David M. Goldfarb

Detection of Plasmid-Mediated KPC-Producing Klebsiella pneumoniae in Ottawa, Canada: Evidence of Intrahospital Transmission

ABSTRACT Klebsiella pneumoniae isolates from three patients admitted to the Ottawa Hospital, a 1,040-bed teaching hospital, were found to contain the plasmid-borne K. pneumoniae carbapenemase (KPC)-producing bla gene (blaKPC). There was evidence of person-to-person transmission for two patients. Screening of 186 clinical isolates revealed no additional blaKPC-containing isolates.

Impact of Rotavirus Vaccination on Hospitalizations and Deaths From Childhood Gastroenteritis in Botswana.

BACKGROUND A monovalent human rotavirus vaccine (RV1) was introduced in Botswana in July 2012. We assessed the impact of RV1 vaccination on childhood gastroenteritis-related hospitalizations and deaths in 2013 and 2014. METHODS We obtained data from registers of 4 hospitals in Botswana on hospitalizations and deaths from gastroenteritis, regardless of cause, among children <5 years of age. Gastroenteritis hospitalizations and deaths during the prevaccine period (January 2009-December 2012) were compared to the postvaccine period (January 2013-December 2014). Vaccine coverage was estimated from data collected through a concurrent vaccine effectiveness study at the same hospitals. RESULTS By December 2014, coverage with ≥1 dose of RV1 was an estimated 90% among infants <1 year of age and 76% among children 12-23 months of age. In the prevaccine period, the annual median number of gastroenteritis-related hospitalizations in children <5 years of age was 1212, and of gastroenteritis-related deaths in children <2 years of age was 77. In the postvaccine period, gastroenteritis-related hospitalizations decreased by 23% (95% confidence interval [CI], 16%-29%) to 937, and gastroenteritis-related deaths decreased by 22% (95% CI, -9% to 44%) to 60. Declines were most prominent during the rotavirus season (May-October) and among infants <1 year of age, with reductions of 43% (95% CI, 34%-51%) in gastroenteritis hospitalizations and 48% (95% CI, 11%-69%) in gastroenteritis deaths. CONCLUSIONS Following introduction of RV1 into the national immunization program, significant declines in hospitalizations and deaths from gastroenteritis were observed among children in Botswana, suggestive of the beneficial public health impact of rotavirus vaccination.

Nanolitre real-time PCR detection of bacterial, parasitic, and viral agents from patients with diarrhoea in Nunavut, Canada

Background Little is known about the microbiology of diarrhoeal disease in Canadas Arctic regions. There are a number of limitations of conventional microbiology testing techniques for diarrhoeal pathogens, and these may be further compromised in the Arctic, given the often long distances for specimen transport. Objective To develop a novel multiple-target nanolitre real-time reverse transcriptase (RT)-PCR platform to simultaneously test diarrhoeal specimens collected from residents of the Qikiqtani (Baffin Island) Region of Nunavut, Canada, for a wide range of bacterial, parasitic and viral agents. Study design/methods Diarrhoeal stool samples submitted for bacterial culture to Qikiqtani General Hospital in Nunavut over an 18-month period were tested with a multiple-target nanolitre real-time PCR panel for major diarrhoeal pathogens including 8 bacterial, 6 viral and 2 parasitic targets. Results Among 86 stool specimens tested by PCR, a total of 50 pathogens were detected with 1 or more pathogens found in 40 (46.5%) stool specimens. The organisms detected comprised 17 Cryptosporidium spp., 5 Clostridium difficile with toxin B, 6 Campylobacter spp., 6 Salmonella spp., 4 astroviruses, 3 noroviruses, 1 rotavirus, 1 Shigella spp. and 1 Giardia spp. The frequency of detection by PCR and bacterial culture was similar for Salmonella spp., but discrepant for Campylobacter spp., as Campylobacter was detected by culture from only 1/86 specimens. Similarly, Cryptosporidium spp. was detected in multiple samples by PCR but was not detected by microscopy or enzyme immunoassay. Conclusions Cryptosporidium spp., Campylobacter spp. and Clostridium difficile may be relatively common but possibly under-recognised pathogens in this region. Further study is needed to determine the regional epidemiology and clinical significance of these organisms. This method appears to be a useful tool for gastrointestinal pathogen research and may also be helpful for clinical diagnostics and outbreak investigation in remote regions where the yield of routine testing may be compromised.

