Strengthening Bordetella pertussis genomic surveillance by direct sequencing of residual positive specimens.

Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of Bordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA "baits" targeting B. pertussis fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of B. pertussis genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of B. pertussis sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS481 Ct < 35 and >10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.

The genetic landscape of germline DDX41 variants predisposing to myeloid neoplasms.

Germline DDX41 variants are the most common mutations predisposing to acute myeloid leukemia (AML)/myelodysplastic syndrome (MDS) in adults, but the causal variant (CV) landscape and clinical spectrum of hematologic malignancies (HMs) remain unexplored. Here, we analyzed the genomic profiles of 176 patients with HM carrying 82 distinct presumably germline DDX41 variants among a group of 9821 unrelated patients. Using our proposed DDX41-specific variant classification, we identified features distinguishing 116 patients with HM with CV from 60 patients with HM with variant of uncertain significance (VUS): an older age (median 69 years), male predominance (74% in CV vs 60% in VUS, P = .03), frequent concurrent somatic DDX41 variants (79% in CV vs 5% in VUS, P < .0001), a lower somatic mutation burden (1.4 ± 0.1 in CV vs 2.9 ± 0.04 in VUS, P = .012), near exclusion of canonical recurrent genetic abnormalities including mutations in NPM1, CEBPA, and FLT3 in AML, and favorable overall survival (OS) in patients with AML/MDS. This superior OS was determined independent of blast count, abnormal karyotypes, and concurrent variants, including TP53 in patients with AML/MDS, regardless of patient's sex, age, or specific germline CV, suggesting that germline DDX41 variants define a distinct clinical entity. Furthermore, unrelated patients with myeloproliferative neoplasm and B-cell lymphoma were linked by DDX41 CV, thus expanding the known disease spectrum. This study outlines the CV landscape, expands the phenotypic spectrum in unrelated DDX41-mutated patients, and underscores the urgent need for gene-specific diagnostic and clinical management guidelines.

Increased TIM-3 and galectin-9 serum levels in patients with advanced systemic mastocytosis.

BACKGROUND: Systemic mastocytosis is characterized by expansion of clonal mast cells in various tissues. Several biomarkers with diagnostic and therapeutic potential have recently been characterized in mastocytosis, such as the serum marker tryptase and the immune checkpoint molecule PD-L1. OBJECTIVE: We aimed to investigate whether serum levels of other checkpoint molecules are altered in systemic mastocytosis and whether these proteins are expressed in mastocytosis infiltrates in the bone marrow. METHODS: Levels of different checkpoint molecules were analyzed in serum of patients with different categories of systemic mastocytosis and healthy controls and correlated to disease severity. Bone marrow biopsies from patients with systemic mastocytosis were stained to confirm expression. RESULTS: Serum levels of TIM-3 and galectin-9 were increased in systemic mastocytosis, particularly in advanced subtypes, compared with healthy controls. TIM-3 and galectin-9 levels were also found to correlate with other biomarkers of systemic mastocytosis, such as serum tryptase and KIT D816V variant allele frequency in the peripheral blood. Moreover, we observed expression of TIM-3 and galectin-9 in mastocytosis infiltrates in bone marrow. CONCLUSIONS: Together, our results demonstrate for the first time that serum levels of TIM-3 and galectin-9 are increased in advanced systemic mastocytosis. Moreover, TIM-3 and galectin-9 are expressed in bone marrow infiltrates in mastocytosis. These findings provide a rationale for exploring TIM-3 and galectin-9 as diagnostic markers and eventually therapeutic targets in systemic mastocytosis, particularly in advanced forms.

Challenges to the delivery and utilisation of child healthcare services: a qualitative study of the experiences of nurses and caregivers in a rural district in Ghana.

