Sebastien Breurec

The Peopling of the Pacific from a Bacterial Perspective

Two prehistoric migrations peopled the Pacific. One reached New Guinea and Australia, and a second, more recent, migration extended through Melanesia and from there to the Polynesian islands. These migrations were accompanied by two distinct populations of the specific human pathogen Helicobacter pylori, called hpSahul and hspMaori, respectively. hpSahul split from Asian populations of H. pylori 31,000 to 37,000 years ago, in concordance with archaeological history. The hpSahul populations in New Guinea and Australia have diverged sufficiently to indicate that they have remained isolated for the past 23,000 to 32,000 years. The second human expansion from Taiwan 5000 years ago dispersed one of several subgroups of the Austronesian language family along with one of several hspMaori clades into Melanesia and Polynesia, where both language and parasite have continued to diverge.

Acute myelitis due to Zika virus infection

In January, 2016, a 15-year-old girl with a history only of an ovarian cyst was admitted to hospital in Pointe-a-Pitre, Guadeloupe, with left hemiparesis. 7 days previously she had presented to the emergency department with left arm pain, frontal headaches, and conjunctival hyperaemia, but no fever, signs of meningeal irritation, or sensory or motor defi cits. The day of admission, she developed acute lower back pain, paraesthesia on the left side of her body, and weakness in her left arm. On admission she had slight left-sided weakness and proximal pain of the left arm and leg, exacerbated on movement, but no fever or signs of meningism, and Glasgow Coma Score (GCS) 15. Laboratory analyses were normal except for raised leucocytes (11·5 × 109/L) and polymorphonuclear leucocytes (9·2 × 109/L). Brain MRI was normal. On day 2, she developed dysuria and urinary retention needing catheterisation, but no abnormal urinary frequency or urgency. The left-sided hemiparesis and pain worsened, and we noted loss of temperature sensation below the T2 dermatome on the left and T4 on the right, and bilateral Hoff man signs. Spinal MRI showed lesions of the cervical and thoracic spinal cord. The cervical lesion was enlarged, suggesting oedema (fi gure). Conus medullaris and lumbar roots were normal, suggesting the bladder dysfunction could be linked to spinal damage. Electromyography and cerebrospinal fl uid examination (including isoelectric focusing protein profi le) were normal. We detected high concentrations of Zika virus on specifi c real-time reverse PCR (Eurobio, Les Ulis, France) in serum, urine, and cerebrospinal fl uid on the second day of her admission (9 days after symptom onset). PCR for varicella zoster and herpes simplex viruses, Legionella, and Mycoplasma pneumoniae in her cerebrospinal fl uid were negative. She had no serological signs of acute infection with cytomegalovirus, Epstein-Barr, chikungunya or dengue viruses, syphilis, or Lyme disease; tests for HIV and human T-cell lymphotropic virus (HTLV) were negative; and aquaporin-A antibodies, a marker of neuromyelitis optica, were absent. We started methylprednisolone 1 g daily for 5 days. On the seventh day of admission her neurological condition improved and we could remove the catheter. 1 month after admission she had moderate weakness in both legs but was able to walk unaided. Repeat MRI showed reduced cervical spinal oedema (appendix). The Zika virus epidemic that started in Brazil in May, 2015, spread to 28 countries in February, 2016, including the French Caribbean Islands of Martinique and Guadeloupe. Like dengue, Zika is an arthropod-borne virus of the Flaviviridae family transmitted by Aedes mosquitoes. Until recently, Zika was thought to cause benign infections in humans. The presence of Zika virus in the cerebrospinal fl uid of our patient with acute myelitis suggests that this virus might be neurotropic. In addition to the usual clinical picture of myelitis she had severe pain. Absence of intrathecal immunoglobulins and normal brain MRI excluded acute disseminated encephalomyelitis. The neurotropism of fl aviviruses such as dengue, Japanese encephalitis, and West Nile viruses, which might be responsible for invasive encephalitis and transverse or extensive myelitis, is well documented. West Nile virus might also aff ect lumbosacral nerve roots in addition to the spinal cord, and retrograde axonal transport from infected peripheral nerves has been shown. Zika virus infection should be considered in patients with acute myelitis living in or travelling from endemic areas, and further study should clarify the spectrum and incidence of neurological associations.