Evaluation of Anatomically Designed Flocked Rectal Swabs for Molecular Detection of Enteric Pathogens in Children Admitted to Hospital with Severe Gastroenteritis in Botswana

ABSTRACT Two-hundred eighty matched bulk stool and anatomically designed flocked rectal swab samples were collected from children admitted to the hospital with acute diarrhea in Botswana. Their parents were asked about the acceptability of the swab collection method compared with bulk stool sampling. All samples underwent identical testing with a validated 15-target (9 bacterial, 3 viral, and 3 parasite) commercial multiplex PCR assay. The flocked swabs had a 12% higher yield for bacterial pathogen targets (241 versus 212; P = 0.003) compared with that of stool samples, as well as similar yields for viral targets (110 versus 113; P = 0.701) and parasite targets (59 versus 65; P = 0.345). One hundred sixty-four of the flocked swab-stool pairs were also tested with separate laboratory-developed bacterial and viral multiplex assays, and the flocked rectal swabs had a performance that was similar to that seen with commercial assay testing. Almost all parents/guardians found the swabs acceptable. Flocked rectal swabs significantly facilitate the molecular diagnosis of diarrheal disease in children.

Early childhood diarrhoeal diseases and cognition: are we missing the rest of the iceberg?

Abstract Risk factors which interfere with cognitive function are especially important during the first 2 years of life – a period referred to as early child development and a time during which rapid growth and essential development occur. Malnutrition, a condition whose effect on cognitive function is well known, has been shown to be part of a vicious cycle with diarrhoeal diseases, and the two pathologies together continue to be the leading cause of illness and death in young children in developing countries. This paper reviews the burden of early childhood diarrhoeal diseases globally and the emerging evidence of their relationship with global disparities in neurocognitive development. The strength of evidence which indicates that the severe childhood diarrhoeal burden may be implicated in cognitive impairment of children from low- and middle-income counties is discussed. Findings suggest that greater investment in multi-site, longitudinal enteric infection studies that assess long-term repercussions are warranted. Furthermore, economic analyses using the concept of human capital should play a key role in advancing our understanding of the breadth and complexities of the health, social and economic ramifications of early childhood diarrhoeal diseases and enteric infections. This broadened awareness can serve to help advocate for more effective interventions, particularly in developing economies.

Assessment of Flocked Swabs for Use in Identification of Streptococcal Pharyngitis

ABSTRACT We compared the performance of flocked swabs to that of traditional swabs for culture of beta-hemolytic streptococci in children with pharyngitis. Sensitivity was higher for flocked swabs, but this did not reach statistical significance. We conclude that flocked swabs can be used in place of traditional swabs for diagnosis of streptococcal pharyngitis.

Prevalence and molecular characterization of Cryptosporidium spp. and Giardia duodenalis in diarrhoeic patients in the Qikiqtani Region, Nunavut, Canada

Background Although the prevalences of infection with the protozoan parasites Cryptosporidium spp. and Giardia duodenalis in humans appear to be relatively high in the Canadian North, their transmission patterns are poorly understood. Objective To determine the detection rate and the molecular characteristics of Cryptosporidium spp. and Giardia duodenalis in diarrhoeic patients in the Qikiqtani (Baffin Island) Region of Nunavut, Canada, in order to better understand the burden of illness and the potential mechanisms of transmission. Study design/methods Diarrhoeal stool specimens (n=108) submitted to the Qikiqtani General Hospital for clinical testing were also tested for the presence of Cryptosporidium spp. and Giardia duodenalis using epifluorescence microscopy and polymerase chain reaction (PCR). DNA sequencing and restriction fragment length polymorphism (RFLP) analyses were performed on PCR-positive specimens to determine the species, genotypes and sub-genotypes of the parasites. Results Cryptosporidium was detected in 15.7% of the diarrhoeic patients, while Giardia was detected in 4.6%. DNA sequencing of a fragment of the small subunit rRNA gene indicated that all of the Cryptosporidium amplicons had a 100% homology to C. parvum, and a gp60 assay showed that all aligned with C. parvum sub-genotype IIa. Microsatellite analysis revealed 3 cases of sub-genotype IIaA15G2R1, 2 of IIaA15G1R and 1 case each of sub-genotypes IIaA16G1R1 and IIaA15R1. For Giardia, results based on the amplification of both the 16S rRNA gene and the gdh gene were generally in agreement, and both DNA sequencing and RFLP demonstrated the presence of the G. duodenalis Assemblage B genotype. Conclusions Both C. parvum and G. duodenalis Assemblage B were present in human diarrhoeal stool specimens from Nunavut, which was suggestive of zoonotic transmission, although human-to-human transmission cannot be ruled out. To fully understand the public health significance of the different Cryptosporidium and Giardia species and genotypes in diarrhoeic patients, it will be imperative to establish the extent of genetic diversity within these parasites through comprehensive studies of the molecular epidemiology of cryptosporidiosis and giardiasis in the Nunavut region.

