Etiological misidentification by routine biochemical tests of bacteremia caused by Gordonia terrae infection in the course of an episode of acute cholecystitis

A Patient of Spontaneous Bacterial Peritonitis in Hepatitis C Cirrhosis Caused by Gordonia terrae: A Case Report

Background

Gordonia terrae is an opportunistic pathogen that rarely causes clinical infections. Here, we first report a case of spontaneous bacterial peritonitis in patients with hepatitis C cirrhosis caused by Gordonia terrea.

Case Presentation

A 71-year-old male patient was diagnosed with spontaneous bacteria peritonitis secondary to hepatitis C cirrhosis. The result of bacterial culture in ascites was positive, and the pathogenic bacteria was preliminarily identified as the Gordonia genus by matrix-assisted laser desorption ionization-time of flight mass spectrometry. After 16S rRNA sequencing analysis, it was determined to be the Gordonia terrea. Symptoms relieved after treatment with ceftazidime.

Conclusion

This case indicates that the clinical infections caused by Gordonia terrea should be brought to the forefront. Accurate and rapid bacterial identification results are highly beneficial to the diagnosis and therapeutic regime.

Antimicrobial treatment in invasive infections caused by Gordonia bronchialis: systematic review

Background

Corynebacterium, Nocardia, Rhodococcus, Mycobacterium, as well as Gordonia genera belongs to the genus Gordonia, Actinomycetia class. Gordonia bronchialis is a nitrate-reducing, urease-producing, non-motile, force aerobe with a rod-like figure that is known to arrangement into sessile, cord-like groups. This systematic review aimed to establish whether and what invasive infections in humans were caused by Gordonia bronchialis, and to evaluate outcomes of administered antibiotic treatment.

Methods

We have registered this systematic review in PROSPERO database of systematic reviews and meta-analyses with the number CRD42022369974.

Results

A total of 24 publications were included (22 case reports and two case series) with 28 individual cases. The oldest patients had 92 years, and the youngest patients had 13 years. Clinical signs of infection were present in six patients (21%). All isolates were susceptible to ciprofloxacin, imipenem, and amikacin. Vancomycin was the most frequently used antibiotic with nine cases followed by ciprofloxacin, ceftriaxone, and amoxicillin/clavulanic acid.

Conclusion

Although there are no standardized recommendations to date, successful treatment with a favorable outcome has most often been carried out with fluoroquinolones, vancomycin with or without aminoglycosides, as well as carbapenems.

Focusing on Gordonia Infections: Distribution, Antimicrobial Susceptibilities and Phylogeny

The immunosuppression conditions and the presence of medical devices in patients favor the Gordonia infections. However, the features of this aerobic actinomycete have been little explored. Strains (n = 164) were characterized with 16S rDNA and secA1 genes to define their phylogenetic relationships, and subjected to broth microdilution to profile the antimicrobial susceptibilities of Gordonia species that caused infections in Spain during the 2005-2021 period. Four out of the eleven identified species were responsible for 86.0% of the infections: Gordonia sputi (53.0%), Gordonia bronchialis (18.3%), Gordonia terrae (8.5%) and Gordonia otitidis (6.1%). Respiratory tract infections (61.6%) and bacteremia (21.9%) were the most common infections. The secA1 gene resolved the inconclusive identification, and two major clonal lineages were observed for G. sputi and G. bronchialis. Species showed a wide antimicrobial susceptibility profile. Cefoxitin resistance varies depending on the species, reaching 94.2% for G. sputi and 36.0% for G. terrae. What is noteworthy is the minocycline resistance in G. sputi (11.5%), the clarithromycin resistance in G. bronchialis secA1 lineage II (30.0%) and the amoxicillin-clavulanate and cefepime resistance in G. terrae (21.4% and 42.8%, respectively). G. sputi and G. bronchialis stand out as the prevalent species causing infections in Spain. Resistance against cefoxitin and other antimicrobials should be considered.

