For bacterial typing to be useful, the development, validation and appropriate application of typing methods must follow unified criteria. Over a decade ago, ESGEM, the ESCMID (Europen Society for Clinical Microbiology and Infectious Diseases) Study Group on Epidemiological Markers, produced guidelines for optimal use and quality assessment of the then most frequently used typing procedures. We present here an update of these guidelines, taking into account the spectacular increase in the number and quality of typing methods made available over the past decade. Newer and older, phenotypic and genotypic methods for typing of all clinically relevant bacterial species are described according to their principles, advantages and disadvantages. Criteria for their evaluation and application and the interpretation of their results are proposed. Finally, the issues of reporting, standardisation, quality assessment and international networks are discussed. It must be emphasised that typing results can never stand alone and need to be interpreted in the context of all available epidemiological, clinical and demographical data relating to the infectious disease under investigation. A strategic effort on the part of all workers in the field is thus mandatory to combat emerging infectious diseases, as is financial support from national and international granting bodies and health authorities.

Background. Infants with pertussis infection are at risk of severe clinical illness and death. Several countries, including the United Kingdom, have introduced maternal pertussis vaccination during pregnancy to protect infants from infection following national increases in pertussis notifications. The objective of this study was to estimate the effectiveness of maternal pertussis vaccination in protecting infants against laboratory-confirmed pertussis infection. Methods. A case-control study was undertaken in England and Wales between October 2012 and July 2013. Cases were infants aged <8 weeks at onset with pertussis infection tested by real-time polymerase chain reaction or culture. Family doctors of each case were asked to identify healthy infants born consecutively after the case in each practice, to act as controls. Fifty-eight cases and 55 controls were included in this study. Odds ratios (ORs) were calculated for the association between maternal vaccination and infant pertussis infection. The vaccine effectiveness (VE) was calculated as 1 – OR. This was adjusted for sex, geographical region, and birth period. Results. Mothers of 10 cases (17%) and 39 controls (71%) received pertussis vaccine in pregnancy. This gave an unadjusted VE of 91% (95% confidence interval [CI], 77%–97%). Adjusted VE was 93% (95% CI, 81%–97%). Conclusions. Maternal pertussis vaccination is effective in preventing pertussis infection in infants aged <8 weeks and may be considered in other countries experiencing high levels of pertussis notifications.

Bordetella pertussiscauses pertussis, a respiratory disease that is most severe for infants. Vaccination was introduced in the 1950s, and in recent years, a resurgence of disease was observed worldwide, with significant mortality in infants. Possible causes for this include the switch from whole-cell vaccines (WCVs) to less effective acellular vaccines (ACVs), waning immunity, and pathogen adaptation. Pathogen adaptation is suggested by antigenic divergence between vaccine strains and circulating strains and by the emergence of strains with increased pertussis toxin production. We applied comparative genomics to a worldwide collection of 343B. pertussisstrains isolated between 1920 and 2010. The global phylogeny showed two deep branches; the largest of these contained 98% of all strains, and its expansion correlated temporally with the first descriptions of pertussis outbreaks in Europe in the 16th century. We found little evidence of recent geographical clustering of the strains within this lineage, suggesting rapid strain flow between countries. We observed that changes in genes encoding proteins implicated in protective immunity that are included in ACVs occurred after the introduction of WCVs but before the switch to ACVs. Furthermore, our analyses consistently suggested that virulence-associated genes and genes coding for surface-exposed proteins were involved in adaptation. However, many of the putative adaptive loci identified have a physiological role, and further studies of these loci may reveal less obvious ways in whichB. pertussisand the host interact. This work provides insight into ways in which pathogens may adapt to vaccination and suggests ways to improve pertussis vaccines.IMPORTANCEWhooping cough is mainly caused byBordetella pertussis, and current vaccines are targeted against this organism. Recently, there have been increasing outbreaks of whooping cough, even where vaccine coverage is high. Analysis of the genomes of 343B. pertussisisolates from around the world over the last 100 years suggests that the organism has emerged within the last 500 years, consistent with historical records. We show that global transmission of new strains is very rapid and that the worldwide population ofB. pertussisis evolving in response to vaccine introduction, potentially enabling vaccine escape.

A previously described sequence-based epidemiological typing method for clinical and environmental isolates ofLegionella pneumophilaserogroup 1 was extended by the investigation of three additional gene targets and modification of one of the previous targets. Excellent typeability, reproducibility, and epidemiological concordance were determined for isolates belonging to both serogroup 1 and the other serogroups investigated. Gene fragments were amplified from genomic DNA, and PCR amplicons were sequenced by using forward and reverse primers. Consensus sequences are entered into an online database, which allows the assignment of individual allele numbers. The resulting sequence-based type or allelic profile comprises a string of the individual allele numbers separated by commas, e.g., 1,4,3,1,1,1, in a predetermined order, i.e.,flaA,pilE,asd,mip,mompS, andproA. The index of discrimination (D) obtained with these six loci was calculated following analysis of a panel of 79 unrelated clinical isolates. ADvalue of >0.94 was obtained, and this value appears to be sufficient for use in the epidemiological investigation of outbreaks caused byL. pneumophila. TheDvalue rose to 0.98 when the results of the analysis were combined with those of monoclonal antibody subgrouping. Sequence-based typing ofL. pneumophilais epidemiologically concordant and discriminatory, and the data are easily transportable. This consensus method will assist in the epidemiological investigation ofL. pneumophilainfections, especially travel-associated cases, by which it will allow a rapid comparison of isolates obtained in more than one country.