = WCHECh050004 recovered from a human blood sample and Escherichia coli strain L103-2 recovered from a goose farm in China. Hafnia phage yong1 contains a tRNA gene and 76 predicted open reading frames, 33 of which were annotated. Gene strings similar to the bacteriophage λ cro-cI-rexA-rexB operon conferring Imm and Rex to lysogenic cells were found in Hafnia phage yong1 genome. Hafnia phage yong1 is the first Myoviridae-like phage found to contain such contiguous genes. Hafnia phage yong1 formed an independent branch between two families, Chaseviridae and Drexlerviridae, in the Proteomic tree.

Evolutionarily recent dual obligatory symbiosis among adelgids indicates a transition between fungus- and insect-associated lifestyles

Adelgids (Insecta: Hemiptera: Adelgidae) form a small group of insects but harbor a surprisingly diverse set of bacteriocyte-associated endosymbionts, which suggest multiple replacement and acquisition of symbionts over evolutionary time. Specific pairs of symbionts have been associated with adelgid lineages specialized on different secondary host conifers. Using a metagenomic approach, we investigated the symbiosis of the Adelges laricis/Adelges tardus species complex containing betaproteobacterial ("Candidatus Vallotia tarda") and gammaproteobacterial ("Candidatus Profftia tarda") symbionts. Genomic characteristics and metabolic pathway reconstructions revealed that Vallotia and Profftia are evolutionary young endosymbionts, which complement each other's role in essential amino acid production. Phylogenomic analyses and a high level of genomic synteny indicate an origin of the betaproteobacterial symbiont from endosymbionts of Rhizopus fungi. This evolutionary transition was accompanied with substantial loss of functions related to transcription regulation, secondary metabolite production, bacterial defense mechanisms, host infection, and manipulation. The transition from fungus to insect endosymbionts extends our current framework about evolutionary trajectories of host-associated microbes.

Current Insights: The Impact of Gut Microbiota on Postoperative Complications in Visceral Surgery-A Narrative Review

Postoperative complications are a major problem occurring in up to 50% of patients undergoing major abdominal surgery. Occurrence of postoperative complications is associated with a significantly higher morbidity and mortality in affected patients. The most common postoperative complications are caused by an infectious genesis and include anastomotic leakage in case of gastrointestinal anastomosis and surgical site infections. Recent research highlighted the importance of gut microbiota in health and disease. It is plausible that the gut microbiota also plays a pivotal role in the development of postoperative complications. This narrative review critically summarizes results of recent research in this particular field. The review evaluates the role of gut microbiota alteration in postoperative complications, including postoperative ileus, anastomotic leakage, and surgical site infections in visceral surgery. We tried to put a special focus on a potential diagnostic value of pre- and post-operative gut microbiota sampling showing that recent data are inhomogeneous to identify a high-risk microbial profile for development of postoperative complications.

Hafnia alvei pneumonia: from bees to human beings

Introduction

Hafnia alvei is an enterobacteria that is a common inhabitant of the gastrointestinal flora of bees, birds, fish, and mammals. In humans this enterobacteria has been recovered from the oropharynx and the gastrointestinal tract but it has been rarely reported as a pathogen and usually identified as hospital-acquired enterobacteria.

Case report

We describe a case of a 57-year-old woman, previously healthy, with a 7-day history of cough with brown sputum, sudden onset of chills, subjective fever, malaise, and pleuritic pain in the right hemithorax. A diagnosis of community-acquired pneumonia (CAP) was suspected and empiric antibiotic treatment was started. However, the patient showed no response and developed hemoptysis. A diagnosis of CAP by Hafnia alvei was confirmed with bronchoalveolar lavage and the patient was treated with i.v. cefepime 2 g TID with a good response.

Conclusions

We presented a case of community-acquired pneumonia by Hafnia alvei in a previously healthy patient that, as far as our knowledge reaches, is the third reported case of CAP secondary to this pathogen.

Draft Genome Sequence of Hafnia paralvei Strain VBC_1714, Isolated from Frozen Cod Fillet Imported from Russia to Norway

Hafnia spp. have the potential to cause opportunistic infections in humans and animals. This announcement describes the draft genome sequence of an H₂S-positive Hafnia paralvei strain that was isolated as a presumptive Salmonella sp. from a frozen cod fillet.

