Outbreak of Achromobacter xylosoxidans and Ochrobactrum anthropi Infections after Prostate Biopsies, France, 2014

Metabarcoding using nanopore sequencing enables identification of diverse and zoonotic vector-borne pathogens from neglected regions: A case study investigating dogs from Bhutan

The diversity and prevalence of canine vector-borne pathogens (VBPs) in Bhutan have to date remained unexplored, whilst recent epidemiological surveys in other South Asian nations have found diseases caused by VBPs to be rife in local dog populations. Importantly, many of such VBPs can infect people as well, with a building body of evidence identifying potentially zoonotic rickettsial organisms infecting humans in Bhutan. Given the lack of data on canine pathogens in Bhutan we employed a suite of deep-sequencing metabarcoding methods using Oxford Nanopore Technologies' MinION™ device to holistically characterise the bacterial, apicomplexan and filarial worm blood-borne pathogens of dogs in the country's south. Of the 95 stray, owned and community dogs sampled 78% (95% CI = 69%-85%) were infected with at least one VBP. Pathogen species detected were highly diverse including the bacteria Mycoplasma haemocanis in 16% (95% CI: 10-24%), Ehrlichia canis in 4% (95% CI: 2-10%), Anaplasma platys in 2% (95% CI: 0.5-7%) of dogs as well as the zoonotic species Bartonella clarridgeiae in 1% (95% CI: 0.1-6%), a potentially novel Bartonella spp. and an Ehrlichia chaffeensis-like bacterium, both in 1% (95% CI: 0.1-6%) of dogs. The apicomplexan haemoparasites Hepatozoon canis in 62% (95% CI: 52-71%), Babesia gibsoni in 45% (95% CI: 36-55%) and Babesia vogeli in 3% (95% CI: 1-9%) of dogs were also detected. Finally, 5% (95% CI: 2-12%) of dogs were found to be infected with the filarioid Acanthocheilonema reconditum and 1% (95% CI: 0.1-6%) with zoonotic Dirofilaria sp. hongkongensis. One canine was found positive to the filarioid Setaria tundra, a species normally found infecting cervids. The elucidated diversity of VBP communities highlights the strength of assumption-free diagnostics, such as metabarcoding, in detecting rare, novel, and unexpected pathogens. This approach to identifying pathogen diversity is of critical importance when investigating regions and populations that have thus far been neglected, with the findings aiding the development of future One Health informed strategies for disease control.

Achromobacter cluster related to COVID-19 supply chain issues

Isolation of an unusual organism, Achromobacter xylosoxidans, from 2 cardiac surgical patients on the same day prompted an investigation to search for cases and cause. An extensive review demonstrated a pseudo-outbreak related to practices to conserve laboratory saline due to short supply resulting from supply chain shortage from the coronavirus disease 2019 pandemic.

Comparative in vitro activities of eravacycline in combination with colistin, meropenem, or ceftazidime against various Achromobacter spp. strains isolated from patients with cystic fibrosis

The Achromobacter species is an emerging pathogen causing chronic bacterial infections in patients with certain conditions, such as cystic fibrosis (CF), hematologic and solid organ malignancies, renal failure, and certain immune deficiencies. In the present study, we assessed the in vitro bactericidal activities of eravacycline, either alone or in combination with colistin, meropenem, or ceftazidime, using 50 Achromobacter spp. strains isolated from CF patients. We also investigated the synergistic interactions of these combinations using microbroth dilutions against 50 strains of Achromobacter spp. Bactericidal, and we assessed the synergistic effects of the tested antibiotic combinations using the time-kill curve (TKC) technique. Our studies show that meropenem alone is the most effective antibiotic of those tested. Based on the TKCs, we found that eravacycline-colistin combinations display both bactericidal and synergistic activities for 24 h against 5 of the 6 Achromobacter spp. strains, including colistin-resistant ones, at 4xMIC of colistin. Although we did not observe synergistic interactions with eravacycline-meropenem or eravacycline-ceftazidime combinations, we did not observe antagonism with any combination tested.This study's findings could have important implications for antimicrobial therapy with tested antibiotics.

Outbreak and control of Achromobacter denitrificans at an academic hospital in Pretoria, South Africa

OBJECTIVE

In this study, we sought to determine the source of an outbreak of Achromobacter denitrificans infections in patients at a tertiary-care academic hospital.

