Ochrobactrum anthropi: an unusual pathogen: are we missing them?

Ochrobactrum anthropi infection following corneal transplantation -a case report and review of literature

BACKGROUND

Ochrobactrum anthropi is widely distributed and primarily infects patients with compromised immune functions . Historically, O. anthropi has been considered to possess low toxicity and pathogenicity; however, recent studies suggest that it may in fact cause severe purulent infections. In this case study, we examine a case of O. anthropi infection following corneal transplantation, exploring the occurrence and outcomes of such post-operative infections.

CASE PRESENTATION

A retrospective analysis of cases involved examinations, genetic testing for diagnosis, and subsequent treatment. In patients undergoing partial penetrating keratoplasty with a fungal corneal ulcer perforation, anterior chamber exudation and purulence were observed post-surgery. Despite antifungal treatment, genetic testing of the anterior chamber fluid and purulent material confirmed O. anthropi infection. The use of antimicrobial treatment specifically targeting O. anthropi was found to be effective in treating the infection.

CONCLUSION

Inflammatory reactions following corneal transplantation should be should be monitored for the presence of other infections. Genetic testing has significant implications for clinical diagnosis and treatment.

Two Case Reports of Ochrobactrum anthropi Bacteremia in a Tertiary Care Hospital in Northeast India

Ochrobactrum anthropi is a non-fermenting, Gram-negative bacillus and an emerging opportunistic pathogen. We have isolated this organism from the blood cultures of two patients, a 53-year-old immunocompetent male presenting with an episode of mild fever post craniotomy and an 85-year-old male with chronic obstructive pulmonary disease (COPD) and urinary retention on an indwelling catheter. The organism was identified using VITEK 2 (bioMérieux, France). Both the isolates were resistant to most of the β-lactams, including cephalosporins, and sensitive to quinolones, aminoglycosides, and carbapenems.

Ochrobactrum anthropi - An Emerging Opportunistic Pathogen in Musculoskeletal Disorders - A Case Report and Review of Literature

INTRODUCTION

Ochrobactrum anthropi is an opportunistic and rare human pathogen, which is seen widely in the environment. O. anthropi infections have been reported in both immunocompetent and immunocompromised individuals. There is no proper consensus on the diagnosis and management of O. anthropi related infections.

CASE REPORT

We report a case of O. anthropi related left distal clavicular osteomyelitis in an immunocompetent individual with an elaborative diagnostic and treatment algorithm for its effective management.

CONCLUSION

A comprehensive management strategy with a combination of implant removal (if present) with extensive surgical debridement of bone and soft tissue and intravenous antibiotics results in successful eradication of O. anthropi infection.

The Genus Ochrobactrum as Major Opportunistic Pathogens

Ochrobactrum species are non-enteric, Gram-negative organisms that are closely related to the genus Brucella. Since the designation of the genus in 1988, several distinct species have now been characterised and implicated as opportunistic pathogens in multiple outbreaks. Here, we examine the genus, its members, diagnostic tools used for identification, data from recent Ochrobactrum whole genome sequencing and the pathogenicity associated with reported Ochrobactrum infections. This review identified 128 instances of Ochrobactrum spp. infections that have been discussed in the literature. These findings indicate that infection review programs should consider investigation of possible Ochrobactrum spp. outbreaks if these bacteria are clinically isolated in more than one patient and that Ochrobactrum spp. are more important pathogens than previously thought.

Investigation of the presence of Ochrobactrum spp. and Brucella spp. in Haemaphysalis longicornis

Ticks are common vectors of human and animal diseases. Ochrobactrum spp. belong to the Brucellaceae family and have recently been recognized as emerging human pathogens. The ability of Haemaphysalis longicornis ticks to carry Ochrobactrum spp. remains uncertain. During June and July 2018, 686 ticks were collected from 11 sites in Pingdingshan Henan province in central China. We extracted 169 DNA samples for Brucellaceae 16S rRNA nested PCR and sequenced them in order to identify Ochrobactrum spp. The data sequences were aligned with NCBI BLAST program and phylogenetic tree was constructed using Mega 5.0. Twenty samples were sequenced successfully out of a total forty-one positive for Brucellaceae. Thirteen DNA samples were identical to O. intermedium (99.85 %-100.00 %) and 3 were identical to O. cicer (99.85 %-100.00 %) (15 collected from host and one from vegetation). Four DNA samples (3 collected from host and one from vegetation) had 99.83-100 % B. melitensis identity. This study adds to the growing body of evidence that shows Ochrobactrum spp. are present in H. longicornis. Ochrobactrum spp. and Brucella spp. are phenotypically and genetically closely related pathogens. Our finding highlights the importance of gene sequencing and phylogenetic analysis to differentiate between Ochrobactrum spp. and Brucella spp. in the research and potentially clinical setting. Future work is required to investigate the transmission potential of Ochrobactrum spp. by H. longicornis.

