Genomic Surveillance of Neisseria gonorrhoeae in the Philippines from 2013-2014

AbstractAntimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health, and of particular concern in the Western Pacific Region, where the incidence of gonorrhoea is high. The Antimicrobial Resistance Surveillance Program (ARSP) has been capturing information on resistant gonorrhoea since 1996, but studies of the genomic epidemiology of gonorrhoea in the Philippines are lacking.We sequenced the whole genomes of 21 N. gonorrhoeae isolates collected in 2013-2014 by the ARSP. The multi-locus sequence type, multi-antigen sequence type, presence of antimicrobial resistance (AMR) determinants, and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined.Ten out of 21 isolates were resistant to penicillin, ciprofloxacin and tetracycline, mostly linked to the presence of blaTEM gene, the S91F mutation in the gyrA gene, and the tetM gene, respectively. None of the isolates were resistant to azithromycin, ceftriaxone or cefixime, although we identified the A24-deletion in the mtrR promoter in one isolate. The concordance between phenotypic and genotypic resistance was 92.38% overall for 5 antibiotics in 4 classes. Despite the small number of isolates studied, they were genetically diverse, as shown by the sequence types, the NG-MAST types and the tree. Comparison with global genomes placed the Philippine genomes within global Lineage A and led to the identification of an international transmission route.This first genomic survey of N. gonorrhoeae isolates collected by ARSP will be used to contextualize ongoing prospective surveillance, and it highlights the importance of genomic surveillance in the Western Pacific and other endemic regions to understand the spread of drug-resistant gonorrhoea worldwide.

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Genomic surveillance of Neisseria gonorrhoeae in the Philippines, 2013–2014

Western Pacific Surveillance and Response ◽

10.5365/wpsar.2020.11.1.005 ◽

2021 ◽

Vol 12 (1) ◽

pp. 17-25

Author(s):

Alfred Villamin ◽

Silvia Argimon ◽

Karis Bohme ◽

Melissa Masim ◽

June Gayeta ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Neisseria Gonorrhoeae ◽

Sequence Data ◽

The Philippines ◽

Sequence Type ◽

Surveillance Program ◽

Gyra Gene ◽

Genotypic Resistance ◽

Genomic Epidemiology ◽

Epidemiology Studies

Antimicrobial-resistant Neisseria gonorrhoeae is a major threat to public health and is of particular concern in the Western Pacific Region, where the incidence of gonorrhoea is high. The Antimicrobial Resistance Surveillance Program (ARSP) has been capturing information on resistant gonorrhoea since 1996, but genomic epidemiology studies on this pathogen are lacking in the Philippines. We sequenced the whole genomes of 21 N. gonorrhoeae isolates collected in 2013–2014 by ARSP. The multilocus sequence type, multiantigen sequence type, presence of determinants of antimicrobial resistance and relatedness among the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined. Ten of 21 isolates were resistant to penicillin, ciprofloxacin and tetracycline, due mainly to the presence of the blaTEM gene, the S91F mutation in the gyrA gene and the tetM gene, respectively. None of the isolates was resistant to ceftriaxone or cefixime. The concordance between phenotypic and genotypic resistance was 92.38% overall for five antibiotics in four classes. Despite the small number of isolates studied, they were genetically diverse, as shown by the sequence types, the N. gonorrhoeae multiantigen sequence typing types and the tree. Comparison with global genomes placed the Philippine genomes within global lineage A and led to the identification of an international transmission route.

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Genomic Surveillance of Methicillin-Resistant Staphylococcus aureus in the Philippines from 2013-2014

10.1101/2020.03.19.998401 ◽

2020 ◽

Cited By ~ 1

Author(s):

Melissa L. Masim ◽

Silvia Argimón ◽

Holly O. Espiritu ◽

Mariane A. Magbanua ◽

Marietta L. Lagrada ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Resistance ◽

