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"Smith, Anthony M."
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An Integrated Approach Is Needed for Ecosystem Based Fisheries Management: Insights from Ecosystem-Level Management Strategy Evaluation
An ecosystem approach is widely seen as a desirable goal for fisheries management but there is little consensus on what strategies or measures are needed to achieve it. Management strategy evaluation (MSE) is a tool that has been widely used to develop and test single species fisheries management strategies and is now being extended to support ecosystem based fisheries management (EBFM). We describe the application of MSE to investigate alternative strategies for achieving EBFM goals for a complex multispecies fishery in southeastern Australia. The study was undertaken as part of a stakeholder driven process to review and improve the ecological, economic and social performance of the fishery. An integrated management strategy, involving combinations of measures including quotas, gear controls and spatial management, performed best against a wide range of objectives and this strategy was subsequently adopted in the fishery, leading to marked improvements in performance. Although particular to one fishery, the conclusion that an integrated package of measures outperforms single focus measures we argue is likely to apply widely in fisheries that aim to achieve EBFM goals.
Journal Article
Impacts of Fishing Low–Trophic Level Species on Marine Ecosystems
Low—trophic level species account for more than 30% of global fisheries production and contribute substantially to global food security. We used a range of ecosystem models to explore the effects of fishing low—trophic level species on marine ecosystems, including marine mammals and seabirds, and on other commercially important species. In five well-studied ecosystems, we found that fishing these species at conventional maximum sustainable yield (MSY) levels can have large impacts on other parts of the ecosystem, particularly when they constitute a high proportion of the biomass in the ecosystem or are highly connected in the food web. Halving exploitation rates would result in much lower impacts on marine ecosystems while still achieving 80% of MSY.
Journal Article
Associations Between Early First Sexual Intercourse and Later Sexual and Reproductive Outcomes: A Systematic Review of Population-Based Data
The assumption that early sexual debut leads to adverse outcomes has been used as justification for sexual health interventions and policies aimed at delaying sexual initiation, yet research in the area has been limited. This review identified and synthesized published literature on the association between early first sexual intercourse and later sexual/reproductive outcomes. Literature searches were conducted in Medline, Embase, PsycINFO, and Current Contents. In all, 65 citations met the selection criteria (industrialized, population-based studies). By far the most common sexual behavior to have been investigated has been sexual partners. Studies consistently reported early first intercourse to be associated with more recent, lifetime, and concurrent sexual partners. Early initiators were also more likely to participate in a wider range of sexual practices and report increased sexual satisfaction (among men). Furthermore, early first intercourse, in some studies, was shown to increase the risk of teen pregnancies, teen births, and having an abortion, while findings on STIs and contraceptive use have been mixed. These findings, however, must be interpreted with caution due to methodological problems and limitations present in the research, including a lack of consensus on what constitutes early sexual intercourse and inconsistencies and problems with analyses.
Journal Article
A One Health perspective on Salmonella enterica Serovar Infantis, an emerging human multidrug-resistant pathogen
Salmonella enterica serovar Infantis presents an ever increasing threat to public health because of its spread throughout many countries and association with high levels of antimicrobial resistance (AMR). We analyzed whole genome sequences of 5,284 Salmonella Infantis strains from 74 countries, isolated during 1989–2020 from a wide variety of human, animal, and food sources, to compare genetic phylogeny, AMR determinants, and plasmid presence. The global Salmonella Infantis population structure diverged into 3 clusters: a North American cluster, a European cluster, and a global cluster. The levels of AMR varied by Salmonella Infantis cluster and by isolation source; 73% of poultry isolates were multidrug resistant, compared with 35% of human isolates. This finding correlated with the presence of the pESI megaplasmid; 71% of poultry isolates contained pESI, compared with 32% of human isolates. This study provides key information for public health teams engaged in reducing the spread of this pathogen.
Journal Article
Characterization of Salmonella enterica serovar Isangi from South Africa, 2020–2021
Background
We describe the genotypic characteristics and antimicrobial resistance (AMR) determinants of
Salmonella enterica
serovar Isangi (
Salmonella
Isangi) clinical isolates in South Africa from 2020 through 2021.
Methods
During the years 2020 to 2021, the Centre for Enteric Diseases of the National Institute for Communicable Diseases, a national reference centre in South Africa for human infections resulting from enteric bacterial pathogens, investigated a total of 3549 clinical isolates of
Salmonella
species. Whole genome sequencing (WGS) was performed using Illumina NextSeq Technology. WGS data was analyzed using Centre for Genomic Epidemiology-based tools and EnteroBase web-based platform. Genotypic relatedness and cluster analysis was investigated based on core-genome multilocus sequence typing.
Results
Forty-nine isolates were confirmed to be
Salmonella
Isangi, with most submitted from Gauteng Province (24/49, 49%). The most prevalent sequence type was ST335 (48/49, 98%), and the remaining 1 isolate was ST216. All ST335 isolates were genotypically multidrug-resistant (MDR), with resistance to fluoroquinolones, chloramphenicol, trimethoprim-sulfamethoxazole and tetracycline; the ST216 isolate was resistant only to aminoglycosides. All ST335 isolates carried ESBL genes, the most common being
bla
CTX-M-15
. Five clusters (consisting of isolates related within five allele differences) were detected, all being ST335.