Evolutionary Timeline and Genomic Plasticity Underlying the Lifestyle Diversity in Rhizobiales

Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens.

Members of the order Rhizobiales include those capable of nitrogen fixation in nodules as well as pathogens of animals and plants. This lifestyle diversity has important implications for agricultural and medical research. Leveraging large-scale genomic data, we infer that Rhizobiales originated as a free-living ancestor ∼1,500 million years ago (Mya) and that the later emergence of host-associated lifestyles broadly coincided with the rise of their eukaryotic hosts. In particular, the first nodulating lineage arose from either Azorhizobium or Bradyrhizobium 150 to 80 Mya, a time range in general concurrent with the emergence of legumes. The rates of lifestyle transitions are highly variable; nodule association is more likely to be lost than gained, whereas animal association likely represents an evolutionary dead end. We searched for statistical correlations between gene presence and lifestyle and identified genes likely contributing to the transition and adaptation to the same lifestyle in divergent lineages. Among the genes potentially promoting successful transitions to major nodulation lineages, the nod and nif clusters for nodulation and nitrogen fixation, respectively, were repeatedly acquired during each transition; the fix, dct, and phb clusters involved in energy conservation under micro-oxic conditions were present in the nonnodulating ancestors; and the secretion systems were acquired in lineage-specific patterns. Our study data suggest that increased eukaryote diversity drives lifestyle diversification of bacteria and highlight both acquired and preexisting traits facilitating the origin of host association.

IMPORTANCE Bacteria form diverse interactions with eukaryotic hosts. This is well represented by the Rhizobiales, a clade of Alphaproteobacteria strategically important for their large diversity of lifestyles with implications for agricultural and medical research. To investigate their lifestyle evolution, we compiled a comprehensive data set of genomes and lifestyle information for over 1,000 Rhizobiales genomes. We show that the origins of major host-associated lineages in Rhizobiales broadly coincided with the emergences of their host plants/animals, suggesting bacterium-host interactions as a driving force in the evolution of Rhizobiales. We further found that, in addition to gene gains, preexisting traits and recurrent losses of specific genomic traits may have played underrecognized roles in the origin of host-associated lineages, providing clues to genetic engineering of microbial agricultural inoculants and prevention of the emergence of potential plant/animal pathogens.

Fertility factors affect the vaginal microbiome in women of reproductive age

Problem

For women of reproductive age, achieving a successful pregnancy requires both the normal functioning of reproductive endocrine and the health of the reproductive tract environment. We aimed to study how these fertility factors, such as female age, baseline sexual hormone levels, tubal patency, and vaginal pH, affect the composition of vaginal microbiome.

Method of study

The 16S rRNA sequencing was carried on vaginal microbiome samples from 85 women of reproductive age without vaginal infections or reproductive endocrine diseases. The detailed correlations between fertility factors and vaginal microbiome were quantified by Spearman's rank tests. A linear discriminant analysis was carried out to explore the effects of fertility factors on the relative abundances of vaginal bacterial species.

Results

The vaginal pH, levels of basal E2, LH, and FSH all had significant effects on the distribution of vaginal microbiome. The relative abundances of vaginal bacterial species, including Escherichia coli, Streptococcus agalactiae, and Prevotella intermedia, were significantly different due to the host's state of reproductive endocrine and tubal patency. It was worth noting that women with tubal obstruction, or prolonged menstrual cycle, or antral follicle count >15, or vaginal pH > 4.5 all had a higher abundance of Escherichia coli in vagina.

Conclusion

The fertility factors associated with the reproductive endocrine and the genital tract environment affected vaginal microbiome in women of reproductive age. The species Escherichia coli, Streptococcus agalactiae, Prevotella intermedia, etc could be used as biomarkers to reflect the pathological state of reproductive endocrine and genital tract.