Microbiology of Hafnia alvei

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.

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.

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.

Maize (Zea mays L. Sp.) varieties significantly influence bacterial and fungal community in bulk soil, rhizosphere soil and phyllosphere

The plant-microbe interaction can affect ecosystem function, and many studies have demonstrated that plant species influence relevant microorganisms. In this study, microbial communities in bulk soil, rhizosphere soil and phyllosphere from different maize varieties were investigated using high-throughput sequencing method. Results demonstrated that cultivar Gaoneng 1 (G1) showed higher bacterial diversity in soil (both bulk and rhizosphere soils) and lower bacterial diversity in the phyllosphere, while cultivar Gaoneng 2 (G2) had lower fungal diversity in both the soil and phyllosphere compare to the other cultivars. The bacterial community structure of soils among the three varieties was significantly different; however, no significant differences were found in the soil fungal community and phyllosphere bacterial and fungal community. The soil networks from cultivar G1 and phyllosphere networks from cultivar Zhengdan (ZD) have the highest complexity in contrast to the other two cultivars. In conclusion, the bacterial community structure in bulk soil of different cultivars was significantly different, so do the co-occurrence ecological networks of phyllosphere bacterial community. This study comprehensively analyzed the microbial community among different maize cultivars and could be useful for guiding practices, such as evaluation of new plant cultivars and quality predictions of these varieties at the microbial level.

Bacteria and antibiotic resistance detection in fractures of wild birds from wildlife rehabilitation centres in Spain

Anatomic adaptations make birds more prone to open fractures with exposed bone parts losing vascularization. As a result of this exposure, fractures are colonized by different microorganisms, including different types of bacteria, both aerobic and anaerobic, causing osteomyelitis in many cases. For this reason, antibiotic treatment is common. However, carrying out antibiotic treatment without carrying out a previous antibiogram may contribute to increased resistance against antibiotics, especially in migratory wild birds. In this paper, bacterial counts regarding fracture type, bacterial identification and antibiotic resistance have been analysed in wild birds from wildlife rehabilitation centres in Spain. The results obtained showed that open fractures had higher bacterial counts (CFU/mL) than closed ones. Bacteria in family Enterobacteriaceae, identified were Escherichia spp., Enterobacter spp., Shigella spp., Hafnia alvei, Proteus mirabilis, Leclercia adecarboxylata and Pantoea agglomerans. Other bacteria present in wild birds' fractures were Aeromonas spp., Enterococcus spp. Bacillus wiedmannii and Staphylococcus sciuri. All species found presented resistance to at least one of the antibiotics used. Wild birds can be implicated in the introduction, maintenance and global spreading of antibiotic resistant bacteria and represent an emerging public health concern. Results obtained in this paper support the idea that it is necessary to take this fact into account before antibiotic administration to wild animals, since it could increase the number of bacteria resistant to antibiotics.

Distribution of Antibiotic-Resistant Enterobacteriaceae Pathogens in Potable Spring Water of Eastern Indian Himalayas: Emphasis on Virulence Gene and Antibiotic Resistance Genes in Escherichia coli

Every year millions of people die due to fatal waterborne diseases around the world especially in developing countries like India. Sikkim, a northeastern state of India, greatly depends on natural water sources. About 80% of the population of Sikkim depends on natural spring water for domestic as well as agricultural use. Recent waterborne disease outbreaks in the state raises a concerning question on water quality. In this study, we analyzed water quality especially for the detection of Enterobacteriaceae members from four districts of the state. Isolation with selective culture media techniques and taxonomic characterization of Enterobacteriaceae bacteria with 16S rRNA gene showed the prevalence of Escherichia coli (37.50%), Escherichia fergusonii (29.41%), Klebsiella oxytoca (36.93%), Citrobacter freundii (37.92%), Citrobacter amalonaticus (43.82%), Enterobacter sp. (43.82%), Morganella morganii (43.82%), Hafnia alvei (32.42%), Hafnia paralvei (38.74%), and Shigella flexneri (30.47%) in the spring water of Sikkim. Antibiotic susceptibility test (AST) showed resistance of the isolates to common antibiotics like ampicillin, amoxicillin as well as to third generation antibiotics like ceftazidime and carbapenem. None of the isolates showed resistance to chloramphenicol. E. coli isolated from spring water of Sikkim showed presence of different virulence genes such as stx1 (81.81%), elt (86.66%), and eae (66.66%) along with resistance gene for ampicillin (CITM) (80%), quinolones (qnrB) (44.44%), tetracycline (tetO) (66.66%), and streptomycin (aadA1) (66.66%). The data indicates a high incidence rate of multiple antibiotic resistant enteric bacteria in the spring water of Sikkim. Additionally, the presence of enteric bacteria in the water samples indicates widespread fecal contamination of the spring water.