Association of Respiratory Viruses with Outcomes of Severe Childhood Pneumonia in Botswana

Background The highest incidence of childhood acute lower respiratory tract infection (ALRI) is in low- and middle-income countries. Few studies examined whether detection of respiratory viruses predicts ALRI outcomes in these settings. Methods We conducted prospective cohort and case-control studies of children 1-23 months of age in Botswana. Cases met clinical criteria for pneumonia and were recruited within six hours of presentation to a referral hospital. Controls were children without pneumonia matched to cases by primary care clinic and date of enrollment. Nasopharyngeal specimens were tested for respiratory viruses using polymerase chain reaction. We compared detection rates of specific viruses in matched case-control pairs. We examined the effect of respiratory syncytial virus (RSV) and other respiratory viruses on pneumonia outcomes. Results Between April 2012 and August 2014, we enrolled 310 cases, of which 133 had matched controls. Median ages of cases and controls were 6.1 and 6.4 months, respectively. One or more viruses were detected from 75% of cases and 34% of controls. RSV and human metapneumovirus were more frequent among cases than controls, but only enterovirus/rhinovirus was detected from asymptomatic controls. Compared with non-RSV viruses, RSV was associated with an increased risk of treatment failure at 48 hours [risk ratio (RR): 1.85; 95% confidence interval (CI): 1.20, 2.84], more days of respiratory support [mean difference (MD): 1.26 days; 95% CI: 0.30, 2.22 days], and longer duration of hospitalization [MD: 1.35 days; 95% CI: 0.20, 2.50 days], but lower in-hospital mortality [RR: 0.09; 95% CI: 0.01, 0.80] in children with pneumonia. Conclusions Respiratory viruses were detected from most children hospitalized with ALRI in Botswana, but only RSV and human metapneumovirus were more frequent than among children without ALRI. Detection of RSV from children with ALRI predicted a protracted illness course but lower mortality compared with non-RSV viruses.

The global burden of paediatric and neonatal sepsis: a systematic review.

The incidence of sepsis is highest in neonates and children, yet the global burden of sepsis in these age groups has not been assessed. We reviewed available evidence from observational epidemiological studies to estimate the global burden and mortality of sepsis in neonates and children. We did a systematic review and meta-analysis of studies reporting population-based sepsis incidence in neonates and children, published between 1979 and 2016. Our search yielded 1270 studies, 23 of which met the inclusion criteria; 16 were from high-income countries and seven from middle-income countries. 15 studies from 12 countries reported complete data and were included in the meta-analysis. We found an aggregate estimate of 48 (95% CI 27-86) sepsis cases and 22 (14-33) severe sepsis cases in children per 100 000 person-years. Mortality ranged from 1% to 5% for sepsis and 9% to 20% for severe sepsis. The population-level estimate for neonatal sepsis was 2202 (95% CI 1099-4360) per 100 000 livebirths, with mortality between 11% and 19%. Extrapolating these figures on a global scale, we estimate an incidence of 3·0 million cases of sepsis in neonates and 1·2 million cases in children. Although these results confirm that sepsis is a common and frequently fatal condition affecting neonates and children globally, few population-based data are available from low-income settings and the lack of standardisation of diagnostic criteria and definition of sepsis in the reviewed studies are obstacles to the accurate estimation of global burden. Robust epidemiological monitoring to define global sepsis incidence and mortality in children is urgently needed.

Hospital-based surveillance for rotavirus gastroenteritis using molecular testing and immunoassay during the 2011 season in Botswana.

We describe rotavirus testing and clinical characteristics for children admitted with acute gastroenteritis during Botswanas 2011 rotavirus season. The rotavirus season extended from June to October with rotavirus-specific case fatality being 2.8%. Using molecular testing as reference, the immunochromatographic test had a sensitivity of 76.5% and specificity of 68.0%. Rotavirus vaccine may significantly reduce childhood morbidity and mortality in Botswana.