The introduction of solid foods is an important dietary event during infancy that causes profound shifts in the gut microbial composition towards a more adult-like state. Infant gut bacterial dynamics, especially in relation to nutritional intake remain understudied. Over 2 weeks surrounding the time of solid food introduction, the day-to-day dynamics in the gut microbiomes of 24 healthy, full-term infants from the Baby, Food & Mi and LucKi-Gut cohort studies were investigated in relation to their dietary intake. Microbial richness (observed species) and diversity (Shannon index) increased over time and were positively associated with dietary diversity. Microbial community structure (Bray–Curtis dissimilarity) was determined predominantly by individual and age (days). The extent of change in community structure in the introductory period was negatively associated with daily dietary diversity. High daily dietary diversity stabilized the gut microbiome. Bifidobacterial taxa were positively associated, while taxa of the genus Veillonella, that may be the same species, were negatively associated with dietary diversity in both cohorts. This study furthers our understanding of the impact of solid food introduction on gut microbiome development in early life. Dietary diversity seems to have the greatest impact on the gut microbiome as solids are introduced.

In the hospital environment, carbapenemase-producing Pseudomonas aeruginosa (CPPA) may lead to fatal patient infections. However, the transmission routes of CPPA often remain unknown. Therefore, this case study aimed to trace the origin of CPPA ST357, which caused a hospital-acquired pneumonia in a repatriated critically ill patient suffering from Guillain-Barré Syndrome in 2023. Antimicrobial susceptibility of the CPPA isolate for 30 single and combination therapies was determined by disk-diffusion, Etest or broth microdilution. Whole-genome sequencing was performed for three case CPPA isolates (one patient and two sinks) and four distinct CPPA ST357 patient isolates received in the Dutch CPPA surveillance program. Furthermore, 193 international P. aeruginosa ST357 assemblies were collected via three genome repositories and analyzed using whole-genome multi-locus sequence typing in combination with antimicrobial resistance gene (ARG) characterization. A Dutch patient who carried NDM-1-producing CPPA was transferred from Kenya to the Netherlands, with subsequent dissemination of CPPA isolates to the local sinks within a month after admission. The CPPA case isolates presented an extensively drug-resistant phenotype, with susceptibility only for colistin and cefiderocol-fosfomycin. Phylogenetic analysis showed considerable variation in allelic distances (mean = 150, max = 527 alleles) among the ST357 isolates from Asia (n = 92), Europe (n = 58), Africa (n = 21), America (n = 16), Oceania (n = 2) and unregistered regions (n = 4). However, the case isolates (n = 3) and additional Dutch patient surveillance program isolates (n = 2) were located in a sub-clade of isolates from Kenya (n = 17; varying 15–49 alleles), the United States (n = 7; 21–115 alleles) and other countries (n = 6; 14–121 alleles). This was consistent with previous hospitalization in Kenya of 2/3 Dutch patients. Additionally, over half of the isolates (20/35) in this sub-clade presented an identical resistome with 9/17 Kenyan, 5/5 Dutch, 4/7 United States and 2/6 other countries, which were characterized by the blaNDM-1, aph(3’)-VI, ARR-3 and cmlA1 ARGs. This study presents an extensively-drug resistant subclone of NDM-producing P. aeruginosa ST357 with a unique resistome which was introduced to the Netherlands via repatriation of critically ill patients from Kenya. Therefore, the monitoring of repatriated patients for CPPA in conjunction with vigilance for the risk of environmental contamination is advisable to detect and prevent further dissemination.

