Pantoea dispersa bacteremia caused by central line-associated bloodstream infection

Whole genome analysis of Pantoea species identified from sepsis patients in selected Ethiopian referral hospitals: emerging pathogens

BACKGROUND

The burden of sepsis worsens due to the continuation of emerging pathogens such as multidrug-resistant Pantoea species.

METHODS

A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in central, southern, and northern parts of Ethiopia. A total of 1416 sepsis patients were recruited and blood cultures were performed. At each study site, positive cultures were characterized by their colony characteristics, gram stain, and conventional biochemical tests. All Pantoea species were identified using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI TOF) and subjected to whole genome sequencing (WGS) using Illumina HiSeq 2500. The phylogeny structure of Pantoea isolates was calculated using IQ-TREE v1.6.12 from single-nucleotide polymorphisms detected by Snippy v.4.6.0 and filtered by Gubbins v.2.3.4. Average nucleotide identity was estimated by using OrthoANI v.0.93.1 on Shovill v.1.1.0 assemblies. Antimicrobial resistance genes and plasmid replicons were detected using ARIBA v.2.14.6. Phylogenetic trees were visualized using iTOLv.6.5.2.

RESULTS

Multiple Pantoea species include: P. dispersa (n = 19), P. septica (n = 1), and a novel Pantoea spp. (n = 1), were identified among sepsis patients. All P. dispersa isolates and the novel Pantoea species were isolated at Dessie Referral Hospital and displayed phylogenetic clonality, including the ubiquity of an IncM1 plasmid and identical antimicrobial resistance (AMR) gene profiles, encoding blaCTX-M-15, blaTEM-1D, blaSCO-1, and aac(3)-lla. The novel Pantoea spp. isolate harboured blaCTX-M-9 and blaTEM-1D and carried an IncN3 plasmid replicon. The P. septica was isolated at Tikur Anbessa Specialized Hospital in Addis Ababa and carried no detectable acquired AMR genes.

CONCLUSION

The emerging Pantoea spp. carrying multiple AMR genes were identified from sepsis patients. Implementation of strong infection prevention strategies and building surveillance capacity with advanced bacteriology laboratories capable of identifying multidrug-resistant emerging pathogens is strongly recommended.

Hemodialysis Catheter-Related Bloodstream Infection Caused by Pantoea: Report of Two Cases and Literature Review

Species of Pantoea are mainly environmental strains and plant pathogens, rarely causing human infections. Here, we describe two cases of hemodialysis catheter-related bloodstream infection caused by Pantoea in patients with uremia. To our knowledge, this is the first reported case of catheter related bloodstream infection caused by Pantoea dispersa (P. dispersa) in hemodialysis patients, as well as the first case of bloodstream infection caused by Pantoea anthophila (P. anthophila). Multiple blood cultures from the catheter showed the presence of Pantoea, and the isolated P. dispersa and P. anthophila were found to be highly sensitive to various antibiotics. Prompt use of antibiotics and catheter lock with gentamicin or amikacin led to rapid recovery of the patients, avoiding the economic burden of catheter replacement. Infections caused by Pantoea might be underestimated as methods such as VITEK® MS system often result in misidentification. Therefore, we recommend using advanced techniques such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) or 16S ribosomal RNA analysis to detect more cases of Pantoea infections. By sharing these cases, we hope to increase awareness among clinicians about the potential pathogenicity of Pantoea in hemodialysis patients. It is crucial to strengthen noting the primary concern for sources of infection with Pantoea species (plant and environmental exposures) to prevent outbreaks of Pantoea-related bloodstream infections in hospitals.

Pantoea dispersa peritoneal dialysis catheter-related infection

Enteric gram-negative bacteria-associated peritoneal dialysis (PD) peritonitis is common. These organisms are such as Escherichia coli, Klebsiella and Enterobacter species. Pantoea dispersa belongs to the order Enterobacterales, it has known benefits and a role in agricultural and environmental biotechnology. Pantoea dispersa, although still relatively rare, is being increasingly recognised to cause human infections. We are reporting a case of PD peritonitis caused by Pantoea dispersa in a kidney failure patient on continuous ambulatory peritoneal dialysis (CAPD). His peritonitis was treated well with intraperitoneal antibiotics and the patient can resume his CAPD therapy. The increasing reports of Pantoea dispersa-related human infections warrant concerns, both in immunocompromised and immunocompetent patients.