Sequence Data ◽

The Philippines ◽

Surveillance Program ◽

Genotypic Resistance ◽

Methicillin Resistant ◽

Whole Genomes ◽

Invasive Infections ◽

The Western Pacific

AbstractMethicillin Resistant Staphylococcus aureus (MRSA) remains one of the leading causes of both nosocomial and community infections worldwide. In the Philippines, MRSA rates have remained above 50% since 2010, but resistance to other antibiotics, including vancomycin, is low. The MRSA burden can be partially attributed to pathogen-specific characteristics of the circulating clones, but little was known about the S. aureus circulating clones in the Philippines.We sequenced the whole genomes of 116 S. aureus isolates collected in 2013-2014 by the Antimicrobial Resistance Surveillance Program. The multi-locus sequence type, spa type, SCC-mec type, presence of antimicrobial resistance (AMR) determinants and virulence genes, and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined.The MRSA population in the Philippines was composed of a limited number of genetic clones, including several international epidemic clones, such as CC30-spa-t019-SCCmec-IV-PVL+, CC5-SCCmec-typeIV, and ST239-spa-t030-SCCmec-typeIII. The CC30 genomes were related to the South West Pacific clone, but formed a distinct and diverse lineage, with evidence of global dissemination. We showed the independent acquisition of resistance to sulfamethoxazole/trimethoprim across different locations and genetic clones, but mostly in pediatric patients with invasive infections. The concordance between phenotypic and genotypic resistance was 99.68% overall for 8 antibiotics in 7 classes.We produced the first comprehensive genomic survey of S. aureus in the Philippines, which bridges the gap in genomic data from the Western Pacific region and will constitute the genetic background to contextualize ongoing prospective surveillance.

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Genomic surveillance of methicillin-resistant Staphylococcus aureus in the Philippines, 2013–2014

Western Pacific Surveillance and Response ◽

10.5365/wpsar.2020.11.1.004 ◽

2021 ◽

Vol 12 (1) ◽

pp. 6-16

Author(s):

Melissa Masim ◽

Silvia Argimon ◽

Holly Espiritu ◽

Mariane Magbanua ◽

Agnettah Olorosa ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Antimicrobial Resistance ◽

Methicillin Resistant Staphylococcus Aureus ◽

Sequence Data ◽

Sccmec Type ◽

The Philippines ◽

Surveillance Program ◽

Genotypic Resistance ◽

Methicillin Resistant ◽

Invasive Infections

Methicillin-resistant Staphylococcus aureus (MRSA) remains one of the leading causes of both nosocomial and community infections worldwide. In the Philippines, MRSA rates have remained above 50% since 2010, but resistance to other antibiotics, including vancomycin, is low. The MRSA burden can be partially attributed to pathogen-specific characteristics of the circulating clones, but little was known about the S. aureus clones circulating in the Philippines. We sequenced the whole genomes of 116 S. aureus isolates collected in 2013–2014 within the Antimicrobial Resistance Surveillance Program. The multilocus sequence type, spa type, SCCmec type, presence of antimicrobial resistance (AMR) determinants and virulence genes and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined. The MRSA population in the Philippines comprised a limited number of genetic clones, including several international epidemic clones, such as CC30-spa-t019-SCCmec-IV-PVL+, CC5-SCCmec-typeIV and ST239-spa-t030-SCCmec-typeIII. The CC30 genomes were related to the South-West Pacific clone but formed a distinct, diverse lineage, with evidence of global dissemination. We showed independent acquisition of resistance to sulfamethoxazole/trimethoprim in various locations and genetic clones but mostly in paediatric patients with invasive infections. The concordance between phenotypic and genotypic resistance was 99.68% overall for eight antibiotics in seven classes. We have made the first comprehensive genomic survey of S. aureus in the Philippines, which bridges the gap in genomic data from the Western Pacific Region and will constitute the genetic background for contextualizing prospective surveillance.