BACKGROUND: Sub-Saharan Africa has one of the poorest child health outcomes in the world. Children born in this region face significant health challenges that jeopardise their proper growth and development. Even though the utilisation of child healthcare services safeguards the health of children, the challenges encountered by nurses in the delivery of services, and caregivers in the utilisation of these services, especially in rural areas, have contributed to poor child health outcomes in this region. AIM: This study explored the experiences of nurses and caregivers in respect of the nursing human resource challenges to the delivery and utilisation of child healthcare services in a rural district in Ghana. METHODS: Individual qualitative interviews were conducted with ten nurses, who rendered child healthcare services; nine caregivers, who regularly utilised the available child healthcare services; and seven caregivers, who were not regular users of these services. These participants were purposively selected for the study. Data were collected using individual semi-structured interview guides and analysed qualitatively using content analysis. Themes and sub-themes were generated during the data analysis. The Ghana Health Service Research Ethics Review Committee and the Nelson Mandela University's Research Ethics Committee approved the study protocol prior to data collection. RESULTS: Three main themes emerged from the data analysis. Theme One focused on the shortage of nurses, which affected the quality and availability of child healthcare services. Theme Two focused on inexperienced nurses, who struggled to cope with the demands related to the delivery of child healthcare services. Theme Three focused on the undesirable attitude displayed by nurses, which discouraged caregivers from utilising child healthcare services. CONCLUSION: Nurses contribute significantly to the delivery of child healthcare services; hence, the inadequacies amongst nurses, in terms of staff numbers and nursing expertise, affect the quality and availability of child healthcare services. Also, caregivers' perceptions of the quality of child healthcare services are based on the treatment they receive at the hands of nurses and other healthcare workers. In this respect, the bad attitude of nurses may disincentivise caregivers in terms of their utilisation of these services, as and when needed. There is an urgent need to comprehensively address these challenges to improve child healthcare outcomes in rural areas in Ghana. Relevant authorities should decentralise training workshops for nurses in rural areas to update their skills. Additionally, health facilities should institute proper orientation and mentoring systems to assist newly recruited nurses to acquire the requisite competences for the delivery of quality family-centred care child healthcare services.

Burkitt Lymphoma After Cardiac Transplantation: Therapeutic Considerations.

Postsolid organ transplant Burkitt lymphoma (PSOT-BL) is rare but more aggressive than other post-transplant lymphoproliferative disorders (PTLD). Little is known about optimal treatment and outcome of postcardiac transplant Burkitt lymphoma (BL). We report an 8-year-old boy with a history of heart transplant who developed Epstein-Barr virus positive, late-onset PSOT-BL. He was successfully treated with BL specific chemoimmunotherapy and cessation of baseline immunosuppression. In this pediatric case of PSOT-BL, the use of standard intensive pediatric based chemoimmunotherapy regimen without modifications was feasible, well tolerated and resulted in complete remission. Long-term toxicities need further study.

Impact of brief educational intervention on knowledge of cancer among community pharmacists.

INTRODUCTION: Community pharmacists may play a vital role in early detection and prevention of cancer. Findings from our pre-assessment studies showed that the Ghanaian community have inadequate knowledge of cancer. We assessed the impact of a brief educational intervention on knowledge level of cancer among Ghanaian community pharmacists. METHOD: The study was a descriptive interventional study. Knowledge of cancer, signs and symptoms, risk factors and cancer screening tests were assessed before in a pre-assessment study and after a brief online education in our current study. A total of 435 community pharmacists were recruited in both studies. RESULTS: The mean ± SD total knowledge score of cancer increased from 9.03 ± 2.65 to 12.97 ± 1.43 out of a maximum score of 15 points. The mean ± SD total knowledge score of signs and symptoms of cancer increased from 4.15 ± 2.14 to 6.86 ± 0.76 out of a maximum score of 7 points. For the total knowledge score of causes and risk factors of cancer, the mean ± SD score increased from 8.13 ± 3.31 to 11.59 ± 0.87 out of a maximum score of 12 points. Lastly, the mean ± SD total knowledge score of cancer screening tests increased from 9.04 ± 5.01 to 16.39 ± 0.86 out of a maximum score of 18 points. CONCLUSION: There were overall statistically significant improvements of participants knowledge in all aspects of cancer in this study compared to the pre-assessment study. Our study presents evidence of the effectiveness of a brief educational intervention tailor-made for Ghanaian community pharmacists.

Socio-cultural barriers to the delivery and utilisation of child healthcare services in rural Ghana: a qualitative study.

