Melioidosis Queensland: An analysis of clinical outcomes and genomic factors

BACKGROUND

The clinical and genomic epidemiology of melioidosis varies across regions.

AIM

To describe the clinical and genetic diversity of B. pseudomallei across Queensland, Australia.

METHODS

Whole genome sequencing of clinical isolates stored at the melioidosis reference lab from 1996-2020 was performed and analysed in conjunction with available clinical data.

RESULTS

Isolates from 292 patients were analysed. Bacteraemia was present in 71% and pneumonia in 65%. The case-fatality rate was 25%. Novel sequence types (ST) accounted for 51% of all isolates. No association was identified between the variable virulence factors assessed and patient outcome. Over time, the proportion of First Nation's patients declined from 59% to 26%, and the proportion of patients aged >70 years rose from 13% to 38%.

CONCLUSION

This study describes a genomically diverse and comparatively distinct collection of B. pseudomallei clinical isolates from across Queensland, Australia. An increasing incidence of melioidosis in elderly patients may be an important factor in the persistently high case-fatality in this region and warrants further investigation and directed intervention.

Determining the in vitro susceptibility of tebipenem, an oral carbapenem, against third-generation cephalosporin-resistant Escherichia coli and Klebsiella pneumoniae isolated from bloodstream infections

Background

Antimicrobials for bloodstream infections due to ESBL- and AmpC-producing Escherichia coli and Klebsiella pneumoniae are significantly limited due to widespread antimicrobial resistance. Tebipenem, an oral carbapenem, exhibits stability against these resistance mechanisms and may prove an attractive alternative.

Methods

The in vitro susceptibility of tebipenem was assessed against previously whole-genome sequenced ESBL- and AmpC-producing E. coli (274 isolates) and K. pneumoniae (42 isolates) derived from bloodstream infections using broth microdilution testing. Resulting tebipenem MICs were compared with those of other carbapenems previously tested against the isolate collection. Tebipenem activity was also compared against those isolates expressing co-resistance to the common oral antibiotics ciprofloxacin and trimethoprim/sulfamethoxazole.

Results

The tebipenem MIC₉₀ value was found to be 0.03 mg/L for E. coli and 0.125 mg/L for K. pneumoniae. For E. coli, the tebipenem MIC₉₀ value was equivalent to that of meropenem, 2-fold lower than that of doripenem, and 8-fold and 4-fold lower than that of imipenem and ertapenem, respectively. For K. pneumoniae, the tebipenem MIC₉₀ value was 2-fold higher than that of meropenem, equivalent to that of doripenem, and 4-fold and 2-fold lower than that of imipenem and ertapenem, respectively. Tebipenem MICs were also unaffected by the expression of co-resistance to ciprofloxacin and trimethoprim/sulfamethoxazole.

Conclusions

The in vitro activity of tebipenem was unaffected by the production of ESBL and AmpC enzymes. Tebipenem also retained its activity against those isolates expressing co-resistance to ciprofloxacin and trimethoprim/sulfamethoxazole. These findings therefore highlight tebipenem as a potential option for the treatment of invasive MDR infections.

Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission

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Identification of closely related (< 50 SNV) clinical and environmental aquatic Elizabethkingia anophelis isolates.

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Identification of a provisional novel species Elizabethkingia umaracha.

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Novel bla_GOB and bla_B carbapenemases and extended spectrum β-lactamase bla_CME alleles identified in Elizabethkingia spp.

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Analysis of the global phylogeny and pangenome of Elizabethkingia spp.

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Identification of novel ICE elements carrying uncharacterised genetic cargo in 67 / 94 (71.3%) of the aquatic environments Elizabethkingia spp.

Elizabethkingia species are ubiquitous in aquatic environments, colonize water systems in healthcare settings and are emerging opportunistic pathogens with reports surfacing in 25 countries across six continents. Elizabethkingia infections are challenging to treat, and case fatality rates are high. Chromosomal bla_B, bla_GOB and bla_CME genes encoding carbapenemases and cephalosporinases are unique to Elizabethkingia spp. and reports of concomitant resistance to aminoglycosides, fluoroquinolones and sulfamethoxazole-trimethoprim are known. Here, we characterized whole-genome sequences of 94 Elizabethkingia isolates carrying multiple wide-spectrum metallo-β-lactamase (bla_Band bla_GOB) and extended-spectrum serine‑β-lactamase (bla_CME) genes from Australian aquatic environments and performed comparative phylogenomic analyses against national clinical and international strains. qPCR was performed to quantify the levels of Elizabethkingia species in the source environments. Antibiotic MIC testing revealed significant resistance to carbapenems and cephalosporins but susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole. Phylogenetics show that three environmental E. anophelis isolates are closely related to E. anophelis from Australian clinical isolates (∼36 SNPs), and a new species, E. umeracha sp. novel, was discovered. Genomic signatures provide insight into potentially shared origins and a capacity to transfer mobile genetic elements with both national and international isolates.