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Genomic Surveillance of Pseudomonas aeruginosa in the Philippines from 2013-2014

10.1101/2020.03.19.998229 ◽

2020 ◽

Author(s):

Jeremiah Chilam ◽

Silvia Argimón ◽

Marilyn T. Limas ◽

Melissa L. Masim ◽

June M. Gayeta ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Antimicrobial Resistance ◽

Sequence Data ◽

Acquired Resistance ◽

Carbapenem Resistance ◽

The Philippines ◽

Surveillance Program ◽

Drug Resistant ◽

Loss Of Function ◽

Genotypic Resistance

AbstractPseudomonas aeruginosa is an opportunistic pathogen often causing nosocomial infections that are resilient to treatment due to an extensive repertoire of intrinsic and acquired resistance mechanisms. In recent years, increasing resistance rates to antibiotics such as carbapenems and extended-spectrum cephalosporins have been reported, as well as multi-drug resistant and possible extremely drug-resistant rates of approximately 21% and 15%, respectively. However, the molecular epidemiology and AMR mechanisms of this pathogen remains largely uncharacterized.We sequenced the whole genomes of 176 P. aeruginosa isolates collected in 2013-2014 by the Antimicrobial Resistance Surveillance Program. The multi-locus sequence type, presence of antimicrobial resistance (AMR) determinants, and relatedness between the isolates were derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined.Carbapenem resistance was associated namely with loss-of function of the OprD porin, and acquisition of the metallo-β-lactamase VIM. The concordance between phenotypic and genotypic resistance was 93.27% overall for 6 antibiotics in 3 classes, but varied widely between aminoglycosides. The population of P. aeruginosa in the Philippines was diverse, with clonal expansions of XDR genomes belonging to multi-locus sequence types ST235, ST244, ST309, and ST773. We found evidence of persistence or reintroduction of the predominant clone ST235 in one hospital, as well as transfer between hospitals. Most of the ST235 genomes formed a distinct Philippine lineage when contextualized with international genomes, thus raising the possibility that this is a lineage unique to the Philippines. This was further supported by long-read sequencing of one representative XDR isolate, which revealed the presence of an integron carrying multiple resistance genes, including blaVIM-2, with differences in gene composition and synteny to other P. aeruginosa class 1 integrons described before.We produced the first comprehensive genomic survey of P. aeruginosa in the Philippines, which bridges the gap in genomic data from the Western Pacific region and will constitute the genetic background to contextualize ongoing prospective surveillance. Our results also highlight the importance of infection control interventions aimed to curtail the spread of international epidemic clone ST235 within the country.

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Antimicrobial resistance trends in community-acquired respiratory tract pathogens in the Western Pacific Region and South Africa: report from the SENTRY antimicrobial surveillance program, (1998–1999) including an in vitro evaluation of BMS284756

International Journal of Antimicrobial Agents ◽

10.1016/s0924-8579(01)00475-7 ◽

2002 ◽

Vol 19 (2) ◽

pp. 125-132 ◽

Cited By ~ 23

Author(s):

J.M. Bell ◽

J.D. Turnidge ◽

R.N. Jones

Keyword(s):

South Africa ◽

Antimicrobial Resistance ◽

Respiratory Tract ◽

Western Pacific ◽

Surveillance Program ◽

Pacific Region ◽

Western Pacific Region ◽

Antimicrobial Surveillance ◽

The Western Pacific

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See and Sequence: Integrating Whole-Genome Sequencing Within the National Antimicrobial Resistance Surveillance Program in the Philippines

10.1101/808378 ◽

2019 ◽

Cited By ~ 6

Author(s):

Silvia Argimón ◽

Melissa A. L. Masim ◽

June M. Gayeta ◽

Marietta L. Lagrada ◽

Polle K. V. Macaranas ◽

...

Keyword(s):