Conclusions
Most
Salmonella
Isangi isolates in South Africa are MDR and ESBL-positive. Ongoing monitoring of the epidemiology and AMR profile of this serovar is important for public health and treatment guidelines.
Journal Article
Imported Cholera Cases, South Africa, 2023
Since February 2022, Malawi has experienced a cholera outbreak of >54,000 cases. We investigated 6 cases in South Africa and found that isolates linked to the outbreak were Vibrio cholerae O1 serotype Ogawa from seventh pandemic El Tor sublineage AFR15, indicating a new introduction of cholera into Africa from south Asia.
Journal Article
Population structure and phylogenetic analysis of Vibrio cholerae non-O1/O139 by whole genome sequencing
Toxigenic Vibrio cholerae serogroups O1 and O139 are well known for causing excessive diarrhea leading to devastating cholera epidemics and pandemics. Over 200 other serogroups, usually lacking the cholera toxin, are denoted non-O1/O139 V. cholerae (NOVC), and cause vibriosis leading to sporadic gastroenteritis and other extraintestinal infections. NOVC infections are not a notifiable disease in Canada and thus underreported. From 2010 to 2023, 160 cases and a small 2018 outbreak were reported in Canada caused by NOVC, provoking considerable public health concern. In this study, 242 Canadian V. cholerae isolates were sequenced, characterized and compared with over 1500 other V. cholerae isolates from around the world to determine their genetic relationships. All Canadian NOVC and two O139 isolates lacked the cholera toxin-producing genes typically harbored by pathogenic O1 and O139. All 14 Canadian O1 isolates were identified from travel-related cases as members of the toxigenic 7 th pandemic lineage, whereas one O139 isolate was acquired domestically. Phylogenetic analysis based on core genome single nucleotide polymorphisms classified the Canadian isolates into five clades. Eight new lineages of NOVC, denoted CAD1–8, were identified from the Canadian isolates. A new lineage was defined as clusters formed by three or more isolates in the phylogeny. These lineages were comprised of isolates from clinical origin alone, environmental origin, or a mixture of both. Some lineages spanned multiple years and regions. CAD-2 was comprised of clinical and environmental isolates associated with the 2018 outbreak. Several virulence genes were detected among NOVC, including hemolysins, toxins and secretion system encoding genes. A proportion of virulence genes differed between isolation source (clinical or environmental) and clinical manifestations (gastrointestinal or extraintestinal). Our study identified environmental sources of NOVC with the potential to cause human infection. Tracking the emergence of NOVC with pathogenic potential is essential for understanding the risk to Canadians.
Journal Article
Metagenomics analysis of sewage for surveillance of antimicrobial resistance in South Africa
Our 24-month study used metagenomics to investigate antimicrobial resistance (AMR) abundance in raw sewage from wastewater treatment works (WWTWs) in two municipalities in Gauteng Province, South Africa. At the AMR class level, data showed similar trends at all WWTWs, showing that aminoglycoside, beta-lactam, sulfonamide and tetracycline resistance was most abundant. AMR abundance differences were shown between municipalities, where Tshwane Metropolitan Municipality (TMM) WWTWs showed overall higher abundance of AMR compared to Ekurhuleni Metropolitan Municipality (EMM) WWTWs. Also, within each municipality, there were differing trends in AMR abundance. Notably, within TMM, certain AMR classes (macrolides and macrolides_streptogramin B) were in higher abundance at a WWTW serving an urban high-income area, while other AMR classes (aminoglycosides) were in higher abundance at a WWTW serving a semi-urban low income area. At the AMR gene level, all WWTWs samples showed the most abundance for the sul1 gene (encoding sulfonamide resistance). Following this, the next 14 most abundant genes encoded resistance to sulfonamides, aminoglycosides, macrolides, tetracyclines and beta-lactams. Notably, within TMM, some macrolide-encoding resistance genes ( mefC , msrE , mphG and mphE ) were in highest abundance at a WWTW serving an urban high-income area; while sul1 , sul2 and tetC genes were in highest abundance at a WWTW serving a semi-urban low income area. Differential abundance analysis of AMR genes at WWTWs, following stratification of data by season, showed some notable variance in six AMR genes, of which bla KPC-2 and bla KPC-34 genes showed the highest prevalence of seasonal abundance differences when comparing data within a WWTW. The general trend was to see higher abundances of AMR genes in colder seasons, when comparing seasonal data within a WWTW. Our study investigated wastewater samples in only one province of South Africa, from WWTWs located within close proximity to one another. We would require a more widespread investigation at WWTWs distributed across all regions/provinces of South Africa, in order to describe a more comprehensive profile of AMR abundance across the country.
Journal Article
Emergence of Vibrio cholerae O1 Sequence Type 75, South Africa, 2018–2020
We describe the molecular epidemiology of cholera in South Africa during 2018-2020. Vibrio cholerae O1 sequence type (ST) 75 recently emerged and became more prevalent than the V. cholerae O1 biotype El Tor pandemic clone. ST75 isolates were found across large spatial and temporal distances, suggesting local ST75 spread.
Journal Article