Epidemiology of methicillin-susceptible Staphylococcus aureus lineages in five major African towns: high prevalence of Panton-Valentine leukocidin genes

The epidemiology of methicillin-susceptible Staphylococcus aureus (MSSA) in Africa is poorly documented. From January 2007 to March 2008, 555 S. aureus isolates were collected from five African towns in Cameroon, Madagascar, Morocco, Niger, and Senegal; among these, 456 unique isolates were susceptible to methicillin. Approximately 50% of the MSSA isolates from each different participating centre were randomly selected for further molecular analysis. Of the 228 isolates investigated, 132 (58%) belonged to five major multilocus sequence typing (MLST) clonal complexes (CCs) (CC1, CC15, CC30, CC121 and CC152) that were not related to any successful methicillin-resistant S. aureus (MRSA) clones previously identified in the same study population. The luk-PV genes encoding Panton-Valentine leukocidin (PVL), present in 130 isolates overall (57%), were highly prevalent in isolates from Cameroon, Niger, and Senegal (West and Central Africa). This finding is of major concern, with regard to both a source of severe infections and a potential reservoir for PVL genes. This overrepresentation of PVL in MSSA could lead to the emergence and spread of successful, highly virulent PVL-positive MRSA clones, a phenomenon that has already started in Africa.

Epidemiology of methicillin-resistant Staphylococcus aureus lineages in five major African towns: emergence and spread of atypical clones.

The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in Africa is poorly documented. From January 2007 to March 2008, we collected 86 MRSA isolates from five African towns, one each in Cameroon, Madagascar, Morocco, Niger and Senegal. Although one or two major clones, defined by the sequence type and staphylococcal cassette chromosome mec type, predominated at each site, genetic diversity (ten clones) was relatively limited in view of the large geographical area studied. Most of the isolates (n = 76, 88%) belonged to three major clones, namely ST239/241-III, a well-known pandemic clone (n = 34, 40%), ST88-IV (n = 24, 28%) and ST5-IV (n = 18, 21%). The latter two clones have only been sporadically described in other parts of the world. The spread of community-associated MRSA carrying the Panton-Valentine leukocidin genes is a cause for concern, especially in Dakar and possibly throughout Africa.