Whole-genome analysis and description of an outbreak due to carbapenem-resistant Ochrobactrum anthropi causing pseudo-bacteraemias

Ochrobactrum anthropi, a rare human pathogen, has been isolated predominantly from patients with catheter-related bacteraemia and rarely from other infections. In 2016, six cases of pseudo-bacteraemia caused by carbapenem-resistant O. anthropi isolates were recovered from an Argentinian hospital. The resistant phenotype exposed by the isolates caught our attention and led to an extensive epidemiologic investigation. Here we describe the characterization of a carbapenem-resistant O. anthropi outbreak whose probable cause was by contaminated collection tubes. The genome analysis of one strain revealed the presence of various resistant determinants. Among them, a metal-dependent hydrolase of the β-lactamase superfamily I, phnP, was found. Lately the recovery of unusual multidrug-resistant pathogens in the clinical setting has increased, thus emphasizing the need to implement standardized infection control practice and epidemiologic investigation to identify the real cause of hospital outbreaks.

Clinical characteristics of patients with Ochrobactrum anthropi bloodstream infection in a Chinese tertiary-care hospital: A 7-year study

BACKGROUND

Ochrobactrum anthropi has become an emerging pathogen for bloodstream infection (BSI).

METHODS

From January 1st 2010 to June 30th 2017, inpatients with one or more blood cultures positive for O. anthropi isolates at Chinese People's Liberation Army General Hospital in Beijing, China, were enrolled in this study. Clinical and laboratory data were collected by reviewing electronic records.

RESULTS

A total of 11 patients with O. anthropi BSI were identified, of which 10 patients survived. There were 6 males and 5 females, whose age ranged from 2 to 83 years. 7 infections were hospital-acquired. In 8 cases O. anthropi was the only pathogen. The most common symptoms of O. anthropi BSI were fever (100%) and disorders of consciousness (45.5%). All patients had undergone indwelling catheter placement. O. anthropi isolates in this study were most susceptible to levofloxacin (100%), ciprofloxacin (85.7%), imipenem (85.7%) and cotrimoxazole (85.7%), while they were widely resistant to penicillins and cephalosporins.

CONCLUSIONS

O. anthropi BSI usually happens in patients with indwelling catheters, and often begins with no distinctive symptom or laboratory finding. O. anthropi seldom form polymicrobial BSIs. Quinolones and carbapenems are optimal antibiotics for O. anthropi BSI. Catheter removal is essential when O. anthropi BSI happens recurrently.

Ochrobactrum anthropi Fulminant Early-onset Neonatal Sepsis: A Case Report and Review of Literature

Ochrobactrum anthropi is Gram-negative bacteria that cause infection in humans, particularly immunocompromised patients and those with indwelling central venous catheters. O. anthropi is unlikely to cause fulminant sepsis in infected patients. A few cases of late-onset neonatal sepsis have been reported in preterm infants with congenital anomalies. We hereby present the first published case of fulminant early-onset neonatal sepsis in a premature newborn.

Prevalence, Host Range, and Comparative Genomic Analysis of Temperate Ochrobactrum Phages

Ochrobactrum and Brucella are closely related bacteria that populate different habitats and differ in their pathogenic properties. Only little is known about mobile genetic elements in these genera which might be important for survival and virulence. Previous studies on Brucella lysogeny indicated that active phages are rare in this genus. To gain insight into the presence and nature of prophages in Ochrobactrum, temperate phages were isolated from various species and characterized in detail. In silico analyses disclosed numerous prophages in published Ochrobactrum genomes. Induction experiments showed that Ochrobactrum prophages can be induced by various stress factors and that some strains released phage particles even under non-induced conditions. Sixty percent of lysates prepared from 125 strains revealed lytic activity. The host range and DNA similarities of 19 phages belonging to the families Myoviridae, Siphoviridae, or Podoviridae were determined suggesting that they are highly diverse. Some phages showed relationship to the temperate Brucella inopinata phage BiPB01. The genomic sequences of the myovirus POA1180 (41,655 bp) and podovirus POI1126 (60,065 bp) were analyzed. Phage POA1180 is very similar to a prophage recently identified in a Brucella strain isolated from an exotic frog. The POA1180 genome contains genes which may confer resistance to chromate and the ability to take up sulfate. Phage POI1126 is related to podoviruses of Sinorhizobium meliloti (PCB5), Erwinia pyrifoliae (Pep14), and Burkholderia cenocepacia (BcepIL02) and almost identical to an unnamed plasmid of the Ochrobactrum intermedium strain LMG 3301. Further experiments revealed that the POI1126 prophage indeed replicates as an extrachromosomal element. The data demonstrate for the first time that active prophages are common in Ochrobactrum and suggest that atypical brucellae also may be a reservoir for temperate phages.

