One Health Determinants of Escherichia coli Antimicrobial Resistance in Humans in the Community: An Umbrella Review

To date, the scientific literature on health variables for Escherichia coli antimicrobial resistance (AMR) has been investigated throughout several systematic reviews, often with a focus on only one aspect of the One Health variables: human, animal, or environment. The aim of this umbrella review is to conduct a systematic synthesis of existing evidence on Escherichia coli AMR in humans in the community from a One Health perspective. PubMed, EMBASE, and CINAHL were searched on "antibiotic resistance" and "systematic review" from inception until 25 March 2022 (PROSPERO: CRD42022316431). The methodological quality was assessed, and the importance of identified variables was tabulated across all included reviews. Twenty-three reviews were included in this study, covering 860 primary studies. All reviews were of (critically) low quality. Most reviews focused on humans (20), 3 on animals, and 1 on both human and environmental variables. Antibiotic use, urinary tract infections, diabetes, and international travel were identified as the most important human variables. Poultry farms and swimming in freshwater were identified as potential sources for AMR transmission from the animal and environmental perspectives. This umbrella review highlights a gap in high-quality literature investigating the time between variable exposure, AMR testing, and animal and environmental AMR variables.

Time-to-positivity in bloodstream infection for Candida species as a prognostic marker for mortality

Time-to-positivity (TTP) may assist in predicting outcome of candidaemia. We analysed a candidaemia dataset collected prospectively in Australia over 1 year (2014-2015). Time to positivity was defined as the period from blood culture sampling to the blood culture flagging positive. Of 415 candidaemia episodes, overall 30-day mortality was 29% (120/415); mortality with Candida albicans was 35% (59/169), C. glabrata complex, 37% (43/115), C. tropicalis, 43% (10/23), Pichia kudriavzevii 25% (3/12) and C. parapsilosis complex 7% (5/71). Each day of increased TTP multiplied the odds ratio (OR) of survival at 30 days by a factor of 1.32 (95%CI 1.06-1.69). Shorter TTP was associated with increased mortality, with 1 day TTP associated with 30-day mortality 37% (41/112) (95%CI: 28%-46%) and 5-day TTP 11% (2/18) (95%CI: 2%-36%).

What's New in Cryptococcus gattii: From Bench to Bedside and Beyond

Cryptococcus species are a major cause of life-threatening infections in immunocompromised and immunocompetent hosts. While most disease is caused by Cryptococcus neoformans, Cryptococcus gattii, a genotypically and phenotypically distinct species, is responsible for 11-33% of global cases of cryptococcosis. Despite best treatment, C. gattii infections are associated with early mortality rates of 10-25%. The World Health Organization's recently released Fungal Priority Pathogen List classified C. gattii as a medium-priority pathogen due to the lack of effective therapies and robust clinical and epidemiological data. This narrative review summarizes the latest research on the taxonomy, epidemiology, pathogenesis, laboratory testing, and management of C. gattii infections.

Whole Genome Sequencing Shows Genetic Diversity, as Well as Clonal Complex and Gene Polymorphisms Associated with Fluconazole Non-Susceptible Isolates of Candida tropicalis

Resistance to azoles in Candida tropicalis is increasing and may be mediated by genetic characteristics. Using whole genome sequencing (WGS), we examined the genetic diversity of 82 bloodstream C. tropicalis isolates from two countries and one ATCC strain in a global context. Multilocus sequence typing (MLST) and single nucleotide polymorphism (SNP)-based phylogenies were generated. Minimum inhibitory concentrations (MIC) for antifungal agents were determined using Sensititre YeastOne YO10. Eleven (13.2%) isolates were fluconazole-resistant and 17 (20.5%) were classified as fluconazole-non susceptible (FNS). Together with four Canadian isolates, the genomes of 12 fluconazole-resistant (18 FNS) and 69 fluconazole-susceptible strains were examined for gene mutations associated with drug resistance. Fluconazole-resistant isolates contained a mean of 56 non-synonymous SNPs per isolate in contrast to 36 SNPs in fluconazole-susceptible isolates (interquartile range [IQR] 46−59 vs. 31−48 respectively; p < 0.001). Ten of 18 FNS isolates contained missense ERG11 mutations (amino acid substitutions S154F, Y132F, Y257H). Two echinocandin-non susceptible isolates had homozygous FKS1 mutations (S30P). MLST identified high genetic diversity with 61 diploid sequence types (DSTs), including 53 new DSTs. All four isolates in DST 773 were fluconazole-resistant within clonal complex 2. WGS showed high genetic variation in invasive C. tropicalis; azole resistance was distributed across different lineages but with DST 773 associated with in vitro fluconazole resistance.