A Practical Method to Implement Strain-Level Metagenomics-Based Foodborne Outbreak Investigation and Source Tracking in Routine

The management of a foodborne outbreak depends on the rapid and accurate identification of the responsible food source. Conventional methods based on isolation of the pathogen from the food matrix and target-specific real-time polymerase chain reactions (qPCRs) are used in routine. In recent years, the use of whole genome sequencing (WGS) of bacterial isolates has proven its value to collect relevant information for strain characterization as well as tracing the origin of the contamination by linking the food isolate with the patient's isolate with high resolution. However, the isolation of a bacterial pathogen from food matrices is often time-consuming and not always successful. Therefore, we aimed to improve outbreak investigation by developing a method that can be implemented in reference laboratories to characterize the pathogen in the food vehicle without its prior isolation and link it back to human cases. We tested and validated a shotgun metagenomics approach by spiking food pathogens in specific food matrices using the Shiga toxin-producing Escherichia coli (STEC) as a case study. Different DNA extraction kits and enrichment procedures were investigated to obtain the most practical workflow. We demonstrated the feasibility of shotgun metagenomics to obtain the same information as in ISO/TS 13136:2012 and WGS of the isolate in parallel by inferring the genome of the contaminant and characterizing it in a shorter timeframe. This was achieved in food samples containing different E. coli strains, including a combination of different STEC strains. For the first time, we also managed to link individual strains from a food product to isolates from human cases, demonstrating the power of shotgun metagenomics for rapid outbreak investigation and source tracking.

Composition of the cutaneous bacterial community of a cave amphibian, Proteus anguinus

The European cave salamander Proteus anguinus is a charismatic amphibian endemic to the concealed and inaccessible subterranean waters of the Dinaric Karst. Despite its exceptional conservation importance not much is known about its ecology and interactions with the groundwater microbiome. The cutaneous microbiota of amphibians is an important driver of metabolic capabilities and immunity, and thus a key factor in their wellbeing and survival. We used high-throughput 16S rRNA gene sequencing based on seven variable regions to examine the bacteriome of the skin of five distinct evolutionary lineages of P. anguinus and in their groundwater environment. The skin bacteriomes turned out to be strongly filtered subsamples of the environmental microbial community. The resident microbiota of the analyzed individuals was dominated by five bacterial taxa. Despite an indicated functional redundancy, the cutaneous bacteriome of P. anguinus presumably provides protection against invading microbes by occupying the niche, and thus could serve as an indicator of health status. Besides conservation implications for P. anguinus, our results provide a baseline for future studies on other endangered neotenic salamanders.

