Comparative genomics of Acinetobacter baumannii and therapeutic bacteriophages from a patient undergoing phage therapy

In 2016, a 68-year-old patient with a disseminated multi-drug resistant Acinetobacter baumannii infection was treated using lytic bacteriophages in one of the first modern human clinical uses of phage therapy in the United States. Due to the emergency nature of the treatment there was little time to thoroughly characterize the phages used in this intervention or the pathogen itself. Here we report the genomes of the nine phages used for treatment and three strains of A. baumannii isolated prior to and during treatment. The eight phages used in the initial treatment were found to be a group of closely related T4-like myophages; the ninth phage, AbTP3Φ1, was found to be an unrelated Fri1-like podophage. Analysis of 19 A. baumannii isolates collected before and during phage treatment showed that resistance to the T4-like phages appeared as early as two days following the start of treatment. Three A. baumannii strains (TP1, TP2 and TP3) collected before and during treatment were sequenced to closure, and all contained a 3.9 Mb chromosome of sequence type 570 with a KL116 capsule locus and identical 8.7 kb plasmids. Phage-insensitive mutants of A. baumannii strain TP1 were generated in vitro and the majority of identified mutations were located in the bacterial capsule locus. The presence of the same mutation in both the in vitro mutants and in phage-insensitive isolates TP2 and TP3, which evolved in vivo during phage treatment, indicate that in vitro investigations can produce results that are relevant and predictive for the in vivo environment.

Draft Genome Sequences of Two Clinical Actinobacillus pleuropneumoniae Serotype 19 Strains from Pigs in Switzerland

Actinobacillus pleuropneumoniae serotype 19 is a very recently described new serotype with a novel type II capsule locus. Here, we report the draft genome sequences of two Actinobacillus pleuropneumoniae serotype 19 strains with a serogroup 3/6/8/12/15 O-antigen locus that were isolated in 2018 and 2021 from two different pig farms in Switzerland.

Relationships of capsular polysaccharides belonging to Campylobacter jejuni HS1 serotype complex

The Campylobacter jejuni capsule type HS1 complex is one of the most common serotypes identified worldwide, and consists of strains typing as HS1, HS1/44, HS44 and HS1/8. The capsule structure of the HS1 type strain was shown previously to be composed of teichoic-acid like glycerol-galactosyl phosphate repeats [4-)-α-D-Galp-(1–2)-Gro-(1-P-] with non-stoichiometric fructose branches at the C2 and C3 of Gal and non-stoichiometric methyl phosphoramidate (MeOPN) modifications on the C3 of the fructose. Here, we demonstrate that the capsule of an HS1/44 strain is identical to that of the type strain of HS1, and the capsule of HS1/8 is also identical to HS1, except for an additional site of MeOPN modification at C6 of Gal. The DNA sequence of the capsule locus of an HS44 strain included an insertion of 10 genes, and the strain expressed two capsules, one identical to the HS1 type strain, but with no fructose branches, and another composed of heptoses and MeOPN. We also characterize a HS1 capsule biosynthesis gene, HS1.08, as a fructose transferase responsible for the attachment of the β-D-fructofuranoses residues at C2 and C3 of the Gal unit. In summary, the common component of all members of the HS1 complex is the teichoic-acid like backbone that is likely responsible for the observed sero-cross reactivity.

The success of particular Acinetobacter baumannii clones: accumulating resistance and virulence inside a sugary shield