BACKGROUND: Over half of global deaths among children under five years of age occur in sub-Saharan Africa. Prompt and consistent access to and utilisation of child healthcare services improves child health outcomes. However, socio-cultural barriers impede the utilisation of child healthcare services among rural dwellers in Ghana. There is a paucity of studies that explore the experiences of nurses and caregivers regarding the socio-cultural barriers to the delivery and utilisation of child healthcare services in rural areas in Ghana such as the Nkwanta South Municipality. PURPOSE: The purpose of this study was to explore the experiences of nurses and caregivers regarding the socio-cultural barriers that impede the delivery and utilisation of child healthcare services by caregivers for their children in the Nkwanta South Municipality, Ghana. METHODS: Data were collected through semi-structured interviews conducted with a purposive sample of ten nurses and nine caregivers of children under five years of age who utilised the available child healthcare services in a rural setting. The consent of all participants was sought and given before interviews were conducted. Data analysis entailed coding and the generation of themes the codes. RESULTS: The exploration of experiences of nurses and caregivers of children under-five years of age revealed that certain socio-cultural beliefs and practices, language barriers and reliance of caregivers on self-medication were the main socio-cultural barriers that impeded the delivery and utilisation of child healthcare services in the Nkwanta South Municipality. CONCLUSION: Nurses and caregivers experienced several socio-cultural barriers which either delayed care seeking by caregivers for their sick children or interfered with the smooth and prompt delivery of needed child healthcare services by nurses. Some of the barriers negatively affected the interaction between nurses and caregivers with the tendency to affect subsequent child healthcare service utilisation. It is recommended that healthcare managers and nurses should foster close collaboration with caregivers and community leaders to address these socio-cultural barriers and facilitate prompt and consistent utilisation of child healthcare service in rural areas.

Integrative literature review of evidence-based guidelines on antiretroviral therapy adherence among adult persons living with HIV.

AIM: To summarize recommendations from available evidence-based guidelines that enhance, address or guide antiretroviral therapy adherence among adult persons living with human immunodeficiency virus. DESIGN: An integrative literature review approach. DATA SOURCE: Guidelines were accessed through Google from the databases of the Canadian Medical Association InfoBase clinical practice database, National Guidelines Clearinghouse, Writer's Guidelines database, the National Institute for Health and Clinical Excellence, UNICEF and WHO. Databases such as PubMed, Google Scholar, EBSCOhost (CINAHL, ERIC, Academic search complete, E-journals, Psych Info and MEDLINE), EMERALD INSIGHT, JSTOR, SCIENCE DIRECT and FINDPLUS were also searched, followed by a citation search. Data sources were searched between 1996 and January 2022. REVIEW METHODS: The five steps of the integrative literature review process, as described by Whittemore and Knafl, were used. These steps are as follows: step one; problem identification, step two; literature search, step three; data evaluation; step four: data analysis and the final step was data presentation. RESULTS: Sixteen guidelines related to antiretroviral therapy adherence were included for data extraction and synthesis. The findings revealed two themes as follows: theme 1: monitoring antiretroviral therapy adherence and theme 2: interventions to promote antiretroviral therapy adherence related to education and counselling, adherence tools, health service delivery and antiretroviral strategies. CONCLUSION: Antiretroviral therapy adherence in adult persons requires both interventions as well as monitoring. The various contributing factors relating to antiretroviral therapy adherence should be further explored. IMPACT: Evidence from the included guidelines can assist nurses in promoting a person's adherence to antiretroviral treatment, which could improve their health and well-being.

Investigation of a Large Diphtheria Outbreak and Cocirculation of Corynebacterium pseudodiphtheriticum Among Forcibly Displaced Myanmar Nationals, 2017-2019.