Up to 14 co-occurring antimicrobial resistance genes (ARG) were previously detected in multiple outbreaks in the Netherlands involving various Enterobacteriaceae species, clones and plasmids, but similar multidrug resistance regions (MRR). This study aimed to map the reported occurrence, mosaic and modular genetic context of the involved ARG. Google Scholar and PubMed Central were queried for articles describing long-read assemblies with ≥ 6 co-occurring ARG. Plasmid (n = 119) and chromosomal (n = 8) sequences of 9 bacterial taxa originating from North America (n = 39), Europe (n = 34), Africa (n = 16), Asia (n = 14), Oceania (n = 13) and South America (n = 7) were extracted from NCBI. Based on colocalized insertions sequences, transposons and integrons, the ARGs could be divided into nine distinct resistance elements. These elements presented a total of 118 mosaic structural variants (SV): qnrB1 (SV = 27; n = 102), blaCTX‑M‑15 (SV = 23; n = 137), tet(A) (SV = 18; n = 93), dfrA14 (SV = 14; n = 115), sul2—strA—strB (SV = 13; n = 120), blaTEM‑1b (SV = 12; n = 119), aac(6’)‑Ib‑cr—blaOXA‑1—catB3 (SV = 7; n = 137), aac(3)‑IIe (SV = 2; n = 92), and aadA1—catA1 SV = 2; n = 12). The MRR showed high modularity with no clear ARG order. Still, three frequent sub-configurations were found. Firstly, blaTEM‑1b was flanked by sul2—strA—strB downstream (92.6%) and blaCTX‑M‑15 upstream (84.0%). Secondly, qnrB1 was flanked by tet(A) upstream (62.4%) and dfrA14 (63.4%) downstream. Thirdly, aac(3)‑IIe was flanked by aac(6’)‑Ib‑cr—blaOXA‑1—catB3 upstream (80.4%). In conclusion, the 14 ARG co-occur globally in similar MRR that are complex to interpret due to modularity and mosaicism. Still, the preservation of these clinically relevant resistance elements infers a potential means of transfer between distinct Enterobacteriaceae isolates.

Up to 14 co-occurring antimicrobial resistance genes (ARG) were previously detected in multiple outbreaks in the Netherlands involving various Enterobacteriaceae species, clones and plasmids, but similar multidrug resistance regions (MRR). This study aimed to map the reported occurrence, mosaic and modular genetic context of the involved ARG. Google Scholar and PubMed Central were queried for articles describing long-read assemblies with ≥ 6 co-occurring ARG. Plasmid (n = 119) and chromosomal (n = 8) sequences of 9 bacterial taxa originating from North America (n = 39), Europe (n = 34), Africa (n = 16), Asia (n = 14), Oceania (n = 13) and South America (n = 7) were extracted from NCBI. Based on colocalized insertions sequences, transposons and integrons, the ARGs could be divided into nine distinct resistance elements. These elements presented a total of 118 mosaic structural variants (SV): qnrB1 (SV = 27; n = 102), blaCTX‑M‑15 (SV = 23; n = 137), tet(A) (SV = 18; n = 93), dfrA14 (SV = 14; n = 115), sul2—strA—strB (SV = 13; n = 120), blaTEM‑1b (SV = 12; n = 119), aac(6’)‑Ib‑cr—blaOXA‑1—catB3 (SV = 7; n = 137), aac(3)‑IIe (SV = 2; n = 92), and aadA1—catA1 SV = 2; n = 12). The MRR showed high modularity with no clear ARG order. Still, three frequent sub-configurations were found. Firstly, blaTEM‑1b was flanked by sul2—strA—strB downstream (92.6%) and blaCTX‑M‑15 upstream (84.0%). Secondly, qnrB1 was flanked by tet(A) upstream (62.4%) and dfrA14 (63.4%) downstream. Thirdly, aac(3)‑IIe was flanked by aac(6’)‑Ib‑cr—blaOXA‑1—catB3 upstream (80.4%). In conclusion, the 14 ARG co-occur globally in similar MRR that are complex to interpret due to modularity and mosaicism. Still, the preservation of these clinically relevant resistance elements infers a potential means of transfer between distinct Enterobacteriaceae isolates.