Background In Portugal, carbapenem-resistant Acinetobacter baumannii (CRAB) has been associated with ST98, ST103 and ST208 (Oxford Scheme, Oxf) and a clone has usually been associated with a particular period of time. These clonal shifts were primarily explained by an increased antimicrobial resistance profile. Here we explore genomic and biochemical differences among these and more recent clones, which could further explain the diversity and evolution of this species. Methods A total of 116 CRAB isolates (2010–15), together with representatives of a previously described CRAB collection (4 isolates, 2001–06) were characterized by attenuated total reflection Fourier transform infrared spectroscopy (FTIR-ATR) and MLST. Representatives of different FTIR-ATR/MLST clusters were selected for WGS (n = 13), which allowed the in silico extraction of resistance and virulence genes, capsule locus and SNP analysis. Results A. baumannii clonal shifts of OXA-58-producing ST103Oxf (2001–04), OXA-40-producing ST98Oxf (2002–06), OXA-23-producing ST208Oxf (2006–10) and OXA-23-producing ST218Oxf (2010–15) were accompanied by an increase in AMR genes and virulence factors. FTIR-ATR clustering was congruent with sugar composition predicted from the capsular locus: a fucosamine cluster comprising ST98Oxf, ST103Oxf and a single ST218Oxf isolate; a pseudaminic acid cluster of ST208Oxf and ST1557Oxf isolates; and legionaminic acid, resembling the sialic acid from mammalian cells, in a cluster comprising ST218Oxf isolates. The whole-genome phylogenetic tree was congruent with MLST, with isolates presenting 5–28 938 SNPs. ST208Oxf and ST218Oxf presented ∼1900 SNPs while ST103Oxf and ST1557Oxf showed a greater number of SNPs (∼28 000). Conclusions Clonal shifts of CRAB were promoted, in our country, by consecutive virulence and AMR gene pool enlargement, together with features increasing pathogen–host adaptation. Worldwide dominance of ST218Oxf is supported by the combination of high AMR and virulence levels.

Transformation of nonencapsulated Streptococcus pneumoniae during systemic infection

Streptococcus pneumoniae (pneumococcus) is a principal cause of bacterial middle ear infections, pneumonia, and meningitis. Capsule-targeted pneumococcal vaccines have likely contributed to increased carriage of nonencapsulated S. pneumoniae (NESp). Some NESp lineages are associated with highly efficient DNA uptake and transformation frequencies. However, NESp strains lack capsule that may increase disease severity. We tested the hypothesis that NESp could acquire capsule during systemic infection and transform into more virulent pneumococci. We reveal that NESp strains MNZ67 and MNZ41 are highly transformable and resistant to multiple antibiotics. Natural transformation of NESp when co-administered with heat-killed encapsulated strain WU2 in a murine model of systemic infection resulted in encapsulation of NESp and increased virulence during bacteremia. Functional capsule production increased the pathogenic potential of MNZ67 by significantly decreasing complement deposition on the bacterial surface. However, capsule acquisition did not further decrease complement deposition on the relatively highly pathogenic strain MNZ41. Whole genome sequencing of select transformants demonstrated that recombination of up to 56.7 kbp length occurred at the capsule locus, along with additional recombination occurring at distal sites harboring virulence-associated genes. These findings indicate NESp can compensate for lack of capsule production and rapidly evolve into more virulent strains.

Advancing Genetic Tools in Streptococcus pneumoniae

Streptococcus pneumoniae is the causative agent of a multitude of diseases, and further study into its pathogenies is vital. The pneumococcus is genetically malleable, and several tools are available to manipulate this pathogen. In this study, we attempted to utilize one such tool, the Sweet Janus cassette, to replace the capsule locus with other capsule loci in our strain background and found that the efficiency of allelic replacement was low and the number of revertant false-positive colonies was high. We determined that the capacity to recombine capsule varied by the initial isolated colony, suggesting that frequency of reversion is dependent on the bacterial clone. Alternative selection markers may further expand the application of Sweet Janus. We created novel cassettes that utilized chlorinated phenylalanine as an alternative counter-selection agent in conjunction with the Janus or Sweet Janus cassette, providing a new dual or triple selection marker. Moreover, we created cassettes that do not require engineered resistance in the background strain, including both single and dual selection markers. We were able to utilize all constructs in allelic replacement of the capsule loci. These novel constructs provide a new means for generating gene deletions in S. pneumoniae that expand experimental applications.

