Consumption of antibiotics in a small Pacific island nation: Samoa

Salmonella enterica Serovar Typhi on an Island: No H58, No Multidrug Resistance, but for How Long?

Little genomic data is available for typhoid fever from island nations, though the disease has a moderately high burden there. Sikorski et al. (M. J. Sikorski, T. H. Hazen, S. N. Desai, S. Nimarota-Brown, et al., mBio 13:e01920-22, 2022, https://doi.org/10.1128/mbio.01920-22) studied 306 Salmonella enterica serovar Typhi genomes from the Samoan Islands collected during 1983 to 2020 and reported dominance of a rare genotype, 2.5.4, and no H58 (genotype 4.3.1). They found pansusceptibility of all isolates to three first lines of antimicrobial agents (ampicillin, chloramphenicol, and cotrimoxazole). This commentary evaluates the importance of these findings for the Samoan Islands and how they can help the global typhoid community. The microbial community in the environment and human gut could have played a role in the lack of antimicrobial resistance (AMR). However, drug-resistant strains may arrive soon at the island, as their international spread is common. Further investigation would help the global typhoid community to better understand the evolution of an isolated pathogen community and the effect of vaccination there.

Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa

For decades, the remote island nation of Samoa (population ~200,000) has faced endemic typhoid fever despite improvements in water quality, sanitation, and economic development. We recently described the epidemiology of typhoid fever in Samoa from 2008 to 2019 by person, place, and time; however, the local Salmonella enterica serovar Typhi (S. Typhi) population structure, evolutionary origins, and genomic features remained unknown. Herein, we report whole genome sequence analyses of 306 S. Typhi isolates from Samoa collected between 1983 and 2020. Phylogenetics revealed a dominant population of rare genotypes 3.5.4 and 3.5.3, together comprising 292/306 (95.4%) of Samoan versus 2/4934 (0.04%) global S. Typhi isolates. Three distinct 3.5.4 genomic sublineages were identified, and their defining polymorphisms were determined. These dominant Samoan genotypes, which likely emerged in the 1970s, share ancestry with other 3.5 clade isolates from South America, Southeast Asia, and Oceania. Additionally, a 106-kb pHCM2 phenotypically cryptic plasmid, detected in a 1992 Samoan S. Typhi isolate, was identified in 106/306 (34.6%) of Samoan isolates; this is more than double the observed proportion of pHCM2-containing isolates in the global collection. In stark contrast with global S. Typhi trends, resistance-conferring polymorphisms were detected in only 15/306 (4.9%) of Samoan S. Typhi, indicating overwhelming susceptibility to antibiotics that are no longer effective in most of South and Southeast Asia. This country-level genomic framework can help local health authorities in their ongoing typhoid surveillance and control efforts, as well as fill a critical knowledge gap in S. Typhi genomic data from Oceania. IMPORTANCE In this study, we used whole genome sequencing and comparative genomics analyses to characterize the population structure, evolutionary origins, and genomic features of S. Typhi associated with decades of endemic typhoid fever in Samoa. Our analyses of Samoan isolates from 1983 to 2020 identified a rare S. Typhi population in Samoa that likely emerged around the early 1970s and evolved into sublineages that are presently dominant. The dominance of these endemic genotypes in Samoa is not readily explained by genomic content or widespread acquisition of antimicrobial resistance. These data establish the necessary framework for future genomic surveillance of S. Typhi in Samoa for public health benefit.

Global antibiotic consumption and usage in humans, 2000-18: a spatial modelling study

BACKGROUND

Antimicrobial resistance (AMR) is a serious threat to global public health. WHO emphasises the need for countries to monitor antibiotic consumption to combat AMR. Many low-income and middle-income countries (LMICs) lack surveillance capacity; we aimed to use multiple data sources and statistical models to estimate global antibiotic consumption.

METHODS

In this spatial modelling study, we used individual-level data from household surveys to inform a Bayesian geostatistical model of antibiotic usage in children (aged <5 years) with lower respiratory tract infections in LMICs. Antibiotic consumption data were obtained from multiple sources, including IQVIA, WHO, and the European Surveillance of Antimicrobial Consumption Network (ESAC-Net). The estimates of the antibiotic usage model were used alongside sociodemographic and health covariates to inform a model of total antibiotic consumption in LMICs. This was combined with a single model of antibiotic consumption in high-income countries to produce estimates of antibiotic consumption covering 204 countries and 19 years.

FINDINGS

We analysed 209 surveys done between 2000 and 2018, covering 284 045 children with lower respiratory tract infections. We identified large national and subnational variations of antibiotic usage in LMICs, with the lowest levels estimated in sub-Saharan Africa and the highest in eastern Europe and central Asia. We estimated a global antibiotic consumption rate of 14·3 (95% uncertainty interval 13·2-15·6) defined daily doses (DDD) per 1000 population per day in 2018 (40·2 [37·2-43·7] billion DDD), an increase of 46% from 9·8 (9·2-10·5) DDD per 1000 per day in 2000. We identified large spatial disparities, with antibiotic consumption rates varying from 5·0 (4·8-5·3) DDD per 1000 per day in the Philippines to 45·9 DDD per 1000 per day in Greece in 2018. Additionally, we present trends in consumption of different classes of antibiotics for selected Global Burden of Disease study regions using the IQVIA, WHO, and ESAC-net input data. We identified large increases in the consumption of fluoroquinolones and third-generation cephalosporins in North Africa and Middle East, and south Asia.

