Strongyloidiasis in Auckland: A ten-year retrospective study of diagnosis, treatment and outcomes of a predominantly Polynesian and Fijian migrant cohort.

BackgroundStrongyloides stercoralis is not endemic in Aotearoa New Zealand (AoNZ). However, approximately one third of Auckland residents are born in endemic countries. This study aimed to describe the epidemiology and management of strongyloidiasis in Auckland, with a focus on migrants from Pacific Island Countries and Territories.MethodsThis study retrospectively reviewed clinical, laboratory and pharmacy records data for all people diagnosed with strongyloidiasis in the Auckland region between July 2012 and June 2022. People with negative Strongyloides serology were included to estimate seropositivity rate by country of birth.FindingsOver ten years, 691 people were diagnosed with strongyloidiasis. Most diagnoses were made by serology alone (622, 90%). The median age was 63 years (range 15-92), 500 (72%) were male, and the majority were born in Polynesia (350, 51%), Fiji (130, 19%) or were of Pasifika ethnicity (an additional 7%). Twelve participants (1.7%) had severe strongyloidiasis at diagnosis. The total proportion treated with ivermectin was only 70% (484/691), with no differences between immunocompromised and immunocompetent participants, nor by ethnicity. The outcome of treatment (based on a combination of serology and/or eosinophilia and/or stool microscopy) could only be determined in 50% of the treated cohort. One participant failed treatment with ivermectin, experiencing recurrent strongyloidiasis, and another participant died in association with severe strongyloidiasis. The rate of 'positive' Strongyloides serology was highest among participants born in Samoa (48%), Fiji (39%), and Southeast Asian countries (34%).InterpretationStrongyloidiasis was common and under-treated in Auckland during the study period. Clinicians should have a low threshold for considering strongyloidiasis in migrants from endemic countries, including Polynesia and Fiji

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Hospital-Onset MRSA Bacteremia Rates Are Significantly Correlated With Sociodemographic Factors: A Step Toward Risk Adjustment

The correlations between census-derived sociodemographic variables and hospital-onset methicillin-resistant Staphylococcus aureus bacteremia (HO-MRSAB) rates were examined at the US state level. On multivariable analysis, only percent African American remained statistically significant. This finding highlights an important disparity and suggests that risk adjustment is needed when comparing HO-MRSAB rates among US states.Infect Control Hosp Epidemiol 2018;39:479–481</jats:p

Diagnostic Performance of Pleural Fluid Adenosine Deaminase for Tuberculous Pleural Effusion in a Low-Incidence Setting

The challenges associated with diagnosing tuberculous pleural effusion have led to the use of pleural fluid adenosine deaminase (pfADA) as a biomarker for Mycobacterium tuberculosis infection. This study retrospectively reviewed the diagnostic performance of pfADA, the pleural fluid lactate dehydrogenase (LD)/ADA ratio, and combinations of these two parameters in 1,637 episodes of pleural effusion in the low-tuberculosis (TB)-incidence setting of Auckland, Aotearoa New Zealand, from between March 2008 and November 2014. </jats:p

The clear and present danger of carbapenemase-producing Enterobacteriaceae (CPE) in New Zealand: time for a national response plan

Antimicrobial resistance (AMR) in general poses a threat to the sustainability of modern healthcare, but a particularly urgent and serious threat is posed by a specific group of antibiotic-resistant bacteria known as carbapenemase-producing Enterobacteriaceae (CPE). CPE are resistant to nearly all antibiotics and include common pathogens such as Escherichia coli and Klebsiella pneumoniae. In New Zealand, the incidence of CPE has increased from three isolates in 2012 to 45 in 2016. The current epidemiology of CPE in New Zealand has similarities with the extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) epidemic in the early 2000s (just before ESBL-PE underwent a non-linear increase in incidence). Although to date in New Zealand, nearly all CPE have been imported from overseas, this situation appears to be changing, with evidence of secondary spread in both households and healthcare facilities over the last year. In this article, we argue that CPE should be regarded as the foremost AMR threat currently facing New Zealand, and highlight the need for a comprehensive national response plan, analogous to plans for other emerging transmissible infections, such as pandemic influenza and Ebola. We also make recommendations about the components of such a plan and advocate that CPE should be recognised as a key priority in New Zealand's national AMR strategy, due to be published in May 2017

Epidemiology of carbapenem resistant Acinetobacter baumannii in New Zealand

AIM: Carbapenem resistant Acinetobacter baumannii have limited treatment options and a propensity to cause hospital outbreaks. In recent years an increase in their detection has been observed in New Zealand. This study aimed to describe the molecular epidemiology of these isolates. METHOD: This study utilised carbapenem resistant A. baumannii complex isolates identified across New Zealand between January 2010 to April 2018. Whole genome sequence analysis and associated demographic information was used to contextualise local isolates within the global epidemiology and establish the relationship between isolates. RESULTS: Thirty-three carbapenem resistant A. baumannii complex isolates (31 A. baumannii sensu stricto) were identified. Twenty-four (73%) were from January 2015 onwards. Twenty-four (73%) had an identifiable epidemiological link to overseas hospitalisation. Twenty-three (74%) of 31 A. baumannii sensu stricto were sequence type (ST) 2 (Pasteur scheme). Phylogenetic analysis identified three ST2 clusters. The largest cluster, of 12 isolates, was from 2015 onwards; with nine (75%) associated with recent hospitalisation in Fiji or Samoa. CONCLUSION: Increasing numbers of carbapenem resistant A. baumannii are being identified in New Zealand. Our data show that this is in large part associated with transnational spread of a single A. baumannii sensu stricto ST 2 strain between Fiji, Samoa and New Zealand.</p

Household transmission of NDM-producing E. coli in New Zealand

This report describes the introduction of an extensively antibiotic-resistant carbapenemase-producing Escherichia coli into a hospital in Auckland, New Zealand, by a patient who was a household contact of recent travellers to the Indian subcontinent. The carbapenemase was identified as New Delhi metallo beta-lactamase (NDM) and reflects probable household transmission in the context of a recent upsurge in NDM-producing Enterobacteriaceae isolation in New Zealand. The observations in this report suggest that hospital screening practices to identify carbapenemase-producing Enterobacteriaceae (CPE) colonised patients may need to be extended to include travellers to high-risk countries who were not hospitalised during their trip, and possibly also their close contacts