Catheter-associated Hafnia alvei-induced Urosepsis

Hafnia alvei, belonging to the Enterobacteriaceae family, is a gram-negative, facultative anaerobe. The organism predominantly colonizes the gastrointestinal tract and, less often, the tissues, urine, and catheters. A 75-year-old male presented with a dry cough, fatigue, decreased appetite, intermittent disorientation, and difficulty ambulating. He had a history of self-catheterization due to urinary retention. He was scheduled to undergo transcatheter aortic valve replacement for enterococcal endocarditis. Physical examination was not significant for any changes. Urine analysis revealed positive leukocyte esterase, the presence of red and white blood cells, urine bacteria, and hyaline casts. The patient was started on empiric intravenous ceftriaxone. Urine culture grew Hafnia alvei and he was switched over to cefepime due to greater susceptibility. On day four, he started deteriorating clinically and was treated with four pressors but remained hypotensive and eventually became anuric. The patient developed septic shock with multiple organ dysfunction syndromes. Despite all measures, his clinical condition failed to improve, and he was continued with comfort measures only. The literature on Hafnia alvei-induced urosepsis is poor and fragmentary. Our patient showed resistance to most beta-lactam antibiotics, including cefuroxime, ceftriaxone, and ceftazidime, along with intermediate susceptibility to piperacillin/tazobactam and was managed with intravenous cefepime based on the sensitivity report. Inducible Bush group 1 beta-lactamase produced by Hafnia alvei is postulated to be responsible for antibiotic resistance. Physicians should remain vigilant of Hafnia alvei-induced urosepsis in patients with long-term catheterization initiating appropriate treatment.

Optimizing the Management of Cadmium Bioremediation Capacity of Metal-Resistant Pseudomonas sp. Strain Al-Dhabi-126 Isolated from the Industrial City of Saudi Arabian Environment

In this study, 23 bacterial strains were isolated from a Cadmium (Cd) contaminated soil in the industrial city, Riyadh of Saudi Arabia. Among these isolates six strains were found to withstand cadmium contamination and grow well. From the six isolates Pseudomonas sp. strain Al-Dhabi-122-127 were found to resist cadmium toxicity to a higher level. The isolates were subjected to biochemical and 16S rDNA gene sequence characterization to confirm their identification. The bacterial strain Al-Dhabi-124 showed 1.5 times higher Cd-degrading activity than Al-Dhabi-122 and Al-Dhabi-123, and Al-Dhabi-126 exhibited 3.5 times higher Cd-degrading activity, higher than the other strains. An atomic absorption spectrophotometer study showed that the strain Al-Dhabi-126 absorbed Cd, and that the bacterial strain Al-Dhabi-126 was found to tolerate cadmium level up to 2100 µg/mL. The bacterial strain Al-Dhabi-126 showed a maximum Cd removal efficacy at pH between 6.0 and 8.0. The efficacy decreased sharply after an increase in pH (9.0). An optimum temperature of 50 °C and pH 6.0 were found to be effective for the Cd removal process by the isolate. The study indicated that the bacterial strain Al-Dhabi-126 can be used effectively for the bioremediation of heavy metals like cadmium, a major toxic pollutant in industrial effluents.

Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

BACKGROUND

The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis.

RESULTS

One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei.

CONCLUSIONS

Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

Faecal indicator bacteria and antibiotic-resistant β-lactamase producing Escherichia coli in blackwater: a pilot study

The aim of this study was to identify and quantify faecal indicator bacteria in blackwater collected from a source separation unit and determine the amount of E. coli isolates resistant to antimicrobials and their potential to produce extended spectrum β-lactamases (ESβLs) and metallo-β-lactamases (MβLs), which hydrolyse the most important antibiotics used in clinical practice. Most of the isolates were resistant to amoxicillin with clavulanic acid (36.4 %), followed by ticarcillin with clavulanic acid (22.7 %) and tetracycline (18.2 %). ESβL-producing genes bla CTX-M and bla TEM were found in three (13.6 %) and four (18.2 %) E. coli strains, respectively, while MβL genes were found in two (9.1 %). By separating at source, this pilot study clearly shows that gastrointestinal bacteria of healthy people can be an important source of antibiotic resistance released into the environment through wastewaters. One way to prevent that is to treat wastewater with a combination of TiO2, UV light, or ozone, as successful methods to remove resistant bacteria and prevent their spread in the environment.

