Highlights d Cities possess a consistent ''core'' set of non-human microbes d Urban microbiomes echo important features of cities and city-life d Antimicrobial resistance genes are widespread in cities d Cities contain many novel bacterial and viral species

Background Microbial communities present in environmental waters constitute a reservoir for antibiotic-resistant pathogens that impact human health. For this reason, a diverse variety of water environments are being analyzed using metagenomics to uncover public health threats. However, the composition of these communities along the coastal environment of a whole city, where sewage and beach waters are mixed, is poorly understood. Results We shotgun-sequenced 20 coastal areas from the city of Montevideo (capital of Uruguay) including beach and sewage water samples to characterize bacterial communities and their virulence and antibiotic resistance repertories. As expected, we found that sewage and beach environments present significantly different bacterial communities. This baseline allowed us to detect a higher prevalence and a more diverse repertory of virulence and antibiotic-resistant genes in sewage samples. Many of these genes come from well-known enterobacteria and represent carbapenemases and extended-spectrum betalactamases reported in hospital infections in Montevideo. Additionally, we were able to genotype the presence of both globally disseminated pathogenic clones and emerging antibiotic-resistant bacteria in sewage waters. Conclusions Our study represents the first in using metagenomics to jointly analyze beaches and the sewage system from an entire city, allowing us to characterize antibiotic-resistant pathogens circulating in urban waters. The data generated in this initial study represent a baseline metagenomic exploration to guide future longitudinal (time-wise) studies, whose systematic implementation will provide useful epidemiological information to improve public health surveillance. Electronic supplementary material The online version of this article (10.1186/s40168-019-0648-z) contains supplementary material, which is available to authorized users.

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An iron-regulated outer-membrane protein of Proteus mirabilis is a haem receptor that plays an important role in urinary tract infection and in in vivo growth Proteus mirabilis, a common cause of urinary tract infections, expresses iron-regulated outer-membrane proteins (OMPs) in response to iron restriction. It has been suggested that a 64 kDa OMP is involved in haemoprotein uptake and that this might have a role in pathogenesis. In order to confirm this hypothesis, this study generated a P. mirabilis mutant strain (P7) that did not express the 64 kDa OMP, by insertion of the TnphoA transposon. The nucleotide sequence of the interrupted gene revealed that it corresponded to a haemin receptor precursor. Moreover, in vitro growth assays showed that the mutant was unable to grow using haemoglobin and haemin as unique iron sources. The authors also carried out in vivo growth and infectivity assays and demonstrated that P7 was not able to survive in an in vivo model and was less efficient than wild-type strain Pr 6515 in colonizing the urinary tract. These results confirmed that the P. mirabilis 64 kDa iron-regulated OMP is a haem receptor that has an important role for survival and multiplication of these bacteria in the mammalian host and in the development of urinary tract infection. INTRODUCTIONIron plays a central role in bacterial metabolism and pathogenesis. In the mammalian host, iron is unavailable for bacterial uptake (Litwin & Calderwood, 1993) as most of it is located intracellularly, stored in ferritin or linked to haem or haem-containing compounds, whilst extracellular iron is bound to transferrin, lactoferrin, haemopexin and haptoglobin (Braun, 2001).To overcome this problem, Gram-negative pathogenic bacteria have evolved iron-regulated systems to acquire this element in the host. These include the direct binding of iron-containing proteins to outer-membrane receptors and the secretion of siderophores or haemophores (Wandersman & Stojiljkovic, 2000). Transport of haem, iron-binding proteins and Fe 3+-siderophore complexes towards the cytoplasm represents an active process. Bacteria have developed a system formed by an outer-membrane receptor and a cytoplasmic membrane complex composed of ExbB, ExbD and TonB proteins that transduces the proton-motive force of the cytoplasmic membrane to the high-affinity outer-membrane receptors, known as TonB-dependent receptors (Olczak et al., 2005;Llamas & Bitter, 2006).Proteus mirabilis is an important cause of urinary tract infections (UTIs) in humans, especially in patients with urinary catheters and structural abnormalities. It shows a predilection for the upper urinary tract where it can cause serious renal damage (Stamm et al., 1977;Senior, 1978). Several potential virulence factors have been described for P. mirabilis, including haemolysin production and ironuptake systems (Rò zalski et al., 1997). Piccini et al. (1998) studied the effect of iron deprivation on the expression of outer-membrane proteins (OMPs) in uropathogenic isolates of P. mirabilis. They fo...

Paenibacillus larvae causes American foulbrood (AFB), a severe disease that affects the brood of honey bee Apis mellifera. AFB is worldwide distributed and causes great economic losses to beekeepers, but in many cases early diagnosis could help in its prevention and control. The aim of the present work was to design a reliable protocol for DNA extraction of P. larvae spores from naturally contaminated honey and adult bees. A novel method that includes a step of spore-decoating followed by an enzymatic spore disruption and DNA purification was developed. Also a freeze-thaw cycle protocol was tested and the results were compared. The DNA extracted was used as template for specific bacterial detection by amplification of a 16S rDNA fragment. Both methods allowed the direct detection by polymerase chain reaction (PCR) of P. larvae spores present in naturally contaminated material. The sporedecoating strategy was the most successful method for DNA extraction from spores, allowing specific and remarkably sensitive PCR detection of spores in all honey and bees tested samples. On the other hand freeze-thawing was only effective for detection of spores recovered from bees, and extensive damage to DNA affected detection by PCR. This work provides new strategies for spore DNA extraction and detection by PCR with high sensitivity, and brings an alternative tool for P. larvae detection in natural samples.