Diagnosis of melioidosis: the role of molecular techniques

Melioidosis is an emerging infectious disease with an estimated global burden of 4.64 million disability-adjusted life years per year. A major determinant related to poor disease outcomes is delay to diagnosis due to the fact that identification of the causative agent Burkholderia pseudomallei may be challenging. Over the last 25 years, advances in molecular diagnostic techniques have resulted in the potential for rapid and accurate organism detection and identification direct from clinical samples. While these methods are not yet routine in clinical practice, laboratory diagnosis of infectious diseases is transitioning to culture-independent techniques. This review article aims to evaluate molecular methods for melioidosis diagnosis direct from clinical samples and discuss current and future utility and limitations.

Burkholderia pseudomallei Clinical Isolates Are Highly Susceptible In Vitro to Cefiderocol, a Siderophore Cephalosporin

Cefiderocol is a cephalosporin designed to treat multidrug-resistant Gram-negative infections. By forming a chelated complex with ferric iron, cefiderocol is transported into the periplasmic space via bacterial iron transport systems and primarily binds to penicillin-binding protein 3 (PBP3) to inhibit peptidoglycan synthesis. This mode of action results in cefiderocol having greater in vitro activity against many Gram-negative bacilli than currently used carbapenems, β-lactam/β-lactamase inhibitor combinations, and cephalosporins. Thus, we investigated the in vitro activity of cefiderocol against a total of 246 clinical isolates of Burkholderia pseudomallei from Queensland, Australia. The collection was composed primarily of bloodstream (56.1%), skin and soft tissue (16.3%), and respiratory (15.9%) isolates. MICs of cefiderocol ranged from ≤0.03 to 16 mg/liter, whereas the MIC90 was 0.125 mg/liter. Based upon CLSI clinical breakpoints for cefiderocol against Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia, three isolates (1.2%) would be classified as nonsusceptible (MIC > 4 mg/liter). Using EUCAST non-species-specific (pharmacokinetic/pharmacodynamic [PK/PD]) clinical breakpoints or those set for Pseudomonas aeruginosa, four isolates (1.6%) would be resistant (MIC > 2 mg/liter). Further testing for coresistance to meropenem, ceftazidime, trimethoprim-sulfamethoxazole, amoxicillin-clavulanate, and doxycycline was performed on the four isolates with elevated cefiderocol MICs (>2 mg/liter); all isolates exhibited resistance to amoxicillin-clavulanic acid, while three isolates also displayed resistance to at least one other antimicrobial. Cefiderocol was found to be highly active in vitro against B. pseudomallei primary clinical isolates. This compound shows great potential for the treatment of melioidosis in countries of endemicity and should be explored further.

Comparative Genomics and Antimicrobial Resistance Profiling of Elizabethkingia Isolates Reveal Nosocomial Transmission and In Vitro Susceptibility to Fluoroquinolones, Tetracyclines, and Trimethoprim-Sulfamethoxazole

The Elizabethkingia genus has gained global attention in recent years as containing sporadic, worldwide, nosocomial pathogens. Elizabethkingia spp. are intrinsically multidrug resistant, primarily infect immunocompromised individuals, and are associated with high mortality (∼20 to 40%). As yet, gaps remain in our understanding of transmission, global strain relatedness, antimicrobial resistance, and effective therapy. Over a 16-year period, 22 clinical and 6 hospital environmental isolates were collected from Queensland, Australia. Identification using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (Vitek MS) and whole-genome sequencing was compared with a global strain data set. Phylogenomic reconstruction robustly identified 22 Elizabethkingia anophelis, 3 Elizabethkingia miricola, 2 Elizabethkingia meningoseptica, and 1 Elizabethkingia bruuniana isolates, most of which branched as unique lineages. Global analysis revealed that some Australian E. anophelis isolates are genetically closely related to strains from the United States, England, and Asia. Comparative genomics of clinical and environmental strains identified evidence of nosocomial transmission in patients, indicating probable infection from a hospital reservoir. Furthermore, broth microdilution against 39 antimicrobials revealed almost ubiquitous resistance to aminoglycosides, carbapenems, cephalosporins, and penicillins. Like other international strains, our isolates expressed susceptibility to minocycline and levofloxacin and the less common trimethoprim-sulfamethoxazole. Our study demonstrates important new insights into the genetic diversity, environmental persistence, and transmission of and potential effective therapy for Australian Elizabethkingia species.

