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.

A total of 73 nontyphoidal Salmonella enterica isolates, 33 from raw chicken meat and 40 from routine clinical specimens, were collected between 2015 and 2017 from eight cities in Sri Lanka for a pilot study of whole-genome sequencing for Salmonella surveillance. The isolates were characterized by conventional serotyping and whole-genome sequencing. The raw sequenced data were assembled and analyzed to predict Salmonella serotypes, determine sequence type (ST) profiles of genome and plasmid, and identify plasmid replicon sequences and antimicrobial resistance (AMR) genes. The most common serovar isolated from chicken meat was Salmonella enterica serovar Agona of ST13 ( n = 16), in contrast to Salmonella enterica serovar Enteritidis of ST11 ( n = 21) in human. Salmonella enterica serovar Corvallis is the only serovar that was overlapping between human and chicken meat. The level of agreement between serotyping and serotype prediction results was 100%. Among the 33 chicken isolates, multidrug resistance (MDR) was observed in five isolates, including two Salmonella enterica serovar Kentucky ST314, which harbored six different classes of AMR determinants. Among the 40 human isolates, MDR was detected in two Salmonella enterica serovar Chester (ST2063) isolates containing five different antibiotic classes of AMR determinants. Out of 73 isolates, the only human Salmonella enterica serovar Typhimurium strain of ST36 was found to possess extended-spectrum beta-lactamase (ESBL) gene, bla CTX-M-15 , and it was positive for ESBL production. In summary, this study identified S . enterica serovars that were dominating in chicken meat and human and showed the genomic differences among the chicken meat and human strains. It should be noted that the limited number of isolates and sampling at a different time period means that thorough source attribution is not possible. To the best of our knowledge, this is the first report on the use of whole-genome sequencing analysis of nontyphoidal S . enterica isolated from chicken meat and human in Sri Lanka.

Biofilms have been associated with chronic wound infections in diabetic patients. The study assessed the occurrence of biofilms in chronic diabetic wounds (CDWs) in a Sri Lankan cohort. Tissue specimens collected during surgical debridement were analysed by quantitative differential viable counting, scanning electron microscopy (SEM), fluorescence insitu hybridization (FISH) and light microscopy with Gram and Haematoxylin‐Eosin staining. All specimens harboured >5·0 log10 CFU per g bacteria and 2–9 distinct species per specimen were recovered from twenty wounds by culture. The most frequently isolated bacterium was Pseudomonas spp. (12/20;60%). Strict anaerobes were isolated from 10/20 specimens. Gram and Haematoxylin‐Eosin staining showed aggregated micro‐colonies, embedded in the wound tissue bed (20/20) but the exopolymer matrix was not visible in all samples (13/20). Fluorescence microscopy using a eubacteria‐specific FISH probe indicated the presence of bacterial aggregates within the deep layers of the wound tissues (20/20). SEM revealed the presumptive architecture of matrix‐embedded microbial clusters (20/20). The approximate diameter of bacterial aggregates in tissues ranged between 12 and 400 µm. Bacterial infiltration into the internal portions of the tissues was apparent using FISH, Gram, and Haematoxylin‐Eosin staining. All CDWs carried biofilm‐specific morphological features. FISH was more specific than SEM and indicated the presence of microcolonies within deeper tissues.

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Background: Group B Streptococcus (GBS) causes significant morbidity and mortality in neonates, pregnant women and patients with underlying comorbidities. Intrapartum antibiotic prophylaxis (IAP) is currently the mainstay of prevention and effective vaccine against invasive GBS disease is under clinical trial.Objectives: To describe the serotype distribution of invasive and colonizing GBS isolates in Sri Lanka.Methods: Probable GBS isolates from high vaginal swabs (HVS) and sterile body sites were collected from eight selected hospital laboratories. Following confirmation of the identification as group B Streptococcus by phenotypic methods including Lancefield grouping test (Plasmatic UK), isolates were tested for serotyping by latex agglutination test kit (STATEN serum institute, Denmark).Results: Out of the 145 probable GBS isolates only 100 from HVS and 37 from sterile body sites were confirmed as GBS. Serotype III was the most predominant in invasive GBS isolates followed by Ia, Ib, VI, II and V in the descending order of frequency. Serotype VI was the most predominant in HVS isolates followed by serotype III, V, Ia, II, Ib and IV. Difference of GBS serotype distribution between the invasive and HVS group was statistically significant (P value = 0.038) Conclusion: Serotype distribution pattern of the study isolates was comparable to most of the other developing and developed countries and hence will be beneficial in future vaccine introduction. GBS vaccine which is currently under clinical trial (Ia, Ib and III) is potentially effective for preventing 68% of the early onset disease in neonates in this study setting.