INTERPRETATION

To our knowledge, this is the first study that incorporates antibiotic usage and consumption data and uses geostatistical modelling techniques to estimate antibiotic consumption for 204 countries from 2000 to 2018. Our analysis identifies both high rates of antibiotic consumption and a lack of access to antibiotics, providing a benchmark for future interventions.

FUNDING

Fleming Fund, UK Department of Health and Social Care; Wellcome Trust; and Bill & Melinda Gates Foundation.

Antimicrobial resistance in the Pacific Island countries and territories

Antimicrobial resistance (AMR) is a critical global health threat with a disproportionate impact on low-income and middle-income countries (LMICs) due to their higher burden of infections, reduced laboratory surveillance infrastructure and fewer regulations governing antimicrobial use among humans or animals. While there have been increasing descriptions of AMR within many LMICs in WHO's Western Pacific and South East Asian regions, there remains a paucity of data from Pacific Island countries and territories (PICTs). The PICTs represent 22 predominantly middle-income countries and territories with a combined population of 12 million people and 20 official languages, spread over hundreds of separate islands spanning an area corresponding to more than 15% of the earth's surface. Our paper outlines the present state of the evidence regarding AMR in PICTs-discussing the present estimates of AMR and their accompanying limitations, important drivers of AMR, as well as outlining key priorities and potential solutions for tackling AMR in this region. Significant areas for action include developing National Action Plans, strengthening laboratory surveillance systems and educational activities targeted at both healthcare workers and the wider community. Ensuring adequate funding for AMR activities in PICTs is challenging given competing health and environmental priorities, in this context global or regional funding initiatives such as the Fleming Fund can play a key role.

High prescription of antimicrobials in a rural district hospital in India

Background

The World Health Organization (WHO) recommends surveillance of antibiotic use as part of the strategy to fight against antimicrobial resistance. However, there is little information about the antibiotic consumption in developing countries, especially in rural areas.

Objective

The objective of this study was to describe the antimicrobial consumption in a rural hospital in India

Methods

The study was performed in a district hospital situated in Anantapur, Andhra Pradesh. In accordance with WHO recommendations, we used the defined daily dose (DDD) methodology to measure the antibiotic use during one year (from 1st August 2011 to 1st August 2012). The antibiotic use was measured using DDDs/100 admissions and DDDs/100 patient-days for inpatients, and DDDs/100 visits for outpatients.

Results

During the study period, there were 15,735 admissions and 250,611 outpatient visits. Antibiotics were prescribed for 86% of inpatients and 12.5% of outpatients. Outpatient prescriptions accounted for 2/3 of the overall antibiotic consumption. For inpatients, the total antibiotic use was 222 DDDs/ 100 patient-days, 693 DDDs/ 100 admissions and the mean number of antibiotics prescribed was 1.8. For outpatients, the total antibiotic use was 86 DDDs/ 100 outpatient visits and the mean number of antibiotics prescribed was 1.2. The most common antibiotics prescribed were aminopenicillins and 3rd generation cephalosporins for inpatients, and tetracyclines and quinolones for outpatients. In a sample of patients with diarrhoea or upper respiratory tract infections (URTI), the proportion of patients who received antibiotics was 84% (95% confidence interval [CI], 67-93) and 52% (95% CI, 43-62), respectively.

Conclusion

In this rural setting, the use of antimicrobials was extremely high, even in conditions with a predominantly viral aetiology such as diarrhoea or URTI.

Methicillin-resistant Staphylococcus aureus, Samoa, 2007-2008

Little is known about the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in most Pacific Island nations. Relatively high rates of MRSA have been reported in Polynesian people living outside the Pacific Islands. To determine the prevalence and characteristics of MRSA, we assessed wound swabs from 399 persons with skin and soft tissue infection living in Samoa. MRSA was isolated from 9% of study participants; 34 of the 196 S. aureus isolates were MRSA. Five MRSA genotypes were identified; the 3 most common were USA300, the Queensland clone, and a sequence type 1 MRSA strain that shares <85% homology with the sequence type 1 MRSA strain common in the region (WA MRSA-1). The Southwest Pacific MRSA clone was identified but accounted for only 12% of MRSA isolates. The high prevalence of MRSA in Samoa provides impetus for initiatives to improve antimicrobial drug resistance surveillance, infection control, and antimicrobial drug use in Pacific Island nations.

Methicillin-resistant Staphylococcus aureus, Samoa, 2007-2008

TOC Summary: A wide range of MRSA genotypes cause wound infections.

Little is known about the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in most Pacific Island nations. Relatively high rates of MRSA have been reported in Polynesian people living outside the Pacific Islands. To determine the prevalence and characteristics of MRSA, we assessed wound swabs from 399 persons with skin and soft tissue infection living in Samoa. MRSA was isolated from 9% of study participants; 34 of the 196 S. aureus isolates were MRSA. Five MRSA genotypes were identified; the 3 most common were USA300, the Queensland clone, and a sequence type 1 MRSA strain that shares <85% homology with the sequence type 1 MRSA strain common in the region (WA MRSA-1). The Southwest Pacific MRSA clone was identified but accounted for only 12% of MRSA isolates. The high prevalence of MRSA in Samoa provides impetus for initiatives to improve antimicrobial drug resistance surveillance, infection control, and antimicrobial drug use in Pacific Island nations.