Class D OXA-48 Carbapenemase in Multidrug-Resistant Enterobacteria, Senegal

To the Editor: Class D OXA β-lactamases are characterized as penicillinases that can hydrolyze oxacillin and cloxacillin and are poorly inhibited by clavulanic acid and EDTA. OXA-48 is one of the few members of this family to possess notable carbapenem-hydrolyzing activity (1). First described in 2004 in Turkey, OXA-48 has recently started to spread in Europe and the Middle East (2). We report the recent emergence of the plasmid-encoded blaOXA-48 gene in multidrug-resistant Enterobacteriaceae recovered from patients in Dakar, Senegal, in hospitals and in the community. From November 2008 through October 2009, 11 Enterobacteriaceae isolates (8 Klebsiella pneumoniae, 1 Escherichia coli, 1 Enterobacter cloacae, and 1 Enterobacter sakazakii) with reduced susceptibility to imipenem were identified at the Institut Pasteur (Dakar, Senegal). Antibacterial drug susceptibility was determined by the disk diffusion method and interpreted according to the European Committee on Antimicrobial Susceptibility Testing guidelines (www.eucast.org). Nine isolates were resistant to expanded-spectrum cephalosporins and also to other antibacterial drug classes. The isolates were recovered from 6 patients with urinary tract infections, 4 patients with surgical infections, and 1 patient with omphalitis. Nine infections were hospital acquired (Le Dantec and Principal Hospitals). Because the patients died before antibacterial drug susceptibility testing could be completed, all 5 patients with surgical infections or omphalitis received only empirical therapy with amoxicillin/clavulanate. One patient with a nosocomial urinary tract infection caused by a co-trimoxazole–susceptible strain was successfully treated with this antibacterial agent. The antibacterial drug regimens of the remaining 4 patients were not known, and they were lost to follow-up. We determined the MICs of imipenem, meropenem, and ertapenem by using the Etest method (AB Biodisk, Solna, Sweden), which showed that 9 isolates were susceptible to imipenem and meropenem but either intermediately susceptible or resistant to ertapenem (Table). The 2 imipenem-nonsusceptible isolates were susceptible or intermediately susceptible to meropenem, and both were resistant to ertapenem. We used previously described PCRs (1,3–7) to screen for carbapenem-hydrolyzing β-lactamase genes (blaVIM, blaIMP, blaKPC, and blaOXA-48), as well as plasmid-encoded blaCTX-M, blaAmpC, blaOXA-1, and blaTEM β-lactamase genes; the aac(6′)-Ib aminoglycoside resistance gene; the quinolone resistance genes qnrA,B,S; the tetracycline resistance genes tetA,B,D; and class 1 integron. The blaOXA-48, blaCTX-M, blaAmpC, and aac(6′)-Ib genes and the variable region of class 1 integron were then characterized by direct DNA sequencing of the PCR products. blaOXA-48 was present in all 11 isolates. blaVIM, blaIMP, and blaKPC were not detected. The qnr genes were present in 7 isolates resistant to ciprofloxacin. The aac(6′)-Ib-cr variant was present in 7 isolates resistant to gentamicin, tobramycin, and ciprofloxacin. The 9 isolates resistant to expanded-spectrum cephalosporins all harbored the blaCTX-M-15 gene. The E. coli isolate also harbored the plasmid-encoded blaAmpC gene ACT-1; blaCTX-M-15, blaOXA-1, blaTEM, and aac(6′)lb-cr were associated in 6 isolates. Long-range PCRs showed that these latter 4 genes were located in the same “multidrug resistance region,” as described in Senegal (6). Positive conjugation experiments with sodium azide–resistant E. coli J53 showed through PCR results, plasmid DNA extraction, and antibiogram patterns of the obtained transconjugants that blaOXA-48 was located on a 70-kb self-conjugative plasmid. The genetic environment of blaOXA-48 was then investigated by PCR with primers specific for insertion sequence IS1999 and for the 5′ part of blaOXA-48 (1). blaOXA-48 was found to be part of a Tn1999 composite transposon composed of 2 copies of the insertion sequence IS1999, as reported (2). Further sequencing of the IS1999 located upstream of blaOXA-48 showed that it was consistently truncated by the insertion sequence IS1R, as initially described in Turkey and more recently in Lebanon and Egypt (2,8). XbaI pulsed-field gel electrophoresis was then used to study the genetic relatedness of the 8 K. pneumoniae isolates. Three isolates had similar restriction profiles and had been recovered from 3 patients concurrently hospitalized at Le Dantec Hospital, suggesting nosocomial transmission. A class 1 integron harboring the dfrA1 trimethoprim-resistance gene was detected in the 3 clonal isolates. Together, these findings show the recent emergence of blaOXA-48 in Senegal in community and hospital settings. They may also suggest the spread of the same major carrying plasmid between the Middle East and Africa. Although 9 of the 11 isolates were found to be susceptible to imipenem on the basis of their MICs, their MICs were nonetheless higher than those of blaOXA-48–negative isolates. This raises 2 issues. First, these strains might go undetected during routine antibacterial drug susceptibility testing, a problem that could be overcome by using ertapenem, a compound more susceptible to carbapenemases. Second, the clinical efficacy of imipenem on such strains is uncertain. The frequency of acquired carbapenemases, which emerged early after imipenem introduction in Senegal (2008), is probably strongly underestimated, partly owing to the limited availability of reliable clinical laboratories (9). Because multidrug resistance is prevalent among Enterobacteriaceae isolated in Dakar hospitals (B. Garin, unpub. data) and in rural communities (6), the emergence of blaOXA-48 is a clear cause for concern. Table Resistance genes and carbapenem MICs of 11 Enterbacteriaceae isolates, Senegal, 2008–2009*

Genetic Diversity and Quinolone Resistance in Campylobacter jejuni Isolates from Poultry in Senegal

ABSTRACT We used the multilocus sequence typing (MLST) method to evaluate the genetic diversity of 46 Campylobacter jejuni isolates from chickens and to determine the link between quinolone resistance and sequence type (ST). There were a total of 16 ST genotypes, and the majority of them belonged to seven clonal complexes previously identified by using isolates from human disease. The ST-353 complex was the most common complex, whereas the ST-21, ST-42, ST-52, and ST-257 complexes were less well represented. The resistance phenotype varied for each ST, and the Thr-86-Ile substitution in the GyrA protein was the predominant mechanism of resistance to quinolone. Nine of the 14 isolates having the Thr-86-Ile substitution belonged to the ST-353 complex. MLST showed that the emergence of quinolone resistance is not related to the diffusion of a unique clone and that there is no link between ST genotype and quinolone resistance. Based on silent mutations, different variants of the gyrA gene were shown to exist for the same ST. These data provide useful information for understanding the epidemiology of C. jejuni in Senegal.