Gordonia sputi-associated bloodstream infection in a renal transplant patient with chronic indwelling central venous catheter: a case report and literature review

Introduction

Although rare, human infections caused by Gordonia spp. have been reported, especially within the immunocompromised population and those with long-term indwelling devices. We report a case of Gordonia spp. bacteraemia in a renal transplant patient and present a literature review on microbiological identification methods of this organism.

Case Presentation

A 62-year-old female renal transplant recipient admitted to hospital with a 2-month history of dry cough and fevers occurring weekly when receiving electrolyte replacement infusions via a Groshong line. Over 2 weeks, blood cultures repeatedly isolated a Gram-positive bacillus solely in aerobic bottles, and this was initially reported as Rhodococcus spp. by the local microbiology laboratory. Chest computed tomography (CT) showed multiple ground-glass lung opacities suggestive of septic pulmonary emboli. As central line-associated bloodstream infection was suspected, empirical antibiotics were initiated and the Groshong line was removed. The Gram-positive bacillus was later confirmed by the reference laboratory as Gordonia sputi via 16S rRNA sequencing. Vancomycin and ciprofloxacin for a duration of 6 weeks were completed as targeted antimicrobial therapy. After treatment, the patient remained symptom-free with marked improvement on repeat CT chest imaging.

Conclusion

This case illustrates the challenges surrounding identification of Gordonia spp. and other aerobic actinomycetes. 16S rRNA gene sequencing may be a preferred identification method, especially when initial workup of a weakly acid-fast organism fails to make an identification or shows discrepant results using traditional diagnostic modalities.

Methods of Identifying Gordonia Strains in Clinical Samples

Gordonia spp. are members of the family Gordoniacea in the suborder Corynebacteriales; their habitat, in most cases, is soil. Many representatives of this genus are human or veterinary pathogens. The main cause of the lack of a standardized approach to dealing with infections caused by Gordonia is their erroneous identification and little information regarding their susceptibility to antimicrobial drugs. This review presents the most common methods for identifying Gordonia strains, including modern approaches for identifying a species. The main prospects and future directions of this field of knowledge are briefly presented.

Trends and Species Diversity of Non-tuberculous Mycobacteria Isolated From Respiratiroy Samples in Northern China, 2014–2021

Background

Pulmonary non-tuberculous mycobacteria (NTM) infection has become a public health concern in China and around the world. The objective of this study was to describe the longitudinal changes in the frequency and diversity of NTM in northern China.

Methods

We retrospectively analyzed data on mycobacterium species in Beijing Chest Hospital from January 2014 to December 2021. The isolates were identified to species level by targeted DNA sequencing.

Results

After excluding duplicates, 1,755 NTM strains were analyzed, which were from 27 provinces in China over 8 years. Among all mycobacteria, the proportion of NTM increased each year, from 4.24% in 2014 to 12.68% in 2021. Overall, 39 different NTM species were identified, including 23 slow growing mycobacteria (SGM) and 16 rapid growing mycobacteria (RGM). The most common species were M. intracellulare (51.62%), M. abscessus (22.22%), M. kansasii (8.32%), M. avium (7.75%) and M. fortuitum (2.05%). The number of NTM species identified also increased each year from 9 in 2014 to 26 in 2021. Most species showed stable isolation rates over the years; however, the proportion of M. avium increased from 3.85 to 10.42% during the study period. Besides, 81 non-mycobacteria strains, including Gordonia (21 isolates), Nocardia (19 isolates) and Tsukamurella (17 isolates), etc., were also discovered.

Conclusion

The proportion of NTM and species diversity increased considerably in northern China from 2014 to 2021. M. intracellulare was the most common NTM isolated among respiratory specimens, followed by M. abscessus and M. kansasii. Rare NTM species and non-mycobacteria pathogens also need attention.

