Amos Phiri

Epidemics of Invasive Salmonella enterica Serovar Enteritidis and S. enterica Serovar Typhimurium Infection Associated with Multidrug Resistance among Adults and Children in Malawi

BACKGROUND Nontyphoidal salmonellae (NTS) have become the most common cause of bacteremia in tropical Africa, particularly among susceptible children and HIV-infected adults. METHODS We describe 4956 episodes of NTS bacteremia (2439 episodes in adults and 2517 episodes in children) that occurred in Blantyre, Malawi, during the 7-year period 1998-2004. RESULTS A total of 75% of the cases of NTS bacteremia were due to Salmonella enterica serovar Typhimurium, and 21% were due to S. enterica serovar Enteritidis. Epidemic increases in the incidence of NTS bacteremia were seen sequentially, occurring first among cases caused by S. Enteritidis and then among cases caused by S. Typhimurium. Increased incidence of bacteremia was temporally associated with the acquisition of multidrug resistance to ampicillin, cotrimoxazole, and chloramphenicol by each serovar and occurred while the incidence of infection due to other common bloodstream pathogens remained constant. These epidemics were observed among adults and children. A seasonal pattern was also seen, with increased incidence during and after the rainy season. The median age of the patients was 32 years among adults and 22 months among children. Acquisition of multidrug-resistant infection was not associated with an increased case-fatality rate among children (22%), and the case-fatality rate among adults showed a significant trend toward decreasing (from 29% to 20%). CONCLUSIONS These data have important implications for the treatment of severe febrile illness in adults and children in tropical Africa. Further understanding of the molecular basis of these epidemics of multidrug-resistant NTS infection, including ongoing whole-genome sequencing of multidrug-resistant isolates, will yield important tools for the study of NTS pathogenesis, transmission, epidemiology, and prevention.

Bacteremia in Malawian Children with Severe Malaria: Prevalence, Etiology, HIV Coinfection, and Outcome

BACKGROUND Previous prospective studies of bacteremia in African children with severe malaria have mainly included children with cerebral malaria, and no study has examined the impact of human immunodeficiency virus (HIV) infection. We examined the prevalence and etiology of bacteremia and the impact of HIV infection on bacteremia in Malawian children with severe malaria, as well as the impact of bacteremia and HIV infection on outcome. METHODS From 1996 until 2005, blood for culture was obtained on admission from all children admitted with severe malaria during the rainy season to the Paediatric Research Ward at the Queen Elizabeth Central Hospital in Blantyre, Malawi. HIV testing was performed prospectively from 2001 to 2005 and retrospectively for those admitted from 1996 to 2000. Multivariate regression analysis examined independent risk factors for bacteremia and death. RESULTS Sixty-four (4.6%) of 1388 children with severe malaria had bacteremia; nontyphoidal Salmonellae (NTS) accounted for 58% of all bacteremias. The prevalence of any bacteremia and of NTS bacteremia was highest in children with severe malarial anemia (11.7% and 7.6%), compared with the prevalence in children with cerebral malaria and severe anemia (4.7% and 3.8%) and in those with cerebral malaria alone (3.0% and 0.9%). HIV infection status was determined in 1119 patients. HIV prevalence was 16% (and was highest in those with severe malaria anemia, at 20.4%), but HIV infection was not significantly associated with bacteremia. Neither bacteremia nor HIV infection was associated with death. CONCLUSIONS Antibiotics are not routinely indicated for children with severe malaria in this region, in which HIV is endemic. However, antibiotic therapy should be used to treat NTS infection if bacteremia is suspected in children with severe malarial anemia.

Bacteremia in febrile Malawian children : Clinical and microbiologic features

Background. There are no published data for the incidence or etiology of childhood bacteremia in Malawi. We describe the clinical and microbiologic features of children admitted to hospital from whom blood cultures yielded bacterial pathogens. Methods. Any neonate or child admitted to the pediatric wards of the Queen Elizabeth Central Hospital had a blood culture taken in the event of fever without obvious clinical explanation. Clinical and microbiologic data were prospectively collected for children with a significant positive culture. Results. Between September, 1996, and August, 1997, we processed 2123 cultures. Of these, 365 (17.2%) grew a pathogen. Non‐typhi salmonellae (NTS) and enteric Gram‐negative bacilli constituted 67.4% of isolates, and Streptococcus pneumoniae constituted 16.4%. More than two‐thirds of NTS episodes coincided with the peak malaria transmission season (January to June); 67% of bacteremic children were malnourished, 28% severely so. Patients with NTS bacteremia were significantly more likely to have coincident malaria and to have splenomegaly and anemia than children with other infecting organisms. The overall mortality was 38% but varied considerably according to age and nutritional status. Prior antibiotic use, coincident malaria or meningitis did not adversely affect outcome. In vitro resistance to the commonly available antibiotics ampicillin and trimethoprim‐sulfamethoxazole was found in 76 and 71% of NTS isolates. Screening tests for penicillin resistance suggested a rate of 21% among pneumococci. Conclusions. Bacteremia is common in hospitalized Malawian children and has a high mortality. There are high rates of resistance to some of the commonly used antibacterial agents.