Reactive arthritis secondary to Hafnia alvei enterocolitis

Diagnosis of postenteritic reactive arthritis (ReA) is a challenge and might have a broad range of differential diagnoses. A 50-year-old man was referred to our attention because of persistent inflammatory low back pain and asymmetric oligoarthritis. The clinical history was positive for diarrhoea in the previous 3 months. Inflammatory bowel disease, Whipple and celiac diseases were carefully excluded. In addition, serology, stool cultures, biopsies from the upper gastrointestinal tract yielded negative results for infections. A presumptive diagnosis of ReA was done and a non-steroidal anti-inflammatory drug trial prescribed. Persistence of symptoms prompted us for a second look of the colon. Biopsy collected from the terminal ileum were cultured and surprisingly colonies of Hafnia alvei, a rod-shaped Enterobacteriaceae, were detected. Treatment with ciprofloxacin leads to fast symptoms resolution. Although enterocolitis from H. alvei has been rarely reported, the culture of intestinal specimens might be recommended in the work-up of patients with suspected postenteritic ReA.

Occurrence of Selected Zoonotic Fecal Pathogens and First Molecular Identification of Hafnia paralvei in Wild Taihangshan Macaques (Macaca mulatta tcheliensis) in China

Rhesus macaques (Macaca mulatta) are hosts to a range of zoonotic and potentially zoonotic pathogens. The present study firstly provides a broader investigation of the presence and prevalence of zoonotic fecal pathogens in wild Taihangshan macaques, a subspecies of rhesus macaque in China. A total of 458 fecal samples were collected between September 2015 and November 2016. Fourteen genera of intestinal parasites (four genera of protozoans and ten genera of helminths) and twelve genera of bacteria were tested for using PCR amplification. The overall samples prevalence of parasitic infection was 98.25%. Entamoeba spp. (89.96%), Balantidium coli (70.09%), and Isospora spp. (28.38%) were the most prevalent protozoa, whereas the predominant prevalent helminths were Trichuris sp. (93.23%), Strongyloides spp. (73.36%), and Oesophagostomum sp. (31.66%). Ten genera of intestinal bacteria were detected in samples of rhesus macaques, including Shigella (31.66%), Escherichia coli (29.91%), Klebsiella pneumoniae (28.38%), Leptospira (26.64%), Campylobacter jejuni (18.34%), Salmonella (13.32%), etc. Eight samples (1.75%) were tested Hafnia-positive based on sequences analysis of 16S rRNA and ampC gene. This is the first molecular characterization of Hafnia infection in NHPs. Our cross-sectional prevalence study provides important information for monitoring the potential transmission of zoonotic infections from wild rhesus macaques.

Effects of Sulfide Flavors on AHL-Mediated Quorum Sensing and Biofilm Formation of Hafnia alvei

In this study, 10 different sulfide flavor compounds commonly used as food additives were screened for antiquorum-sensing activity. Among these, diallyl disulfide (DADS) and methyl 2-methyl-3-furyl disulfide (MMFDS) were found to exert the strongest inhibition against violacein production in Chromobacterium violaceum 026, the tested biosensor strain. DADS and MMFDS also inhibited the growth of Hafnia alvei H4, yielding MIC values of 48 and 41.6 mM, respectively. In addition, DADS and MMFDS also inhibited the ability of H. alvei H4 to produce acyl-homoserine lactone as demonstrated by the reduced level of C6-HSL in the supernatant of DADS-treated culture. At concentrations corresponding to 1/4 MIC, DADS, and MMFDS inhibited the swarming ability of H. alvei H4 by 73.50% and 76.43%, respectively, while having virtually no effect on cell growth. The same concentrations of DADS and MMFDS also completely inhibited the formation of biofilm. These antiquorum sensing effects of DADS and MMFDS involved changes in the expression of the quorum-sensing genes luxI and luxR. Quantitative RT-PCR analysis showed that the mRNA levels of both genes were significantly reduced by DADS and MMDFS at concentrations below their MICs. However, further test using a mutant strain of H. alvei lacking luxR (ΔluxR) revealed significant reduction in luxI mRNA level upon treatment of the strain with DADS or MMDFS, but no change in luxR mRNA level occurred when a luxI-lacking mutant (ΔluxI) was treated with these compounds. The result therefore suggested that the antiquorum-sensing effect of DADS and MMFDS against H. alvei H4 might operate mainly through the inhibition of luxI expression in the cells.

PRACTICAL APPLICATION

The sulfide flavors compounds used in this paper are commonly used in food processing in China and are listed in the national standard of Chinese food additives GB2760-2014. The application of sulfide flavors in food processing can enhance aroma and prevent food spoilage.