Whole genome sequencing for antimicrobial resistance mechanisms, virulence factors and clonality in invasive Streptococcus agalactiae blood culture isolates recovered in Australia

Invasive Streptococcus agalactiae (Group B streptococci, GBS) infections result in a large burden of disease globally. Changes in clinical and molecular epidemiology, as well as antibiotic resistance patterns, are being described globally amongst GBS isolates. Very little is known about the characteristics of invasive GBS disease in the Australian setting. Therefore, this study aimed to define the clinical and genomic characteristics of invasive GBS isolates from the Sunshine Coast region in Australia. Thirty-two isolates were identified over a 3-year period. Known risk factors for disease were present in 71.9% and the leading site of disease was the skin and soft tissue (40.6%). Sequence types (ST) 1, 17 and 23 made up 50% with ST17 making up 56.2% of the total. Serotype Ia was the most prevalent (9/32, 28.1%). Clindamycin and erythromycin resistance was seen in 12.5% and 25%, respectively. Active surveillance and local knowledge of GBS epidemiology and antibiotic resistance has both patient and public health importance. Vaccine candidates are currently in their clinical phase of development.

Evidence for Co-evolutionary History of Early Diverging Lycopodiaceae Plants With Fungi

Lycopods are tracheophytes in the Kingdom Plantae and represent one of the oldest lineages of living vascular plants. Symbiotic interactions between these plants with fungi and bacteria, including fine root endophytes in Endogonales, have been hypothesized to have helped early diverging plant lineages colonize land. However, attempts to study the lycopod rhizobiome in its natural environment are still limited. In this study, we used Illumina amplicon sequencing to characterize fungal and bacterial diversity in nine Lycopodiaceae (club moss) species collected in New Zealand. This was done with generic fungal ITS rDNA primers, as well as Endogonales- and arbuscular mycorrhizal fungi (AMF)-selective primer sets targeting the 18S rDNA, and generic bacterial primers targeting the V4 region of the 16S rDNA. We found that the Lycopodiaceae rhizobiome was comprised of an unexpected high frequency of Basidiomycota and Ascomycota coincident with a low abundance of Endogonales and Glomerales. The distribution and abundance of Endogonales varied with host lycopod, and included a novel taxon as well as a single operational taxonomic unit (OTU) that was detected across all plant species. The Lycopodiaceae species with the greatest number and also most unique OTUs was Phlegmariurus varius, while the plant species that shared the most fungal OTUs were Lycopodiella fastigiatum and Lycopodium scariosum. The bacterial OTU distribution was generally not consistent with fungal OTU distribution. For example, community dissimilarity analysis revealed strong concordance between the evolutionary histories of host plants with the fungal community but not with the bacterial community, indicating that Lycopodiaceae have evolved specific relationships with their fungal symbionts. Notably, nearly 16% of the ITS rDNA fungal diversity detected in the Lycopodiaceae rhizobiome remained poorly classified, indicating there is much plant-associated fungal diversity left to describe in New Zealand.

Novel Chlamydiales genotypes identified in ticks from Australian wildlife

Background

Members of the order Chlamydiales are known for their potential as human and veterinary bacterial pathogens. Despite this recognition, epidemiological factors such as routes of transmission are yet to be fully defined. Ticks are well known vectors for many other infections with several reports recently describing the presence of bacteria in the order Chlamydiales in these arthropods. Australian wildlife are hosts to an extensive range of tick species. Evidence is also growing that the marsupial hosts these ticks parasitise can also be infected by a number of bacteria in the order Chlamydiales, with at least one species, Chlamydia pecorum, posing a significant conservation threat. In the current study, we investigated the presence and identity of Chlamydiales in 438 ixodid ticks parasitizing wildlife in Australia by screening with a pan-Chlamydiales specific targeting the 16S rRNA gene.

Results

Pan-Chlamydiales specific PCR assays confirmed the common presence of Chlamydiales in Australian ticks parasitising a range of native wildlife. Interestingly, we did not detect any Chlamydiaceae, including C. pecorum, the ubiquitous pathogen of the koala. Instead, the Chlamydiales diversity that could be resolved indicated that Australian ticks carry at least six novel Chlamydiales genotypes. Phylogenetic analysis of the 16S rRNA sequences (663 bp) of these novel Chlamydiales suggests that three of these genotypes are associated with the Simkaniaceae and putatively belong to three distinct novel strains of Fritschea spp. and three genotypes are related to the “Ca. Rhabdochlamydiaceae” and putatively belong to a novel genus, Rhabdochlamydia species and strain, respectively.