Isolation and characterization of a crude oil degrading bacteria from formation water: comparative genomic analysis of environmental Ochrobactrum intermedium isolate versus clinical strains

In this study, we isolated an environmental clone of Ochrobactrum intermedium, strain 2745-2, from the formation water of Changqing oilfield in Shanxi, China, which can degrade crude oil. Strain 2745-2 is aerobic and rod-shaped with optimum growth at 42 °C and pH 5.5. We sequenced the genome and found a single chromosome of 4 800 175 bp, with a G+C content of 57.63%. Sixty RNAs and 4737 protein-coding genes were identified: many of the genes are responsible for the degradation, emulsification, and metabolizing of crude oil. A comparative genomic analysis with related clinical strains (M86, 229E, and LMG3301(T)) showed that genes involved in virulence, disease, defense, phages, prophages, transposable elements, plasmids, and antibiotic resistance are also present in strain 2745-2.

Draft Genome Sequence of Organophosphate-Degrading Ochrobactrum anthropi FRAF13

Ochrobactrum anthropi FRAF13 was isolated from farmland soil in Jersey Village, Texas. FRAF13 is a bacterial microorganism with broad antibiotic resistance that possesses a number of metal-dependent β-lactam enzymes with secondary phosphotriesterase activity that can initiate the breakdown of organophosphate compounds.

Extensive Identification of Bacterial Riboflavin Transporters and Their Distribution across Bacterial Species

Riboflavin, the precursor for the cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide, is an essential metabolite in all organisms. While the functions for de novo riboflavin biosynthesis and riboflavin import may coexist in bacteria, the extent of this co-occurrence is undetermined. The RibM, RibN, RfuABCD and the energy-coupling factor-RibU bacterial riboflavin transporters have been experimentally characterized. In addition, ImpX, RfnT and RibXY are proposed as riboflavin transporters based on positional clustering with riboflavin biosynthetic pathway (RBP) genes or conservation of the FMN riboswitch regulatory element. Here, we searched for the FMN riboswitch in bacterial genomes to identify genes encoding riboflavin transporters and assessed their distribution among bacteria. Two new putative riboflavin transporters were identified: RibZ in Clostridium and RibV in Mesoplasma florum. Trans-complementation of an Escherichia coli riboflavin auxotroph strain confirmed the riboflavin transport activity of RibZ from Clostridium difficile, RibXY from Chloroflexus aurantiacus, ImpX from Fusobacterium nucleatum and RfnT from Ochrobactrum anthropi. The analysis of the genomic distribution of all known bacterial riboflavin transporters revealed that most occur in species possessing the RBP and that some bacteria may even encode functional riboflavin transporters from two different families. Our results indicate that some species possess ancestral riboflavin transporters, while others possess transporters that appear to have evolved recently. Moreover, our data suggest that unidentified riboflavin transporters also exist. The present study doubles the number of experimentally characterized riboflavin transporters and suggests a specific, non-accessory role for these proteins in riboflavin-prototrophic bacteria.

16S ribosomal DNA sequence-based identification of bacteria in laboratory rodents: a practical approach in laboratory animal bacteriology diagnostics

Correct identification of bacteria is crucial for the management of rodent colonies. Some bacteria are difficult to identify phenotypically outside reference laboratories. In this study, we evaluated the utility of 16S ribosomal DNA (rDNA) sequencing as a means of identifying a collection of 30 isolates of rodent origin which are conventionally difficult to identify. Sequence analysis of the first approximate 720 to 880 bp of the 5'- end of 16S rDNA identified 25 isolates (83.33%) with ≥ 99% similarity to a sequence of a type strain, whereas three isolates (10%) displayed a sequence similarity ≥ 97% but <99% to the type strain sequences. These similarity scores were used to define identification to species and genus levels, respectively. Two of the 30 isolates (6.67%) displayed a sequence similarity of ≥ 95 but <97% to the reference strains and were thus allocated to a family. This technique allowed us to document the association of mice with bacteria relevant for the colonies management such as Pasteurellaceae, Bordetella hinzii or Streptococcus danieliae. In addition, human potential pathogens such as Acinetobacter spp., Ochrobactrum anthropi and Paracoccus yeei or others not yet reported in mouse bacterial species such as Leucobacter chironomi, Neisseria perflava and Pantoea dispersa were observed. In conclusion, the sequence analysis of 16S rDNA proved to be a useful diagnostic tool, with higher performance characteristics than the classical phenotypic methods, for identification of laboratory animal bacteria. For the first time this method allowed us to document the association of certain bacterial species with the laboratory mouse.