Bloodstream Infections by Pantoea Species: Clinical and Microbiological Findings from a Retrospective Study, Italy, 2018-2023

(1) Background: The widespread use of MALDI-TOF coupled to mass spectrometry has improved diagnostic accuracy by identifying uncommon bacteria. Among Enterobacterales, Pantoea species have been seen to be implicated in several human infections, but their clinical and microbiological framework is currently based on a few anecdotal reports. (2) Methods: We conducted this five-year (2018-2023) single-center study aimed at investigating the prevalence and clinical and microbiological findings of Pantoea species bloodstream infections. (3) Results: Among the 4996 bloodstream infection Gram-negative isolates collected during the study period, Pantoea species accounted for 0.4% (n = 19) of isolates from 19 different patients, 5 of them being pediatric cases. Among Pantoea species isolates, P. agglomerans was the most frequently detected (45%; n = 9) followed by P. eucrina (30%; n = 6) and P. septica (15%; n = 3). Malignancy (35.7%) in adults and malignancy (40%) and cerebrovascular disease following meconium aspiration (40%) in pediatric patients as comorbidities and shivering and/or fever following parenteral infusion (36.8%) as a symptom/sign of Pantoea species bloodstream infection onset were the most frequently observed clinical features. Among adults, primary bloodstream infection was the most frequent (50%), whereas among pediatric patients, the most commonly identified sources of infection were catheter-related (40%) and the respiratory tract (40%). Overall, Pantoea species bloodstream infection isolates displayed high susceptibility to all the antibiotics except for ampicillin (63.2%), fosfomycin (73.7%), and piperacillin/tazobactam (84.2%). Targeted antibiotic treatment was prescribed as monotherapy for adults (71.4%) and combination therapy for pediatric patients (60%). The most prescribed antibiotic regimens were piperacillin/tazobactam (21.4%) in adults and meropenem- (40%) and aminoglycoside-containing (40%) antibiotics in pediatric patients. The overall 28-day all-cause mortality rate was 5.3% (n = 1). (4) Conclusions: The prevalence and 28-day mortality rate of Pantoea species bloodstream infections were low. The prescription of targeted therapy including broad-spectrum antibiotics could indicate an underestimation of the specific involvement of the Pantoea species in the onset of the disease, warranting further studies defining their pathogenic potential.

Genomic characterization of Pantoea anthophila strain UI705 causing urinary tract infections in China

Introduction

Pantoea anthophila (P. anthophila) is a Gram-negative bacterium initially isolated from Impatiens balsamina in India. P. anthophila has been characterized with low pathogenicity, and no human infections caused by this organism have been reported yet. We report the first case of urinary tract infection caused by P. anthophila in a 73-year-old man after bladder cancer surgery.

Methods

The bacterial isolate gained from urine was named UI705 and identified as P. anthophila by MALDI-TOF mass spectrometry. The genome sequencing and analysis were performed to further characterize the pathogenesis of the clinical isolate.

Result and discussion

To the best of our knowledge, this is the first report of human infection caused by P. anthophila in China. The draft genome sequence of P. anthophila UI705 provides a fundamental resource for subsequent investigation of its virulence factors, antibiotic resistance, host-pathogen interactions, and comparative genomics of genus Pantoea.

Pantoea abscess mimicking sarcoma in a HTLV-1-infected Indigenous Australian man: Case report and literature review

Gram-negative bacteria of the genus Pantoea are emerging bacterial causes of diverse sporadic and outbreak-linked infections. Chronic Pantoea abscesses are unusual and may give rise to a differential diagnosis of malignancy. Foreign body retention and host immune defects may be risk factors for such chronic infections.

Sepsis: emerging pathogens and antimicrobial resistance in Ethiopian referral hospitals

Background

Sepsis due to multidrug resistant (MDR) bacteria is a growing public health problem mainly in low-income countries.