Clinical presentation of non-typhoidal Salmonella bacteraemia in Malawian children.

We report the clinical presentation and outcome of 299 Malawian children with non-typhoidal Salmonella (NTS) bacteraemia and no evidence of focal sepsis, admitted to Queen Elizabeth Central Hospital (QECH), Blantyre, over a 26-month period (February 1996-April 1998). A peak incidence during the rainy season was noted. Salmonella typhimurium (79%) and S. enteritidis (13%) were the commonest isolates. For children aged > 6 months, NTS bacteraemia was significantly associated with malarial parasitaemia (RR 1.5 [1.2, 2.2], P < 0.01) and with severe anaemia (RR 7.2 [3.4, 15.3], P < 0.0001), when compared to other common pathogens causing childhood bacteraemia. Clinical overlap with malaria and anaemia, and the presence of malarial parasitaemia on admission, may delay diagnosis. NTS bacteraemia was commonly diagnosed following blood transfusion. Resistance in vitro to ampicillin (79%), co-trimoxazole (72%) and gentamicin (55%) was very common, and was rare to chloramphenicol (0.3%) which is the antibiotic of choice for NTS sepsis at QECH. Overall mortality was high (23%). Young age and clinical HIV infection were risk factors for mortality. Recurrences of NTS bacteraemia following antibiotic therapy were common among children with clinical HIV infection.

Invasive Group B Streptococcal Infection in Infants, Malawi

Incidence and serotype distribution of disease in Malawi are similar to those reported from industrialized countries, but case-fatality rate is high.

Acute bacterial meningitis in children admitted to the Queen Elizabeth Central Hospital, Blantyre, Malawi in 1996–97

To design appropriate interventions, we collected clinical and demographic data prospectively on all children aged one day to 14 years admitted with a diagnosis of bacterial meningitis (BM) from April 1st 1996 to March 31st 1997 to the Queen Elizabeth Central Hospital (QECH), Blantyre, Malawi. During the study period 267 children (2.7% of all paediatric admissions) were found to have BM; 83% were under 5 years of age, 61% under one year and 23% under one month. The most common causative organisms in the post neonatal period (n= 206) were Streptococcus pneumoniae (27%), Haemophilus influenzae type b (Hib) 21%, and Salmonella typhimurium (6%). In the neonatal group (< 1 month, n= 61) the most common causes were Streptococcus agalactiae (23%), S. typhimurium (15%), S. pneumoniae (11.5%) and other Gram negative rods (11.5%). Nineteen of 21 salmonella infections were in children under one year of age and all S. agalactiae were in infants under three months. There was delay on presentation: the average length of fever was 4.6 days, 39.5% had convulsed prior to arrival and 57% had an altered level of consciousness. An initial diagnosis of malaria had probably contributed to the delay in 22.5% (42 of 186 tested). 48% were < 80% weight for age, with 18% < 60% weight for age. The overall mortality was 40%. The outcome was worst in salmonella infections, particularly neonatal salmonella BM with a case fatality rate (CFR) of 89% (8 of 9 cases). Coma on presentation worsened prognosis (mortality 64% if Blantyre Coma Score < 3, 26% if > 3). 15% of survivors had sequelae on discharge. 20% of Hib isolates were resistant to chloramphenicol, but all salmonellae were sensitive. 5% of S. pneumoniae were resistant to penicillin and 8% to chloramphenicol. Earlier access to adequate health care and awareness of BM in a malaria‐endemic area would reduce mortality and morbidity. Vaccination against Hib infection would have reduced death by 18 (17%) and prevented sequelae in 7 cases.

Aetiology of neonatal sepsis in Blantyre, Malawi: 1996–2001

Abstract Aim: The aim of this retrospective study was to report causes, antibiotic resistance and outcome of neonatal sepsis (often fatal in developing countries) in Malawi. Methods: All blood and cerebrospinal fluid isolates collected between January 1996 and December 2001 from inpatients aged 0–30 days with suspected sepsis at Queen Elizabeth Central Hospital, Blantyre, Malawi were reviewed. In vitro resistance to antibiotics commonly used in Malawi was assessed. Case fatality rate was analysed with respect to age, bacterial pathogen and infection site. Results: A total of 801 bacteria were isolated from 784 neonates over 6 years—599 isolates from blood and 202 from cerebrospinal fluid. Overall, 54% of bacteria were gram-positive and 46% gram-negative. The commonest causes of neonatal sepsis were group B Streptococcus (17%) and non-typhoidal Salmonella (14%). In vitro antibiotic susceptibility to the first-line antibiotic combination of penicillin and gentamicin was 78% for all isolates, but in vitro sensitivities to gentamicin for Klebsiella spp and non-typhoidal Salmonella were only 33% and 53%, respectively. In-hospital case fatality rate was known for only 301 cases and was high at 48%. Group B Streptococcus was associated with the best outcome. Mortality was significantly higher if presentation was in the 1st week of life or if sepsis was caused by gram-negative bacteria. The causes of neonatal sepsis in this population show a different pattern from other studies in developing countries.