Interaction of Mannose-Binding Lectin With Lipopolysaccharide Outer Core Region and Its Biological Consequences

Lipopolysaccharide (LPS, endotoxin), the main surface antigen and virulence factor of Gram-negative bacteria, is composed of lipid A, core oligosaccharide, and O-specific polysaccharide (O-PS) regions. Each LPS region is capable of complement activation. We have demonstrated that LPS of Hafnia alvei, an opportunistic human pathogen, reacts strongly with human and murine mannose-binding lectins (MBLs). Moreover, MBL-LPS interactions were detected for the majority of other Gram-negative species investigated. H. alvei was used as a model pathogen to investigate the biological consequences of these interactions. The core oligosaccharide region of H. alvei LPS was identified as the main target for human and murine MBL, especially l-glycero-d-manno-heptose (Hep) and N-acetyl-d-glucosamine (GlcNAc) residues within the outer core region. MBL-binding motifs of LPS are accessible to MBL on the surface of bacterial cells and LPS aggregates. Generally, the accessibility of outer core structures for interaction with MBL is highest during the lag phase of bacterial growth. The LPS core oligosaccharide-MBL interactions led to complement activation and also induced an anaphylactoid shock in mice. Unlike Klebsiella pneumoniae O3 LPS, robust lectin pathway activation of H. alvei LPS in vivo was mainly the result of outer core recognition by MBL; involvement of the O-PS is not necessary for anaphylactoid shock induction. Our results contribute to a better understanding of MBL-LPS interaction and may support development of therapeutic strategies against sepsis based on complement inhibition.

Superbugs in the supermarket? Assessing the rate of contamination with third-generation cephalosporin-resistant gram-negative bacteria in fresh Australian pork and chicken

Background

Antibiotic misuse in food-producing animals is potentially associated with human acquisition of multidrug-resistant (MDR; resistance to ≥ 3 drug classes) bacteria via the food chain. We aimed to determine if MDR Gram-negative (GNB) organisms are present in fresh Australian chicken and pork products.

Methods

We sampled raw, chicken drumsticks (CD) and pork ribs (PR) from 30 local supermarkets/butchers across Melbourne on two occasions. Specimens were sub-cultured onto selective media for third-generation cephalosporin-resistant (3GCR) GNBs, with species identification and antibiotic susceptibility determined for all unique colonies. Isolates were assessed by PCR for SHV, TEM, CTX-M, AmpC and carbapenemase genes (encoding IMP, VIM, KPC, OXA-48, NDM).

Results

From 120 specimens (60 CD, 60 PR), 112 (93%) grew a 3GCR-GNB (n = 164 isolates; 86 CD, 78 PR); common species were Acinetobacter baumannii (37%), Pseudomonas aeruginosa (13%) and Serratia fonticola (12%), but only one E. coli isolate. Fifty-nine (36%) had evidence of 3GCR alone, 93/163 (57%) displayed 3GCR plus resistance to one additional antibiotic class, and 9/163 (6%) were 3GCR plus resistance to two additional classes. Of 158 DNA specimens, all were negative for ESBL/carbapenemase genes, except 23 (15%) which were positive for AmpC, with 22/23 considered to be inherently chromosomal, but the sole E. coli isolate contained a plasmid-mediated CMY-2 AmpC.

Conclusions

We found low rates of MDR-GNBs in Australian chicken and pork meat, but potential 3GCR-GNBs are common (93% specimens). Testing programs that only assess for E. coli are likely to severely underestimate the diversity of 3GCR organisms in fresh meat.

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes

Most studies of bacterial motility have examined small-scale (micrometer–centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes.

Interactions with other microbes may inhibit or facilitate the dispersal of bacteria. Here, Zhang et al. use cheese rind microbiomes as a model to show that physical networks created by filamentous fungi can affect the dispersal of motile bacteria and thus shape the diversity of microbial communities.