DESIGN

Outbreak report study with intervention. The study period extended from February 2018 to December 2018.

SETTING

The study was conducted at a tertiary-care academic hospital in Pretoria, South Africa.

PATIENTS AND PARTICIPANTS

All patients who cultured A. denitrificans from any site were included in this study. During the study period, 43 patients met this criterion.

INTERVENTIONS

Once an outbreak was confirmed, the microbiology laboratory compiled a list of affected patients. A common agent, chlorhexidine-and-water solution, was used as a disinfectant-antiseptic for all affected patients. The laboratory proceeded to culture this solution. Environmental and surface swabs were also cultured from the hospital pharmacy area where this solution was prepared. Repetitive-element, sequence-based, polymerase chain reaction (rep-PCR) was performed on the initial clinical isolates to confirm the relatedness of the isolates.

RESULTS

In total, 43 isolates of A. denitrificans were cultured from patient specimens during the outbreak. The laboratory cultured A. denitrificans from all bottles of chlorhexidine-and-water solutions sampled from the wards and the pharmacy. The culture of the dispenser device used to prepare this solution also grew A. denitrificans. The rep-PCR confirmed the clonality of the clinical isolates with 2 genotypes dominating.

CONCLUSIONS

Contaminated chlorhexidine-and-water solutions prepared at the hospital pharmacy was determined to be the source of the outbreak. Once this item was removed from the hospital, the laboratory did not culture any further A. denitrificans isolates from patient specimens.

Recurrent environmental contamination in a centralized radiopharmacy unit by Achromobacter spp: results of a large microbiological investigation

BACKGROUND

Radiopharmaceuticals preparation unit, such as every aseptic preparation units, are strictly monitored in terms of microbiological contamination. Despite all biocontamination control procedures, our radiopharmacy unit faced repeated environnmental contamination by Achromobacter spp which necessitated a large environmental investigation.

METHOD

Microbiological controls were carried out using Count Tact agars (Biomérieux) for flat surfaces, dry swabbing for hard to reach areas and containers were filled with a sterile water solution (then filtrated on 0.45µm membrane and seeded). Microbiological identification was performed by mass spectrometry (MALDI-TOF-MS, Brucker) on each positive sample.

RESULTS

Achromobacter spp was found in 10% of the 413 samples during the 8 months investigation period. The proportion of positive samples was stable among time but their location was unpredictable. The highest inoculum was finally found in the buckets used for biocleaning.

DISCUSSION

Samples from cleaning buckets taken by dry swabbing were at first negative, but the use of a non-routinely used sampling method allowed to discover the reservoir of this persistent contamination.

CONCLUSION

This investigation alerted us on the high microbiological risk associated with reusable plastic containers and the importance of a sampling method adapted to critical locations.

Genomics of Ochrobactrum pseudogrignonense (newly named Brucella pseudogrignonensis) reveals a new bla OXA subgroup

Ochrobactrum pseudogrignonense (newly named Brucella pseudogrignonensis) is an emerging pathogen in immunodeficient and immunocompetent patients. Most documented cases associated with Ochrobactrum are frequently catheter-related and exhibit wide-spectrum β-lactam resistance. Misidentification of this pathogen using commercial bacterial identification kits is common. We identified a case of O. pseudogrignonense infection associated with cholelithiasis. The O. pseudogrignonense genome was sequenced and reconstructed using a Nanopore and Illumina hybrid strategy. A novel bla _OXA-919 divergent from existing OXA members was identified and subsequent analysis revealed its existence in all available O. pseudogrignonense genomes, which forms a new phylogenetic subgroup distinct from other OXA clusters. Further analysis demonstrated the presence of the novel bla _OXA-919 in the chromosome of several other Ochrobactrum species. Our study indicated that Ochrobactrum chromosomes may be a reservoir of bla _OXA-919 β-lactamases.

