Abstract:e Herbaspirillum bacteria are best known as plant growth-promoting rhizobacteria but have also been recovered from clinical samples. Here, biochemical tests, matrix-assisted laser deionization-time of flight (MALDI-TOF) mass spectrometry, adherence, and cytotoxicity to eukaryotic cells were used to compare clinical and environmental isolates of Herbaspirillum spp. Discrete biochemical differences were observed between human and environmental strains. All strains adhered to HeLa cells at low densities, and cyto… Show more
“…No genes related to the nif cluster were found in the WT00C strain, which is in agreement with a previous analysis of the genome of this strain [18]. These results also confirm previous analyses showing that clinical strains are not able to reduce atmospheric nitrogen [11]. Considering that the nif gene cluster in the genus Herbaspirillum seems to be an early acquisition, and considering its high degree of conservation in H. frisingense GSF30 T [19] and H. rubrisubalbicans [20], it is probable that the nif genes and upstream region were lost in strains AU14040, AU13965 and, interestingly, in the environmental isolate WT00C.Fig.…”
Section: Resultssupporting
confidence: 92%
“…In addition, 18 isolates that could not be classified were named lineages 1, 2 and 3 [10]. Comparison of Herbaspirillum isolates recovered from environmental and clinical sources showed no differences in adhesion capacity and cytotoxicity in human HeLa cells [11]. Although the above cases are related to immunocompromised patients, Regunath et al described a case of bacteremia caused by gentamicin-resistant Herbaspirillum in an immunocompetent adult male farmer [12].…”
Background
Herbaspirillum seropedicae
is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of
H. seropedicae
have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of
H. seropedicae
, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin.
Results
Both genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus
Herbaspirillum
. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (
nif
) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes. The clinical strains also acquired new genes and genomic islands that may be related to host interactions. Among the acquired islands was a cluster of genes related to lipopolysaccharide (LPS) biosynthesis. Although highly conserved in environmental strains, the LPS biosynthesis genes in the two clinical strains presented unique and non-orthologous genes within the genus
Herbaspirillum
. Furthermore, the AU14040 strain cluster contained the
neuABC
genes, which are responsible for sialic acid (Neu5Ac) biosynthesis, indicating that this bacterium could add it to its lipopolysaccharide. The Neu5Ac-linked LPS could increase the bacterial resilience in the host aiding in the evasion of the immune system.
Conclusions
Our findings suggest that the lifestyle transition from environment to opportunist led to the loss and acquisition of specific genes allowing adaptations to colonize and survive in new hosts. It is possible that these substitutions may be the starting point for interactions with new hosts.
Electronic supplementary material
The online version of this article (10.1186/s12864-019-5982-9) contains supplementary material, which is available to authorized users.
“…No genes related to the nif cluster were found in the WT00C strain, which is in agreement with a previous analysis of the genome of this strain [18]. These results also confirm previous analyses showing that clinical strains are not able to reduce atmospheric nitrogen [11]. Considering that the nif gene cluster in the genus Herbaspirillum seems to be an early acquisition, and considering its high degree of conservation in H. frisingense GSF30 T [19] and H. rubrisubalbicans [20], it is probable that the nif genes and upstream region were lost in strains AU14040, AU13965 and, interestingly, in the environmental isolate WT00C.Fig.…”
Section: Resultssupporting
confidence: 92%
“…In addition, 18 isolates that could not be classified were named lineages 1, 2 and 3 [10]. Comparison of Herbaspirillum isolates recovered from environmental and clinical sources showed no differences in adhesion capacity and cytotoxicity in human HeLa cells [11]. Although the above cases are related to immunocompromised patients, Regunath et al described a case of bacteremia caused by gentamicin-resistant Herbaspirillum in an immunocompetent adult male farmer [12].…”
Background
Herbaspirillum seropedicae
is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of
H. seropedicae
have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of
H. seropedicae
, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin.
Results
Both genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus
Herbaspirillum
. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (
nif
) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes. The clinical strains also acquired new genes and genomic islands that may be related to host interactions. Among the acquired islands was a cluster of genes related to lipopolysaccharide (LPS) biosynthesis. Although highly conserved in environmental strains, the LPS biosynthesis genes in the two clinical strains presented unique and non-orthologous genes within the genus
Herbaspirillum
. Furthermore, the AU14040 strain cluster contained the
neuABC
genes, which are responsible for sialic acid (Neu5Ac) biosynthesis, indicating that this bacterium could add it to its lipopolysaccharide. The Neu5Ac-linked LPS could increase the bacterial resilience in the host aiding in the evasion of the immune system.
Conclusions
Our findings suggest that the lifestyle transition from environment to opportunist led to the loss and acquisition of specific genes allowing adaptations to colonize and survive in new hosts. It is possible that these substitutions may be the starting point for interactions with new hosts.
Electronic supplementary material
The online version of this article (10.1186/s12864-019-5982-9) contains supplementary material, which is available to authorized users.
