Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes

Background: The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods: This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results: Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal ‘sentinel’ surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (=3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has becomedominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions: The consortium’s aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies

Synthesis of pacific ocean climate and ecosystem dynamics

The goal of the Pacific Ocean Boundary Ecosystem and Climate Study (POBEX) was to diagnose the large-scale climate controls on regional transport dynamics and lower trophic marine ecosystem variability in Pacific Ocean boundary systems. An international team of collaborators shared observational and eddyresolving modeling data sets collected in the Northeast Pacific, including the Gulf of Alaska (GOA) and the California Current System (CCS), the Humboldt or Peru-Chile Current System (PCCS), and the Kuroshio-Oyashio Extension (KOE) region. POBEX investigators found that a dominant fraction of decadal variability in basin and regional-scale salinity, nutrients, chlorophyll, and zooplankton taxa is explained by a newly discovered pattern of ocean-climate variability dubbed the North Pacific Gyre Oscillation (NPGO) and the Pacific Decadal Oscillation (PDO). NPGO dynamics are driven by atmospheric variability in the North Pacific and capture the decadal expression of Central Pacific El Niños in the extratropics, much as the PDO captures the low-frequency expression of eastern Pacific El Niños. By combining hindcasts of eddy-resolving ocean models over the period 1950-2008 with model passive tracers and long-term observations (e.g., CalCOFI, Line-P, Newport Hydrographic Line, Odate Collection), POBEX showed that the PDO and the NPGO combine to control low-frequency upwelling and alongshore transport dynamics in the North Pacific sector, while the eastern Pacific El Niño dominates in the South Pacific. Although different climate modes have different regional expressions, changes in vertical transport (e.g., upwelling) were found to explain the dominant nutrient and phytoplankton variability in the CCS, GOA, and PCCS, while changes in alongshore transport forced much of the observed long-term change in zooplankton species composition in the KOE as well as in the northern and southern CCS. In contrast, cross-shelf transport dynamics were linked to mesoscale eddy activity, driven by regional-scale dynamics that are largely decoupled from variations associated with the large-scale climate modes. Preliminary findings suggest that mesoscale eddies play a key role in offshore transport of zooplankton and impact the life cycles of higher trophic levels (e.g., fish) in the CCS, PCCS, and GOA. Looking forward, POBEX results may guide the development of new modeling and observational strategies to establish mechanistic links among climate forcing, mesoscale circulation, and marine population dynamics. © 2013 by The Oceanography Society. All rights reserved

Synthesis of pacific ocean climate and ecosystem dynamics

The goal of the Pacific Ocean Boundary Ecosystem and Climate Study (POBEX) was to diagnose the large-scale climate controls on regional transport dynamics and lower trophic marine ecosystem variability in Pacific Ocean boundary systems. An international team of collaborators shared observational and eddyresolving modeling data sets collected in the Northeast Pacific, including the Gulf of Alaska (GOA) and the California Current System (CCS), the Humboldt or Peru-Chile Current System (PCCS), and the Kuroshio-Oyashio Extension (KOE) region. POBEX investigators found that a dominant fraction of decadal variability in basin and regional-scale salinity, nutrients, chlorophyll, and zooplankton taxa is explained by a newly discovered pattern of ocean-climate variability dubbed the North Pacific Gyre Oscillation (NPGO) and the Pacific Decadal Oscillation (PDO). NPGO dynamics are driven by atmospheric variability in the North Pacific and capture the decadal expression of Central Pacific El Niños in the extratropics, much as the PDO captures the low-frequency expression of eastern Pacific El Niños. By combining hindcasts of eddy-resolving ocean models over the period 1950-2008 with model passive tracers and long-term observations (e.g., CalCOFI, Line-P, Newport Hydrographic Line, Odate Collection), POBEX showed that the PDO and the NPGO combine to control low-frequency upwelling and alongshore transport dynamics in the North Pacific sector, while the eastern Pacific El Niño dominates in the South Pacific. Although different climate modes have different regional expressions, changes in vertical transport (e.g., upwelling) were found to explain the dominant nutrient and phytoplankton variability in the CCS, GOA, and PCCS, while changes in alongshore transport forced much of the observed long-term change in zooplankton species composition in the KOE as well as in the northern and southern CCS. In contrast, cross-shelf transport dynamics were linked to mesoscale eddy activity, driven by regional-scale dynamics that are largely decoupled from variations associated with the large-scale climate modes. Preliminary findings suggest that mesoscale eddies play a key role in offshore transport of zooplankton and impact the life cycles of higher trophic levels (e.g., fish) in the CCS, PCCS, and GOA. Looking forward, POBEX results may guide the development of new modeling and observational strategies to establish mechanistic links among climate forcing, mesoscale circulation, and marine population dynamics. © 2013 by The Oceanography Society. All rights reserved

Genetic connectivity of the ecosystem engineer Perumytilus purpuratus north to the 32ºS southeast Pacific ecological discontinuity

Connectivity in benthic marine animals with complex life cycles occurs primarily during the pelagic lar-val stage and depends deterministically on oceanographic dynamics. The scale of such larval dispersal is highly uncertain due the difficulty of direct measurement and poor knowledge of larval dynamics and ocean flow variability. This study characterizes the pattern of genetic connectivity in the ecosystem engineer Perumytilus purpuratus between latitudes 23°S and 33°S, which includes the ecological discontinuity reported for many taxa north to 32°S at the southeast Pacific. The genetic discontinuity observed in P. purpuratus around 26°S is described herein while that detected at 28°S is in line with the ecological discontinuity (in coverage, recruitment and density) previously reported for this mussel between 28°S and 32°S. Both discontinui-ties delimitate two major gene pools upon Bayesian infer-ences on geographical variation of five microsatellite loci. Interestingly, marker Pepu 1 was responsible for most vari-ation between pools and was potentially under selection. In fact, inferences excluding Pepu 1 produced a single gene pool ( k = 1) in central-northern Chile. The IBD connec-tivity pattern observed among P. purpuratus beds distrib-uted in the interval 23°S–33°S is congruent with processes driven by larval dynamics, and the dominant equatorward Humboldt Current along a coast largely unaffected by ice during the last Pleistocene glaciation. However, the selec-tive scenario unveiled by microsatellite Pepu 1 inside the 25°S–28°S ecological discontinuity is consistent with selective processes associated with specific mesoscale properties operating in this area. This study highlights the usefulness of integrating different oceanographic scales, ecological data and population genetics to better under-stand connectivity of benthic marine species.Versión del editor2,011