Candida auris: Diagnostic Challenges and Emerging Opportunities for the Clinical Microbiology Laboratory

Purpose of Review

This review summarises the epidemiology of Candida auris infection and describes contemporary and emerging diagnostic methods for detection and identification of C. auris.

Recent Findings

A fifth C. auris clade has been described. Diagnostic accuracy has improved with development of selective/differential media for C. auris. Advances in spectral databases of matrix-associated laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) systems have reduced misidentification. Direct detection of C. auris in clinical specimens using real time PCR is increasingly used, as is whole genome sequencing (WGS) to track nosocomial spread and to study phylogenetic relationships and drug resistance.

Summary

C. auris is an important transmissible, nosocomial pathogen. The microbiological laboratory diagnostic capacity has extended beyond culture-based methods to include PCR and WGS. Microbiological techniques on the horizon include the use of MALDI-TOF MS for early echinocandin antifungal susceptibility testing (AST) and expansion of the versatile and information-rich WGS methods for outbreak investigation.

Preventing Early-Onset Group B Streptococcus neonatal infection and reducing antibiotic exposure using a rapid PCR test in term prelabour rupture of membranes

BACKGROUND

How best to target intrapartum antibiotic prophylaxis (IAP) to minimise both Early-Onset Group B Streptococcus (EOGBS) neonatal infection and maternal/fetal antibiotic exposure is uncertain, with both routine-screening and risk-factor approaches available.

AIMS

This retrospective cohort study was undertaken to examine the outcomes of a hybrid risk-and-screen approach to EOGBS prevention using GBS polymerase chain reaction (PCR). The target population was women with term prelabour rupture of membranes (TermPROM) having the risk factor of prolonged rupture of membranes (ROM) ≥18 h.

MATERIALS AND METHODS

Non-labouring TermPROM women had rapid GBS PCR testing at presentation. GBS screen-positive women proceeded to induction of labour and received IAP. GBS screen-negative women were allowed home to await spontaneous labour and not given IAP regardless of duration of ROM, unless other risk factors developed. For all other women, the risk-factor approach was followed.

RESULTS

From 2009 to 2018, there were 20 cases of culture-positive EOGBS, a rate of 0.36/1000 live births (95% CI 0.22-0.56/1000), comparable to other recent reports. Over 2010-2018 when laboratory data were available, 1120 TermPROM women with ROM ≥18 h avoided antibiotics because they were GBS PCR-negative (2.3% of all births, 3.6% of vaginal births) while 338 TermPROM women with ROM <18 h received targeted antibiotics for being GBS-positive. No cases of EOGBS occurred in TermPROM women, those with ROM ≥18 h, or due to protocol-compliance failure.

CONCLUSIONS

A hybrid approach involving risk-factor-based IAP and intrapartum GBS PCR screening of non-labouring TermPROM women delivers acceptably low rates of EOGBS while minimising and better targeting antibiotic exposure.

Out Of Hospital And In Hospital Management Of Cellulitis Requiring Intravenous Therapy

Background

Cellulitis requiring intravenous therapy can be managed via out of hospital programs, but a high number of patients are still admitted to hospital.

Objective

We aimed to review the clinical features, management and outcomes of patients with cellulitis requiring intravenous therapy in a Hospital in the Home (HITH) program compared to patients who are admitted to hospital.

Methods

A prospective cohort study of patients with limb cellulitis requiring intravenous antibiotics was conducted at a metropolitan principal referral hospital.

Results

A total of 100 patients out of 113 eligible patients were recruited. Forty-eight were treated entirely in hospital and 52 were treated entirely or partially via HITH. Patients treated in hospital were older (mean 69.2 vs 56.7 years, p<0.001), less mobile, have more comorbidities (Charlson Comorbidity Index mean 2.2 vs 1.2, P=0.005) and more associated active illness. All patients with Eron Class III were admitted to hospital. Patients treated in hospital had a higher incidence of acute renal failure (27.1% vs 3.8%, p=0.001), nosocomial infection (10.4% vs 0.0%, P=0.023), and a higher 28-day hospital readmission rate (10.4% vs 0.0%, P=0.023).