Advancing Genetic Tools in Streptococcus Pneumoniae

Streptococcus pneumoniae is the causative agent of a multitude of diseases and further study into its pathogenies is vital. The pneumococcus is genetically malleable and several tools are available to manipulate this pathogen. In this study, we attempted to utilize one such tool, the Sweet Janus cassette, to replace the capsule locus with other capsule loci in our strain background and found that the efficiency of allelic replacement was low and the number of revertant false-positive colonies was high. We determined that the capacity to recombine capsule varied by the initial isolated colony, suggesting that frequency of reversion is dependent on the bacterial cell line. Alternative selection markers may further expand the application of Sweet Janus. We created novel cassettes that utilized chlorinated phenylalanine as an alternative counter-selection agent in conjunction with the Janus or Sweet Janus cassette, providing a new dual or triple selection marker. Moreover, we created cassettes that do not require engineered resistance in the background strain, including both single and dual selection markers. We were able to utilize all constructs in allelic replacement of the capsule loci. These novel constructs provide a new means for generating gene deletions in S. pneumoniae that expand experimental applications.

Epidemiologia da doença meningocócica no Estado de Goiás, Brasil no período de 2010 a 2016

A doença meningocócica (DM) é uma infecção bacteriana aguda, potencialmente fatal causada pela bactéria Neisseria meningitidis, apresenta grande potencial epidêmico devido as suas características de evolução clínica rápida, gravidade e letalidade. O objetivo deste trabalho foi descrever a situação epidemiológica da doença meningocócica no Estado de Goiás, Brasil entre os anos de 2010 e 2016. Foi realizado levantamento de estudos descritivos dos casos confirmados de doença meningocócica registrados no Sistema de Informação de Agravos de Notificação (Sinan), datando de 1º de janeiro de 2010 a 31 de outubro de 2016 com taxas de incidência, mortalidade e projeções anuais populacionais calculadas com base nos registros do Sinan e Instituto Brasileiro de Geografia e Estatística (IBGE). O processamento e a análise de dados foi realizado com os programas: EpiInfoTM, TabWin e TabNet. No Estado de Goiás foram registrados 2.483 casos da doença. Houve, variação da taxa de incidência entre os anos de 2007 e 2011, tendo um decréscimo significativo igual a 33,3% em relação ao ano de 2010. Foram registrados 573 óbitos, com maior incidência em crianças menores de 1 ano. A maioria dos casos registrados é de residentes da zona urbana. O sorogrupo C foi mais incidente. Os principais achados foram: redução da taxa de incidência da doença meningocócica, constância da taxa de mortalidade geral, aumento na taxa de letalidade e predominância do sorogrupo C. A epidemiologia permite analisar o impacto da vacina sobre a carga da doença e a necessidade de estratégias de intervenção. Descritores: Meningite; Sepse; Epidemiologia. Referências Brasil. Ministério da Saúde. Influenza, Doença Meningocócica e Outras Meningites: Doença Meningocócica. In: SAÚDE, Ministério da. Guia de Vigilância em Saúde. 2. ed. Brasília: MS, 2017. Cap. 1. p. 33-44. Brasil. Ministério da Saúde. Influenza, Doença Meningocócica e Outras Meningites: Doença Meningocócica. In: SAÚDE, Guia de Vigilância em Saúde. 3. ed. Brasília: MS, 2019. Cap. 1. p. 33-44. Berezin EN. Doença meningocócica: epidemiologia da infecção meningocócica. SBP. Sociedade Brasileira de Pediatria. São Paulo. 2015. Santos ML, Ruffino-Netto A. Doença meningocócica: situação epidemiológica no Município de Manaus, Amazonas, Brasil, 1998/2002. Cad Saúde Pública. 2005;21(3):823-29. Castiñeiras TMPP, Pedro LGF, Martins FSV. Doença meningocócica. 2006. CIVES- Centro de Informação em Saúde para Viajantes - UFRJ. Rio de Janeiro. 2006 Barroso DE, Carvalho DM, Nogueira SA, Solari CA. Doença meningocócica: epidemiologia e controle de casos secundários. Rev Saúde Pública. 1998;32(1):89-97. Teixeira AB, Cavalcante JCV, Moreno IC, Soares IA, Holanda FOA. Meningite bacteriana: uma atualização. RBAC. 2018;50(4):327-29. Brasil. Ministério da Saúde. Secretaria de Vigilância em Saúde. Boletim Epidemiológico. Volume 50, nº 3, Brasília. 2019. Emmerick ICM, Campos MR, Schramm JMA, Silva RS, Costa MFS. Estimativas corrigidas de casos de meningite, Brasil 2008-2009. Epidemiol Serv Saúde. 2014;23(2):215-26. Brasil. Ministério da Saúde. Doenças Infecciosas e Parasitárias: Guia de Bolso. 3. ed. Brasília/DF; 2004.v.1. Harrison OB, Claus H, Jiang Y, Bennett JS, Bratcher HB, Jolley KA et al. Description and nomenclature of Neisseria meningitidis capsule locus. Emerg Infect Dis. 2013;19(4):566-73. Brasil. Ministério da Saúde. Secretaria da Vigilância em Saúde. Boletim Epidemiológico. Meningite bacteriana não especificada no Brasil 2007 - 2016. Brasília. 2016. Brasil. Ministério da Saúde. Casos de meningite em crianças brasileiras diminuíram nos últimos dois anos, 2012. Brasília. 2012. Brasil. Portaria nº 204, de 17 de fevereiro de 2016. Define a Lista Nacional de Notificação Compulsória de doenças, agravos e eventos de saúde pública nos serviços de saúde públicos e privados em todo o território nacional, nos termos do anexo, e dá outras providências. Diário Oficial da República Federativa do Brasil; Seção 1:23. Brasil. Ministério da Saúde. Secretaria de Vigilância em Saúde. Coordenação-Geral de Desenvolvimento da Epidemiologia em Serviços. Guia de Vigilância em Saúde: volume único, 2 ed. Brasília. 2017. Goias. Secretaria de Estado da Saúde (SES). Dia Mundial de combate às meningites é celebrado nesta quarta-feira. Governo do Estado de Goiás. 2019. Ministério da Saúde. Meningite. Sinan.Sistema de Informação de Agravos de Notificação. Brasília. 2019.