Methods

A multicenter study was conducted between October 2019 and September 2020 at four hospitals located in central (Tikur Anbessa and Yekatit 12), southern (Hawassa) and northern (Dessie) parts of Ethiopia. A total of 1416 patients clinically investigated for sepsis were enrolled. The number of patients from Tikur Anbessa, Yekatit 12, Dessie and Hawassa hospital was 501, 298, 301 and 316, respectively. At each study site, blood culture was performed from all patients and positive cultures were characterized by their colony characteristics, gram stain and conventional biochemical tests. Each bacterial species was confirmed using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI TOF). Antimicrobial resistance pattern of bacteria was determined by disc diffusion. Logistic regression analysis was used to assess associations of dependent and independent variables. A p-value < 0.05 was considered as statistically significant. The data was analyzed using SPSS version 25.

Results

Among 1416 blood cultures performed, 40.6% yielded growth. Among these, 27.2%, 0.3% and 13.1%, were positive for pathogenic bacteria, yeast cells and possible contaminants respectively. Klebsiella pneumoniae (26.1%), Klebsiella variicola (18.1%) and E. coli (12.4%) were the most frequent. Most K. variicola were detected at Dessie (61%) and Hawassa (36.4%). Almost all Pantoea dispersa (95.2%) were isolated at Dessie. Rare isolates (0.5% or 0.2% each) included Leclercia adecarboxylata, Raoultella ornithinolytica, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Burkholderia cepacia, Kosakonia cowanii and Lelliottia amnigena. Enterobacteriaceae most often showed resistance to ampicillin (96.2%), ceftriaxone (78.3%), cefotaxime (78%), cefuroxime (78%) and ceftazidime (76.4%). MDR frequency of Enterobacteriaceae at Hawassa, Tikur Anbessa, Yekatit 12 and Dessie hospital was 95.1%, 93.2%, 87.3% and 67.7%, respectively. Carbapenem resistance was detected in 17.1% of K. pneumoniae (n = 111), 27.7% of E. cloacae (n = 22) and 58.8% of Acinetobacter baumannii (n = 34).

Conclusion

Diverse and emerging gram-negative bacterial etiologies of sepsis were identified. High multidrug resistance frequency was detected. Both on sepsis etiology types and MDR frequencies, substantial variation between hospitals was determined. Strategies to control MDR should be adapted to specific hospitals. Standard bacteriological services capable of monitoring emerging drug-resistant sepsis etiologies are essential for effective antimicrobial stewardship.

Nosocomial bloodstream infection pathogen Pantoea dispersa: a case report and literature review

Pantoea dispersa is a gram-negative bacterium frequently found in plants, soil, and water. The genus Pantoea is a rare pathogen in human infectious diseases. The known susceptible populations include infants and postoperative and immunocompromised patients. To date, there are no reports of nosocomial bloodstream infection due to P. dispersa following chest puncture. A 72-year-old Chinese woman suffering from chest distress was found to be blood culture positive for a gram-negative bacterium. The organism was identified as P. dispersa through VITEK 2, MALDI-TOF MS, and 16S rRNA gene sequencing. Although cefoperazone-sulbactam and imipenem were used for treatment, the patient died four days later. To the best of our knowledge, this is the first case of nosocomial bloodstream infection caused by P. dispersa in China. We hope that this article would help clinicians understand better the potential pathogenicity of this pathogen.

Characteristics and accurate identification of Pantoea dispersa with a case of spontaneous rupture of hepatocellular carcinoma in China: A case report

INTRODUCTION

Pantoea dispersa belongs to the genus Pantoea, which is isolated from Enterobacteriaceae. It has been reported to cause some kinds of infections, but there are few detailed studies on it, especially its characteristics and identification methods, which has caused a lot of trouble in clinical work.

PATIENT CONCERNS

A 51-year-old Chinese man was admitted to our hospital with a 7-hour history of progressive abdominal pain. He was previously diagnosed with liver cirrhosis secondary to chronic hepatitis B infection and hepatocellular carcinoma. An emergency hepatic artery embolization for hemostasis was performed under local anesthesia. Forty-eight hours later, the patient presented sudden onset of high fever up to 39.0 °C and chill.