Evolutionary History of Helicobacter pylori Sequences Reflect Past Human Migrations in Southeast Asia

The human population history in Southeast Asia was shaped by numerous migrations and population expansions. Their reconstruction based on archaeological, linguistic or human genetic data is often hampered by the limited number of informative polymorphisms in classical human genetic markers, such as the hypervariable regions of the mitochondrial DNA. Here, we analyse housekeeping gene sequences of the human stomach bacterium Helicobacter pylori from various countries in Southeast Asia and we provide evidence that H. pylori accompanied at least three ancient human migrations into this area: i) a migration from India introducing hpEurope bacteria into Thailand, Cambodia and Malaysia; ii) a migration of the ancestors of Austro-Asiatic speaking people into Vietnam and Cambodia carrying hspEAsia bacteria; and iii) a migration of the ancestors of the Thai people from Southern China into Thailand carrying H. pylori of population hpAsia2. Moreover, the H. pylori sequences reflect iv) the migrations of Chinese to Thailand and Malaysia within the last 200 years spreading hspEasia strains, and v) migrations of Indians to Malaysia within the last 200 years distributing both hpAsia2 and hpEurope bacteria. The distribution of the bacterial populations seems to strongly influence the incidence of gastric cancer as countries with predominantly hspEAsia isolates exhibit a high incidence of gastric cancer while the incidence is low in countries with a high proportion of hpAsia2 or hpEurope strains. In the future, the host range expansion of hpEurope strains among Asian populations, combined with human motility, may have a significant impact on gastric cancer incidence in Asia.

First case of Elizabethkingia anophelis meningitis in the Central African Republic

An 8-day-old girl of indigenous origin delivered by caesarean section to an HIV-negative mother with an uneventful pregnancy presented to the Complexe Pediatrique in Bangui, Central African Republic, in March 2011 with a 3-day history of fever at 38.5 °C. The newborn had a history of intubation and mechanical ventilation at birth due to asphyxia, followed by 2 days of hospitalization. At admission, she was irritable, feeding poorly, had a seizure and had lost 1500 g (32%) of her birth weight. She showed ...

Primary antibiotic resistance and associated mechanisms in Helicobacter pylori isolates from Senegalese patients

BackgroundAntibiotic combination therapy for Helicobacter pylori eradication must be adapted to local resistance patterns, but the epidemiology of H. pylori resistance to antibiotics is poorly documented in Africa. The aim was to determine the antibiotic resistance rates, as well as the associated molecular mechanisms, of strains isolated in Dakar, Senegal.MethodsOne hundred and eight H. pylori strains were isolated between 2007 and 2009 from 108 patients presenting with upper abdominal pain to the Gastroenterology Department of Le Dantec Hospital. Antimicrobial susceptibility testing was performed for amoxicillin, clarithromycin, metronidazole, levofloxacin and tetracyclin using the E-test method. Mutations in the 23S rRNA gene of clarithromycin-resistant strains and in gyrA and gyrB of levofloxacin-resistant strains were investigated.ResultsIsolates were characterized by no resistance to amoxicillin (0%), tetracycline (0%), and very low rate of resistance to clarithromycin (1%), but a high rate of resistance to metronidazole (85%). The clarithromycin-resistant strain displayed the A2143G mutation. A worrying rate of levofloxacin resistance was detected (15%). N87I and D91N were the most common mutations in the quinolone-resistance-determining region of gyrA.ConclusionsThe first-line empirical regimen for H. pylori eradication in Senegal should include clarithromycin. Increasing rates of fluoroquinolone resistance detected should discourage the use of levofloxacin-containing regimens without prior antimicrobial susceptibility testing.

Epidemiology of Staphylococcus aureus in pigs and farmers in the largest farm in Dakar, Senegal.

Between December 2009 and November 2011, we collected 57 (12.3%) Staphylococcus aureus isolates from 464 pigs and 16 (30.8%) isolates from 52 farmers in the largest farm in Dakar. Fifty-one isolates (70%) belonged to four major multilocus sequence typing clonal complexes (CCs): CC152 (26.0%), CC15 (19.2%), CC5 (13.7%), and CC97 (10.9%). The CC variability among the pigs was similar to that observed among the farmers. Six isolates that were recovered only among pigs were resistant to methicillin (10.5%). They were assigned to the ST5-staphylococcal cassette chromosome mec type (SCCmec) IV (n = 5) and ST88-SCCmec IV (n = 1) clones. The luk-PV genes encoding Panton-Valentine leukocidin (PVL), present in 43 (58.9%) isolates overall, including all major CCs and the MRSA ST5-SCCmec IV clone, were highly prevalent compared to data from industrialized countries. This finding is of major concern with regard to the potential virulence of these strains.