Conclusion

Approximately half of the patients who require intravenous therapy can be treated via an out of hospital program. Patients admitted to hospital were more unwell and more likely to suffer complications. The presence of comorbid illness does not necessarily exclude participation in HITH and careful selection is essential to ensure safe outcomes.

Cellulitis in older people over 75 years - are there differences?

Aim

To examine differences in risk factors, clinical features and outcomes of cellulitis between those 75 + years and those <75 years admitted to a metropolitan hospital.

Methods

A prospective study of patients with limb cellulitis requiring intravenous antibiotics conducted at Bankstown-Lidcombe Hospital, Australia from June 2014 to April 2015.

Results

Thirty one patients were 75 + years and 69 less than 75 years. A greater proportion of older patients resided in nursing home (25.8% vs 2.9% respectively, p = 0.001) and mobilized with walking aid(s) (58.1% vs 11.6% respectively, p < 0.001). Significantly more older patients had documented hypertension (45.2% vs 23.2% respectively p = 0.035), atrial fibrillation (33.5% vs 5.8% respectively, p < 0.001), dementia (22.6% vs 1.4% respectively, p = 0.001) and malignancy (16.1% vs 1.4% respectively, p = 0.010). The clinical presentation of cellulitis and cellulitis severity (Eron classification) did not significantly differ in both groups; however older patients were more likely to have dependent edema (OR 4.0, 95%CI 1.3-12.6, p = 0.018) and less likely to be obese (OR 0.3, 95%CI 0.1-0.8, p = 0.012) or had a past history of cellulitis (OR 0.3, 95%CI 0.1-1.0, p = 0.044) on presentation. Despite the age difference, there were no major differences in intravenous antibiotic choice, hospital length of stay, and hospital readmission rates in both groups. Older patients however, were more likely to experience complications such as falls and/or decreased mobility (38.7% vs 15.9% respectively, p = 0.020) during the cellulitis episode.

Conclusion

There are minor differences in the risk factors and clinical features of cellulitis in older patients as compared to the young. Outcomes are similar except for a higher incidence of hospital related complications.

Candidaemia and a risk predictive model for overall mortality: a prospective multicentre study

Background

Candidaemia is associated with high mortality. Variables associated with mortality have been published previously, but not developed into a risk predictive model for mortality. We sought to describe the current epidemiology of candidaemia in Australia, analyse predictors of 30-day all-cause mortality, and develop and validate a mortality risk predictive model.

Methods

Adults with candidaemia were studied prospectively over 12 months at eight institutions. Clinical and laboratory variables at time of blood culture-positivity were subject to multivariate analysis for association with 30-day all-cause mortality. A predictive score for mortality was examined by area under receiver operator characteristic curves and a historical data set was used for validation.

Results

The median age of 133 patients with candidaemia was 62 years; 76 (57%) were male and 57 (43%) were female. Co-morbidities included underlying haematologic malignancy (n = 20; 15%), and solid organ malignancy in (n = 25; 19%); 55 (41%) were in an intensive care unit (ICU). Non-albicans Candida spp. accounted for 61% of cases (81/133). All-cause 30-day mortality was 31%. A gastrointestinal or unknown source was associated with higher overall mortality than an intravascular or urologic source (p < 0.01). A risk predictive score based on age > 65 years, ICU admission, chronic organ dysfunction, preceding surgery within 30 days, haematological malignancy, source of candidaemia and antibiotic therapy for ≥10 days stratified patients into < 20% or ≥ 20% predicted mortality. The model retained accuracy when validated against a historical dataset (n = 741).

Conclusions

Mortality in patients with candidaemia remains high. A simple mortality risk predictive score stratifying patients with candidaemia into < 20% and ≥ 20% 30-day mortality is presented. This model uses information available at time of candidaemia diagnosis is easy to incorporate into decision support systems. Further validation of this model is warranted.

Electronic supplementary material

The online version of this article (10.1186/s12879-019-4065-5) contains supplementary material, which is available to authorized users.