The outcome of non-typhoidal salmonella meningitis in Malawian children, 1997–2006

Abstract Introduction: The clinical course and outcome of non-typhoidal salmonella (NTS) meningitis in Malawian children over a 10-year period (1997–2006) is described. Methods: Demographic, clinical and laboratory data were collected for all children over 2 months of age admitted with salmonella meningitis to Queen Elizabeth Central Hospital from 1997 to 2006. In the 1st year, salmonellae were susceptible to chloramphenicol, and children received 2 weeks of chloramphenicol treatment. When NTS resistance to chloramphenicol started to appear in 1998, treatment was changed to ceftriaxone. From 2002, the duration of antibiotic therapy was extended to 4-weeks which included 2 weeks of intravenous ceftriaxone and a further 2 weeks of oral ciprofloxacin. Results: The in-hospital case fatality rate (CFR) was 52.3% (48.2% until 2002 and 53.9% after prolonged antibiotic therapy was introduced). Of the survivors, one in 12 (8.3%) became completely well (sequelae-free) in the period 1997–2001 while 18 of 31 survivors (58.1%) made a complete recovery during 2002–2006 (p<0.01). After the 4-week course of antimicrobial therapy was introduced, the number of relapses or recurrences fell from nine in 15 (60%) survivors treated with chloramphenicol or ceftriaxone to three in 35 (8.7%) survivors who received 4 weeks of antibiotics (p<0.0001). Conclusion: In Malawi, salmonella meningitis has a CFR of ∼50%, which has remained constant over many years. Residual morbidity, however, has decreased over 10 years, despite rising numbers of multi-drug-resistant cases of NTS. This improvement might be owing to better treatment and management and/or reduced pathogenicity of the multi-drug-resistant bacteria.

Nontyphoidal Salmonellae in United Kingdom Badgers: Prevalence and Spatial Distribution

ABSTRACT Eighteen (72%) of 25 badger social groups were found to excrete Salmonella enterica serovar Ried, S. enterica serovar Binza, S. enterica serovar Agama, or S. enterica serovar Lomita. Each serovar was susceptible to a panel of antimicrobials. Based on results of pulsed-field gel electrophoresis, the S. enterica serovar Agama and S. enterica serovar Binza isolates were very similar, but two clones each of S. enterica serovar Lomita and S. enterica serovar Ried were found. Badgers excreting S. enterica serovar Agama were spatially clustered.

Genomic characterisation of invasive non-typhoidal salmonella enterica subspecies enterica serovar bovismorbificans isolates from Malawi

Background Invasive Non-typhoidal Salmonella (iNTS) are an important cause of bacteraemia in children and HIV-infected adults in sub-Saharan Africa. Previous research has shown that iNTS strains exhibit a pattern of gene loss that resembles that of host adapted serovars such as Salmonella Typhi and Paratyphi A. Salmonella enterica serovar Bovismorbificans was a common serovar in Malawi between 1997 and 2004. Methodology We sequenced the genomes of 14 Malawian bacteraemia and four veterinary isolates from the UK, to identify genomic variations and signs of host adaptation in the Malawian strains. Principal Findings Whole genome phylogeny of invasive and veterinary S. Bovismorbificans isolates showed that the isolates are highly related, belonging to the most common international S. Bovismorbificans Sequence Type, ST142, in contrast to the findings for S. Typhimurium, where a distinct Sequence Type, ST313, is associated with invasive disease in sub-Saharan Africa. Although genome degradation through pseudogene formation was observed in ST142 isolates, there were no clear overlaps with the patterns of gene loss seen in iNTS ST313 isolates previously described from Malawi, and no clear distinction between S. Bovismorbificans isolates from Malawi and the UK. The only defining differences between S. Bovismorbificans bacteraemia and veterinary isolates were prophage-related regions and the carriage of a S. Bovismorbificans virulence plasmid (pVIRBov). Conclusions iNTS S. Bovismorbificans isolates, unlike iNTS S. Typhiumrium isolates, are only distinguished from those circulating elsewhere by differences in the mobile genome. It is likely that these strains have entered a susceptible population and are able to take advantage of this niche. There are tentative signs of convergent evolution to a more human adapted iNTS variant. Considering its importance in causing disease in this region, S. Bovismorbificans may be at the beginning of this process, providing a reference against which to compare changes that may become fixed in future lineages in sub-Saharan Africa.