Clonal expansion of a virulent Streptococcus suis serotype 9 lineage distinguishable from carriage subpopulations

Streptococcus suis is a porcine pathogen, causing severe invasive infections. S. suis serotype 9 is increasingly causing disease in Dutch and Chinese pig herds, but it is unknown whether all serotype 9 isolates are equally virulent and markers that can identify virulent strains are not available. Therefore, discrimination between virulent isolates and carriage isolates typically not associated with disease, is currently not possible. We collected tonsillar S. suis isolates from 6 herds not previously diagnosed with S. suis infections, and clinical S. suis isolates of previously diseased pigs. We confirmed the virulence of a virulent type strain and one representative clinical isolate, and the lack of virulence of two carriage isolates, in a pig infection model. Phylogenetic analysis of whole genome sequences of 124 isolates resulted in 10 groups, of which two were almost uniquely populated by clinical isolates. The population structure of S. suis serotype 9 appears highly diverse. However, analysis of the capsule loci sequences showed variation in a single region which fully correlated with a virulent genotype. Transmission electron microscopy suggested differences in capsule thickness between carriage and clinical genotypes. In conclusion, we found that that the S. suis serotype 9 population in the Netherlands is diverse. A distinct virulence-associated lineage was identified and could be discriminated based on the capsule locus sequence. Whilst the difference in virulence cannot be directly attributed to the DNA sequence, the correlation of capsule locus sequence with virulence could be used in the development of diagnostic tests to identify potential virulent S. suis serotype 9 in pigs.