DIAGNOSIS

Morphological and phenotypic profiles were performed for preliminary identification for P dispersa. The biochemical features were obtained by VITEK 2 Test Kit. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis and 16S ribosomal RNA sequencing were performed to accurately identify P dispersa.

INTERVENTION

Antibiotic therapy of intravenous ceftazidime was started empirically. The antibiotic treatment was switched to intravenous cefepime at the same time because of suspected ceftazidime treatment failure and microbiological sensitivity.

OUTCOMES

The patient remained afebrile, and the second blood culture results were negative. Chest X-ray was normal as well. In order to control the progression of the hepatic lesion, transarterial chemoembolization was performed under local anesthesia. After completion of 14 days of antibiotic treatment, the patient was discharged with no signs of recurrence.

CONCLUSION

P dispersa, a gram-negative bacterium rod, were facultative anaerobic, which displayed yellow pigmentation, round, raised, smooth on culture plates. Conventional analysis was difficult to complete its identification. With biochemical tests, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis and 16S ribosomal RNA sequencing, P dispersa can be accurately identified. It will help physicians understand the related clinical manifestations and make timely and effective treatment for patients.

Pantoea agglomerans: An Elusive Contributor to Chronic Obstructive Pulmonary Disease Exacerbation

The ubiquitously present gram-negative bacteria Pantoea agglomerans is not a commonly known human pathogen. Recently, increasing recognition of the species as a human pathogen has led to controversy as limited documented cases of P.agglomerans bacteremia and infections have been reported in the literature, with most cases reported among immunocompromised patients or the pediatric population. Here, we present the case of a 54-year-old female with P. agglomerans and Enterococcus faecium bacteremia along with chronic obstructive pulmonary disease.

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

The use and misuse of antibiotics have made antibiotic-resistant bacteria widespread nowadays, constituting one of the most relevant challenges for human health at present. Among these bacteria, opportunistic pathogens with an environmental, non-clinical, primary habitat stand as an increasing matter of concern at hospitals. These organisms usually present low susceptibility to antibiotics currently used for therapy. They are also proficient in acquiring increased resistance levels, a situation that limits the therapeutic options for treating the infections they cause. In this article, we analyse the most predominant opportunistic pathogens with an environmental origin, focusing on the mechanisms of antibiotic resistance they present. Further, we discuss the functions, beyond antibiotic resistance, that these determinants may have in the natural ecosystems that these bacteria usually colonize. Given the capacity of these organisms for colonizing different habitats, from clinical settings to natural environments, and for infecting different hosts, from plants to humans, deciphering their population structure, their mechanisms of resistance and the role that these mechanisms may play in natural ecosystems is of relevance for understanding the dissemination of antibiotic resistance under a One-Health point of view.

Molecular validation of clinical Pantoea isolates identified by MALDI-TOF

The Enterobacterial genus Pantoea contains both free-living and host-associating species, with considerable debate as to whether documented reports of human infections by members of this species group are accurate. MALDI-TOF-based identification methods are commonly used in clinical laboratories as a rapid means of identification, but its reliability for identification of Pantoea species is unclear. In this study, we carried out cpn60-based molecular typing of 54 clinical isolates that had been identified as Pantoea using MALDI-TOF and other clinical typing methods. We found that 24% had been misidentified, and were actually strains of Citrobacter, Enterobacter, Kosakonia, Klebsiella, Pseudocitrobacter, members of the newly described Erwinia gerundensis, and even several unclassified members of the Enterobacteriaceae. The 40 clinical strains that were confirmed to be Pantoea were identified as Pantoea agglomerans, Pantoea allii, Pantoea dispersa, Pantoea eucalypti, and Pantoea septica as well as the proposed species group, Pantoea latae. Some species groups considered largely environmental or plant-associated, such as P. allii and P. eucalypti were also among clinical specimens. Our results indicate that MALDI-TOF-based identification methods may misidentify strains of the Enterobacteriaceae as Pantoea.