From NTM (Nontuberculous mycobacterium) to Gordonia bronchialis—A Diagnostic Challenge in the COPD Patient

In patients with chronic obstructive pulmonary disease, respiratory infections are of various aetiology, predominantly viral and bacterial. However, due to structural and immunological changes within the respiratory system, such patients are also prone to mycobacterial and other relatively rare infections. We present the 70-year old male patient with chronic obstructive pulmonary disease (COPD) and coexisting bronchial asthma, diagnosed due to cough with purulent sputum expectoration lasting over three months. The first microbiological investigation of the sputum sample revealed the growth of mycobacteria. The identification test based on protein MPT64 production indicated an organism belonging to NTM (nontuberculous mycobacterium). However, further species identification by genetic testing verified the obtained culture as not belonging to the Mycobacterium genus. Based on observed morphology, the new characterisation identified an aerobic actinomycete, possibly a Nocardia spp. The isolated strain was recultured on standard microbiological media. The growth of colonies was observed on Columbia blood agar plates and solid Löewenstein-Jensen medium. The Gram and Zhiel-Nielsen stains revealed the presence of Gram-positive acid-fast bacilli. The extraction protocol and identification were performed in two repetitions; the result was G. bronchialis, with a confidence value of 99% and 95%, respectively. The gene sequencing method was applied to confirm the species affiliation of this isolate. The resulting sequence was checked against the 16S ribosomal RNA sequences database (Bacteria and Archaea). The ten best results indicated the genus Gordonia (99.04–100%) and 100% similarity of the 16S sequenced region was demonstrated for Gordonia bronchialis. The case described indicates that the correct interpretation of microbiological test results requires the use of advanced microbiology diagnosis techniques, including molecular identification of gene sequences. From a clinical point of view, Gordonia bronchialis infection or colonization may present a mild course, with no febrile episodes and no significant patient status deterioration and thus, it may remain undiagnosed more often than expected.

Sternal osteomyelitis by Gordonia Bronchialis in an immunocompetent patient after open heart surgery

Gordonia is a catalase-positive, aerobic, nocardioform, Gram-positive staining actinomycete that also shows weak acid-fast staining. Several Gordonia species are commonly found in the soil. The bacterium has been isolated from the saliva of domesticated/wild dogs as well. In hospitalized patients, most commonly it is found in the setting of intravascular catheter-related infections. However, recent reports show that it is being increasingly isolated from sternal wounds, skin/neoplastic specimens and from pleural effusions. Gordonia shares many common characteristics with Rhodococcus and Nocardia. Ergo, it is commonly misrecognized as Nocardia or Rhodococcus. Since this pathogen requires comprehensive morphological and biochemical testing, it is often difficult and cumbersome to isolate the species. Broad-range Polymerase Chain Reaction (PCR) and sequencing with genes like 16S rRNA or hsp65 are used to correctly identify the species. Identification is essential for choosing and narrowing the right antimicrobial agent. Herein, we report our experience with a patient who presented with sternal osteomyelitis after infection with this elusive bug.

Gordonia bronchialis-Associated Endophthalmitis, Oregon, USA

Gordonia bronchialis is an aerobic actinomycetes that rarely causes infections in humans. Few reports describe Gordonia spp. causing eye-related infections. We report a case of chronic infectious endophthalmitis in Oregon, USA, associated with infection by G. bronchialis.

Yet More Evidence of Collusion: a New Viral Defense System Encoded by Gordonia Phage CarolAnn

Temperate phages play important roles in the physiology of their bacterial hosts and establish a lysogenic relationship with the host through which prophage-expressed genes confer new phenotypes. A key phenotype is prophage-mediated defense against heterotypic viral attack, in which temperate phages collude with their bacterial host to prevent other phages from attacking, sometimes with exquisite specificity. Such defense systems have been described in Pseudomonas and Mycobacterium phages but are likely widespread throughout the microbial community. Here, we describe a novel prophage-mediated defense system encoded by Gordonia phage CarolAnn, which defends against infection by unrelated phages grouped in cluster CZ. CarolAnn genes 43 and 44 are coexpressed with the repressor and are necessary and sufficient to confer defense against phage Kita and its close relatives. Kita and these relatives are targeted through Kita gene 53, a gene that is of unknown function but which is the location of defense escape mutations that overcome CarolAnn defense. Expression of Kita gene 53 is toxic to Gordonia terrae in the presence of CarolAnn genes 43 and 44, suggesting that defense may be mediated by an abortive infection type of mechanism. CarolAnn genes 43 and 44 are distant relatives of mycobacteriophage Sbash genes 31 and 30, respectively, which also confer viral defense but use a different targeting system.IMPORTANCE Prophage-mediated viral defense systems play a key role in microbial dynamics, as lysogeny is established relatively efficiently, and prophage-expressed genes can strongly inhibit lytic infection of other, unrelated phages. Demonstrating such defense systems in Gordonia terrae suggests that these systems are widespread and that there are a multitude of different systems with different specificities for the attacking phages.