Conclusions

Sequence results suggest Australian wildlife ticks harbour a range of unique Chlamydiales bacteria that belong to families previously identified in a range of arthropod species. The results of this work also suggest that it is unlikely that arthropods act as vectors of pathogenic members of the family Chlamydiaceae, including C. pecorum, in Australian wildlife. The biology of novel Chlamydiales identified in arthropods remain unknown. The pathogenic role of the novel Chlamydiales identified in this study and the role that ticks may play in their transmission needs to be explored further.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-017-1994-y) contains supplementary material, which is available to authorized users.

Chlamydial infections in wildlife-conservation threats and/or reservoirs of 'spill-over' infections?

Members of the order Chlamydiales are biphasic intracellular pathogens known to cause disease in both humans and animals. As we learn more about the genetic diversity of this group of pathogens, evidence is growing that these bacteria infect a broader range of animal hosts than previously thought. Over 400 host species are now documented globally with the majority of these being wild animals. Given the impact of chlamydial infections on humans and domesticated animals, the identification of members of the order Chlamydiales in wildlife raises significant questions over a) their impact on animal health and b) the relationships to those strains also found in humans and domestic animals. In some species such as the iconic marsupial, the koala, the conservation impact is known with chlamydial infections associated with debilitating disease, however, in general, little is known about the pathogenic potential of Chlamydiae infecting most wildlife hosts. Accumulating evidence suggests contact with wild animals is a risk factor for infections in domestic animals and/or humans. Beyond the well-recognised zoonotic pathogen, Chlamydia psittaci, a range of studies have now reported traditional pathogens in the family Chlamydiaceae such as Chlamydia pecorum, Chlamydia suis, Chlamydia pneumoniae and Chlamydia abortus in wild animals. The spectre of cross-host transmission 'spill-over' and 'spill-back' in the epidemiology of infections is of potential concern, however, comprehensive epidemiological studies are lacking for most of these. Accurate evaluation of the significance of chlamydial infections in wildlife is otherwise hampered by i) the cross-sectional nature of most impact studies, ii) a lack of standardised diagnostic approaches, iii) limited study sizes, and iv) biases associated with opportunistic sampling.

Chemically-mediated sexual display postures in pre-ovulatory female topmouth gudgeon, Pseudorasbora parva

While mating systems vary considerably throughout the animal kingdom, smell is increasingly recognised as a common factor in successful copulation. However, the full range of olfactory- induced mating behaviours among animals is undoubtedly underestimated in comparison to visual or contact stimuli, and this underestimation suggests that our understanding of courtship rituals may be incomplete. Here, we use the highly invasive topmouth gudgeon, Pseudorasbora parva as a biological model to separate and validate the induction of headstands as courtship behaviour in many fish species. Conspecific odour was isolated using solid phase extraction (SPE) and fractionated using high-performance liquid chromatography (HPLC). Active fractions were characterised using nuclear magnetic resonance (NMR). Electrophysiological responses of pre-ovulatory females to conspecific odour were also tested via the electro-olfactogram (EOG). Results revealed that pre-ovulatory females adopted headstand body postures during exposure to nest guarding male odour (4/12) and SPE extract (5/12) but did not display during exposure to any other odour. Fractions from HPLC yielded 1 active fraction that induced headstand body postures in pre-ovulatory females (4/12). The active fraction eluted at 30–35 min and showed no response in the UV. NMR imaging revealed low intensity levels of aliphatic protons: methylene protons (CH2) at around 2 parts per million (ppm) and methin (CH) at around 3 ppm. EOG response amplitudes were approximately double in response to pre-ovulatory female odour than to odour derived from post-ovulatory females (Mann–Whitney U-test, , ). This study provides evidence of sex-specific chemical cues and responsive, adaptive sexual behaviour in P. parva and demonstrates that female display postures may be induced by chemical stimuli alone.

Utility of the Gd scale for the measurement of Gender-Dysphoria in males

Responses on the 31-item Gender Dysphoria ( Gd) scale of the MMPI of 104 primary gender-dysphoric males who had undergone or were about to undergo gender-reassignment surgery, 25 secondary gender-dysphoric patients from the same clinics, and 563 male psychiatric outpatients were tabulated and specificities and sensitivities calculated. The scale had satisfactory specificity, correctly identifying 98.1% of subjects. Sensitivity was unsatisfactory (40%) in distinguishing secondary gender-dysphorics in the Gender Clinic samples but adequate (88.4%) in the combined psychiatric outpatient and Gender Clinic samples. Factor analysis yielded 8 dimensions, but only 2 of these were easily interpretable or had sufficient items to ensure reliability, suggesting that there was little possibility of utilizing subscales. It is concluded that the Gd scale is an appropriate instrument for excluding primary gender dysphoria when used in conjunction with conventional diagnostic assessments.