Anncaliia algerae Microsporidial Myositis, New South Wales, Australia

We describe the successful management of Anncaliia algerae microsporidial myositis in a man with graft versus host disease after hemopoietic stem cell transplantation. We also summarize clinical presentation and management approaches and discuss the importance of research into the acquisition of this infection and strategies for prevention.

Contemporary management and clinical outcomes of mucormycosis: A systematic review and meta-analysis of case reports

With the advent of newer antifungals, optimum treatment of mucormycosis remains to be fully elucidated. This study systematically evaluated the contemporary management and outcomes of mucormycosis. Mucormycosis cases in patients aged ≥18 years published between January 2000 and January 2017 were identified through Ovid MEDLINE and Embase. Of the 3619 articles identified, 600 (851 individual patient cases) were included in the review. Of the 851 patient cases, antifungal treatment details were available for 785. Intravenous (i.v.) amphotericin B formulations remained the most commonly prescribed first-line antifungals (760/785; 96.8%): 88.2% (670/760) were initiated as monotherapy and 11.8% (90/760) as combination antifungal therapy. Posaconazole oral suspension monotherapy was prescribed as an initial antifungal in 11 cases. It was also administered as maintenance or salvage therapy in 39 and 25 cases, respectively. Itraconazole capsule monotherapy (n = 10) was prescribed primarily for cutaneous disease in patients not receiving any immunosuppressive therapy. All-cause 90-day mortality was 41.0% (349/851). Initial treatment with combination antifungals did not reduce 90-day mortality compared with i.v. conventional amphotericin B or i.v. liposomal amphotericin B monotherapy [35/90 (38.9%) vs. 146/369 (39.6%) vs. 91/258 (35.3%), respectively; P = 0.541]. Concomitant surgical and antifungal therapy was associated with significantly lower 90-day mortality compared with treatment with antifungals alone (OR = 0.23, 95% CI 0.13-0.41; P < 0.001). The findings suggest that first-line antifungals with good efficacy remain an urgent unmet need. Whilst surgery is fundamental to improving survival, the clinical utility of combination antifungal therapy or posaconazole monotherapy requires further investigation.

A series of three cases of severe Clostridium difficile infection in Australia associated with a binary toxin producing clade 2 ribotype 251 strain

Three patients with severe Clostridium difficile infection (CDI) caused by an unusual strain of C. difficile, PCR ribotype (RT) 251, were identified in New South Wales, Australia. All cases presented with severe diarrhoea, two had multiple recurrences and one died following a colectomy. C. difficile RT251 strains were isolated by toxigenic culture. Genetic characterisation was performed using techniques including toxin gene profiling, PCR ribotyping, whole genome sequencing (WGS), in-silico multi-locus-sequence-typing (MLST) and core-genome single nucleotide variant (SNV) analyses. Antimicrobial susceptibility was determined using an agar incorporation method. In vitro toxin production was confirmed by Vero cell cytotoxicity assay and pathogenicity was assessed in a murine model of CDI. All RT251 isolates contained toxin A (tcdA), toxin B (tcdB) and binary toxin (cdtA and cdtB) genes. Core-genome analyses revealed the RT251 strains were clonal, with 0-5 SNVs between isolates. WGS and MLST clustered RT251 in the same evolutionary clade (clade 2) as RT027. Despite comparatively lower levels of in vitro toxin production, in the murine model RT251 infection resembled RT027 infection. Mice showed marked weight loss, severe disease within 48 h post-infection and death. All isolates were susceptible to metronidazole and vancomycin. Our observations suggest C. difficile RT251 causes severe disease and emphasise the importance of ongoing surveillance for new and emerging strains of C. difficile with enhanced virulence.

Changing epidemiology of candidaemia in Australia

Objectives

Knowledge of contemporary epidemiology of candidaemia is essential. We aimed to identify changes since 2004 in incidence, species epidemiology and antifungal susceptibilities of Candida spp. causing candidaemia in Australia.

Methods

These data were collected from nationwide active laboratory-based surveillance for candidaemia over 1 year (within 2014-2015). Isolate identification was by MALDI-TOF MS supplemented by DNA sequencing. Antifungal susceptibility testing was performed using Sensititre YeastOne™.