Bacteremia due to Gordonia polyisoprenivorans: case report and review of literature

Background

Gordonia polyisoprenivorans is a ubiquitous aerobic actinomycetes bacterium that rarely cause infections in humans. Here, we report a case of G. polyisoprenivorans catheter-related bacteremia in an AIDS patient.

Case presentation

A 37-year-old man with a past medical history of AIDS-related lymphoma suffered bacteremia caused by a Gram-positive corynebacterium. The strain was identified as a Gordonia species by matrix-assisted laser desorption ionization–time of flight mass spectrometry and confirmed to G. polyisoprenivorans by 16S rRNA combined with gyrB gene sequencing analyses. The patient was treated with imipenem and had a good outcome.

Conclusions

The findings from our case and previously reported cases indicate that malignant hematologic disease, immunosuppression, and indwelling catheter heighten the risk for G. polyisoprenivorans infection. Molecular methods should be employed for proper identification of G. polyisoprenivorans to the species level.

A Chinese patient with peritoneal dialysis-related peritonitis caused by Gordonia terrae: a case report

Background

Gordonia terrae is a rare cause of clinical infections, with only 23 reported cases. We report the first case of peritoneal dialysis-related peritonitis caused by Gordonia terrae in mainland China.

Case presentation

A 52-year-old man developed peritoneal dialysis-related peritonitis and received preliminary antibiotic treatment. After claiming that his symptoms had been resolved, the patient insisted on being discharged (despite our recommendations) and did not receive continued treatment after leaving the hospital. A telephone follow-up with the patient’s relatives revealed that the patient died 3 months later. Routine testing did not identify the bacterial strain responsible for the infection, although matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identified the strain as Gordonia rubropertincta. However, a 16S rRNA sequence analysis using an isolate from the peritoneal fluid culture revealed that the responsible strain was actually Gordonia terrae. Similar to this case, all previously reported cases have involved a delayed diagnosis and initial treatment failure, and the definitive diagnosis required a 16S rRNA sequence analysis. Changes from an inappropriate antibiotic therapy to an appropriate one have relied on microbiological testing and were performed 7–32 days after the initial treatment.

Conclusions

The findings from our case and the previously reported cases indicate that peritoneal dialysis-related peritonitis caused by Gordonia terrae can be difficult to identify and treat. It may be especially challenging to diagnose these cases in countries with limited diagnostic resources.

Electronic supplementary material

The online version of this article (doi:10.1186/s12879-017-2283-2) contains supplementary material, which is available to authorized users.

Complete Genome Sequence of Gordonia terrae 3612

Here, we report the complete genome sequence of Gordonia terrae 3612, also known by the strain designations ATCC 25594, NRRL B-16283, and NBRC 100016. The genome sequence reveals it to be free of prophage and clustered regularly interspaced short palindromic repeats (CRISPRs), and it is an effective host for the isolation and characterization of Gordonia bacteriophages.

Sternal Osteomyelitis Caused by Gordonia bronchialis after Open-Heart Surgery

We report the case of a deep sternal wound infection with sternal osteomyelitis caused by Gordonia bronchialis after open-heart surgery. The isolate was identified as a G. bronchialis by 16S rRNA and hsp65 gene sequencing, having initially been misidentified as a Rhodococcus by a commercial phenotypic identification system.

