Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.

Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a threat to public health in India because of its high dissemination, mortality, and limited treatment options. Its genomic variability is reflected in the diversity of sequence types, virulence factors, and antimicrobial resistance (AMR) mechanisms. This study aims to characterize the clonal relationships and genetic mechanisms of resistance and virulence in CRKP isolates in India. Materials and Methods We characterized 344 retrospective K. pneumoniae clinical isolates collected from 8 centers across India collected in 2013–2019. Susceptibility to antibiotics was tested with VITEK 2. Capsular types, multilocus sequence type, virulence genes, AMR determinants, plasmid replicon types, and a single-nucleotide polymorphism phylogeny were inferred from their whole genome sequences. Results Phylogenetic analysis of the 325 Klebsiella isolates that passed quality control revealed 3 groups: K. pneumoniae sensu stricto (n = 307), K. quasipneumoniae (n = 17), and K. variicola (n = 1). Sequencing and capsular diversity analysis of the 307 K. pneumoniae sensu stricto isolates revealed 28 sequence types, 26 K-locus types, and 11 O-locus types, with ST231, KL51, and O1V2 being predominant. blaOXA-48-like and blaNDM-1/5 were present in 73.2% and 24.4% of isolates, respectively. The major plasmid replicon types associated with carbapenase genes were IncF (51.0%) and Col group (35.0%). Conclusion Our study documents for the first time the genetic diversity of K and O antigens circulating in India. The results demonstrate the practical applicability of genomic surveillance and its utility in tracking the population dynamics of CRKP. It alerts us to the urgency for longitudinal surveillance of these transmissible lineages.

The objective of this study was to determine Salmonella numbers on retail raw chicken carcasses in Guatemala and to phenotypically characterize the isolates (serotyping and antibiotic susceptibility). In total, 300 chicken carcasses were collected from seven departments in Guatemala. Salmonella numbers were determined using the most-probable-number method following the U. S. Department of Agriculture's Food Safety and Inspection Service protocol. In total, 103 isolates were obtained, all of which were tested for antibiotic susceptibility, whereas 46 isolates were serotyped. Overall, Salmonella prevalence and mean number (mean log most probable number per carcass) was 34.3% and 2.3 (95% confidence interval: 2.1 to 2.5), respectively. Significant differences (P < 0.05) in Salmonella prevalence were found by storage condition (refrigerated or ambient temperature), market type (wet markets, supermarkets, and independent poultry stores), chicken production system (integrated or nonintegrated production company), and chicken skin color (white or yellow). Chickens produced by integrated companies had lower Salmonella numbers (P < 0.05) than nonintegrated companies, and white-skin carcasses had lower numbers (P < 0.05) than yellow-skin carcasses. Among 13 different Salmonella serovars identified, Paratyphi B (34.8%) was most prevalent, followed by Heidelberg (16.3%) and Derby (11.6%). Of all the Salmonella isolates, 59.2% were resistant to one to three antibiotics and 13.6% to four or more antibiotics. Among all the serovars obtained, Salmonella Paratyphi B and Heidelberg were the most resistant to the antibiotics tested. Salmonella levels and antibiotic resistant profiles among isolates from raw poultry at the retail market level were high relative to other reports from North and South America. These data can be used by Guatemalan stakeholders to develop risk assessment models and support further research opportunities to control transmission of Salmonella spp. and antibiotic-resistant isolates from chicken meat to humans.

Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)’s 2013–2017 sample collection. Methods A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance (AMR), and AGROSAVIA. Results Of the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases bla KPC-3 , bla KPC-2 , bla NDM-1 , bla NDM-9 , bla VIM-2 , bla VIM-4 , and bla VIM-24 , and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin ( clb3 ) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI > 99.9%). Conclusions The study outlines complex CRKP epidemiology in Colombia. CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of sequence types (STs), MGE, and resistance and virulence genes.

In this Supplement, we detail outputs of the National Institute for Health Research Global Health Research Unit on Genomic Surveillance of Antimicrobial Resistance project, covering practical implementation of whole-genome sequencing across our consortium, which consists of laboratories in Colombia, India, Nigeria, and the Philippines.