Bacterias aisladas de biosólidos de la PTAR San Fernando en Medellín-Colombia con capacidad para reducir cromo hexavalente

En las últimas décadas se ha trabajado activamente para reducir el impacto ambiental generado por las actividades antrópicas que constantemente liberan componentes tóxicos al ambiente generando inestabilidad y daños en la salud de las comunidades biológicas. Entre los diferentes contaminantes, los metales pesados revisten importancia en virtud de sus propiedades, que dificultan su degradación o transformación en otros compuestos menos tóxicos. El cromo es uno de los metales de mayor interés a nivel global por su uso en múltiples industrias. Los métodos convencionales que utilizan materiales cromados en sus procesos, no sólo arrojan cantidades considerables de residuos al ambiente, sino que dan poca cuenta de la fracción de Cr6+ presente en determinados ecosistemas. La biorremediación se ha propuesto como una alternativa económicamente viable y ambientalmente sostenible. El propósito del presente trabajo fue evaluar la capacidad de reducción de cromo por bacterias, aisladas de una matriz de biosólidos de la Planta de tratamiento de aguas residuales (PTAR) San Fernando en la ciudad de Medellín-Colombia. Muestras de biosólidos se cultivaron en Agar Nutritivo enriquecido con diferentes concentraciones de Cr6+. Las cepas que presentaron mayor tolerancia al cromo fueron aisladas para realizar ensayos de reducción por triplicado, monitoreando la concentración del metal en el tiempo. Se obtuvieron siete especies bacterianas diferentes dentro de las cuales se destacaron Staphylococcus saprophyticus, Ochrobactrum anthropi y Bacillus cereus por la capacidad de reducir Cr6+ a 96 h con eficiencias de 29.0%, 61.1% y 100%,  respectivamente.

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.

Prevalence of antibiotic-resistant, toxic metal-tolerant and biofilm-forming bacteria in hospital surroundings

The emergence and rapid spread of antibiotic-resistant bacteria due to unethical and non-scientific disposal of hospital wastes and clinical by-products caused an alarming environmental concern and associated public health risks. The present study aims to assess the co-selection of antibiotic resistance and heavy metal tolerance by bacteria isolated from hospital effluents. These isolates were also tested for hemolytic activity, pH-tolerance, thermal inactivation, auto-aggregation, cell-surface hydrophobicity and interaction with other bacteria. The study reports the prevalence of antibiotic-resistant and heavy metal tolerant bacteria in clinical effluents and water samples. Most of these isolates were resistant to vancomycin, clindamycin, ampicillin, rifampicin, penicillin-G, methicillin and cefdinir, and evidenced the production of extended-spectrum β-lactamase enzyme. Toxic metals such as cadmium, copper, iron, lead and zinc also exert a selection pressure towards antibiotic resistance. Pseudomonas aeruginosa strain GCC_19W3, Bacillus sp. strain GCC_19S2 and Achromobacter spanius strain GCC_SB1 showed β-hemolysis, evidenced by the complete breakdown of the red blood cells. Highest auto-aggregation was exhibited by Bacillus sp. strain GCC_19S2; whereas, maximum cell-surface hydrophobicity was displayed by P. aeruginosa strain GCC_19W1. Antagonistic activity by Stenotrophomonas maltophilia strain GCC_19W2, P. aeruginosa strain GCC_19W3 and strains of Achromobacter restricts the growth of other microorganisms by producing some bactericidal substances. The study emphasises undertaking safety measures for the disposal of clinical effluents directly into the environment. The study suggests adopting necessary measures and regulations to restrict the spread of emerging pathogens within the hospital biome and community, which if unnoticed, might pose a significant clinical challenge.

Hematogenous pleural infection caused by Achromobacter xylosoxidans in a patient undergoing maintenance hemodialysis

A 78-year-old Japanese man, undergoing maintenance hemodialysis for 20 years and having received coronary artery bypass grafting two months before, was hospitalized because of fever with subclinical left-sided pleurisy. Achromobacter xylosoxidans strains exhibiting identical genomic patterns on a macrorestriction analysis were isolated from the blood and the pleural effusion obtained on admission. Physical and radiological examinations did not reveal any lesions in either chest wall or lung adjacent to the effusion, indicating that the organism in the effusion had entered the pleural space via the bloodstream. Immunocompromising conditions due to undergoing maintenance hemodialysis and the presence of the antecedently accumulated pleural effusion may have been associated with the development of hematogenous dissemination. The patient fully recovered only with antibiotic therapy. To our knowledge, the present report is the first describing a case of hematogenous pleural infection caused by A. xylosoxidans.