Geochemistry and microbial diversity of cave waters in the gypsum karst aquifers of Emilia Romagna region, Italy

Fifty-seven control points of waters (sinking streams, rivers in caves, and resurgences) hosted in gypsum karst areas in Emilia Romagna region (N-Italy) were sampled in the framework of a Project LIFE+08NAT/IT/000369 "Gypsum" in the period 2010-2014. The microbiology and chemistry of these waters have been analyzed to evaluate the impact of human activities or natural factors, in the gypsum karst systems. Waters have been analyzed for major chemistry (Ca, Mg, Na, K, SO₄, HCO₃, Cl, NO₃) and some minor constituents (F, Br, NH₄ and PO₄), measuring pH, electric conductivity (EC), total dissolved solids (TDS) and temperature (T) in situ. The same samples have been analyzed with traditional microbiology techniques focused on total microbial count and on fecal microbiota, as index of human and/or animal contamination, and molecular biology techniques (sequencing of 16S rRNA segment and PCR-DGGE), focused on the characterization of microbial populations in the different sampling sites and determination of their variations and/or changes during the five years of the project. As expected, waters tend to be increasingly mineralized from sinking streams to resurgences, with only local and temporarily high contents in nitrates and ammonium, often related to the presence of bat colonies. PCR-DGGE revealed ecological changes, in terms of microbial populations present in the bulk water samples, in different sampling sites within the same cave. Although the impact of fecal microorganisms only rarely exceeded 2 log UFC/ml, the results evidenced fluctuations of these microorganisms mainly correlated to the season and to the biological activity of bats.

Phylogenetic Analysis and Antimicrobial Profiles of Cultured Emerging Opportunistic Pathogens (Phyla Actinobacteria and Proteobacteria) Identified in Hot Springs

Hot spring water may harbour emerging waterborne opportunistic pathogens that can cause infections in humans. We have investigated the diversity and antimicrobial resistance of culturable emerging and opportunistic bacterial pathogens, in water and sediment of hot springs located in Limpopo, South Africa. Aerobic bacteria were cultured and identified using 16S ribosomal DNA (rDNA) gene sequencing. The presence of Legionella spp. was investigated using real-time polymerase chain reaction. Isolates were tested for resistance to ten antibiotics representing six different classes: β-lactam (carbenicillin), aminoglycosides (gentamycin, kanamycin, streptomycin), tetracycline, amphenicols (chloramphenicol, ceftriaxone), sulphonamides (co-trimoxazole) and quinolones (nalidixic acid, norfloxacin). Gram-positive Kocuria sp. and Arthrobacter sp. and gram-negative Cupriavidus sp., Ralstonia sp., Cronobacter sp., Tepidimonas sp., Hafnia sp. and Sphingomonas sp. were isolated, all recognised as emerging food-borne pathogens. Legionella spp. was not detected throughout the study. Isolates of Kocuria, Arthrobacter and Hafnia and an unknown species of the class Gammaproteobacteria were resistant to two antibiotics in different combinations of carbenicillin, ceftriaxone, nalidixic acid and chloramphenicol. Cronobacter sp. was sensitive to all ten antibiotics. This study suggests that hot springs are potential reservoirs for emerging opportunistic pathogens, including multiple antibiotic resistant strains, and highlights the presence of unknown populations of emerging and potential waterborne opportunistic pathogens in the environment.

Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human feces

BACKGROUND

Members of the genus Hafnia have been isolated from the feces of mammals, birds, reptiles, and fish, as well as from soil, water, sewage, and foods. Hafnia alvei is an opportunistic pathogen that has been implicated in intestinal and extraintestinal infections in humans. However, its pathogenicity is still unclear. In this study, we isolated H. alvei from human feces and performed sequencing as well as comparative genomic analysis to better understand its pathogenicity.

RESULTS

The genome of H. alvei CBA7124 comprised a single circular chromosome with 4,585,298 bp and a GC content of 48.8%. The genome contained 25 rRNA genes (9 5S rRNA genes, 8 16S rRNA genes, and 8 23S rRNA genes), 88 tRNA genes, and 4043 protein-coding genes. Using comparative genomic analysis, the genome of this strain was found to have 72 strain-specific singletons. The genome also contained genes for antibiotic and antimicrobial resistance, as well as toxin-antitoxin systems.