Up to 14 co-occurring antimicrobial resistance genes (ARG) were previously detected in multiple outbreaks in the Netherlands involving various Enterobacteriaceae species, clones and plasmids, but similar multidrug resistance regions (MRR). This study aimed to map the reported occurrence, mosaic and modular genetic context of the involved ARG. Google Scholar and PubMed Central were queried for articles describing long-read assemblies with ≥ 6 co-occurring ARG. Plasmid (n = 119) and chromosomal (n = 8) sequences of 9 bacterial taxa originating from North America (n = 39), Europe (n = 34), Africa (n = 16), Asia (n = 14), Oceania (n = 13) and South America (n = 7) were extracted from NCBI. Based on colocalized insertions sequences, transposons and integrons, the ARGs could be divided into nine distinct resistance elements. These elements presented a total of 118 mosaic structural variants (SV): qnrB1 (SV = 27; n = 102), blaCTX‑M‑15 (SV = 23; n = 137), tet(A) (SV = 18; n = 93), dfrA14 (SV = 14; n = 115), sul2—strA—strB (SV = 13; n = 120), blaTEM‑1b (SV = 12; n = 119), aac(6’)‑Ib‑cr—blaOXA‑1—catB3 (SV = 7; n = 137), aac(3)‑IIe (SV = 2; n = 92), and aadA1—catA1 SV = 2; n = 12). The MRR showed high modularity with no clear ARG order. Still, three frequent sub-configurations were found. Firstly, blaTEM‑1b was flanked by sul2—strA—strB downstream (92.6%) and blaCTX‑M‑15 upstream (84.0%). Secondly, qnrB1 was flanked by tet(A) upstream (62.4%) and dfrA14 (63.4%) downstream. Thirdly, aac(3)‑IIe was flanked by aac(6’)‑Ib‑cr—blaOXA‑1—catB3 upstream (80.4%). In conclusion, the 14 ARG co-occur globally in similar MRR that are complex to interpret due to modularity and mosaicism. Still, the preservation of these clinically relevant resistance elements infers a potential means of transfer between distinct Enterobacteriaceae isolates.

Up to 14 co-occurring antimicrobial resistance genes (ARG) were previously detected in multiple outbreaks in the Netherlands involving various Enterobacteriaceae species, clones and plasmids, but similar multidrug resistance regions (MRR). This study aimed to map the reported occurrence, mosaic and modular genetic context of the involved ARG. Google Scholar and PubMed Central were queried for articles describing long-read assemblies with ≥ 6 co-occurring ARG. Plasmid ( n = 119) and chromosomal ( n = 8) sequences of 9 bacterial taxa originating from North America ( n = 39), Europe ( n = 34), Africa ( n = 16), Asia ( n = 14), Oceania ( n = 13) and South America ( n = 7) were extracted from NCBI. Based on colocalized insertions sequences, transposons and integrons, the ARGs could be divided into nine distinct resistance elements. These elements presented a total of 118 mosaic structural variants (SV): qnrB1 (SV = 27; n = 102), bla _CTX‑M‑15 (SV = 23; n = 137), tet (A) (SV = 18; n = 93), dfrA14 (SV = 14; n = 115), sul2—strA—strB (SV = 13; n = 120), bla _TEM‑1b (SV = 12; n = 119), aac(6’)‑Ib‑cr — bla _OXA‑1 — catB3 (SV = 7; n = 137), aac(3)‑IIe (SV = 2; n = 92), and aadA1 — catA1 SV = 2; n = 12). The MRR showed high modularity with no clear ARG order. Still, three frequent sub-configurations were found. Firstly, bla _TEM‑1b was flanked by sul2—strA—strB downstream (92.6%) and bla _CTX‑M‑15 upstream (84.0%). Secondly, qnrB1 was flanked by tet (A) upstream (62.4%) and dfrA14 (63.4%) downstream. Thirdly, aac(3)‑IIe was flanked by aac(6’)‑Ib‑cr — bla _OXA‑1 — catB3 upstream (80.4%). In conclusion, the 14 ARG co-occur globally in similar MRR that are complex to interpret due to modularity and mosaicism. Still, the preservation of these clinically relevant resistance elements infers a potential means of transfer between distinct Enterobacteriaceae isolates.