Results

A total of 527 candidaemia episodes (yielding 548 isolates) were evaluable. The mean annual incidence was 2.41/105 population. The median patient age was 63 years (56% of cases occurred in males). Of 498 isolates with confirmed species identity, Candida albicans was the most common (44.4%) followed by Candida glabrata complex (26.7%) and Candida parapsilosis complex (16.5%). Uncommon Candida species comprised 25 (5%) isolates. Overall, C. albicans (>99%) and C. parapsilosis (98.8%) were fluconazole susceptible. However, 16.7% (4 of 24) of Candida tropicalis were fluconazole- and voriconazole-resistant and were non-WT to posaconazole. Of C. glabrata isolates, 6.8% were resistant/non-WT to azoles; only one isolate was classed as resistant to caspofungin (MIC of 0.5 mg/L) by CLSI criteria, but was micafungin and anidulafungin susceptible. There was no azole/echinocandin co-resistance.

Conclusions

We report an almost 1.7-fold proportional increase in C. glabrata candidaemia (26.7% versus 16% in 2004) in Australia. Antifungal resistance was generally uncommon, but azole resistance (16.7% of isolates) amongst C. tropicalis may be emerging.

Implant salvage in breast reconstruction with severe peri-prosthetic infection

BACKGROUND

Although treatment of mild peri-prosthetic infection in implant-based breast reconstruction results in high rates of resolution, successful management of severe peri-prosthetic infection remains a significant challenge.

METHODS

In this case series, a protocol utilizing a novel dressing - negative pressure wound therapy with instillation (NPWTi) - for the management of severe peri-prosthetic infection in breast reconstruction patients is described. This is an operative technique involving: (i) explantation of the breast prosthesis and application of the NPWTi dressing to the implant pocket; (ii) change of the NPWTi dressing; (iii) intraoperative fluid/tissue cultures; and (iv) reimplantation of the breast prosthesis when cultures yield no growth.

RESULTS

This protocol was utilized in six cases of severe peri-prosthetic infection in five patients with immediate breast reconstruction for breast cancer or risk-reducing surgery. Cultures of fluid/tissue grew typical and/or unusual organisms. Only one case did not yield an organism. The hospital length of stay upon completion of the protocol ranged from 7-16 days (mean, 12 days). Successful implant salvage was achieved in five of six cases. The protocol was aborted in one case to allow for completion of adjuvant chemotherapy.

CONCLUSIONS

Early findings from this case series suggest that in cases of severe peri-prosthetic infection this novel operative protocol may result in successful implant salvage for breast reconstruction patients. Further studies are needed to more fully elaborate the role of NPWTi to achieve implant salvage in challenging cases of peri-prosthetic infection.

Uncommon manifestations of Listeria monocytogenes infection

BACKGROUND

Listeria monocytogenes causes gastroenteritis, meningitis and bacteraemia in immunocompromised, pregnant patients, the elderly as well in immunocompetent patients. Focal infections with this organism are uncommon, especially in sporadic (non-outbreak) setting, require high index of suspicion and are challenging to diagnose. We present 3 cases of Listeria monocytogenes presenting as focal infections to our hospitals, all of which are the first reported cases from Australia.

CASE PRESENTATION

Three unrelated cases of unique focal infections caused by Listeria monocytogenes are presented. 1) A 73 year old Caucasian lady on immunosuppression for colorectal cancer presented with prosthetic knee joint septic arthritis, 2) An 83 year old Caucasian man presented with prosthetic vascular graft infection and 3) A 60 year old Asian man with perianal abscess. Except for case 1, the other cases had a prolonged duration of symptoms on presentation. Listeria was not thought to be causative organism in any of these cases until microbiological specimens isolated the organism. Matrix Associated Laser Desorption/Ionization-Time of Flight Mass Spectrometry (MALDI-TOF MS) assisted in making an earlier diagnosis of the infection in all three cases. All of these patients had Listeria monocytogenes isolated from clinical specimens. They were managed with antibiotics and surgery with favourable outcomes. Public health investigations to determine any dietary association were done, however no intervention was thought to be necessary in any of the cases except provide dietary advice. The first two cases highlight the importance of microbiological sampling in serious infections for definitive antibiotic therapy to be administered.