Gordonia bacteremia

Gordonia species are ubiquitous aerobic actinomycetes that rarely cause infection in humans. We report the second known case of Gordonia otitidis catheter-related bacteremia in an immunocompromised patient and review four additional cases of Gordonia bacteremia seen at our institution over the past 14 years. In addition, the existing literature on Gordonia infections is reviewed.

Peritonitis caused by Haemophilus parainfluenzae, Leifsonia aquatica, and Gordonia spp. in a patient undergoing continuous ambulatory peritoneal dialysis

BACKGROUND

Peritonitis has remained the most common serious complication of continuous ambulatory peritoneal dialysis (CAPD). In most cases, these infections are monomicrobial, and the pathogens involved most commonly are Staphylococci. Recently, polymicrobial infections with rare organisms have been reported more often.

CASE REPORT

We describe a patient who developed recurrent episodes of CAPD-associated peritonitis with a total of four pathogens: Methicillin-resistant S. aureus, Haemophilus parainfluenzae, Leifsonia aquatica, and Gordonia spp. The infection most likely was acquired when the patient used tap water for dialysis during a camping trip. All episodes were treated successfully with antibiotics. Finally, the device was removed, and later, a new catheter was implanted, which still is in use.

CONCLUSION

Peritoneal dialysis-associated peritonitis may be caused by rare organisms. Antibiotics may be able to treat disease temporarily, but removal of contaminated catheters usually is required.

The strengths and weaknesses of Gordonia: a review of an emerging genus with increasing biotechnological potential

This review about the genus Gordonia provides a current overview of recent research on a young genus that was introduced in the year 1997 ( Stackebrandt et al., 1997 ). This emerging genus has attracted increasing environmental, industrial, biotechnological and medical interest during the last few years, in particular due to the capabilities of its members to degrade, transform, and synthesize organic compounds as well as to the pathogenic effects that have been described in many case studies. The number of publications about Gordonia has increased significantly after the year 2004 (the year of the first Gordonia review published by Arenskötter et al.) describing 13 new validly published species (type strains), many newly described physiological and metabolic capabilities, new patent applications and many new case reports of bacterial infections. Members of the genus Gordonia are widely distributed in nature and it is therefore important to unravel the species richness and metabolic potential of gordoniae in future studies to demonstrate their environmental impact especially on the degradation of persistent organic compounds and their ecological participation in the carbon cycle of organic material in soil and water. This review summarizes mainly the current state of importance and potential of the members of this genus for the environmental and biotechnological industry ("the strengthsâ) and briefly its pathogenic impact to humans ("the weaknessesâ).

Cutaneous infection caused by Gordonia amicalis after a traumatic injury

Gordonia amicalis infection has never been reported in humans. We report here the first case of G. amicalis-related cutaneous infection after a traumatic injury. The isolate was confirmed by 16S rRNA sequencing analysis, and the patient responded well to repeated debridement and antibiotic treatment.

Gordonia bronchialis bacteremia and pleural infection: case report and review of the literature

Gordonia species are aerobic actinomycetes recently recognized as causing human disease, often in the setting of intravascular catheter-related infections. We describe a case of Gordonia bronchialis bacteremia and pleural space infection in the absence of an indwelling intravascular catheter and review the breadth of reported infections with this emerging pathogen.

Five cases of bacteraemia due to Gordonia species

Gordonia species are aerobic Gram-positive bacilli and a rare cause of human disease. To our knowledge, there are only two cases of human infection with Gordonia sputi reported in the literature. We report five cases of bacteraemia due to Gordonia species at our institution since 2005, including four caused by G. sputi. Three of these cases were likely related to chronic indwelling central venous catheters.

Gordonia species: emerging pathogens in pediatric patients that are identified by 16S ribosomal RNA gene sequencing

Gordonia species are emerging pathogens that are often misidentified as Rhodococcus or Nocardia species but are reliably distinguished by 16S ribosomal RNA gene sequencing. We present a case series of 6 episodes of catheter-associated infection caused by Gordonia species in 5 patients seen at a tertiary care pediatric hospital and describe the management and outcomes of this infection in adults and children.