Pantoea dispersa bacteremia in an immunocompetent patient: a case report and review of the literature

Background

Pantoea is a Gram-negative, non-encapsulated, non-spore-forming, ubiquitous straight rod which can be isolated from geographical and ecological sources such as plant surfaces, buckwheat seeds, human feces, and the environment. The genus Pantoea is a rare pathogen in a clinical setting, and is divided into 20 different species such as Pantoea agglomerans, Pantoea ananatis, Pantoea deleyi, Pantoea dispersa, Pantoea septica, Pantoea stewartii or Pantoea rwandensis. Pantoea dispersa has been reported to cause other infections, including respiratory infections, neonatal sepsis, and bloodstream infections. We report a case of Pantoea dispersa bacteremia caused by acute cholangitis. This is the first case report of Pantoea dispersa bacteremia caused by acute cholangitis as far as we had searched.

Case presentation

A 38-year-old Japanese woman suffered from acute cholangitis; a blood culture showed that Gram-negative rod was positive. The treatment was successful with intravenously administered meropenem, and it was switched to orally administered levofloxacin according to microbiological susceptibility. The organism was identified as Pantoea dispersa by both genetic investigation by 16S ribosomal RNA and additional biochemical tests. To the best of our knowledge, this is the first case report of Pantoea dispersa bacteremia caused by acute cholangitis.

Conclusion

The epidemiology and clinical features of Pantoea dispersa are still unknown. More cases of infections caused by Pantoea dispersa might be revealed with advancing technical methods, such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or 16S ribosomal RNA analysis. Physicians must know that a variety of infections caused by Pantoea dispersa could occur in immunocompromised as well as immunocompetent patients.

Pantoea dispersa: Is it the Next Emerging "Monster" in our Intensive Care Units? A Case Report and Review of Literature

Hospital-acquired infections and their consequences are the main cause of morbidity/mortality in critically ill and immunocompromised patients. It becomes interesting when an unusual and uncommon microorganism is found to be the causative agent, rather than the known commensals and opportunists. We present such a case, when a multiparous female, in post lower uterine segment cesarean section period presented with fulminant septic shock, hepatic failure, coagulopathy, and ventilator-associated pneumonitis. The organism grown in the tracheal secretions turned out to be an uncommon, unusual Gram-negative Coccobacillus by the name of Pantoea dispersa, resistant to almost all the conventional antimicrobial agents. In spite of all the efforts, the patient could not be saved. However, the case has opened up a virtual “Pandora's box” of questions. Are these microorganisms, known plant pathogens, really harmful to humans? Are they commensals or virulent opportunists? Are we once again on the way to a new “Acinetobacter,” like near-epidemic? This is an attempt to try and find some insight about this presently uncommon and not well known genus of Pantoea! We have tried to trace and review the related available literature in the clinical medicine.

Endogenous microbial contamination of melons (Cucumis melo) from international trade: an underestimated risk for the consumer?

BACKGROUND

Fruits and vegetables have increasingly been related to foodborne outbreaks. Besides surface contamination, a possible internalization of microorganisms into edible parts of plants during growth has already been observed. To examine an actual risk for the consumer, microbial contamination of the rind and pulp of 147 muskmelons from international trade was assessed using cultural and biochemical methods, polymerase chain reaction and matrix-assisted laser desorption/ionization-time of flight mass spectrometry.

RESULTS

One hundred percent of the rind samples [3.69-8.92 log colony forming units (CFU) g^-1 ] and 89.8% of the pulp samples (maximum load 3.66 log CFU g^-1 ) were microbiologically contaminated. Among the 432 pulp isolates, opportunistic and potentially pathogenic bacteria were identified, mainly Staphylococcus spp. (48.9%), Clostridium spp. (42.9%) and Enterobacteriaceae (27.9%). Salmonella spp., Escherichia coli and isolates of the Bacillus cereus group were found on the rind (1.4%, 0.7% and 42.9%, respectively) and in the pulp (0.7%, 1.4% and 4.7%). Clostridium perfringens was isolated from the rind of seven melons.

CONCLUSION

The present study revealed a regularly occurring internal contamination of melons. Possible health risks for consumers because of an occurrence of microorganisms in melon pulp should be considered in future food safety assessments. © 2018 Society of Chemical Industry.