“…These species do not ferment lactose or grow in nitrogen-free medium (1,2). A number of Herbaspirillum species have been identified and studied, but only a few species have been reported to be human pathogens (3).…”
cHerbaspirillum spp. are Gram-negative bacteria that inhabit soil and water. Infections caused by these organisms have been reported in immunocompromised hosts. We describe severe community-acquired pneumonia and bacteremia caused by Herbaspirillum aquaticum or H. huttiense in an immunocompetent adult male.
CASE REPORT
In early September 2014, a 46-year-old white male presented to a referring facility with fever, fatigue, and shortness of breath. His illness began 5 days prior to admission to our facility after he was drenched in rain during a fishing trip. He had a fever of 40°C, despite use of antipyretics, with chills, night sweats, anorexia, myalgia, and headache. Three days prior to admission, he had a transient period of dry cough for half a day that resolved spontaneously. The next day he developed sharp right-sided pleuritic chest pain, worsening dyspnea, and severe fatigue. When he presented to the referring facility, clinical findings were remarkable for a respiratory rate (RR) of 28/min with an oxygen saturation (SpO 2 ) level of 77% on room air which improved to 91% on 4 liters/min of oxygen via nasal cannula. His white blood cell (WBC) count was 7.7 ϫ 10 Ϫ3 /l with 55% bands, and bilateral alveolar infiltrates were noted on a chest X-ray. Analysis of his arterial blood gas revealed a pH level of 7.46, partial pressure of CO 2 (pCO 2 ) of 34 mm Hg, pO 2 of 53 mm Hg, SpO 2 of 89% on 4 liters/min of oxygen via nasal cannula, and HCO 3 of 24 meq/liter. Blood cultures were drawn, and he was treated with intravenous vancomycin, ceftriaxone, and azithromycin. His condition worsened and he was transferred to our university teaching hospital.The patient's past medical history was unremarkable, except for childhood asthma, atypical pneumonia as a teenager, and tonsillectomy. He was on no home medications. He lived on a farm in rural Missouri with his wife and had close contact with cattle and turkeys (he had birthed calves 6 months earlier and handled 15,000 baby turkeys 3 weeks prior to the onset of illness). A few weeks prior to admission, the patient returned from work with about 20 loosely attached ticks. He also cleaned a grain bin in his barn (contained mold and possible rat excreta) a week prior to presentation. He smoked cigarettes for 30 years and also consumed alcohol regularly. He denied sick contacts, animal bites or scratches, and recent travel.The results of a physical examination conducted on presentation to our facility were remarkable for temperature (38°C), heart rate (HR) (98 beats/min), blood pressure (BP) (141/88 mm Hg), and RR (30/min with use of accessory muscles). There was bilateral lower chest wall tenderness, coarse inspiratory crepitations were heard in left axilla and left lower chest, and diminished breath sounds were noted in the right axilla and right lower chest.The rest of the exam was unremarkable. Laboratory measurements on admission revealed a WBC count of 9.0 ϫ 10 Ϫ3 /l, granulocytes at 89.6% and no bands on automated differential determinations, hemoglobin at 13.4 g/dl, ...
“…Herbaspirillum seropedicae are Gram-negative oxidasepositive nonfermenting rods of Betaproteobacteria class, commonly found in the rhizosphere of maize and rice, which promote plant growth via biological nitrogen fixation and phytohormone production [1,2]. More recently, some Herbaspirillium species have transitioned from environment (water, contaminated soil, plant internal tissues, and root nodules) to human hosts, mostly as opportunistic (pathogenic) bacteria.…”
Introduction. Herbaspirillum seropedicae are Gram-negative oxidase-positive nonfermenting rods of Betaproteobacteria class, commonly found in rhizosphere. More recently, some Herbaspirillium species have transitioned from environment to human hosts, mostly as opportunistic (pathogenic) bacteria. We present a 58-year-old female with non-small-cell lung cancer (NSCLC) who presented with pneumonia and was found to have Herbaspirillum seropedicae bacteremia. Case History. A 58-year-old woman with NSCLC on Pralsetinib presented with fevers and rigors for 2 days. Coarse breath sounds were auscultated on the right upper lung field. Labs revealed leukopenia and mild neutropenia. CT chest revealed right upper lobe pneumonia. She was admitted for sepsis secondary to pneumonia and placed on broad spectrum antibiotics with intravenous piperacillin-tazobactam and vancomycin. The patient continued to have fever 2 days after admission (max: 102.8°F). Preliminary blood cultures grew Gram-negative rods. The patient continued to have temperature spikes on the 3rd day of antibiotics (Tmax 101.5°F). Blood cultures revealed oxidase-positive nonfermenting rods. The patient’s antibiotic was changed to IV meropenem on the 4th day of hospitalization. Ultimately, on the seventh day of hospitalization, the blood culture was confirmed from outside lab as Herbaspirillum seropedicae. The patient started feeling better and defervesced after about 24 hours. Discussion. More recently, Herbaspirillum spp. have been recovered from humans. Our patient had Herbaspirillum bacteremia, and reported regularly cleaning her pond and weeding her garden with possible exposure to this environmental proteobacterium. Herbaspirillum may be more prevalent than earlier thought owing to misidentification. With the institution of appropriate antimicrobial therapy, the outcomes seem mostly favorable.
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