Public Health ◽

Antimicrobial Resistance ◽

Genome Sequencing ◽

Genomic Data ◽

Carbapenem Resistance ◽

The Philippines ◽

Surveillance Program ◽

Whole Genome ◽

Genomic Epidemiology ◽

Carbapenem Resistant

AbstractDrug-resistant bacterial infections constitute a growing threat to public health globally 1. National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor the emergence and spread of resistance and are central to the dissemination of these data to AMR stakeholders 2. Whole-genome sequencing (WGS) can support these efforts by pinpointing resistance mechanisms and uncovering transmission patterns 3, 4. However, genomic surveillance is rare in low- and middle-income countries (LMICs), which are predicted to be the most affected by AMR 5. We implemented WGS within the established Antimicrobial Resistance Surveillance Program (ARSP) of the Philippines via ongoing technology transfer, capacity building in and binational collaboration. In parallel, we conducted an initial large-scale retrospective sequencing survey to characterize bacterial populations and dissect resistance phenotypes of key bug-drug combinations, which is the focus of this article. Starting in 2010, the ARSP phenotypic data indicated increasing carbapenem resistance rates for Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae and Escherichia coli. We first identified that this coincided with a marked expansion of specific resistance phenotypes. By then linking the resistance phenotypes to genomic data, we revealed the diversity of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying this expansion. We discovered a previously unreported plasmid-driven hospital outbreak of carbapenem-resistant K. pneumoniae, uncovered the interplay of carbapenem resistance genes and plasmids in the geographic circulation of epidemic K. pneumoniae ST147, and found that carbapenem-resistant E. coli ST410 consisted of diverse lineages of global circulation that carried both international and local plasmids, resulting in a combination of carbapenemase genes variants previously unreported for this organism. Thus, the WGS data provided an enhanced understanding of the interplay between strains, genes and vehicles driving the dissemination of carbapenem resistance in the Philippines. In addition, our retrospective survey served both as the genetic background to contextualize local prospective surveillance, and as a comprehensive dataset for training in bioinformatics and genomic epidemiology. Continued prospective sequencing, capacity building and collaboration will strengthen genomic surveillance of AMR in the Philippines and the translation of genomic data into public-health action. We generated a blueprint for the integration of WGS and genomic epidemiology into an established national system of laboratory-based surveillance of AMR through international collaboration that can be adapted and utilized within other locations to tackle the global challenge of AMR.

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Trends in antimicrobial resistance in Neisseria gonorrhoeae in Hanoi, Vietnam, 2017–2019

BMC Infectious Diseases ◽

10.1186/s12879-020-05532-3 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Paul C. Adamson ◽

Hung Van Le ◽

Hai Ha Long Le ◽

Giang Minh Le ◽

Trung Vu Nguyen ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Linear Regression ◽

Neisseria Gonorrhoeae ◽

Antibiotic Susceptibility ◽

Western Pacific ◽

Diffusion Method ◽

Categorical Variables ◽

Pacific Region ◽

Western Pacific Region ◽

The Western Pacific

Abstract Background Antimicrobial resistance (AMR) in Neisseria gonorrhoeae is an emerging global health threat. Surveillance of AMR in N. gonorrhoeae in the Western Pacific Region is important, as resistant strains have typically emerged from this region. There are sparse data regarding antibiotic susceptibility of N. gonorrhoeae from Vietnam. This study aimed to provide updated data on antibiotic susceptibilities in N. gonorrhoeae isolates from Hanoi, Vietnam. Methods From 2017 to 2019, 409 N. gonorrhoeae clinical isolates were collected at the National Hospital for Venereology and Dermatology in Hanoi, Vietnam. Antibiotic susceptibility testing was performed by disk diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) protocol. The zone diameters of inhibition were recorded and interpreted according to standard CLSI criteria, except for azithromycin, due to the absence of CLSI interpretation. Categorical variables were analyzed by Chi-square and Fisher’s exact tests. Linear regression was used to evaluate zones of inhibition by year. Results Among the 409 isolates, no isolates were susceptible to penicillin, 98.3% were resistant to ciprofloxacin, and all isolates were susceptible to spectinomycin. There were 122/407 (30.0%) isolates resistant to azithromycin and there was an association between resistance and year (p < 0.01), ranging from 15.3% of isolates in 2017 to 46.7% of the isolates in 2018. Resistance to cefixime was found in 13/406 (3.2%) of isolates and there was no association by year (p = 0.30). Resistance to ceftriaxone occurred in 3/408 (0.7%) of isolates. Linear regression indicated the zone of inhibition diameters decreased by 0.83 mm each year for ceftriaxone (95% CI: − 1.3, − 0.4; p < 0.01) and decreased by 0.83 mm each year (95% CI: − 1.33, − 0.33; p < 0.01) for azithromycin; the association was not significant for cefixime (p = 0.07). Conclusions We found decreasing susceptibility of N. gonorrhoeae to ceftriaxone and azithromycin, as well as a high prevalence of resistance to azithromycin, among isolates in Hanoi, Vietnam from 2017 to 2019. The trends of decreasing susceptibility to first-line treatments are concerning and highlight the urgency of addressing antimicrobial resistance in N. gonorrhoeae. Expanded surveillance efforts within the Western Pacific Region are critical to monitoring trends and informing treatment guidelines.