CONCLUSIONS

We revealed the complete genome sequence of the opportunistic gut pathogen, H. alvei CBA7124. We also performed comparative genomic analysis of the sequences in the genome of H. alvei CBA7124, and found that it contained strain-specific singletons, antibiotic resistance genes, and toxin-antitoxin systems. These results could improve our understanding of the pathogenicity and the mechanism behind the antibiotic resistance of H. alvei strains.

Microbiology and foodborne pathogens in honey

Honey has been considered a relatively safe foodstuff due to its compositional properties, with infant botulism caused by Clostridium botulinum being the most prominent health risk associated with it. Our review is focused on the honey microflora along the food chain and evaluates the pathogenic potential of those microorganisms found in honey. This product may contain a great variety of bacteria and, particularly, fungi that eventually entered the food chain at an early stage (e.g., via pollen). For many of these microorganisms, opportunistic infections in humans have been recorded (e.g., infections by Staphylococcus spp., Citrobacter spp., Escherichia coli, Hafnia alvei, Aspergillus spp., Fusarium spp., Trichoderma spp., Chaetomium spp.), although direct infections via honey were not registered.

Hafnia alvei: A new pathogen in open fractures

Background

Deep infection following open both bone forearm fractures is a rare complication. Prophylactic antibiotic regimens are targeted at the most common pathogens, which include primarily Staph aureus followed by gram-negative bacteria. Hafnia alvei is an unusual pathogen that is rarely pathogenic in humans and has never been reported as a cause of infection following open fracture.

Methods

We present a 12-year-old male with an open forearm fracture who developed a late deep infection. Cultures grew only Hafnia alvei. The patient was treated with debridement, placement of antibiotic beads, and ciprofloxacin.

Results

At 6 months following the initial debridement, the patient had no clinical evidence of infection and regained full function of the affected forearm without any residual deficits.

Conclusions

This is the first report of deep infection following an open forearm fracture owing to Hafnia alvei, a pathogen rarely responsible for human infection.

Whole-Genome Sequence of Hafnia alvei HUMV-5920, a Human Isolate

A clinical isolate of Hafnia alvei (strain HUMV-5920) was obtained from a urine sample from an adult patient. We report here its complete genome assembly using PacBio single-molecule real-time (SMRT) sequencing, which resulted in a chromosome with 4.5 Mb and a circular contig of 87 kb. About 4,146 protein-coding genes are predicted from this assembly.

Genome Sequence of Hafnia alvei bta3_1, a Bacterium with Antimicrobial Properties Isolated from Honey Bee Gut

Hafnia alvei bta3_1, a strain with antibacterial properties, was isolated from honey bee gut and cultured under aerobic and anaerobic conditions. To explore the potential genetic bases of its antibacterial and possible pathogenic properties, the complete genome of this organism was sequenced and analyzed.

Genetic Diversity of O-Antigens in Hafnia alvei and the Development of a Suspension Array for Serotype Detection

Hafnia alvei is a facultative and rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. Although it has been more than 50 years since the genus was identified, very little is known about variations among Hafnia species. Diversity in O-antigens (O-polysaccharide, OPS) is thought to be a major factor in bacterial adaptation to different hosts and situations and variability in the environment. Antigenic variation is also an important factor in pathogenicity that has been used to define clones within a number of species. The genes that are required to synthesize OPS are always clustered within the bacterial chromosome. A serotyping scheme including 39 O-serotypes has been proposed for H. alvei, but it has not been correlated with known OPS structures, and no previous report has described the genetic features of OPS. In this study, we obtained the genome sequences of 21 H. alvei strains (as defined by previous immunochemical studies) with different lipopolysaccharides. This is the first study to show that the O-antigen gene cluster in H. alvei is located between mpo and gnd in the chromosome. All 21 of the OPS gene clusters contain both the wzx gene and the wzy gene and display a large number of polymorphisms. We developed an O serotype-specific wzy-based suspension array to detect all 21 of the distinct OPS forms we identified in H. alvei. To the best of our knowledge, this is the first report to identify the genetic features of H. alvei antigenic variation and to develop a molecular technique to identify and classify different serotypes.