Imaging of microbial interactions has so far been based on well‐established electron microscopy methods. This study presents a new way to study bacterial colonies and interactions between bacteria and their viruses, bacteriophages (phages), in situ on agar plates using helium ion microscopy (HIM). In biological imaging, HIM has advantages over traditional scanning electron microscopy with its sub‐nanometer resolution, increased surface sensitivity, and the possibility to image nonconductive samples. Furthermore, by controlling the He beam dose or by using heavier Ne ions, the HIM instrument provides the possibility to mill out material in the samples, allowing for subsurface imaging and in situ sectioning. Here, the first HIM‐images of bacterial colonies and phage–bacterium interactions are presented at different stages of the infection as they occur on an agar culture. The feasibility of neon and helium milling is also demonstrated to reveal the subsurface structures of bacterial colonies on agar substrate, and in some cases also structure inside individual bacteria after cross‐sectioning. The study concludes that HIM offers great opportunities to advance the studies of microbial imaging, in particular in the area of interaction of viruses with cells.

The use of bacteriophages to treat bacterial infections (phage therapy) is considered a possible solution to the antimicrobial resistance crisis. However, phage therapy is not a new concept. The discovery of phages in the early twentieth century was closely tied to clinical practice, and phage therapy quickly spread around the world.The use of phage therapy in twentieth century South America is still shrouded in mystery and has been mentioned only briefly in recent scientific literature. Research on Brazilian reference collections of medical texts revealed that Brazil was an important, but so far little-known, player of phage therapy, uncovers interesting priority claims and missing pieces of phage therapy history. Of note, there is the widespread use of phages against bacillary dysentery and staphylococcal infections, with Dr José da Costa Cruz from the Institute Oswaldo Cruz as Brazil's leading expert and pioneer. This review about historical phage use in a South American country fills gaps in our knowledge about the "golden years" of phage therapy, providing information about successful experiences that can be useful against dangerous pathogens in our time. Key points• Brazil had an important role in the golden years of phage therapy, which lasted until the mid-twentieth century.• Dr José da Costa Cruz from the Institute Oswaldo Cruz in Rio de Janeiro was the leading expert.• The first phage therapy cases in Brazil took place in 1921 during an outbreak of dysentery in Barbacena.• The mass testing of the Institute Oswaldo Cruz phage product during the Paulista revolution of 1924 preceded Dr d'Herelle's tests in India and the Soviet Union's tests on military troops.• Successful phage use in Brazil was against bacillary dysentery and staphylococcal infections.• The available information about phage therapy clinical cases and phage products was retrieved from the literature investigated and presented in this publication. Research in contextEvidence before this study Reports summarising the use of phage therapy in Brazil were scarce before this review. Only three recent publications mentions, briefly and without details, that Brazilian doctors were involved with phage therapy in the 1920s. Sixteen sources of Brazilian medical publications were checked for phage-related information, looking at the period from 1915 (when Dr Frederik Twort published his phage discovery) to 1952. Any phage or phage therapy related words in titles and abstracts were used as inclusion criteria. The risk of bias associated with data inclusion is minimal, because the objective was to have all published material concerning phages.However, since routine phage therapy cases were not always published, the data presented here are probably only a fraction of the actual phage use at the time.

Intensive aquaculture conditions expose fish to bacterial infections, leading to significant financial losses, extensive antibiotic use and risk of antibiotic resistance in target bacteria. Flavobacterium columnare causes columnaris disease in aquaculture worldwide. To develop a bacteriophage-based control of columnaris disease, we isolated and characterized 126 F. columnare strains and 63 phages against F. columnare from Finland and Sweden. Bacterial isolates were virulent on rainbow trout (Oncorhynchus mykiss) and fell into four previously described genetic groups A, C, E and G, with genetic groups C and E being the most virulent. Phage host range studied against a collection of 228 bacterial isolates demonstrated modular infection patterns based on host genetic group. Phages infected contemporary and previously isolated bacterial hosts, but bacteria isolated most recently were generally resistant to previously isolated phages. Despite large differences in geographical origin, isolation year or host range of the phages, whole genome sequencing of 56 phages showed high level of genetic similarity to previously isolated F. columnare phages (Ficleduovirus, Myoviridae). Altogether, this phage collection demonstrates a potential to be used in phage therapy.

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