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Genomic epidemiology of Neisseria gonorrhoeae elucidating the gonococcal antimicrobial resistance and lineages/sublineages across Brazil, 2015–16

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkaa318 ◽

2020 ◽

Vol 75 (11) ◽

pp. 3163-3172

Author(s):

Daniel Golparian ◽

Maria Luiza Bazzo ◽

Lisléia Golfetto ◽

Pamela Cristina Gaspar ◽

Marcos André Schörner ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Neisseria Gonorrhoeae ◽

Genomic Diversity ◽

Surveillance Program ◽

Phylogenomic Analysis ◽

Resistance Mutations ◽

Genomic Epidemiology ◽

Antimicrobial Surveillance ◽

Genomic Studies ◽

Azithromycin Resistance

Abstract Objectives Neisseria gonorrhoeae antimicrobial resistance (AMR) surveillance is imperative internationally, but only eight (22.9%) countries in the WHO Region of the Americas reported complete AMR data to the WHO Global Gonococcal Antimicrobial Surveillance Program (WHO GASP) in 2016. Genomic studies are ideal for enhanced understanding of gonococcal populations, including the spread of AMR strains. To elucidate the circulating gonococcal lineages/sublineages, including their AMR determinants, and the baseline genomic diversity among gonococcal strains in Brazil, we conducted WGS on 548 isolates obtained in 2015–16 across all five macroregions in Brazil. Methods A total of 548 gonococcal isolates cultured across Brazil in 2015–16 were genome sequenced. AMR was determined using agar dilution and/or Etest. Genome sequences of isolates from Argentina (n = 158) and the 2016 WHO reference strains (n = 14) were included in the analysis. Results We found 302, 68 and 214 different NG-MAST, MLST and NG-STAR STs, respectively. The phylogenomic analysis identified one main antimicrobial-susceptible lineage and one AMR lineage, which was divided into two sublineages with different AMR profiles. Determination of NG-STAR networks of clonal complexes was shown as a new and valuable molecular epidemiological analysis. Several novel mosaic mtrD (and mtrR and mtrE) variants associated with azithromycin resistance were identified. Conclusions We describe the first genomic baseline data to support the Brazilian GASP. The high prevalence of resistance to ciprofloxacin, tetracycline and benzylpenicillin, and the high number of isolates with mosaic penA and azithromycin resistance mutations, should prompt continued and strengthened AMR surveillance, including WGS, of N. gonorrhoeae in Brazil.

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Making War upon the Chart

To Master the Boundless Sea ◽

10.5149/northcarolina/9781469640440.003.0007 ◽

2018 ◽

pp. 166-201

Author(s):

Jason W. Smith

Keyword(s):

The United States ◽

Central Place ◽

The Philippines ◽

Western Pacific ◽

American Empire ◽

The Caribbean ◽

Post War ◽

The Western Pacific ◽

Hydrographic Surveying

This chapter examines the place of charts and hydrographic surveying in the consolidation of a formal American empire after 1898 and the central place of environmental knowledge in the broader strategic debates concerning American empire in the post war period, 1899-1903. It follows the work of surveying vessels off Cuba and the Philippines, the emerging role of the Hydrographic Office and its leaders, and the strategic debates among officer-students at the United States Naval War College and the Navy’s top leadership in the General Board of the Navy in recognizing and debating the importance of the marine environment generally and the specific strategic features of various harbors and coastlines from the Caribbean to the Western Pacific. The chapter argues that charts, hydrographic surveying, and a larger cartographic discourse were central to the geography of American empire, particularly in projecting American sea power into the Western Pacific and the Caribbean.

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