BACKGROUND: Diphtheria, a life-threatening respiratory disease, is caused mainly by toxin-producing strains of Corynebacterium diphtheriae, while nontoxigenic corynebacteria (eg, Corynebacterium pseudodiphtheriticum) rarely causes diphtheria-like illness. Recently, global diphtheria outbreaks have resulted from breakdown of health care infrastructures, particularly in countries experiencing political conflict. This report summarizes a laboratory and epidemiological investigation of a diphtheria outbreak among forcibly displaced Myanmar nationals in Bangladesh. METHODS: Specimens and clinical information were collected from patients presenting at diphtheria treatment centers. Swabs were tested for toxin gene (tox)-bearing C. diphtheriae by real-time polymerase chain reaction (RT-PCR) and culture. The isolation of another Corynebacterium species prompted further laboratory investigation. RESULTS: Among 382 patients, 153 (40%) tested tox positive for C. diphtheriae by RT-PCR; 31 (20%) PCR-positive swabs were culture confirmed. RT-PCR revealed 78% (298/382) of patients tested positive for C. pseudodiphtheriticum. Of patients positive for only C. diphtheriae, 63% (17/27) had severe disease compared to 55% (69/126) positive for both Corynebacterium species, and 38% (66/172) for only C. pseudodiphtheriticum. CONCLUSIONS: We report confirmation of a diphtheria outbreak and identification of a cocirculating Corynebacterium species. The high proportion of C. pseudodiphtheriticum codetection may explain why many suspected patients testing negative for C. diphtheriae presented with diphtheria-like symptoms.

Genomic Surveillance and Improved Molecular Typing of Bordetella pertussis Using wgMLST.

Multilocus sequence typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, classical MLST schemes for Bordetella pertussis, the causative agent of whooping cough, seldom reveal diversity among the small number of gene targets and thereby fail to delineate population structure. To improve the discriminatory power of allele-based molecular typing of B. pertussis, we have developed a whole-genome MLST (wgMLST) scheme from 225 reference-quality genome assemblies. Iterative refinement and allele curation resulted in a scheme of 3,506 coding sequences and covering 81.4% of the B. pertussis genome. This wgMLST scheme was further evaluated with data from a convenience sample of 2,389 B. pertussis isolates sequenced on Illumina instruments, including isolates from known outbreaks and epidemics previously characterized by existing molecular assays, as well as replicates collected from individual patients. wgMLST demonstrated concordance with whole-genome single nucleotide polymorphism (SNP) profiles, accurately resolved outbreak and sporadic cases in a retrospective comparison, and clustered replicate isolates collected from individual patients during diagnostic confirmation. Additionally, a reanalysis of isolates from two statewide epidemics using wgMLST reconstructed the population structures of circulating strains with increased resolution, revealing new clusters of related cases. Comparison with an existing core genome (cgMLST) scheme highlights the stable gene content of this bacterium and forms the initial foundation for necessary standardization. These results demonstrate the utility of wgMLST for improving B. pertussis characterization and genomic surveillance during the current pertussis disease resurgence.

Detection and Characterization of Diphtheria Toxin Gene-Bearing Corynebacterium Species through a New Real-Time PCR Assay.

Respiratory diphtheria, characterized by a firmly adherent pseudomembrane, is caused by toxin-producing strains of Corynebacterium diphtheriae, with similar illness produced occasionally by toxigenic Corynebacterium ulcerans or, rarely, Corynebacterium pseudotuberculosis While diphtheria laboratory confirmation requires culture methods to determine toxigenicity, real-time PCR (RT-PCR) provides a faster method to detect the toxin gene (tox). Nontoxigenic tox-bearing (NTTB) Corynebacterium isolates have been described, but impact of these isolates on the accuracy of molecular diagnostics is not well characterized. Here, we describe a new triplex RT-PCR assay to detect tox and distinguish C. diphtheriae from the closely related species C. ulcerans and C. pseudotuberculosis Analytical sensitivity and specificity of the assay were assessed in comparison to culture using 690 previously characterized microbial isolates. The new triplex assay characterized Corynebacterium isolates accurately, with 100% analytical sensitivity for all targets. Analytical specificity with isolates was 94.1%, 100%, and 99.5% for tox, Diph_rpoB, and CUP_rpoB targets, respectively. Twenty-nine NTTB Corynebacterium isolates, representing 5.9% of 494 nontoxigenic isolates tested, were detected by RT-PCR. Whole-genome sequencing of NTTB isolates revealed varied mutations putatively underlying their lack of toxin production, as well as eight isolates with no mutation in tox or the promoter region. This new Corynebacterium RT-PCR method provides a rapid tool to screen isolates and identify probable diphtheria cases directly from specimens. However, the sporadic occurrence of NTTB isolates reinforces the viewpoint that diphtheria culture diagnostics continue to provide the most accurate case confirmation.

