Wave upon wave of disease: The cholera pathogen, Vibrio cholerae , is considered to be ubiquitous in water systems, making the design of eradication measures apparently fruitless. Nevertheless, local and global Vibrio populations remain distinct. Now, Weill et al. and Domman et al. show that a surprising diversity between continents has been established. Latin America and Africa bear different variants of cholera toxin with different transmission dynamics and ecological niches. The data are not consistent with the establishment of long-term reservoirs of pandemic cholera or with a relationship to climate events. Science , this issue p. 785 , p. 789

Background: Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. In addition, genetic variability of all the P. aeruginosa strains whose genomes have been sequenced is extremely low. This low genomic variability might be explained if clinical strains constitute a subpopulation of this bacterial species present in environments that are close to human populations, which preferentially produce virulence associated traits. Results: In this work, we sequenced the genomes and performed phenotypic descriptions for four non-human P. aeruginosa isolates collected from a plant, the ocean, a water-spring, and from dolphin stomach. We show that the four strains are phenotypically diverse and that this is not reflected in genomic variability, since their genomes are almost identical. Furthermore, we performed a detailed comparative genomic analysis of the four strains studied in this work with the thirteen previously reported P. aeruginosa genomes by means of describing their core and pan-genomes. Conclusions: Contrary to what has been described for other bacteria we have found that the P. aeruginosa core genome is constituted by a high proportion of genes and that its pan-genome is thus relatively small. Considering the high degree of genomic conservation between isolates of P. aeruginosa from diverse environments, including human tissues, some implications for the treatment of infections are discussed. This work also represents a methodological contribution for the genomic study of P. aeruginosa, since we provide a database of the comparison of all the proteins encoded by the seventeen strains analyzed.

In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

Objective: In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. Results: Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved.

Studies based on the analysis of housekeeping genes indicate thatEscherichia coliand allShigellaspecies, except forShigellaboydiitype 13, belong to a single species. This study analysed the phenotypicand genotypic characteristics of 23E.colistrains isolatedin different countries from faecal specimens taken from children with diarrhoea.Strains were identified using the VITEK system and typed with rabbit seraobtained against 186 somatic and 53 flagellarE. coliantigens andagainst 45Shigellasomatic antigens. Biochemical analysis of thesestrains showed a typicalE. coliprofile with a defined reactionagainst bothE.coliO179 andS.boydii16 somatic antisera. Agglutination assays for flagellar antigens showed aresponse against H2 in 7 (30 %) strains, H10 in 2 (9 %)strains, H32 in 12 (52 %) strains and H34 in 2 (9 %)strains, demonstrating 4 serotypes associated with this new somatic antigen64474. A serum against one of theseE.colistrains (64474)was prepared. Absorption assays ofS.boydii16 andE.coli64474 antisera withE. coliO179 antigen removedthe agglutination response against this O179 antigen completely, while theagglutination titres against bothS.boydii16 andE. coli64474 remained the same. Four (17 %)E.colistrains showed antimicrobial resistance to piperacillinonly, one (4 %) to piperacillin and trimethoprim/sulfamethoxazole,one (4 %) to ciprofloxacin, nitrofurantoin and piperacillin,and two (9 %) strains were resistant to ciprofloxacin,norfloxacin, ofloxacin, piperacillin and trimethoprim/sulfamethoxazole.With regards to PCR assays, one (4 %) of the strainswas positive forShigellageneipaH, one (4 %)foripaA, two (9 %) foripaB, one (4 %)foripaD, two (9 %) forsepAandthree (13 %) forospF. Therfbgenecluster in theE. colistrains was analysed by RFLP and comparedwith the gene cluster obtained fromS. boydii16. Therfb-RFLPpatterns for all 23E.colistrains were similar to thoseobtained forS.boydii16. The results from PCR tests todetectrfbgeneswzx(encoding O unit flippase)andwzy(encoding polymerase) belonging to a cluster relatedto the biosynthesis of theS. boydii16-specific O antigen were positivein 21 (91 %) and 22 (96 %)of the strains, respectively. PCR assays to detectE.colivirulence genes were also performed. These assays detected enterotoxigenicE.coligenesltA1in 12 of the strains (52 %),st1ain 4 (17 %),cfa1 in 6 (26 %),cs1 in 1 (4 %),cs3 in 3 (13 %),cs13 in 9 (39 %) andcs14 in 5 (22 %)of the strains. Results from the PFGE analyses confirmed the wide geographicaldistribution of these strains suggesting that 64474 : H2, 64474 : H10,64474 : H32 and 64474 : H34 are new serotypesofE.colistrains with a defined virulence capacity, andshare a common O antigen withS. boydii16.

In 2011, an outbreak of hemorrhagic colitis and hemolytic uremic syndrome (HUS) was reported in Europe that was related to a hybrid STEAEC of Escherichia coli (E. coli) O104:H4 strain. The current study aimed to analyze strains of E. coli O104 and O9 isolated before 2011. The study included 47 strains isolated from children with and without diarrhea between 1986 and 2009 from different geographic regions, as well as seven reference strains. Serotyping was carried out on 188 anti-O and 53 anti-H sera. PCR was used to identify DEC genes and phylogenetic groups. Resistance profiles to antimicrobials were determined by diffusion in agar, while PFGE was used to analyze genomic similarity. Five serotypes of E. coli O104 and nine of O9 were identified, as well as an antigenic cross-reaction with one anti-E. coli O9 serum. E. coli O104 and O9 presented diarrheagenic E. coli (DEC) genes in different combinations and were located in commensal phylogenetic groups with different antimicrobial resistance. PFGE showed that O104:H4 and O9:(H4, NM) strains from SSI, Bangladesh and México belong to a diverse group located in the same subgroup. E. coli O104 and O9 were classified as commensal strains containing DEC genes. The groups were genetically diverse with pathogenic potential making continued epidemiologic surveillance important.