CONCLUSION

Sporadic focal infections with Listeria occur infrequently and are often not diagnosed till culture results from microbiological specimens become available. Dietary history should be an important aspect of thorough clinical history and food consumption advice is crucial in immunocompromised patients on similar lines as given to pregnant women about listeriosis.

Dendritic cell biology during malaria

Malaria is an infectious disease that causes serious morbidity and mortality worldwide. The disease is associated with a variety of clinical syndromes ranging from asymptomatic to lethal infections involving anaemia, organ failure, pulmonary and cerebral disease. The molecular and cellular factors responsible for the differences in disease severity are poorly understood but parasite-specific immune responses are thought to play a critical role in pathogenesis. Dendritic cells have an essential role in linking innate and adaptive immune responses and here we review their role in the context of malaria.

Efficacy and safety of direct stenting in coronary angioplasty

BACKGROUND

Direct stenting is the deployment of an intracoronary stent without lesion predilation. Potential advantages include shorter procedural time, lower contrast dose and reduced spiral dissections. There is also the potential financial benefit of less balloon and/or stent usage. Concern still exists among some operators, however, regarding failure of stent deployment and local complications.

METHODS

Of 467 consecutive angioplasty cases at the Alfred Hospital between August 1, 1997 and May 22, 1998, direct stenting was attempted in 93 patients (20%). Interventionalist preference determined whether direct stenting was attempted. Vessels with excessive calcification, severe proximal tortuosity or small caliber were typically considered unsuitable for direct stenting.

RESULTS

A total of 102 lesions (38 type A, 60 type B, and 4 type C) were treated with direct stenting. Initial deployment was successful in 98 of 102 lesions, with a further 3 lesions successfully stented following predilation. A stent was unable to be deployed in only 1 case; however, the lesion was treated with balloon angioplasty alone. The majority of lesions required only 1 stent (an average of 1.1 stents were used per lesion). Distal complications occurred in 5 patients. In 3 patients, a small distal dissection was successfully stented, and in 1 case embolization of debris occurred down the distal vessel, resulting in a small procedural myocardial infarction. Only 1 patient out of 93 (1%) developed a large distal dissection requiring the deployment of multiple stents, compared with 22 of the remaining 374 patients (5.9%) who underwent conventional angioplasty. This was a significant difference in favor of direct stenting (Chi-square, p < 0.05). When compared with a cohort of patients matched by lesion grade treated with conventional stenting, direct stenting used significantly less contrast per case (154 +/- 7.6 ml compared with 202 +/- 9.5 ml for conventional stenting; p = 0.0001).

CONCLUSION

Direct stenting is a safe and effective method for treating coronary artery disease. In appropriately selected cases, it has a low rate of procedural failure and results in less contrast usage and fewer distal complications than conventional angioplasty and stenting.

Efficacy of a low dose of cefotaxime in serious chest infections

The optimal antibiotic dosage in serious chest infections is not established and commonly used regimens may well be excessive. We have compared the efficacy of a low dose of cefotaxime (2 g every 12 h) with a more usual dose (2 g every 8 h) in a prospective, randomized study of the treatment of chest infections in the seriously ill. Fifty intensive care unit patients received either regimen for five days. The two groups appeared demographically comparable. Clinical resolution occurred in 86 percent, no change occurred in 4 percent, and deterioration occurred in 10 percent. Microbiologic clearance occurred in 52 percent of those in whom a pathogen was isolated (46 percent of patients). There was no significant difference in clinical or microbiologic response between the two regimens. It is concluded that cefotaxime in a dose of 2 g twice daily is effective in the treatment of serious chest infections.

Uncertain relevance of gastric colonization in the seriously ill

We have studied the temporal relationship for the same micro-organisms between gastric colonization and both nasopharyngeal colonization and major clinical infections in 100 consecutive, long-stay, intensive care patients. 67% of patients developed positive gastric cultures, mainly with aerobic Gram-negative bacilli and C. albicans; 33% developed positive nasopharyngeal cultures with similar organisms, but in only 8% was the same organism previously cultured from the stomach; 48% of patients developed infections, mainly respiratory, but commonly with different organisms. The presence of a positive gastric culture was not associated with gastric pH, bleeding, severity of illness, or mortality. The results fail to confirm that an ascending migration of organisms from the stomach is.frequent or that there is a relationship between gastric colonization and clinical infections. Firm therapeutic recommendation in these areas may be premature.