Genomic Survey of Bordetella pertussis Diversity, United States, 2000-2013.

We characterized 170 complete genome assemblies from clinical Bordetella pertussis isolates representing geographic and temporal diversity in the United States. These data capture genotypic shifts, including increased pertactin deficiency, occurring amid the current pertussis disease resurgence and provide a foundation for needed research to direct future public health control strategies.

PD-L1 Expression in Mastocytosis.

Programmed death 1 (PD-1), when activated by its ligands PD-L1 and PD-L2, suppresses active immune cells in normal immune regulation to limit autoimmunity and, in tumors, as a mechanism of immune evasion. PD-L1 expression has been described as both a prognostic and predictive marker in many solid and hematologic neoplasms, as targeted therapies against the PD-1/PD-L1 interaction have gained clinical importance. PD-L1 expression has been assessed in a few studies on mastocytosis. We review this literature and the need for further investigation of the tumor-immune interaction in mastocytosis.

Sustained centrosome-cortical contact ensures robust polarization of the one-cell C. elegans embryo.

In C. elegans, the anterior-posterior axis is established at the one-cell stage when the embryo polarizes along its long axis. One model suggests that a cue from the centrosome triggers symmetry breaking and is then dispensable for further steps in the process. In the absence of the initial centrosome cue, a redundant mechanism, reliant on the centrosome's microtubules, can polarize the cell. Despite this model, data from multiple sources suggest that direct centrosome-contact with the cortex may play a role in ensuring robust polarization. Some of this past work includes analysis of pam-1 mutants, which lack a functional puromycin-sensitive aminopeptidase and have aberrant centrosome positioning and variable polarization defects. To better understand the role of centrosome dynamics in polarization, we looked in detail at centrosome behavior in relation to key polarity landmarks in pam-1 mutants as well as those lacking cortical flows. We provide evidence for a model in which sustained direct contact between the centrosome and the cortex acts to reinforce both the actomyosin and the microtubule-dependent pathways. This contact is necessary for polarization when flows are inhibited.

Screening and Genomic Characterization of Filamentous Hemagglutinin-Deficient Bordetella pertussis.

Despite high vaccine coverage, pertussis cases in the United States have increased over the last decade. Growing evidence suggests that disease resurgence results, in part, from genetic divergence of circulating strain populations away from vaccine references. The United States employs acellular vaccines exclusively, and current Bordetella pertussis isolates are predominantly deficient in at least one immunogen, pertactin (Prn). First detected in the United States retrospectively in a 1994 isolate, the rapid spread of Prn deficiency is likely vaccine driven, raising concerns about whether other acellular vaccine immunogens experience similar pressures, as further antigenic changes could potentially threaten vaccine efficacy. We developed an electrochemiluminescent antibody capture assay to monitor the production of the acellular vaccine immunogen filamentous hemagglutinin (Fha). Screening 722 U.S. surveillance isolates collected from 2010 to 2016 identified two that were both Prn and Fha deficient. Three additional Fha-deficient laboratory strains were also identified from a historic collection of 65 isolates dating back to 1935. Whole-genome sequencing of deficient isolates revealed putative, underlying genetic changes. Only four isolates harbored mutations to known genes involved in Fha production, highlighting the complexity of its regulation. The chromosomes of two Fha-deficient isolates included unexpected structural variation that did not appear to influence Fha production. Furthermore, insertion sequence disruption of fhaB was also detected in a previously identified pertussis toxin-deficient isolate that still produced normal levels of Fha. These results demonstrate the genetic potential for additional vaccine immunogen deficiency and underscore the importance of continued surveillance of circulating B. pertussis evolution in response to vaccine pressure.

The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement.

Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology.IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a large number of repetitive mobile genetic elements that obstruct genome analysis. However, these mobile elements facilitate large rearrangements that alter the order and orientation of essential protein-encoding genes, which otherwise exhibit little nucleotide sequence diversity. By comparing the complete genome assemblies from 257 isolates, we show that specific rearrangements have been conserved throughout recent evolutionary history, perhaps by eliciting changes in gene expression, which may also provide useful information for molecular epidemiology.

The quality of life of HIV-infected South African university students: Experiences with the WHOQOL-HIV-Bref.

HIV and AIDS has serious repercussions on psychological, social and physical well-being, and the assessment of Quality of Life (QoL) of people living with HIV and AIDS is essential to gauge how these challenges are met. The WHOQoL-HIV Bref forms part of a suite of instruments developed by the World Health Organisation. The purpose of this paper is to describe the quality of life of a sample of HIV-infected students at a South African university, as well as explain the internal consistency between questions within each of the QoL domains. A descriptive, cross-sectional study design using a quantitative approach was applied. A non-probability, purposive sampling approach was utilized and students enrolled in the antiretroviral therapy or wellness programme were invited to voluntarily participate in this study. The WHOQOL-HIV Bref was self-administered after explanation of the questions by a registered, trained health care professional. A total of 63 students returned completed questionnaires that were included in the analysis. Acceptable to good reliability scores were established for the following domains: Level of Independence; Social Relations; Environment and Spiritual or Personal Beliefs. Assessing QoL in the sample, the lowest score was for "Spirituality" and the highest "Social Relations". The "Physical" and "Psychological" domain scores for females were significantly lower than the score for males. There was no significant difference between any of the domain scores among participants with CD4 cell counts above or below 350 cells/mm3. In general the performance of this sample is encouraging and it is recommended that the measure be utilized for QoL screening, and further research. The WHOQOL-HIV Bref for students does not contain an academic wellness component which should be added considering the significant effects of HIV on neuropsychological functioning. Also further investigation into the reasons for poor scores obtained in physical and psychological well-being in females should be encouraged.

Epidemiology of Pertussis Among Young Pakistani Infants: A Community-Based Prospective Surveillance Study.

BACKGROUND: Pertussis remains a cause of morbidity and mortality among young infants. There are limited data on the pertussis disease burden in this age group from low- and lower-middle-income countries, including in South Asia. METHODS: We conducted an active community-based surveillance study from February 2015 to April 2016 among 2 cohorts of young infants in 4 low-income settlements in Karachi, Pakistan. Infants were enrolled either at birth (closed cohort) or at ages up to 10 weeks (open cohort) and followed until 18 weeks of age. Nasopharyngeal swab specimens were obtained from infants who met a standardized syndromic case definition and tested for Bordetella pertussis using real-time polymerase chain reaction. We determined the incidence of pertussis using a protocol-defined case definition, as well as the US Centers for Disease Control and Prevention (CDC) definitions for confirmed and probable pertussis. RESULTS: Of 2021 infants enrolled into the study, 8 infants met the protocol-defined pertussis case definition, for an incidence of 3.96 (95% confidence interval [CI], 1.84-7.50) cases per 1000 infants. Seven of the pertussis cases met the CDC pertussis case definition (5 confirmed, 2 probable), for incidences of CDC-defined confirmed pertussis of 2.47 (95% CI, .90-5.48) cases per 1000 infants, and probable pertussis of 0.99 (95% CI, .17-3.27) cases per 1000 infants. Three of the pertussis cases were severe according to the Modified Preziosi Scale score. CONCLUSIONS: In one of the first prospective surveillance studies of infant pertussis in a developing country, we identified a moderate burden of pertussis disease in early infancy in Pakistan.

Bordetella pertussis Strain Lacking Pertactin and Pertussis Toxin.

A Bordetella pertussis strain lacking 2 acellular vaccine immunogens, pertussis toxin and pertactin, was isolated from an unvaccinated infant in New York State in 2013. Comparison with a French strain that was pertussis toxin-deficient, pertactin wild-type showed that the strains carry the same 28-kb deletion in similar genomes.