Achromobacter spp. healthcare associated infections in the French West Indies: a longitudinal study from 2006 to 2016

Background

Bacteria of the Achromobacter genus, more particularly xylosoxidans species, are responsible for various healthcare associated infections (HAI) which are increasingly described since the last decade. Cystic fibrosis (CF) patients are considered as potential reservoirs in hospitals. We performed a retrospective study to estimate the frequencies of Achromobacter spp. HAI among patients from French West Indies, to determine characteristics of infected patients and establish a possible link between CF and infections.

Methods

All adults with at least one Achromobacter spp. positive sample and infection criteria in accordance with European official definitions of HAI, hospitalized in University Hospital of Martinique from 2006 to 2016 for more than 48 h, were included. Patient clinical features, immune status and underlying diseases were obtained from medical files. A list of CF patients was given by clinicians.

Antibiotic-susceptibility profiles of the strains were determined using an automated method.

Results

Mean incidence density was 0.038/1000 days of hospitalization. Achromobacter spp. HAI evolved as an endemic situation with a low but pretty much stable incidence rate over the 11-year observation period. An epidemic peak was noticed in 2013. Among the 66 included patients, 56.1% were immunocompetent and no one had CF. Pneumonia and bacteraemia were the two main HAI. Among the 79 isolated strains, 92.4% were resistant to at least 1 major antibiotic and 16.4% met the definition of multidrug-resistant bacteria.

Conclusions

This microorganism, little known in our country because of the scarcity of CF patients, represents a threat for both immunosuppressed and immunocompetent patients and a therapeutic challenge because of its high resistance.

Correct Identification of Ochrobactrum anthropi From Blood Culture Using 16rRNA Sequencing: A First Case Report in an Immunocompromised Patient in Mexico

The present report describes the misidentification of Brucella spp. from a positive blood culture using traditional microbiology tests. A molecular test identified the bacterium as Ochrobactrum anthropi. According to the information available, this report is the first to include this type of case in Mexico.

[Infection control practices while performing prostate biopsies in France: A CIAFU survey]

In 2008, the French Public Health Committee admitted that associating ultrasound probe protection, and related precautions, and low-level disinfection would be equivalent to the intermediate level disinfection. In 2010, the French Urology Association (AFU) updated guidelines regarding trans-rectal prostate biopsies, namely preventive measures related to cross-transmission of infections. We report an evaluation of compliance to them, driven in 2016 by AFU's infection committee. Although not recommended, almost one third of the urologists still perform biopsies under general anesthesia, and two thirds of them ask for a urine culture before biopsies. Several improvements are still needed: sterilization of needle guide should always be done when not of single use, the ultrasonography gel should be sterile, probes protection should be EC labeled, and compliance to probe processing between two patients should increase. Most of urologists happened to experience blood or feces contamination of probes. Less than half of probes are entirely floodable, and when intermediate level disinfection is done, glutaraldehyde is still referred as disinfectant by one third of the urologists.

LEVEL OF EVIDENCE

4.

Diet-induced reconstruction of mucosal microbiota associated with alterations of epithelium lectin expression and regulation in the maintenance of rumen homeostasis

It is unknown whether lectins of the rumen epithelium contribute to the recognition of mucosal microbes and activation of tolerogenic cytokines in ruminant animals. We applied an integrated method of RNA-seq and 16S rRNA gene sequencing to investigate alterations of epithelial lectin expression and regulation with a diet-induced reconstruction of the mucosal microbiota in the goat rumen. Our results showed that the diversity and richness of the rumen mucosal microbiota were promoted by the dietary concentrate. Meantime, in the rumen epithelium, five lectin genes, namely, sialic acid-binding Ig-like lectin 14 (LOC102180073), C-type lectin domain family 4, member E (CLEC4E), C-type lectin domain family 7, member A (CLEC7A), C-type lectin domain family 16, member A (CLEC16A), and lectin, mannose-binding 2 (LMAN2), were indicated to promote the expression of 8 tolerogenic cytokines, transforming growth factor beta 1 (TGFB1) and 4 enzyme genes involved in retinoic acid biosynthesis via 6 signaling pathways. Analysis of the combined data showed that 9 microbial genera (Clostridium_IV, Desulfobulbus, Eubacterium, Ochrobactrum, Propionibacterium, Pseudomonas, Slackia, Staphylococcus and Subdivision5_genera_IS) were highly related to the expression of functional lectins. These findings provide new insights into the interactions between the rumen epithelium and mucosal microbiota in the maintenance of rumen homeostasis.